Complete issue - IMA Fungus

T h e G l o b a l 

M y c o l o g i c a l J o u r n a l 

Volume 2 · No. 2 · December 2011 

N E W S · R E P O R T S · A W A R D S A N D P E R S O N A L I A · R E S E A R C H N E W S 

B O O K N E W S · f o r t h c o m i n g M E E T I N G S · A R T I C L E S

Colofon 

IMA Fungus 

Compiled by the International 

Mycological Association for the 

world’s mycologists. 

Scope: All aspects of pure and 

applied mycological research and 

news. 

Aims: To be the flagship journal 

of the International Mycological 

Association. IMA FUNGUS is 

an international, peer-reviewed, 

open-access, full colour, fast-track 

journal. 

Frequency: Published twice per year 

(June and December). Articles are 

published online with final pagination 

as soon as they have been 

accepted and edited. 

ISSN 

E-ISSN 

2210-6340 (print) 

2210-6359 (online) 

Websites: www. imafungus.org 

www.ima-mycology.org 

E-mail: d.hawksworth@nhm.ac.uk 

Volume 2 · No. 2 · December 2011 

Cover: Crushed, bi-walled spore of 

Pacispora franciscana (ZT Myc) 

extracted from the type locality 

from mycorrhizospheric soil under 

an olive tree close to the Basilica of 

St Francis of Assisi (Umbria, Italy). 

The inner, germinal wall of the brilliant 

white spore stains in Melzer’s 

reagent. Photo Fritz Oehl. 

EDITORIAL BOARD 

Editor-in-Chief 

Prof. dr D.L. Hawksworth CBE, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de 

Madrid, Plaza Ramón y Cajal, 28040 Madrid, Spain; and Department of Botany, Natural History Museum, Cromwell 

Road, London SW7 5BD, UK; E-mail: d.hawksworth@nhm.ac.uk 

Layout Editors 

M.J. van den Hoeven-Verweij & M. Vermaas, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD 

Utrecht, The Netherlands; E-mail: m.verweij@cbs.knaw.nl 

Associate Editors 

Dr T.V. Andrianova, M.G. Kholodny Institute of Botany, Tereshchenkivska Street 2, Kiev, MSP-1, 01601, Ukraine; 

E-mail: tand@darwin.relc.com 

Prof. dr D. Begerow, Lehrstuhl für Evolution und Biodiversität der Pflanzen, Ruhr-Universität Bochum, Universitätsstr. 

150, Gebäude ND 44780, Bochum, Germany; E-mail: dominik.begerow@rub.de 

Dr S. Cantrell, Department of Plant Pathology and Crop Physiology, Louisiana State University, Agricultural Centre, 455 Life 

Sciences Bldg., Baton Rouge, LA 70803, USA; E-mail: scantrel@suagm.edu 

Prof. dr D. Carter, Discipline of Microbiology, School of Molecular Biosciences, Building G08, University of Sydney, 

NSW 2006, Australia; E-mail: d.carter@mmb.usyd.edu.au 

Prof. dr P.W. Crous, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands; E- 

mail: p.crous@cbs.knaw.nl 

Prof. dr J. Dianese, Departamento de Fitopatologia, Universidade de Brasília, 70910-900 Brasília, D.F., Brasil; E-mail: 

jcarmine@unb.br 

Dr P.S. Dyer, School of Biology, Institute of Genetics, University of Nottingham, University Park, Nottingham NG7 2RD, 

UK; E-mail: paul.dyer@nottingham.ac.uk 

Dr M. Gryzenhout, Dept. of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa; 

E-mail: Gryzenhoutm@ufs.ac.za 

Prof. dr L. Guzman-Davalos, Instituto de Botánica, Departamento de Botánica y Zoología, Universidad de Guadalajara, 

A.P. 1-139 Zapopan, 45101, México; E-mail: lguzman@cucba.udg.mx 

Dr K. Hansen, Kryptogambotanik Naturhistoriska Riksmuseet, Box 50007, 104 05 Stockholm, Sweden; E-mail: karen. 

hansen@nrm.se 

Prof. dr K.D. Hyde, School of Science, Mae Fah Luang University, Tasud, Chiang Rai, Thailand; E-mail: kdhyde3@gmail. 

com 

Prof. dr L. Lange, Vice Dean, The Faculties of Engineering, Science and Medicine, Aalborg University; Director of Campus, 

Copenhagen Institute of Technology (CIT), Lautrupvang 15, DK-2750 Ballerup, Denmark; E-mail: lla@adm.aau. 

dk 

Prof. dr L. Manoch, Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand; 

E-mail: agrlkm@ku.ac.th 

Prof. dr W. Meyer, Molecular Mycology Research Laboratory, CIDM, ICPMR, Level 3, Room 3114A, Westmead Hospital, 

Darcy Road, Westmead, NSW, 2145, Australia; E-mail: w.meyer@usyd.edu.au 

Dr D. Minter, CABI Bioservices, Bakeham Lane, Egham, Surrey, TW20 9TY, UK; E-mail: d.minter@cabi.org 

Dr L. Norvell, Pacific Northwest Mycology Service, LLC, 6720 NW Skyline Boulevard, Portland, Oregon 97229-1309, 

USA; E-mail: llnorvell@pnw-ms.com 

Dr G. Okada, Microbe Division / Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, 

Saitama 351-0198, Japan; E-mail: okada@jcm.riken.jp 

Prof. dr N. Read, Fungal Cell Biology Group, Institute of Cell and Molecular Biology, Rutherford Building, University of 

Edinburgh, Edinburgh EH9 3JH, UK; E-mail: nick@fungalcell.org 

Prof. dr K.A. Seifert, Research Scientist / Biodiversity (Mycology and Botany), Agriculture & Agri-Food Canada, K.W. 

Neatby Bldg, 960 Carling Avenue, Ottawa, ON, K1A OC6, Canada; E-mail: seifertk@agr.gc.ca 

Prof. dr J.W. Taylor, Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, 

CA 94720, USA; E-mail: jtaylor@berkeley.edu 

Prof. dr M.J. Wingfield, Forestry and Agricultural Research Institute (FABI), University of Pretoria, Pretoria 0002, South 

Africa; E-mail: mike.wingfield@fabi.up.ac.za 

Prof. dr W.-Y. Zhuang, Systematic Mycology and Lichenology Laboratory, Institute of Microbiology, Chinese Academy of 

Sciences, Beijing 100080, China; E-mail: zhuangwy@sun.im.ac.cn 

 

i m a f U N G U S

ONE FUNGUS ONE NAME: A PLANT PATHOLOGIST’S 

VIEW 

Some eight months have gone by since the significant “One fungus = One name” (1F=1N) symposium was held at the 

historic home of the Netherland’s Academy of Science, Trippenhuis, in Amsterdam. This period might well go down in 

history as amongst the most traumatic, exciting, and important in the history of fungal taxonomy. The outcomes will undoubtedly 

influence the field and the many associated disciplines that rely upon it for decades, if not posterity. 

I 

had the privilege of being invited 

to present one of the introductory 

lectures at the 1F=1N symposium. 

Given the level of tension concerning the 

topic, I am not sure that I was particularly 

excited about doing so at the time. Yet as 

a plant pathologist and academic, I have 

had to grapple with the confusing issue 

of fungi having more than one name, 

sometimes even different species names, 

for most of my career. Like many other 

plant pathologists, in my case working on 

trees, I have been confronted by farmers 

and foresters who have been frustrated, 

sometimes irritated, by the confusing 

names that they have had to contend with, 

while attempting to reduce the impact of 

plant diseases. Likewise, students in classes 

have been baffled by the complexities 

surrounding the dual nomenclature linked 

to anamorph/teleomorph connections and 

further complicated by pleomorphism in 

the asexual morphs of fungi. After many 

years of debate, often heated, the 1F=1N 

symposium in Amsterdam provided us with 

a perfect forum to debate the possibility of 

abandoning the dual nomenclature for the 

fungi. 

The turning point towards abandoning 

Article 59 and adopting a single name 

nomenclature arose as a result of DNA 

sequence data becoming increasingly 

available to mycologists. Effectively the 

“rules” dictated by the Code became 

restrictive, often redundant. Out of sheer 

frustration, some plant pathologists (see 

Crous et al. 2006) found it necessary to 

sidestep these regulations in order to present 

a meaningful taxonomy for important 

agents of plant disease. As John Taylor, the 

opening speaker at the 1F=1N symposium 

aptly stated, in seeking to abandon the dual 

nomenclature for fungi, we were in reality 

dealing with a situation where the proverbial 

“horse had already bolted” (Taylor 2011). 

My presentation followed Johns’ and, while 

also expounding on the inevitable demise of 

a dual nomenclature, as a plant pathologist 

and practitioner using mycology, my 

questions focussed mostly not on 1F=1N, 

but the issue of WHICH NAME we might 

most effectively use. 

The IF=1N symposium presented 

contradictory views regarding the 

opportunities and the hazards of 

abandoning a dual nomenclature for the 

fungi. The debates were lively, sometimes 

heated, and the event culminated in the 

drafting of the Amsterdam Declaration later 

published in this journal (Hawksworth et al. 

2011). It also precipitated the publication 

of a contrary view (Gams et al. 2011), which 

also had a large number of supporters. 

But most importantly, I believe that these 

debates provided the material that was 

essential for the all-important deliberations 

that would follow during discussions 

regarding the next edition of the Code at the 

International Botanical Congress that was to 

follow in Melbourne in July. 

The watershed discussions in Melbourne 

regarding the future of the taxonomy 

of the fungi are over. And the outcomes 

Mike Wingfield entering the rooms of the Royal Netherlands Academy of Arts and Sciences in Amsterdam for 

the One Fungus = One Name symposium on 19–20 April 2011. 

EDITORIAL 

volume 2 · no. 2 

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EDITORIAL 

(Hawksworth 2011, Knapp et al. 2011, 

McNeill et al. 2011, Norvell 2011) are 

monumental to say the least. Some of us 

closely involved in the debate and that 

could not be in Melbourne received “blow 

by blow” accounts of the proceedings from 

Scott Redhead. Scott played an enormously 

important part in the debate, and had 

served as Secretary to a Special Committee 

established by the previous Congress in 

Vienna in 2005 to address this issue which 

had sadly failed to reach a consensus. 

From 1 January 2013, Article 59 will no 

longer provide for the separate naming of 

different morphs of the same fungus; all fungi 

will from then have only one correct name. 

I am absolutely convinced that that this will 

substantially promote our credibility with the 

practitioners of mycology. Certainly, in my 

situation, this will especially support plant 

pathologists and our stakeholders that rely on 

us to manage plant diseases (see Wingfield et 

al. 2011). But the real work post-Melbourne 

has yet to be done. The process towards 

deciding WHICH NAMES we use for the 

fungi now faces us, and another meeting at 

the Trippenhuis in April 2012 lies ahead to 

address this issue. Under the revised rules 

adopted in Melbourne, it will fortunately 

now be possible to develop approved lists 

of names with special protection to help 

minimize disruptions to the mycological 

community. Nevertheless, for some fungi, this 

is likely to be a road not entirely smooth. But 

it is a road towards a long-awaited natural 

classification for the fungi that had to be 

embarked on. Let the games begin. 

Crous PW, Slippers B, Wingfield MJ, Rheeder 

J, Marasas WFO, Philips AJL, Alves A, 

Burgess TI, Barber P, Groenewald JZ (2006) 

Phylogenetic lineages in the Botryosphaeriaceae. 

Studies in Mycology 55: 235–253. 

Gams W, Jaklitsch W, Agerer R, Aguirre-Hudson B, 

Andersen B, et al. (2011) A critical response to 

the ‘Amsterdam Declaration’. Mycotaxon 116: 

501–513. 

Hawksworth DL (2011) A new dawn for the 

naming of fungi: impacts of decisions made 

in Melbourne in July 2011 on the future 

publication and regulation of fungal names. 

MycoKeys 1: 7–20; IMA Fungus 2: 155–162. 

Hawksworth DL, Crous PW, Redhead SA, Reynolds 

DR, Samson RA, Seifert KA, Taylor JW, 

Wingfield MJ, et al. (2011) The Amsterdam 

Declaration on Fungal Nomenclature. IMA 

Fungus 2: 105–112; Mycotaxon 116: 491–500. 

Knapp S, McNeil, J, Turland NJ (2011) Changes to 

publication requirements made at the XVIII 

International Botanical Congress in Melbourne 

— what does e-publication mean for you? 

Taxon 60: 1498–1501; Mycotaxon 117: in press. 

McNeill J, Turland NJ, Monro A, Lepschi B (2011) 

XVIII International Botanical Congress: 

preliminary mail vote and report of Congress 

action on nomenclature proposals. Taxon 60: 

1507–1520. 

Norvell LL (2011) Fungal nomenclature. 1. 

Melbourne approves a new Code. Mycotaxon 

116: 481–490. 

Taylor JE (2011) One Fungus = One Name: DNA 

and fungal nomenclature twenty years after 

PCR. IMA Fungus 2: 113–120. 

Wingfield MJ, de Beer ZW, Slippers B, Wingfield 

BD, Groenewald JZ, Lombard L, Crous 

PW (2011) One fungus one name promotes 

progressive plant pathology. Molecular Plant 

Pathology : in press. 

Michael J. Wingfield 

(Mike.Wingfield@fabi.up.ac.za) 

(40) ima fUNGUS

1000 fungal genomes to be sequenced 

fungi: 1000genomes 

As diverse decomposers, pathogens, and 

mutualistic symbionts, fungi have an 

enormous impact on human affairs and 

ecosystem function. Perhaps more than 

any other group of non-photosynthetic 

eukaryotes, fungi are essential biological 

components of the global carbon cycle. 

Collectively, they are capable of degrading 

almost any naturally occurring and 

manmade biopolymers. As such, fungi hold 

considerable promise in the development of 

alternative fuels, carbon sequestration and 

bioremediation of contaminated ecosystems. 

The use of fungi for the continued 

benefit of society requires an accurate 

understanding of how they interact in 

natural and synthetic communities. The 

ability to sample environments for complex 

fungal metagenomes is rapidly becoming 

a reality and will play an important part 

in harnessing fungi for industrial, energy, 

climate and ecosystem management 

purposes. Our ability to accurately analyze 

these data relies on well-characterized, 

foundational reference genome data of 

phylogenetically diverse fungi. With recent 

advancements in next generation sequencing 

technologies, the sequencing of fungal 

genomes is more tractable and less expensive 

than ever. The result is that sequencing of 

fungal genomes is becoming a relatively 

routine approach to data collection for all 

areas of mycology. This growth in genomics 

is resulting in a more integrated approach 

to biological research with basic tools of 

evolutionary biology (e.g., phylogenetic 

tree reconstruction, tests for selection, etc.) 

being central to comparative genomics. 

There exists a need, however, for systematic 

sampling of the Fungal Tree of Life to fully 

leverage our knowledge of fungal evolution 

and its application to genome-enabled 

mycology. 

To bridge this gap, an international 

research team in collaboration with the 

Joint Genome Institute ( JGI) of the US 

Department of Energy has embarked on a 

five-year project to sequence 1000 fungal 

genomes from across the Fungal Tree of 

Life. The team comprises Joseph Spatafora 

(Oregon State University), Jason Stajich 

(University of California at Riverside), 

Kevin McCluskey (Fungal Genetics Stock 

Center), Pedro Crous (KNAW-CBS Fungal 

Diversity Centre), Gillian Turgeon (Cornell 

University), Daniel Lindner (USDA Forest 

Service), Kerry O’Donnell and Todd Ward 

(USDA Agricultural Research Service), 

Antonis Rokas (Vanderbilt University), N. 

Louise Glass (University of California at 

Berkeley), A. Elizabeth Arnold (University 

of Arizona), Francis Martin (INRA, 

France), and Igor Grigoriev ( JGI). The 

overall plan is to fill gaps in the Fungal Tree 

of Life through the sequencing of at least 

two reference genomes from every accepted 

fungal family. One hundred species from 

27 orders and 55 families will be sequenced 

in the first year of sampling (Tier One) 

with ~225 additional species sequenced 

every year for the next four years. At the 

centre of this sampling effort are the unique 

biological resources that are housed in living 

culture collections, which provide access to 

high quality vouchered material. 

This is an exciting time as we move 

into the genomic era of mycology. This 

project has the core goal of providing 

reference information to inform 

research on comparative genomics, 

evolution of development, plant-microbe 

interactions, industrial mycology, and 

environmental metagenomic sequencing. 

Close cooperation with other large-scale 

genomic sequencing projects is underway 

and we envision building a network for 

global participation in the project. More 

information can be found on the project 

website (). 

Joey Spatafora 

(spatafoj@science.oregonstate.edu) 

NEWS 

The Ug99 stem rust (Puccinia graminis) of wheat 

threatens global supplies 

Ug99 is an aggressive race of 

stem rust of wheat (Puccinia 

graminis) first discovered in 

Uganda in 1998. The discovery 

was startling to pathologists 

and wheat breeders because 

the pathogen could potentially 

overcome the genetic resistance 

built into over half the world’s 

wheat crop. Ug99 is more 

dangerous than other rusts 

because of the number of 

resistance genes it is able to 

overcome. 

The world is starting to 

take notice of this global threat 

to food security. For example, 

even though Ug99 has not 

reached the USA, the threat is 

so urgent that the United States 

Department of Agriculture 

(USDA) recently surveyed 

Puccinia graminis race Ug99 on wheat. Photo Borlaug Global Rust Initiative. 


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NEWS 

World distribution of Puccinia graminis race Ug99 on wheat (November 2011). Courtesy Borlaug Global Rust 

Initiative. 

2. Australia: 

• Oct-‐Nov 2010: Consistent air-flows 

from South Africa 

• Confirmed Ug99 (race PTKST: 

Sr31+Sr24 vir.) at source 

• Abnormal rainfall in Australia 

• SuscepMble hosts in Australia 

Emerging Concerns 

and identified varieties of wheat that show 

Ug99 resistance in efforts to prepare for the 

possibility of a Ug99 outbreak in the USA. 

The Durable Rust Resistance in Wheat 

(DRRW) project, funded by the Bill & 

Melinda Gates Foundation and the UK 

Department for International Development, 

and administered at Cornell University, 

has been established with the mission to 

mitigate this threat to the world’s wheat 

crop and avoid catastrophic losses. Two 

important DRRW objectives are pathogen 

surveillance and breeding wheat varieties 

that are resistant to the family of stem rust 

that includes Ug99, as well as stripe rust 

Jan-‐Mar 2011 

Oct-‐Nov 2010 

1. South Asia: 

• Jan-‐Mar 2011: Consistent air-flows 

from Yemen + Eritrea 

• Stem rust (Ug99?) at source in 

Yemen, Feb 2011 

• High severity of stem rust 

Eritrea, Oct. 2010 

• Highly suscepMble hosts in 

South Asia (PBW343: 6M ha; 

Inqualab-‐91: 4M ha) 

Possible spread of Puccinia graminis race Ug99 on wheat. Prepared by David Hodson (CIMMYT). 

(P. striiformis, syn. P. glumarum). New 

cultivated varieties must also improve 

farmers’ yields to keep pace with a growing 

world population. 

Ug99 is highly mobile, carried by wind 

or accidental human transmission. Because 

it does not recognize political boundaries, 

a surveillance system that is global in 

scope is necessary. The Global Cereal Rust 

Monitoring system is a coordinated network 

of national surveillance teams who collect 

standardized data from wheat fields in 20 

countries in Africa and Asia. The surveyors 

note any instance of rust, collect a sample 

of the rust for genetic testing, and record 

GPS data and other factors. These data are 

incorporated into a centralized database 

which allows researchers a bird’s eye view 

of the track of the pathogen, which helps in 

predicting where it might go next. 

Since its discovery in Uganda, Ug99 

has spread north-easterly through Kenya, 

Ethiopia, crossed the Red Sea into Yemen 

and Iran, and is now currently threatening 

Pakistan (where 24 M tons of wheat were 

produced in 2009) and India (over 80 M 

tons). Both countries have large plantings 

of wheat that are known to be susceptible. 

Historical evidence of the movements of 

rust pathogens indicates that Pakistan and 

India are at-risk. Ug99 has also traveled 

south, down the eastern coast of Africa to 

South Africa. There is a chance it could 

travel via wind currents over the Indian 

Ocean into Australia. 

Screening nurseries in Kenya and 

Ethiopia are key to the resistance breeding 

efforts. The nurseries are administered 

by CIMMYT (International Maize and 

Wheat Improvement Center), KARI 

(Kenya Agricultural Research Institute), and 

EIAR (Ethiopian Institute of Agricultural 

Research). Because Ug99 is present in east 

Africa, breeders from countries where Ug99 

is not present send promising new wheat 

varieties to these nurseries for field testing. 

Wheat breeders at the nurseries plant the 

seeds, expose them to Ug99, and collect 

screening data based on the incidence and 

severity of infection. If a variety is not 

resistant to Ug99 it soon becomes apparent. 

Thirty countries have sent germplasm for 

screening to KARI and EIAR, and 225 

000 lines of wheat have been screened since 

2006. 

Based on this screening process, 14 

varieties of wheat that are resistant to Ug99 

have been identified and are in testing with 

various national governments and seed 

programmes – and Ug99 resistant varieties 

have now been released in Ethiopia. Under 

an USAID (United States Agency for 

International Development) project, Ug99 

resistant seed has been distributed to six 

countries. A total of 12 000 ha of resistant 

varieties of wheat have been sown in Nepal, 

Bangladesh, Afghanistan, Egypt, Ethiopia, 

and Pakistan. 

Scientists on the DRRW project want to 

ensure that any new varieties released are not 

based on single gene resistance. Ug99, like 

any rust pathogen, has a great capability to 

(42) ima fUNGUS

change and evolve through mutation or sexual 

recombination. In fact, eight variants of Ug99 

have already been discovered. A wheat variety 

that only offers single gene resistance could be 

overwhelmed by Ug99 very quickly. 

The DRRW project also supports the 

Borlaug Global Rust Initiative (BGRI), 

founded by Norman Borlaug in 2005. The 

BGRI’s mission is to reduce the world’s 

vulnerability to rusts (stem, yellow, and leaf ) 

and advocate for a sustainable international 

system for improving wheat yields and 

crop protection. The website for the BGRI 

() is regularly updated and 

should be consulted for more information. 

John Bakum 

BGRI Web Administrator and Content 

Developer 

( Jb755@cornell.edu) 

NEWS 

A DNA barcode for Fungi proposed for adoption 

At a meeting of the Fungal Working 

Group of the Consortium for the Barcode 

of Life (CBOL) held in Amsterdam on 

17–18 April 2011, it was agreed that a 

publication be prepared based on the 

studies carried out and which made a formal 

proposal to CBOL as to the barcode to 

be used for Fungi (see Schoch et al., IMA 

Fungius 2: (5), June 2011). The results of 

an evaluation of six DNA regions by an 

international consortium using different 

groups of fungi, concluded that the internal 

transcribed spacer (ITS) region was the 

most appropriate as it had the highest 

probability of successful identification of 

the regions within the ribosomal cistron 

across the broadest range of Fungi. This 

was particularly valuable as the region to 

adopt as while it was not successful in all 

cases, it was the region that most commonly 

provided a barcode gap between the levels 

of within-species and between-species 

sequence variation. This region is therefore 

now to be formally proposed for adoption 

by the Consortium for the Barcode of 

Life as the primary fungal barcode marker, 

although it is recognized that supplementary 

barcodes may need to be proposed for 

adoption in some circumscribed taxonomic 

groups. 

The studies conducted involved the 

mitochondrial cytochrome c oxidase 

subunit 1, three regions from the nuclear 

ribosomal RNA cistron, regions of three 

representative protein coding genes (RPB1, 

RPB2 and MCM7), nuclear ribosomal small 

subunit (SSU), and nuclear ribosomal large 

subunit (LSU) – but all were inferior to 

the ITS. A multiauthored paper, involving 

148 researchers from 71 institutions, and 

describing the work carried out, is currently 

in revision in the Proceedings of the National 

Academy of Sciences of the USA, and is 

expected to appear shortly. 

New world record for the largest fungal basidiome 

A single basidiome of Rigidoporus ulmarius 

growing over the stump of an elm (Ulmus 

sp.) tree killed by Ophiostoma novo-ulmi 

in the grounds of the former International 

Mycological Institute at Kew (Surrey, UK) 

was accepted as the world’s largest in the 

Guiness Book of Records for 1990. That 

specimen measured 1.56 × 1.37 m and had 

a circumference of 4.53 m in January 1993 

(Aitchison & Hawksworth 1993). The 

basidiome continued to grow after that date, 

but it was never weighed, and subsequently 

deteriorated in situ. 

Now, an even larger single basidiome 

has been discovered on Hainan Island 

in southern China which is described 

by Dai & Cui (2011). This is of another 

polyporaceous fungus, Fomitiporia 

ellipsoidea, found on the underside of a 

fallen trunk of Cyclobalanopsis patellifornmis 

in virgin forest. This was judged to be 20 yr 

A portion of the basidiome with Yu-Cheng Dai. 


(43)

NEWS 

old and measured a massive 10.85 m long 

× 0.82–0.88 m wide and 4.6–5.5 cm thick, 

with a volume calculated as 409 000 – 525 

000 cm 3 and a fresh weight estimated at 

400–500 kg. With some 452 million pores, 

in an editorial note at the end of the article 

Nick P. Money suggests that it would have 

been generating around one trillion spores 

per day! 

Aitchison EM, Hawksworth DL (1993) IMI: 

retrospect and prospect. Wallingford: CAB 

International. 

Dai Y-C, Cui B-K (2011) Fomitiporia ellipsoidea 

has the largest fruiting body among the fungi. 

Fungal Biology 115: 813–814. 

A slice through a part of the basidiome showing 

the layers of pores. 

International meetings planned to discuss fungal 

 

nomenclature 

htt 

Following the dramatic revisions to 

nomenclatural rules for fungi enacted at 

the 2011 International Botanical Congress 

in Melbourne in July 2011 (Hawksworth 

2011, McNeill et al. 2011, Norvell 2011), 

members of both the Nomenclature 

Committee for Fungi (NCF) and the 

International Commission for the 

Taxonomy of Fungi (ICTF) have received 

many questions about how mycologists 

should adapt to the changes. Precise 

responses must wait publication of the new 

International Code of Nomenclature for 

algae, fungi, and plants which is expected 

in mid-2012, but the need for coordinated 

action is clear. With that in mind, the 

executives of these two bodies have agreed 

to cooperate to ensure the efficient sharing 

of accurate and consistent information and 

to develop inclusive, open, and transparent 

procedures for acting on the changes. 

Three major issues are: 

(1) the migration away from 

dual nomenclature, based upon 

nomenclatural priority, community 

consensus and the best interests of users, 

via 

(2) the development of ‘Protected 

lists’ of accepted names and their 

nomenclatural types, together with 

those competing synonyms (including 

sanctioned names), and in some cases 

lists of rejected names, and 

(3) the establishment of permanent 

subcommissions or temporary working 

groups focused on specific narrowly or 

broadly delimited taxa to develop and 

recommend names for the ‘Protected’ or 

‘Rejected’ lists. 

Logically, some of these working groups will be 

derived from the permanent Subcommissions 

or associated Commissions of the ICTF 

(Aspergillus/Penicillium, Ceratocystis/ 

Ophiostoma, Fusarium, Trichoderma/ 

Hypocrea). Others are yet to be formed, and 

we hope that many will self-organize among 

existing taxonomic communities, and identify 

themselves to the NCF and ICTF, who can 

then provide support and information. 

As of this writing, four symposia are 

planned for 2012 to begin the process of 

sharing accurate information and formulate 

the expectations for the subcommissions 

and working groups: 

1F 

12–13 

= 

April 

2012 

?N 

CBS Symposium 

CBS symposium: One Fungus = Which 

Name? 12–13 April 2012, Trippenhuis, 

Royal Netherlands Academy of Arts 

and Sciences (KNAW), Amsterdam, 

the Netherlands. This meeting, which 

will focus entirely on understanding the 

nomenclatural changes and developing 

plans for implementation, will be a 

mixture of keynote speakers, breakout 

sessions, and book launches. It is unclear 

whether there will be any side meetings 

among the ICTF Subcommissions or 

other working groups associated with this 

symposium, although both the IMA and 

the ICTF plan to hold general meetings. 

Check the CBS website () 

for more information. 

Mycological Society of Japan, 56th Annual 

Meeting. 26–27 May 2012, Gifu University, 

 

Gifu. This meeting will include a 2 hour 

symposium, “The new nomenclature - what 

is going on and what should be done.” 

Watch the MSJ website () for more information. A subsequent 

“Forum on microbial databases for academia 

and industry,” being organized by the 

Federation of Microbiology Societies, Japan 

(FEMS-Japan), is tentatively scheduled for 

29 May 2012 in Tokyo and will include 

presentations on several mycological 

databases. 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Mycological Society of America, Annual 

Meeting. 15–19 July 2012, Yale University, 

New Haven, CT, USA. This meeting will 

include a symposium, “The mycologist’s 

guide to the new International Code of 

Nomenclature for algae, fungi, and plants.” 

Preliminary plans are also underway 

for a satellite meeting of the ICTF 

Subcommission on Fusarium taxonomy 

(dgeiser@psu.edu) and a new Hypocreales 

working group to be held before or after 

the meeting (contact Amy Rossman, 

Amy.Rossman@ars.usda.gov). Watch 

 

the 

MSA website () for more 

information. 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

(44) ima fUNGUS

INSTITUTE OF MICROBOLOGY CHINESE ACADEMY OF ... 

http://english.im.cas.cn/ 

--> 

Home | Sitemap | Contact | Directory | CAS | 

that all mycologists can indicate their Code Search: is the mandate of the NCF. The 

interest in specific taxonomic orders, in 

Please enter 

ICTF, 

keywords 

although focused primarily on 

About Us News People Research Education & Training International order Cooperation to facilitate Societies data & Publications sharing and Papers the Resources fungi Links of Join economic Us importance, has an 

Chinese Academy of Sciences, Institute of 

Microbiology Special Symposium: New 

development of working groups. 

Seminars 

The mandating of working groups, 

interest in facilitating the process for the 

broadest possible community. We welcome 

era of fungal nomenclature. Tentative dates 

9–10 August 2012, State Key Laboratory 

of Mycology, Beijing. Contact Dr. Cai Lei 

Genetic host resistance to PRRSV 

assurance of fair representation, avoidance participation from all mycologists. 

PresentorRaymond R. R. (Bob) 

of duplication of effort, and accommodation 

Rowland 

UniversityDiagnostic Medicine and 

of overlapping areas of interest are a priority. Pathobiology of Kansas Hawksworth State DL (2011) A new dawn for the 

University’s College of Veterinary 

(mrcailei@gmail.com), and consult the Working groups are encouraged to identify Medicine 

naming of fungi: impacts of decisions made 

Time09:30,11 23,2011 

June 2012 issue of IMA Fungus for more themselves and to form preliminary working Place:A323, Institute of Microbio... in Melbourne in July 2011 on the future 

information. 

relationships. Subcommissions of the ICTF 

Neural regulation of the immune 

publication and regulation of fungal names. 

system and its involvement in 

are expected to give these requirements top 

MycoKeys 1: 7-20; IMA Fungus 2: 155–162. 

inflammatory disease 

We encourage organizers of other 

PresentorLi Tian, PhD 

priority in their work plans, welcoming the McNeill J, Turland N, Monro AM, Lepschi 

mycological meetings to consider adding participation of other interested mycologists BJ (2011) XVIII International Botanical 

Papers 

News 

sessions Over-expression or symposia of an F-box protein on gene nomenclature CAI to Lei Honored IMA who Young might Mycologist not Award be [2011-11-10] formal members. Those 

Congress: preliminary mail vote and report of 

·Prof. 

reduces abiotic stress tolerance and 

Symposium on Advances Fungal Genomics and Evolution -- In Celebration of 

their · programs in 2012 in order to provide interested in forming such groups or in 

Congress action on nomenclature proposals. 

promotes root growth in rice ·Mini 

the Founding of the State Key Laboratory of Mycology [2011-10-26] 

Group II intron-anchored gene deletion in 

accurate information and encourage Host Species Of Famous sharing Tibetan concerns Medicinal Fungus should Identified communicate 

[2011-09-15] 

· 

Taxon 60: 1507–1520. 

Clostridium 

·Insect Multimedia 

Symposium Addresses Increased Demand for Industrial 

PARP and RIP-1 are required for autophagy 

participation by mycologists in all 

·TWAS-ROESEAP 

countries. 

Biotechnology [2011-08-29] with NCF Chair, Scott Redhead (scott. Norvell LL (2011) Melbourne approves a new Code. 

induced by 11’-deoxyverticillin A, which 

· 

precedes caspase-dependent apoptosis 

Executive Director Visits IMCAS [2011-07-22] 

·TWAS 

redhead@agr.gc.ca) and ICTF Chair, Keith Mycotaxon 116: 481–490. 

Probing genomic diversity and evolution of 

two Chinese ever Awarded the Bergey Medal [2011-05-25] 

·First 

The Streptococcus NCF suis and serotype ICTF 2 by NimbleGen are interacting Witnesses First Bergey’s Seifert Meeting (keith.seifert@agr.gc.ca). 

[2011-05-20] 

· 

tiling array 

·Beijing 

Launches World Data Center for Microorganisms [2011-05-18] 

regularly Functional evaluation with of the four putative curators of Index ·IMCAS 

Our goals are to ensure that all 

Scott Redhead (Chair) and 

DNA-binding regions in Thermoanaerobacter 

The 5th Intermational Day o... 

Fungorum · 

tengcongensis reverse and gyrase MycoBank to ensure 

interested mycologists receive an accurate 

Lorelei Norvell (Secretary) 

Research Progress 

Chloropupukeanolides C–E, cytotoxic 

that pupukeanane the data chlorides required with a spiroketal for preparing Silencing in Regulation and of Interactions complete among understanding the Host, Virus Satellite 

· 

of RNA the new Societies & Publications Nomenclature Committee for Fungi (NCF) 

skeleton from Pestalotiopsis fici 

·RNA 

[2011-11-02] 

Protected Enhanced production lists of are recombinant available to working nomenclatural rules so that anyone wishing 

Comprehensive Structural Analysis of Neuraminidase Inhibition Using 

Nattokinase in Bacillus subtilis by promoter ·First 

groups · Laninamivir, a Highly Effective, Novel Influenza Drug [2011-10-26] 

and the community as a whole. to contribute may do so, and to define 

Keith Seifert (Chair) and 

SOD Achieve Industrialization [2011-10-17] 

·Hyperthermostable 

A nomenclatural database of connected of Non-cell-autonomous clearly Silencing the mechanisms of Endogenous Target and Gene expectations in for 

Andrew Miller (Secretary) 

·Restriction 

[More] 

Plants [2011-08-17] 

anamorph and teleomorph genera should participation. The format, standardization International Commission for the Taxonomy 

Genomic Analysis of Pathogenic and Evolution Mechanisms of 

·Comparative 

Streptococcus suis [2011-06-08] 

soon be placed on the IMA website 

and information requirements for the 

of Fungi (ICTF) 

Screening Strategy for Rapid Access to Polyether Antibiotics in 

·Genetic 

(). We intend Actinomycetes [2011-05-27] lists, and the approval of these final lists 

to develop a web-based mechanism so according to the requirements of the 

NEWS 

MycoKeys 

Institute Of Microbiology Chinese Academy of Sciences 

NO.1 West Beichen Road, Chaoyang District, Beijing 100101, China Phone: 0086-10-64807462 Fax: 0086-10-64807468 Email: office@im.ac.cn 

launched on 14 September 2011with the 

aim of accelerating biodiversity research, 

swelling further the options open for 

mycologists to publish their research. A sister 

journal to the already launched PhytoKeys 

and ZooKeys, MycoKeys will consider works 

describing new taxa, taxonomic revisions, 

checklists and catalogues, phylogenetic 

analyses, biogeography, methodology, data 

mining and literature surveys, monographs, 

atlases, letters and points of view, conference 

proceedings and Festschrifts, and data papers 

(manuscripts with large data sets). It is likely 

to be particularly attractive to authors of 

online to readers, though a few hard copies 

will be printed for archival purposes and 

deposited in key mycological libraries. 

Authors will, however, be able to purchase 

hard-copy offprints. There will normally 

be a fee of 15 € per page charge to authors, 

although this is being waived until September 

2012 on articles of up to 20 pages, and for 

the first 20 pages of longer works. Thorsten 

H. Lumbsch has been appointed Editor-in- 

Chief, and the publisher is Pensoft Publishers 

of Sofia, Bulgaria. Further information can 

be found on the journal’s website, . 

lengthy works or ones with many coloured 

1 of 1 

illustrations. The philosophy of the journal 

is discussed further in a leading article 

1 

Not to be confused with the very successful 

MycoKey 11/21/11 CD of keys 3:20 to the PMgenera of ascomycetes 

(Lumbsch et al. 2011), which includes a 

and basidiomycetes of Northern Europe produced 

The number of new mycological journals 

being produced continues to swell. MycoKeys 1 

is a new open-access mycological journal 

vision of automated connections of included 

data to key global databases and repositories. 

MycoKeys will be open-access and free 

by Thomas Læssøe & Jens H. Petersen (Version 2.1, 

2006; Version 3.1 Funga Nordica Edition, 2008); see 

. 

Lumbsch HT, Miller AN, Begerow D, Penev L (2011) MycoKeys, or why we need a new journal in mycology. MycoKeys 1: 1–6. 


(45)

REPORTS 

Genomics in China 

Mycologists at the Second Symposium for China’s Fungal Genome Initiative, Kunming. Photo by Juan Li. 

Mycologists at the Second Symposium for China’s Fungal Genome Initiative, Kunming. From left to right, 

Xingzhong Liu (Director of State Key Laboratory of Mycology at the Chinese Academy of Sciences’ 

campus in Beijing and newly elected President of the Asian Mycological Association), John W. Taylor (IMA 

President), Chungshu Wang (Chinese Institutes for Biological Sciences of the Chinese Academy of Sciences 

in Shanghai), Jiujiang Yu (Research Geneticist, USDA, SRRC in New Orleans), and Ke-Qin Zhang (Vice- 

President of Yunnan University). Photo taken with J. Taylor’s camera, photographer unknown. 

Mycologists at the Second Symposium for China’s Fungal Genome Initiative, Kunming. From left to right, Ke- 

Qin Zhang (Vice-President of Yunnan University), Joan Bennett (Rutgers University), Yunbo Qu (Shangdong 

University), and Zhiqiang An (University of Texas Health Science Center, Houston, Texas). Photo by Kaifang 

Ji. 

Two mycological symposia emphasizing 

fungal genomics were held in China 

in October 2011: a Mini-Symposium 

on Advances in Fungal Genomics and 

Evolution to celebrate the creation of the 

State Key Laboratory of Mycology at the 

Beijing campus of the Chinese Academy 

of Sciences; and the Second Symposium 

for China’s Fungal Genome Initiative, 

held at Yunnan University in Kunming. 

The meetings were organized by a trio of 

eminent Chinese mycologists: Xingzhong 

Liu (Director of the State Key Laboratory 

of Mycology in Beijing and newly elected 

President of the Asian Mycological 

Association), Chengshu Wang (Chinese 

Institutes for Biological Sciences of the 

Chinese Academy of Sciences in Shanghai 

and the vice President of the Mycological 

Society of China), and Keqin Zhang 

(Vice-President of Yunnan University). 

Many impressive presentations were made 

by Chinese scientists, which focused on 

fungi that parasitize insects and nematodes, 

including species of Cordyceps, Metarhizium, 

Beauveria, and Arthrobotrys. A visit by 

international symposium participants to the 

third largest freshwater lake in China, Taihu, 

brought home the importance of research 

into alternative methods of controlling 

agricultural pests in China – during an 

hour’s visit, only one, lone, immature gull 

was seen. 

The contingent of international 

visitors also visited the mycological 

facilities at the State Key Laboratory 

of Mycology, Institute of Microbiology 

in Beijing, and the Research Center 

for Insect Sciences, Institute of Plant 

Physiology and Ecology in Shanghai. 

In Beijing, more than 15 principal 

investigators conduct research in four 

areas: Diversity and Evolution; Functions 

and Interactions; Secondary Metabolism; 

and the Molecular Basis of Growth and 

Development. The four-story building 

that houses most of the PI’s labs also has a 

collection of more than 14 000 cultures, a 

herbarium with nearly 500 000 accessions, 

and a museum for fungi with interactive 

displays that hosts visits by groups 

of school children. In Shanghai, the 

collections and museum feature insects 

and the interaction of fungi and insects 

(46) ima fUNGUS

and the research facilities feature a stateof-the-art 

phytotron used for research on 

plant genetics and plant diseases caused 

by fungi. 

John W. Taylor 

President, International Mycological 

Association 

(jtaylor@berkeley.edu) 

International Association for Lichenology (IAL) 

REPORTS 

The IAL will hold its next quadrennial 

symposium in Bangkok on 9–13 January 

2012 () hosted by 

Ramkhamhaeng University. Most aspects 

of plant/microbial biology are represented 

amongst the session themes ranging 

from genomics and metabolites to 

forest ecology and global change. 

This is the first IAL conference to be 

hosted by a tropical nation, and reflects 

considerable interest and activity 

in lichen research by Thai scientists 

during the past 10 years. There are 

three post-symposium 5-day excursions 

and three workshops (Graphidaceae, 

Parmeliaceae, and Tropical lichens). Over 

300 abstracts for lectures and posters 

had been submitted by the submission 

deadline, promising an interesting and 

science-packed week. The Symposium 

is co-hosted by the universities of 

Chiang Mai, Mahasarakham, Maejo 

and Srinakarinwirot, The Biodiversity 

Research and Training Program, The Thai 

Botanical Society, The Thai Mycological 

Association, and The Queen Sirikit 

Botanical Garden. 

Peter D. Crittenden 

President, International Association for 

Lichenology 

(pdc@nottingham.ac.uk) 

Tourist hotel on stilts in a mangrove forest at Banpu where the post-conference Graphidaceae and Tropical 

Lichen workshops are to be held at IAL7. 

XVI Congress of European Mycologists (CEM XVI) 

The XVI Congress of European Mycologists 

was held in Porto Carras, Halkidiki, 

Greece, on 19–23 September 2011. This 

series of meetings is arguably the longest 

continuously running series of international 

congresses for mycology. Since its inception 

in Brussels in September 1956, it has visited 

widely different places within Europe, in 

accordance with a tradition of being hosted 

by a new country on each occasion. By 

coming to Greece in 2011, this was its first 

visit to this whole huge area of southeastern 

Europe, the Balkan Peninsula. It was also 

the first time ever on the shores of the 

Mediterranean. These congresses have 

always been arranged to ensure a balance is 

maintained between field and laboratory 

mycology. Very appropriately, therefore, 

the present congress, organized under 

the auspices of the European Mycological 

Association (EMA), and the sixteenth in the 

series, was at a resort surrounded by classic 

coastal aleppo pine woodland near the 

attractive seaside village of Neas Marmaras, 

about halfway down the eastern side of 

Sithonia, the central of the three long thin 

peninsulas which make Halkidiki such a 

distinct part of northern Greece. 

The Congress was presided over by 

the EMA President, and the Chair of the 

Organizing Committee was Stephanos 

Diamandis, the EMA Vice-President. The 

meeting was attended by 230 participants 

from 37 countries and every inhabited 

continent. After an ice-breaker party on 

the Sunday evening, formal sessions began 

on the Monday morning with a short 

opening ceremony and speeches of welcome 

from the local mayor, a representative of 

NAGREF, the main Congress sponsor 

in Greece, and the EMA President. The 

scientific programme comprised four days of 

lectures, presentations, workshops, symposia 

and posters, with one day, the Wednesday, 

reserved for field excursions, with a choice 

of two destinations. There was a plenary 

session each day, with keynote addresses, 

and these plenary sessions were followed 

each day by parallel sessions, poster sessions 

and satellite events covering a wide range of 

thematic areas. In addition to the scientific 

programme, there was, on the Thursday, a 

memorable Congress Dinner and, on the 

last day of the Congress, a business meeting 

of the General Assembly of the EMA. 

Plenary session keynote addresses 

• A new imaging nanotechnology for 

mycology (L. Kock). 

• Fungal conservation: insights from 

population biology and the impacts of 

past, present and future human land 

use (A. Dahlberg). 

• Fungal evolution: divergence and 

adaptation ( J. Taylor). 

• Fungal families: morphology, 


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REPORTS 

Stephanos Diamandis making a presentation to IMA 

President John W. Taylor. 

phylogeny and conflict resolution (P.F. 

Cannon). 

• MtDNA and rDNA: two different 

evolutionary lines combined for 

genetic differentiation, taxonomy 

and phylogeny in ascomycetes (M.A. 

Typas). 

• Outdoor airspora: patterns, prevalence 

and impacts (C. Rogers). 

Parallel sessions 

• Aeromycology (moderator E. 

Kapsanaki-Gotsi). 

• Alien and invasive fungi - biological 

control (moderator I. Kalucka). 

• Conservation of fungi (moderator C. 

Perini). 

• Developmental mycology (moderator 

R. Poeder). 

• Edible and medicinal fungi (moderator 

J. Baptista-Ferreira). 

• Fungal biotechnology (moderator J. 

Taylor). 

• Fungal distribution and diversity 

(moderators A. Abdel-Azeem, S. 

Diamandis, Z. Gonou-Zagou, and P.M. 

Kirk). 

• Fungal genetics and genomics 

(moderator M.A. Typas). 

• Fungi in ecosystems: effects of climate 

change (moderator L. Boddy). 

• Fungus-plant interactions: mycorrhizal 

systems (moderator R. Agerer). 

• Insect-fungus associations (moderator 

D. Schigel). 

• Plant pathogenic fungi (moderator J. 

Fatehi). 

• Systematics and evolution of fungi 

(moderators P.F. Cannon and C. 

Denchev). 

Poster sessions 

• Conservation of fungi, Developmental 

mycology, Systematics and evolution of 

fungi. 

• Aeromycology, Fungal distribution and 

diversity, Insect-fungus associations, 

Medical and veterinary mycology, 

Teaching mycology. 

• Biological control, Fungal 

biotechnology, Fungal genetics and 

genomics, Plant pathogenic fungi. 

Satellite events 

• Meeting of the European Council for 

Conservation of Fungi. 

• Symposium on application of IUCN 

criteria to fungi (moderator A. 

Dahlberg). 

• Workshop on conservation of 

ascomycetes (moderator D.W. Minter). 

Field excursions 

Wednesday 21 September, the middle 

day of the Congress, was devoted to two 

field excursions. The first was to Mount 

Holomon, in the main part of Halkidiki, 

some distance from the Congress, and 

at a higher altitude, which provided 

an opportunity to see fine broadleaved 

forests. The second, less than 10 km from 

the Congress site, was to the hill village 

of Parthenon from which an exploration 

of Mediterranean pine woodland, olive 

groves and scrub vegetation was planned. 

Both excursions were made but, very 

unfortunately, their start and finish 

coincided almost exactly with the passage of 

a front of torrential rain – the only rain in 

an otherwise warm and sunny week, making 

any serious field work practically impossible. 

This Congress was, scientifically, superb. 

Congresses of European Mycologists 

have always been strong in respect of 

biogeography, conservation, ecology, field 

mycology, recording and systematics. 

The world’s first group devoted to fungal 

conservation – the European Council for 

Fungal Conservation – arose from the 

1985 Congress of European Mycologists 

in Oslo and, in 2010, the EMA played a 

major role in establishing the International 

Society for Fungal Conservation, the only 

society anywhere exclusively devoted to 

protecting fungi. Not surprisingly, therefore, 

many of the sessions and satellite events 

at the Greek Congress demonstrated that 

the CEMs maintain a leading position in 

the now rapidly developing movement for 

fungal conservation. There has, however, 

been some concern within the EMA that 

other aspects of mycology have not always 

received sufficient attention at these events. 

At the preceding Congresses in Ukraine 

(2003) and Russia (2007) attempts were 

made, with increasing effectiveness, 

to address this imbalance. The Greek 

Congress not only continued that trend, 

but achieved a spectacular leap forward 

in terms of scientific coverage, with many 

aspects of laboratory-based mycology 

taking high-profile positions within 

the programme. The sessions on fungal 

biotechnology and on fungal genetics and 

genomics were highlights in that respect, 

but that did not mean that traditional 

themes were neglected. The session on 

insect-fungal interactions was memorable, 

and a particular achievement was to hold 

what appears to have been the first session 

devoted to aeromycology at a purely 

mycological congress. 

All in all, the Greek Congress has 

established a new high standard which 

will pose real challenges for subsequent 

Congresses to meet. To attract so many 

participants from so many different 

countries was a real achievement, not least 

because this was done at a time of severe 

recession and under the cloud of a huge 

global economic crisis. That achievement 

was a clear indication that the programme 

was as scientifically exciting as the location 

of the Congress was attractive. It was also 

reassuring to see many young mycologists 

present, and especially satisfying that, 

finally, a firm place has been established for 

Greek mycology not only on the European 

map, but also in the global arena. For this, 

mycology owes a great debt of gratitude to 

Stephanos Diamandis and his team on the 

Organizing Committee for their tireless 

work and huge generosity. 

David W. Minter 

President, European Mycological Association 

(d.minter@cabi.org) 

(48) ima fUNGUS

30 th ECCO Annual Meeting in Utrecht 

The European Culture Collections’ 

Organisation (ECCO) held its 30 th Annual 

Meeting in Utrecht, The Netherlands, 

on 16–17 June 2011. The meeting was 

organized by the CBS curators and the 

ECCO board. With 71 participants from 

22 countries, it was the best attended annual 

meeting since the foundation of ECCO in 

1981. The ECCO Annual meetings bring 

together curators and other scientists from 

culture collections of all kinds throughout 

Europe to exchange the latest research, 

novel methods for strain identification and 

preservation, and to build networks and 

share ideas about the challenges faced by the 

collection community. 

The venue for this year’s meeting was 

Hotel Mitland, a choice much appreciated 

by the participants for the beautiful 

surroundings of the historical fortress 

‘De Bilt’ close to Utrecht city centre. The 

detailed programme of the meeting can be 

viewed on the ECCO website (), from where presentations can also 

be downloaded. On Thursday morning, the 

meeting was opened by CBS Director Pedro 

Crous and ECCO President Daina Eze, 

followed by four sessions, viz. phylogeny and 

taxonomy of microorganisms, developments 

in databases, and the Convention on 

Biological Diversity Nagoya protocol for 

Access and Benefit Sharing (ABS); the latter 

was followed by a round-table discussion 

on the consequences of ABS for microbial 

research. Possible strategies to influence the 

decisions national authorities will need to 

take that govern microbial exchange were 

also discussed. After the last session on 

collection network activities such as the 

EU-funded projects European Consortium 

Participants at the ECCO meeting in Utrecht. 

of Microbial Resources Centres (EMbaRC) 

and Microbial Resource Research 

Infrastructure (MIRRI), the party visited 

the CBS building on Thursday evening, 

where the conference dinner was also held. 

Joost Stalpers, who retired in May 2011 

after three decades of CBS curatorship, 

was addressed by former ECCO president 

Dagmar Fritze, thanking him on behalf of 

the entire ECCO community for his many 

contributions to the mission of ECCO. 

On Friday morning the meeting 

continued with a session presenting 

examples of successful collaborations 

between culture collections and industrial 

partners, followed by a series of talks on 

promising methods for strain identification 

and validation. 

After the official business of the 

ECCO General Meeting, poster prizes 

were awarded to the three best posters 

presented, viz. third prize to Celia Soares et 

al., second to Sashka Mihailova et al., and 

first to Marilia Maciel et al. Later that day, 

many participants joined in for a guided 

tour through Utrecht city centre, enjoying 

a selection of historic sites including the 

famous Dom tower. Many ECCO delegates 

also stayed on for a special meeting on 

Saturday 19 June organized by the Global 

Biological Research Centre Network 

demonstration project (GBRCN), where 

the preparations for MIRRI were discussed. 

The next ECCO meeting is to be 

held in Braga, Portugal, at the Micoteca 

Universidade do Minho (MUM), in June 

2012. 

Gerard Verkleij 

(g.verkleij@cbs.knaw.nl) 

REPORTS 

Mycological Society of America 

The Mycological Society of America held 

its 79 th annual meeting in the ‘Land of the 

Midnight Sun’ – Fairbanks, AK – during 

the first week of August 2011. Over 300 

mycologists were in attendance, many from 

foreign lands. Some attendees started the 

week with pre-meeting trips to Denali 

National Park or other local sites, enjoying 

the wilderness and big skies of Alaska. 

Others attended a two-day workshop, 

sponsored by the Fungal Environmental 

Sampling and Informatics Network 

(FESIN) on ‘Metamycology and beyond: 

using fungi in educational contexts’. 

The meeting kicked off with the 

Presidential Address by Thomas Bruns 

on ‘Revised thoughts on the processes 

that maintain local species diversity of 

ectomycorrhizal fungi.’ The invitational 

Karling Lecturer was Joseph Heitman 

from Duke University Medical Center. 

He gave a fascinating overview of the 

evolution of sex in fungi and spent 

the entire week interacting with MSA 

members. Symposia included: Mechanisms 

of fungal-plant interactions: perspectives 

from the interface of ecology, evolutionary 

biology, and genomics; Fungal population 

genetics; Diversification of fungi; Fungal 

contribution to organic matter storage 


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REPORTS 

MSA Annual Foray, Fairbanks, participants. Photo by Andy Hart. 

and sequestration in soils; and Molecular 

ecology and biodiversity of arctic and boreal 

fungi. After spending the day listening to 

exciting contributed and invited talks, there 

were evening discussions on environmental 

sequencing and information from JGI 

on their fungal sequencing and analysis 

capabilities for individual researchers. The 

schedule was full, but there was still time 

to meet with colleagues for stimulating 

discussions of recent research. 

Several prominent mycologists received 

awards at the meeting. These included: 

Amy Rossman (USDA-ARS Systematic 

Mycology and Microbiology Laboratory, 

Beltsville, MD), Distinguished Mycologist; 

Lori Carris (Washington State University), 

Weston Teaching Award; Tim James 

(University of Michigan), Alexopoulus Prize 

for Outstanding Early-Career Mycologist; 

Greg Mueller (Chicago Botanical Garden), 

and Don Pfister (Harvard University), 

MSA Fellows; and Susumu Takamatsu 

(Mie University, Tsu, Japan), Honorary 

Member. Twenty-five students and young 

professionals received awards for travel and 

research excellence. The annual banquet 

included a wine-tasting competition, local 

cuisine, and entertainment by a Native 

American dance group. The annual auction 

featured a wide array of literature and 

mycological curiosities so that everyone left 

with something new (or in some cases, very 

old)! 

The foray was absolutely amazing 

with charismatic macrofungi everywhere! 

The morning was spent in the forests of 

the University of Alaska Large Animal 

Research Station among the musk ox and 

caribou. Later in the day, we left the campus 

to explore some of the local forests, which 

were also well stocked with mushrooms 

of many species. It was an amazing day 

and wonderful to visit with friends and 

colleagues among the trees. 

Preparations are already underway for 

next year’s annual meeting at Yale University 

in New Haven, Connecticut. The theme 

of that meeting will be ‘Integrative fungal 

biology: linking disciplines in basic and 

applied mycology.’ More information on 

this meeting can be found throughout 2012 

at . The east 

coast venue should provide easy access for 

our European colleagues, and we hope to see 

many of you there! 

Jessie A. Glaeser 

Secretary, Mycological Society of America 

(msasec1@yahoo.com) 

MSA Annual Foray, Fairbanks, display table. Photo 

by Andy Hart. 

D. Jean Lodge and friend (Boletus cf. edulis), MSA Annual Foray, Fairbanks. Photo by Jessie Glaeser. 

(50) ima fUNGUS

20 th Nordic Mycological Congress (NMC 20) 

The 20 th Nordic Mycological Congress 

(NMC) took place on the island Gotland 

in Eastern Sweden on 25 September to 1 

October 2011. It was organized by Ellen 

Larsson (University of Gothenburg), Mikael 

Jeppson, and myself (Swedish Museum of 

Natural History), and held in one of the 

Biological Sciences teaching laboratories 

at the University of Gotland in Visby. The 

NMC is primarily a congress for collecting 

and identifying fungi: mornings are used for 

collecting, and late afternoons and evenings 

for microscopic studies and discussions on 

identifications. 

Fifty-five professional and invited 

amateur mycologists attended, mainly from 

the Nordic countries (i.e. Denmark, Finland, 

Iceland, Norway, and Sweden) participated, 

but also including ones from China, Estonia, 

Scotland, and Spain joined. Gotland, situated 

in the Baltic Sea, is especially interesting 

because of its calcareous soil and warm 

climate. Many fungi are found here that are 

otherwise absent or rare in the rest of the 

Nordic countries. The meeting was a great 

success with plenty of fungi fruiting and 

beautiful sunshine all week. More than 32 

localities were visited, including a wide range 

of habitats, such as coniferous and deciduous 

forests, wooded meadows, alvars, and sand 

dunes. During the week 1525 collections 

were made, identified, and registered in a 

database (by Ibai Olariaga and PhD student 

Elisabeth Sjökvist, supported by the Swedish 

Taxonomy Initiative). The collections 

represented 596 species, including a large 

number Red Listed in Sweden. Additional 

collections identified within the three 

months after the meeting will be added and 

all information will be available in the Species 

Gateway database of the Swedish Species 

Information Centre (). 

Fungi were put out on display in the evening 

(in a tent placed outdoors to keep the fungi 

fairly fresh), and selected interesting groups 

of species were discussed. Several students 

from the universities of Gothenburg and 

Gotland attended the meeting and helped 

with the display. It was a very busy week, but 

more than anything the meeting provided an 

opportunity for mycologists to interact, enjoy 

and talk about fungi – and other topical 

issues. 

The NMC is held every second year 

and rotates amongst the Nordic countries. 

Seppo Huhtinen (University of Turku) is 

the organizer of the next NMC, which is to 

be held in the Bear’s Lodge (Pohtimonlampi 

Hotel), close to Rovaniemi, Lappland, in 

northern Finland in 2013. Mycologists 

from outside the Nordic countries will be 

welcome. 

Karen Hansen 

(karen.hansen@nrm.se) 

REPORTS 

Scenes from the 20 th Nordic Mycological Congress on Gotland, Sweden, during field- and laboratory work, presentations, and one of the 47 Cortinarius subgen. 

Phlegmacium species collected, C. terpsichores. Photos by Tapio Kekki and Tor Erik Brandrud. 


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AWARDS AND PERSONALIA 

AWARDS 

IMA Young Mycologist Awards 2011 

It is with great pleasure that the IMA 

officers can now announce the winners of 

the first four of the inaugural International 

Mycological Association Young Mycologist 

Awards. The IMA Executive Committee 

had intended for then President Pedro 

Crous to present the awards last August 

at the XIV International Mycological 

Congress (IMC9) in Edinburgh. Alas, we 

learned that initiating the award process 

was far more complicated than we had 

foreseen. Now, with the process in place and 

functioning, we have received notification of 

the winners from Africa, Asia, Australasia, 

and North America. The committees 

for Europe and Latin America have been 

formed, and their winners will be reported 

in the first issue of IMA Fungus in 2012. All 

winners of the IMC9 round of IMA Young 

Mycologist Awards will receive their awards, 

which include a cheque for 500 €, at IMC10 

in Thailand in 2014. 

Please join me in congratulating the 

recipients: Marieka Gryzenhout (Ethel 

Mary Doidge Medal – African Regional 

Mycological Member Organization), 

Lei Cai (Keisuke Tubaki Medal – 

Asian Regional Mycological Member 

Organization), Ceri Pearce (Daniel 

McAlpine Medal – Australasian Regional 

Mycological Member Organization), and 

A. Elizabeth (‘Betsy’) Arnold (Arthur 

Henry Reginald Buller Medal – North 

American Regional Mycological Member 

Organization). 


President, International Mycological 

Association (IMA) 

Ethel Mary Doidge Medal 

Marieka Gryzenhout, starting with 

her first paper published soon after she 

began graduate school, and continuing 

through to her book on an important 

plant pathogenic fungi (Gryzenhout et al., 

2009, Taxonomy, Phylogeny, and Ecology of 

Bark-Inhabiting Tree-Pathogenic Fungi in 

the Cryphonectriaceae. St Paul, MN: APS 

Press). Marieka has contributed enormously 

to our knowledge of fungi. As a young 

mycologist with energy and intelligence, she 

has already made an impact in Africa as well 

as internationally. Her research has been 

particularly concerned with Diaporthales, 

an order which includes a number of serious 

forest pathogens, including chestnut blight 

fungus, Cryphonectria parasitica. She also 

discovered additional pathogens that threaten 

forests, and has determined the relationships 

between these species, describing new species 

and new genera where warranted, and also 

connecting sexual and asexual morphs. 

Marieka is also now investigating other plant 

pathogens, such as species of Phytophthora. 

She has assumed roles in several scientific 

societies, most spectacularly as the founding 

editor of the African Mycological Association 

(AMA) newsletter MycoAfrica, and is also 

now a member of the Executive Committee 

of the International Mycological Association 

(IMA). One of those supporting her 

nomination for this Medal commented that 

Marieka “represents the bright future for 

mycology in Africa.” 

Keisuke Tubaki Medal 

Lei Cai is an outstanding young mycologist 

in China. He has been working on the 

systematics and biodiversity of fungi from 

aquatic, coprophilous, and thermophilic 

habitats for many years. He has examined 

more than 5000 specimens, which has 

led to the discovery and descriptions of 

five new genera, and 45 new species. He 

is currently focusing on the systematics of 

plant pathogenic fungi using a polyphasic 

approach, and already has an impressive 

research record which includes one 

monograph, two book chapters, and 54 

peer-reviewed papers. 

For his excellent performance 

in mycological research, Lei Cai was 

awarded the prestigious Chinese Academy 

of Sciences (CAS) “Hundred-Talent 

Program”. He has also made significant 

contributions in promoting mycological 

studies in China and elsewhere in Asia. As 

Executive Associate Editor, he has played a 

key role in establishing and managing the 

new international journal, Mycology; he 

also serves as an associate editor of Fungal 

Diversity. He is an active educator in 

mycology who has given lectures at various 

international workshops or courses in the 

Chinese Academy of Sciences. 

Daniel McAlpine Medal 

Ceri Pearce was selected by the Australasian 

IMA Regional Mycological Organization for 

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this Medal based on her research and major 

contributions to the mycological community. 

Her PhD research, which centred on the 

biology and taxonomy of Australian fungi, 

resulted in a book on Phyllachoraceae in 

Australia. More recently, with her research 

now focusing on the increasingly important 

area of biosecurity, she has been involved in 

the development of diagnostic and emergency 

response systems for exotic and introduced 

pests in Australia. Ceri has contributed to the 

mycologicsl community through her roles in 

mycology organizations, which includes the 

Australasian Mycological Society (executive 

councillor and librarian, 1998–2002), 

Australasian Plant Pathology Society 

(executive councillor 2005 –2007, and cochair 

of the Regional Councillor Working 

Group, 2005– 2008. In addition, she won 

the bid and successfully co-organised the 8 th 

International Mycological Congress (IMC8) 

in Cairns in 2006, which was the first time 

that an IMC had been held in the Southern 

Hemisphere. Finally, Ceri has been involved 

in numerous mycological educational and 

training programmes, both within her own 

organization and to agricultural industries, 

peers, and school students. 

Arthur Henry Reginald 

Buller Medal 

A. Elizabeth (‘Betsy’) Arnold received her 

PhD in Ecology and Evolutionary Biology 

in 2002 from the University of Arizona 

where she worked with Lucinda McDade. 

From 2003–2004, she was supported by 

a prestigious NSF Postdoctoral Fellow 

in Microbial Biology with sponsorship 

from François Lutzoni at Duke University. 

Betsy joined the faculty in the Division of 

Plant Pathology and Microbiology in the 

Department of Plant Sciences at the UA 

in 2005, where she is now an Associate 

Professor. Betsy currently teach courses 

in microbial diversity, plant sciences and 

mycology, curates the Robert L. Gilbertson 

Mycological Herbarium, and conducts 

research on the ecology, evolution and 

systematics of plant-associated fungi. She 

is best known for her innovative work in 

evolution and ecology of endophytes of 

terrestrial ecosystems. Her work is truly 

global in scale with sampling occurring 

along continental transects. It has resulted 

in our most complete understanding of the 

biodiversity and distribution of endophytic 

fungi and the World’s largest culture 

collection of endophytes. Betsy is a much 

sought after speaker across a spectrum of 

life science conferences, is an active member 

of the Mycological Society of America, 

and one of mycology’s biggest advocates. 

It is with great pride that North American 

mycologists acknowledge Betsy Arnold 

and her contribution to mycology with this 

Award. 


Distinguished Asian Mycologist Award 

Kevin D. Hyde was given the award of 

Distinguished Asian Mycologist in August 

2011 at the Asian Mycological Congress for 

his services in promoting Asian Mycology. 

Since 2008 Kevin has been Head and 

Associate Professor of the Institute of 

Kevin Hyde looking for freshwater fungi in southern France. Photo Jacques Fornier. 

Excellence in Fungal Research, School of 

Science, Mae Fah Luang University, Chiang 

Rai, Thailand and is also Managing Director 

of the Mushroom Research Foundation in 

Chiang Mai. 

He has held numerous prestigious 

positions in Asian mycological organizations, 

including EASIANET (of BioNet 

International) (Coordinator 2004–2007), 

Mycological Association of Hong Kong 

(Chair, 2002–2007), and IMA Asian 

Mycological Committee (Chair, 2007– 

2011). He founded and edited Fungal 

Diversity, a journal now pre-eminent in its 

field, and has been involved as an editor 

of about ten other journals. A prolific 

researcher, with over 600 publications and 15 

books to his credit, Kevin’s real passion is in 

training students – he has supervised some 20 

postdoctoral fellows, over 60 PhD students, 

and 15 MPhil students who have been drawn 

from Thailand, Sri Lanka, China, Laos, 

Myanmar, Vietnam, India, and Kenya. 

Kevin obtained his PhD from the 

University of Portsmouth, UK, under the 


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Kevin Hyde teaching in the Mushroom Research Centre in Chiang Mai. Students from left to right: Marivic 

Cabanela, Nilam Wulandari, Iman Hidiyat, Subbu and unidentified. 

direction of E. B. Gareth Jones, in 1987. 

He first worked as a school teacher in 

Basingstoke, UK, and then Brunei, before 

moving to Australia where he surveyed 

plant pathogens in north Queensland 

and Papua New Guinea where he became 

fascinated by tropical microfungi. He 

subsequently obtained a tenured lectureship 

in the University of Hong Kong where 

he was based for 15 years before moving 

to Thailand. The Mushroom Research 

Foundation which he established also 

provides scholarships for PhD’s in mycology. 

Kevin strives to mould each of his students 

into renowned mycologists in their own 

right, and two of the first IMA Young 

Mycologists awards now made are to his 

previous students, Ceri Pearce and Lei Cai 

(see above). 

It is difficult to conceive of a more 

fitting recipient of this special award, and 

mycologists world-wide join in extending 

Kevin our congratulations and thanks for 

all he has done and continues to do for 

mycology. One of his current PhD students 

at Mae Fah Luang University, Samantha 

Karunarathna adds: “In Dr Hyde’s 

laboratory, we are budding mycologists, who 

have been taught, trained and mentored 

by Dr Hyde and would like to wish Dr 

Hyde all the very best and good luck in his 

endeavours to train and mould mycologists 

to salvage the world of mycology which is in 

dire need of many more mycologists.” 

BIRTHDAY GREETINGS 

Jiang-Chun Wei’s 80 th 

Jiang-Chun Wei celebrated his 80 th birthday 

on 6 November 2011. Born in Xianyang 

city, Shaanxi Province, China, his childhood 

to1945 was during World War II, and his 

middle-school life from 1945–1949 was the 

time of the Civil War of China. He majored 

in plant pathology at the Northwest 

Agricultural College from 1950, at a time 

when gene theory was opposed in China, 

but he never gave up his belief in science, for 

example, consulting the famous professor 

Sheng-Han Shi on the disease pathway 

of stripe rust of wheat from physiological 

and biochemical aspects. After graduating 

in 1955, Jiang-Chun was sent to work in 

the Institute of Agricultural Biology of 

Northwest China, of the Chinese Academy 

of Sciences (CAS). The first project for 

him was smut disease of millet, guided 

by the myco-pathologist Jian-Yi Li. Then 

in 1956 he was dispatched to the CAS 

Institute of Applied Mycology in Beijing 

where he studied the systematics of rust 

fungi on Rosaceae under the guidance of the 

mycologist Yun-Zhang 

Wang. In 1958, however, 

he was sent to Russia to 

finish his PhD degree 

under the guidance of the 

lichenologist Savicz at 

the Komarov Botanical 

Institute, in what was 

then Leningrad (now St 

Petersburg). He was soon 

publishing on lichens 

in Umbilicariaceae, a 

passion that stayed with 

him from that time, 

obtained his PhD in 

1962, and then returned 

to China. This time 

that was to the recently 

established CAS Institute of Microbiology 

in Beijing where he commenced work on 

the Chinese lichen biota in the Institute’s 

Laboratory of Mycology. His research 

career, however, was soon disrupted by an 

enforced absence from the Institute for 

ten years for the duration of the ‘Cultural 

Revolution’, after which he returned to 

the Institute of Microbiology, where he 

was Director of the Open Laboratory of 

Systematic Mycology and Lichenology 

(1985–1993) – the title of the laboratory 

(54) ima fUNGUS

eflecting his personal interests and which 

was one of the first in the world to embrace 

lichen-forming along with other fungi. 

Further, Jiang-Chun was the founding coeditor 

of Mycosystema (1986–1993). He 

also served as President of the Mycological 

Society of China (1993-2003), of which he 

was then made an Honorary President, and 

in 1995 he was awarded the degree of DSc 

by the Komarov Botanical Institute. To date, 

he has published 107 research papers, and 

also eight books, including An Enumeration 

of Lichens in China (1991, Beijing 

IN MEMORIAM 

International Science Publishers) and a 

monograph of his beloved Umbilicariaceae 

in Asia (with Jiang Yumei, 1993, The Asian 

Umbilicariaceae (Ascomycota), Beijing 

International Science Publishers). 

A celebration in his honour was held 

at the Institute of Microbiology on his 

birthday, where he gave a lecture ‘A glance 

back and prospect at my age of eighty’ 

and enjoyed a huge celebratory cake. 

Jiang-Chung has been an inspiration to 

numerous students and fellow researchers 

in China, both for his vision, perseverance, 

and scientific contributions, and I feel 

honoured to have been privileged to know 

him and enjoy his hospitality in Beijing. All 

mycologists, including lichenologists, wish 

him a productive and fulfilling time. 

Xin Li Wei (Key Laboratory of Systematic 

Mycology and Lichenology, Institute 

of Microbiology, Chinese Academy of 

Sciences, Beijing) kindly provided much 

of the background information and 

photograph presented here. 


Aino Marjatta Henssen (1925–2011) 

A leading lichen taxonomist and systematist, 

Aino passed away on 29 August 2011. She was 

born on 12 April 1925 in Elberfeld, Germany, 

and had a German father and Finnish mother. 

She enroled at university to become a teacher, 

but due to her enthusiasm for research she 

graduated in 1953 with a doctoral thesis in 

plant physiology. After working in Bonn and 

Berlin at agricultural institutes investigating 

microorganisms decomposing manure, she 

started to work taxonomically – describing 

two new actinomycete genera and several 

new species. Following visits to Helsinki and 

Uppsala in 1956–61she turned her focus 

onto lichen fungi, inspired by the Swedish 

school of ascomycete systematics led by Johan 

Axel Nannfeldt, who had introduced ascoma 

development as a major character complex in 

ascomyete classification. Aino’s revision of the 

families Lichinaceae and Ephebaceae (1963, 

Symbolae Botanicae Upsaliensis 18 

(1): 1–123) is a prime example 

of this type of work, illustrated 

by numerous photographs of 

sections showing developmental 

stages. A decade later her textbook 

Lichenes: Eine Einführung in die 

Flechtenkunde (with her former 

PhD student Hans Martin Jahns, 

1973 1 , Stuttgart: Georg Thieme) 

she presented a classification 

that fully integrated lichenized 

with non-lichenized fungi, and 

introduced the “Zwischengruppe” 

for fungi that did not conform to 

the classical concepts of Nannfeldt; 

this was a remarkable work which 

presented ontogenetic data on all major groups 

based on her observations, which included 

many new findings, and descriptions of all 

families and orders she accepted 

In 1963 Aino was appointed curator of 

the herbarium at the Philipps-University in 

Marburg, and in 1970 as Associate Professor, 

a position she held until her retirement 

in 1990. Aino’s enthusiasm for lichens 

and other fungi attracted many students, 

and she continued her research as long as 

health permitted, with her last paper being 

published in 2007. In a series of more than 

120 publications, she described three orders 

(Arthoniales, Gyalectales, Lichinales), three 

families (Coccocarpiaceae, Coccotremataceae, 

Gloeoheppiaceae), 21 genera, and over 

150 new species, as well as numerous new 

combinations, often as a part of critical 

generic revisions. However, one of her mostcited 

works is her 1976 study with Peter W. 

James demonstrating by critical microscopic 

work that different morphologies could be 

produced by the same fungus depending on 

whether it has a cyanobacterial or a green– 

algal partner (in Brown DH et al. (ed.), 

Lichenology: progress and problems: 27–77, 

London: Academic Press). She was also the 

first researcher to appreciate the diversity of 

melanized non-lichenized rock-inhabiting 

fungi, describing many in Lichenothelia. 

Her 65 th birthday was marked with 

a ‘Festschrift’ ( Jahns HM (ed.), 1990, 

Bibliotheca Lichenologica 38: 1–427), and 

she was awarded the Acharius Medal of the 

International Association for Lichenology 

(IAL) in 1992. She will be remembered as 

a scientist who understood and pursued 

lichenology as a field of its own but also as 

an integral part of mycology. 

Prepared from a draft kindly provided by 

Heidi Döring (Royal Botanic Gardens, 

Kew, UK), and a PDF of a fuller obituary 

prepared along with H. T. Lumbsch which 

is to appear in The Lichenologist in 2012. 

1 

This work is dated “1974” but was actually 

published on 6 December 1973. Aino was always 

very concerned to point this out to show that her 

classification came out before that adopted by Josef 

Poelt (in Ahmadjian V, Hale ME (eds), 1974, The 

Lichens: 599–632, New York: Academic Press) – 

and which is dated “1973” but actually appeared on 

25 March 1974. 


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Zang Mu (1930–2011) 

Zang Mu, one of the best-known Chinese 

macromycetologists, who was born on 

28 December 1930, passed away on 10 

November 2011, aged 81. A graduate 

from Soochow University, he worked at 

Nanjing Normal University as a teacher 

from 1954–1973, when he moved to the 

Kunming Institute of Botany (KIB) of 

the Chinese Academy of Sciences (CAS). 

As a research fellow in mycology and 

bryology, his major interests focused on 

systematics, ecology, and geography of 

fungi. He also studied mycorrhizas and their 

application in afforestation. He established 

the cryptogamic herbarium of KIB, and 

served as curator for many years. Other 

positions he was appointed to include that 

of Vice-President of the Mycological Society 

of China, and Vice-Director of the Key 

Laboratory of Mycology and Lichenology 

of CAS in Beijing. He published over 

150 papers on the fungi of China, and 

also several monographs, including the 

well-illustrated and remarkable [Economic 

Macrofungi from Southwestern China] (with 

Ying JZ, 1994, Beijing: Science Press), and 

had only this year completed [Dictionary 

of the Families and Genera of Chinese 

Cryptogams (Spore Plants)] (with Li XJ, 

2011, Beijing: Higher Education Press). 

Zang Mu twice received the secondclass 

Award in National Scientific and 

Technological Progress (1993, 1995), a 

second-class prize in China’s State Natural 

Science Award (2003), and also the N. 

Hiratsuka Award of the Mycological 

Society of Japan (2003). Besides mycology 

and bryology, he was also very interested 

in Chinese calligraphy, paintings, and 

collecting stamps. He contributed his full 

energy to the development of mycology and 

relative research fields in China, and is also 

warmly remembered for his kindness and 

hospitality to numerous visiting mycologists 

from overseas. China has lost a great 

mycologist, whose exceptional knowledge of 

Chinese mushrooms will be sorely missed. 

Prepared from material supplied by Liu 

Peigui and Zhu L. Yang (Kunming Institute 

of Botany, Chinese Academy of Sciences, 

Kunming, China). 

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Horizontal Gene Transfer (HGT) from Fungi is the 

basis for plant pathogenicity in oomycetes 

It always seemed rather odd that some 

oomycetes (Oomycota) were so fungal-like 

in their behaviour as plant pathogens. 

Now whole-genome comparisons are 

starting to reveal just why. Richards et al. 

(2011) have undertaken a painstaking 

gene-by-gene analysis of the proteomes 

of Hyaloperonospora parasitica and three 

species of Phytophthora (P. infestans, P. 

ramorum, and P. sojae) which reveals 

an extensive pattern of cross-kingdom 

horizontal gene transfer (HGT) from Fungi. 

In the case of P. ramorum, an amazing 7.6 

% of the secreted proteome appears to have 

been acquired from true fungi. In all, 34 

cases of HGT were identified, of which the 

case for 21 was strongly supported, most 

of which seem to have occurred close to 

the shift from phagotrophy to osmotrophy 

and the evolution of the fungal cell wall at 

the base of the monophyletic Fungi clade. 

Amongst the genes evidently transferred, 

are one related to features such as the ability 

to break down plant cell walls and take 

up sugars, nitrogen and phosphates, and 

further ones implicated in overcoming plant 

defence mechanisms and attacking plant 

cells. A schematic diagram of the functional 

proteome of oomycetes derived from 

Fungi is provided (their Fig. 2) at which 

one can only marvel at the complexity. The 

phenomenon was already recognized some 

years ago by Richards et al. (2006), but only 

five HGT gene transfers were reported at 

that time. This more detailed study, made 

possible by increasingly available genome 

sequences, reveals that this phenomenon 

is much more extensive than might have 

been imagined. Thus, it is not a matter of 

oomycetes merely being ‘fungal analogues’ 

or ‘pseudofungi’, they are actually partly 

Fungi. 

It should be noted that HGT is not 

only unidirectional from Fungi into to 

other organisms. Indeed, in another paper 

published this summer, this same group of 

researchers report identifying 323 examples 

of HGT into Fungi from prokaryotes 

(principally bacteria) and also other Fungi 

(Richards et al. 2011b). 

RESEARCH NEWS 

Richards TA, Dacks JB, Jenkinson JM, Thornton CR, Talbot NJ (2006) Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms. Current 

Biology 16: 1857–1864. 

Richards TA, Leonard G, Soanes DM, Talbot NJ (2011b) Gene transfer into fungi. Fungal Biology Reviews 25: 98–110. 

Richards TA, Soanes DM, Jones MDM, Vasieva O, Leonard G, Paszkiewicz K, Foster PG, Hall N, Talbot NJ (2011a) Horizontal gene transfer facilitated the evolution 

of plant parasitic mechanisms in the oomycetes. Proceedings of the National Academy of Sciences, USA 108: 15258–15263. 

1 HGTs 

8 HGTs 

2 HGTs 

1 HGTs 

9 HGTs 

Saccharomycotina 

Pezizomycotina Fungi 

‘other fungi’ 

Metazoa 

Amoebozoa 

Archaeplastida 

Alveolata 

Blastocystis hominis 

Diatoms 

Ectocarpus siliculosus 

Aureococcus anophagefferens 

Hyphochytrium catenoides 

Saprolegnia parasitica 

Albugo laibachii 

Phytophthora ramorum 

Phytophthora sojae 

Phytophthora infestans 

Hyaloperonospora parastica 

Unikonts 

S 

t 

r 

a 

m 

e 

n 

o 

p 

i 

l 

e 

s 

Schematic figure showing the pattern of horizontal gene transfer (HGT) between fungi and oomycetes, adapted from Richards et al. (2011a: fig. 1). In total Richards et 

al. (2011) provide evidence of 34 gene transfer events. Using phylogenetic methods combined with alternative topology tests they polarised the ancestry of 21 transfer 

events and are illustrated in this figure. The figure shows the transfers were generally concordant with the diversification of plant parasitic oomycetes, consistent with 

putative annotation of many of these genes which suggest that they are important for plant parasitism. Figure courtesy of Tom A. Richards. 


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RESEARCH News 

Fungal pathogens as a driver of tree species 

diversity in tropical forests 

It has been postulated that at least one of 

the factors promoting the maintenance of 

diversity in tropical forests is the action 

of host-specific parasites and pathogens 

which are more likely to kill seedlings 

near the parent tree species, the so-called 

Janzen-Connell ( J-C) model. In order to 

test whether this held for plant pathogens, 

Konno et al. (2011) isolated Colletotrichum 

anthrisci from seedlings of four trees 

growing below the same tree species 

where they had been killed by dampingoff 

beneath: Cornus controversa, Fraxinus 

lanuginosa, Magnolia obovata, and Prunus 

grayana. The isolates from all four species 

were confirmed as identical by 99–100 % 

similarity in ITS sequences (5.8SrDNA, 

ITS1 and ITS2), and inoculated into 

seedlings of F. lanuginosa and Prunus 

grayana. In all cases some damage to the 

seedlings occurred, but this was most severe 

in seedlings inoculated with isolates from 

the conspecific host tree. This suggests a 

degree of specialization whereby seedlings 

from the same tree species are more 

likely to be eliminated than those from 

different hosts – consequently reducing 

the probability of seedlings of the same 

tree species surviving when growing near 

examples of the same species. Konno et al. 

postulate that if this situation is common 

within several pathogens in a mixed 

tree forest, then diversity will tend to be 

maintained as proposed in the J-C model. 

The study also shows that fungi with 

identical ITS sequences obtained from 

native forest trees can differ in their degree 

of pathogenicity to other tree species. 

Konno M, Iwamoto S, Seiwa K (2011) Specialization of a fungal pathogen on host tree species in a cross-inoculation experiment. Journal of Ecology 99: 1394–1401. 

Colletotrichum anthrisci (from ex-type strain CBS 125334). a–b. acervuli; c. tip of a seta; d–e. conidiophores; f. conidiophores and setae; g–i. appressoria; j–k.conidia; 

all from ex-type culture CBS 125334. a, c–e, j: from Anthriscus stem; b,f, g, k: from SNA. a–b: DM; c–k: DIC. — Scale bars: a = 200 μm; e = 10 μm; a applies to a–b; e 

applies to c–k. Photos courtesy Ulrike Damm. 

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A new system for the arbuscular mycorrhizal fungi 

(Glomeromycota) 

In the course of the last ten years, and 

especially during the last five, immense 

progress has been made in understanding 

the molecular phylogenetic relationships 

of arbuscular mycorrhizal fungi, members 

of the phylum Glomeromycota. As might 

have been expected for a group which was 

already represented by modern-looking 

representatives in the Devonian, and which 

forms mutualistic associations with some 

80--85 % of land plants around today, there 

was much diversity to be detected. In 2011 

a succession of key papers describing new 

classes, families, and genera has appeared, 

mainly prepared by Fritz Oehl (Zürich, 

Switzerland), Gladstone Alves da Silva 

(Recife, Brazil), and Javier Palenzuela 

(Granada, Spain), with various colleagues, 

has appeared (e.g. Oehl et al. 2011ad). 

Building on the pioneering work of 

Christopher Walker, Arthur Schüβler, 

and James B. Morton in particular, these 

researchers have established robust 

correlations between microscopic features 

and the major groupings emerging from 

molecular studies. An elegant consumerfriendly 

digest and synthesis of the new 

system for the phylum has now been 

prepared, which we are proud to include in 

the current issue of IMA Fungus (Oehl et 

al. 2011e). 

In the new system, three classes 

(Archaeosporomycetes, Glomeromycetes, 

and Paraglomeromycetes), five orders 

(Archaeosporales, Diversisporales, 

Gigasporales, Glomerales, and 

Paraglomerales), 14 families, and 29 

genera are recognized. Key anatomical 

and morphological features characterizing 

the molecularly supported taxa are spore 

formation, the number of spore walls, 

germination type and structure, and 

mycorrhizal structures (stained in Trypan 

blue). These characters are illustrated 

and tabulated down to genus level in the 

synthesis paper, and using this many genera 

will now be separable using light microscopy 

alone. This paper is set to become the 

key reference work on this remarkable 

fungal phylum for ecologists and others 

investigating or utilizing endomycorrhizal 

fungi. 

RESEARCH NEWS 

Oehl F, Silva GA, Goto BT, Sieverding E (2011a) Glomeromycetes: three new genera and glomoid species 

reorganized. Mycotaxon 116: 75–120. 

Oehl F, Silva DKA, Maia LC, Sousa NMF de, Vieira HEE, Silva GA (2011b) Orbispora gen. nov., ancestral in 

the Scutellosporaceae (Glomeromycetes). Mycotaxon 116: 161–169. 

Oehl F, Silva GA, Goto BT, Maia LC, Sieverding E (2011c) Glomeromycota: two new classes and a new order. 

Mycotaxon 116: 365–379. 

Oehl F, Silva GA, Sánchez-Castro I, Goto BT, Maia LC, Vieira HEE, Barea JM, Sieverding E, Palenzuela J 

(2011d) Revision of Glomeromycetes with entrophosporoid and glomoid spore formation with three new 

genera. Mycotaxon 117: 297–316. 

Oehl F, Sieverding E, Palenzuela J, Ineichen K, Silva GA (2011e) Advances in Glomeroycota taxonomy and 

classification. IMA Fungus 2:191—199. 

Examples of characteristics of spore bases and subtending hyphae in Glomeromycota. A. Glomus ambisporum. 

B. G. aureum. C. Funneliformis coronatus. D. Septoglomus constrictum. sw = spore wall layers; sp = bridging 

septum; sh = subtending hypha. See Oehl et al. (IMA Fungus 2: 191–199, 2011) for further explanation. 

Photos courtesy Fritz Oehl. 

New insights into global fungal species numbers? 

Blackwell (2011) has revisited the issue of 

how many fungi exist on Earth, and the 

impact that molecular studies, and especially 

high-throughput environmental sequencing 

has had on our understanding of the extent 

of that diversity. She draws attention to the 

state of knowledge of the fungi in particular 

habitats, and the issue of phylogenetic 

species not or hardly separable by other 

features. Attention is drawn to the increased 

number of flowering plants suggested 

to exist beyond the 270 000 used in the 

extrapolations of Hawksworth (1991): for 

example, Paton et al. (2008) provide a figure 

of 352 000 for known species, and Joppa 


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RESEARCH News 

1.5 M + ? 

et al. (2010) expect that to grow by 10–20 

% – i.e. to 387 200–422 400 species. If these 

larger figures are used, then the 6 : 1 ratio of 

fungi : plants used by Hawksworth (1991) 

would yield a figure of 2.3–2.5 M species of 

fungi. 

Blackwell also emphasises the results 

of the study of O’Brien et al. (2005) from 

environmental sequences from soil which 

suggested a total number of 3.5–5.1 M 

fungus species. However, results from highthroughput 

sequencing studies have to be 

approached with some caution as critical 

studies with bacterial populations suggest 

that they may overestimate the number of 

taxa actually present by a factor of about six 

(Quince et al. 2009). If it were justified to 

apply that factor in the O’Brien et al. study, 

their figure would not have been so far 

ahead of other estimates. 

A different approach to estimating 

global species numbers of all organisms was 

taken by Mora et al. (2011), who found 

that the description of taxa according to 

rank followed a predictable pattern across 

different groups of organisms. In the case of 

the fungi, the validity of the approach might 

be questioned as our knowledge is so poor, 

and also as they worked with a figure of just 

43 271 species of fungi – the number in the 

Catalogue of Life 2010 Annual Checklist 

(Bisby et al. 2010) rather than the 100 000 

figure currently in general use (e.g. Kirk et 

al. 2008). However, what was intriguing is 

that based on that data set, they predicted 

611 000 (± 297 000) fungal species which 

implies that only around 7 % (range 

4.5–13.5 %) are now known, perhaps not so 

different from the 5 % previously proposed 

(Hawksworth 1991). 

While it now seems that the 1.5 M 

estimate may indeed be conservative, as 

stated when it was proposed (Hawksworth 

1991), the jury remains out as to how much 

by. For that reason I am inclined to still 

work with “at least 1.5 M” as the additional 

factor is so uncertain, as I concluded a 

decade ago (Hawksworth 2001). Much 

more field-truthed data are needed to 

improve the current estimates, and as 

Blackwell points out, this “can be speeded 

by enlisting more biologists to accomplish 

the goal” (p. 434). But how can that be 

done? The answer may lie in an increasing 

recognition within the scientific community 

of the scale of the problem, the excitement 

of discovering novel taxa, and a hightened 

appreciation of the crucial role of fungi in 

so many aspects of human concern from 

health to food security and climate change. 

A paradigm shift in the foci of biological 

research may be required. 

Bisby FA, Ropskov YR, Orrell TM, Nicolson D, Paglinawan LE, et al. (2010) Species 2000 and ITIS Catalogue of Life: 2010 annual checklist. Reading: Species 2000. 

Blackwell M (2011) The Fungi: 1, 2, 3 . . . . 5.1 million species. American Journal of Botany 98: 426–438. 

Hawksworth DL (1991) The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycological Research 95: 641–655. 

Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycological Research 105: 1422–1432. 

Joppa LN, Roberts DL, Pimm SL (2010) How many species of flowering plants are there? Proceedings of the Royal Society of London, B, 278: 554–559. 

Kirk PM, Cannon PF, Minter DW, Stalpers JA (2008) Ainsworth & Bisby’s Dictionary of the Fungi. 10 th edn. Wallingford: CAB International. 

Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B (2011) How many species are there on Earth and in the Ocean? PLoS Biology 9(8): e1001127. 

O’Brien BL, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R (2005) Fungal community analysis by large-scale sequencing of environmental samples. Applied and 

Environmental Microbiology 71: 5544–5550. 

Paton AJ, Brummitt N, Govaerts R, Harman K, Hinchcliffe S, Allkin B, Lughadha EM (2008) Towards Target 1 of the Global Strategy for Plant Conservation: a 

working list of all known plant species – progress and prospects. Taxon 57: 602–611. 

Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read IF, Sloan WT (2009) accurate determination of microbial diversity from 454 pyrosequencing 

data. Nature Methods 6: 639–641. 

Powdery mildews under scrutiny 

The Special Interest Group (SIG) meetings 

held during IMC9 in August 2010 were 

exceedingly popular. Mini-reviews based on 

the SIG events have already been published 

in previous issues of IMA FUNGUS, and 

a longer review on molecular diagnostic 

methods is included in this issue (pp. 

177–189). In the case of the SIG on 

powdery mildew fungi (Erysiphales), 

convened by Uwe Braun, Levente Kiss and 

Susumu Takamatsu, the papers presented 

are published as an issue of Mycoscience 52 

(3) (May 2011) under the title ‘Biology, 

biodiversity, evolution and systematics of 

the Erysiphales’. 

The focus on the papers is on the 

biology and evolution of pathogenesis and 

variation at the molecular level in particular 

species or complexes. Aleš Lebeda et al. (pp. 

59—164) review the pathotype and race 

designations and tests used in two powdery 

mildews attacking cucurbits, Golvinomyces 

cichoracearum and Podosphaera xanthii. 

The situation has become confusing as 

a result of the use of different Cucumis 

species and cultivars in challenge testing, 

with, for example, three systems being 

used by different research groups for race 

denomination; the adoption of two sets of 

host genotypes and a concise designation 

system are commended. Quercus is host 

to more powdery mildews than any other 

genus, with over 50 species recognized on 

members of the genus. Those present on oak 

in Europe, which had all been considered 

as introduced, are reviewed by Marie-Laure 

Desprez-Loustau et al. (pp. 165–173). 

Molecular phylogenetic studies confirm 

that within Eryisphe three species are 

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involved; E. alphitoides (syn. Microsphaera 

alphitoides) which is the most pathogenic, 

E. hypophylla, and E. quercicola recently 

discovered in France and only known 

from a single ITS sequence. Affinities with 

powdery mildews known from tropical 

hosts discovered were a surprise, and hostjumping 

and specialization on Q. robur is 

postulated to have occurred in the evolution 

of E. alphitoides. Molecular phylogenetic 

studies on Erysiphe species on Ligustrum 

and Syringia (both Oleaceae) by Yusuke 

Seko et al. (pp. 174–182), revealed two 

groups which could also be distinguished 

by the pigmentation of the appendages 

to the ascomata; E. syringiae occurred 

only on Syringa and probably evolved in 

North America, and E. ligustri and E. 

syringae-japonicae on Ligustrum and Syringa 

respectively, with the last species having 

arisen in eastern Asia. 

Three contributions are on biological 

and development aspects. Roger Cook et 

al. (pp. 183–197) report on appressorium 

formation on the germ tubes of 36 Erysiphe 

species. Unlobed appressoria (“alobatustype”) 

occurred in three species, while 

in others they were lobed. Viewed from 

below in the plane in contact with the 

host, five-lobed appressoria were formed by 

120° dichotomous branchings; species of 

Neoerysiphe and Phyllactina branched at the 

same angle. I found the light and scanning 

electron micrographs and explanatory 

drawings particularly illuminating. In 

Oidium neolycopersici, Yoshihiro Takikawa 

et al. (pp. 198–203) endeavoured to fund 

whether the point of initiation of germ 

tubes was triggered by contact with the 

host leaves or if it was predetermined; in 

their experiments using electrostatic spore 

collectors and different substrates, they 

showed germination was always stimulated 

by contact but that they almost exclusively 

arose subterminally regardless of the actual 

point of contact. Takikawa et al. (pp. 

204–209) also studied the behaviour of 

conidia in E. trifoliorum. In that species, on 

host and non-host leaves as well as several 

artificial surfaces; they discovered that the 

so-called “two-step” germination process 

was actually the result of a first unsuccessful 

attempt at host penetration. Microcyclic 

conidiogenesis, the formation of conidia 

directly from a conidium without little 

or no hyphal growth, is documented by 

Alexandra Pintye et al. (pp. 213–216) 

from species of four genera based on light 

and low-temperature scanning electron 

microscopy. 

Finally, Uwe Braun (pp. 210–212) 

provides a brief overview of the current state 

of systematics in these fungi, which includes 

a synopsis of the tribe and subtribe system 

to be used in the forthcoming Manual of 

the Erysiphales (Powdery Mildews) he has 

prepared with Roger Cook and which is 

expected to be published in April 2012; 

that work will evidently recognize about 

820 species, a marked increase from the 515 

accepted in Uwe’s 1987 monograph – it will 

be a “must have” for both field mycologists 

and plant pathologists worldwide. 

RESEARCH NEWS 


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BOOK NEWS 

21 st Century Guidebook to Fungi. By David Moore, Geoffrey D. Robson & Anthony P. J. 

Trinci. 2011. ISBN 978-1-107-00676-8 (hdbk), 978-0-521-18695-7 (pbk). Pp. xii + 627, 

illustr., CD. Cambridge University Press, Cambridge, UK. Price £ 80, US$ 135 (hdbk), 

£ 40, US$ 65 (pbk). 

A modern mycological textbook for use in 

advanced university courses has been much 

needed, as there have already been so many 

advances in our understanding of their 

genetics, development, and relationships 

this century. This book grew out of courses 

the authors have taught at the University 

of Manchester for many years. It aims to 

capture the excitement, and present a new 

look, of fungi as they are now understood in 

a “systems biology” framework, emphasizing 

interactions with other organisms, adopting 

an integrated rather than a reductionist 

approach, utilizing modelling and 

bioinformatics when appropriate - and 

enhancing accessibility by an accompanying 

CD not just with the entire text, but also 

hyperlinks to both key websites and cited 

references. 

The 18 chapters are organized into six 

parts: Nature and origin of fungi; Fungal 

cell biology; Fungal genetics and diversity; 

Biochemistry and developmental biology of 

fungi; Fungi as saprotrophs, symbionts and 

pathogens; and Fungal biotechnology and 

bioinformatics. All are well-illustrated by line 

drawings, half-tones, tables, and “resource 

boxes”, and are accompanied by a list of 

“references and further reading”. Coloured 

versions of the photographs are provided 

in two bound-in signatures and on the CD, 

though the quality of the printed ones is not 

optimal. Also, while there is a note to say in 

the main text if an illustration is also in the 

coloured sections, no precise indication is 

provided which hinders their location. 

While most points that might be 

expected to be in a modern text of fungi 

are there, the balance of coverage reflects 

the research interests of the authors, and 

also the types of courses where fungi might 

still constitute a unit in a UK university 

today. More attention is consequently 

accorded to developmental, physiological, 

and industrial aspects (including massculture 

and fermenter design), for example, 

rather than classification, biogeography, and 

community ecology. However, although the 

overview of the fungi and their classification 

only have 40 pages in the main body of 

the book, and much of that occupied by 

photographs, there is an Appendix which 

includes descriptions down to order with 

example genera indicated. On the ecological 

side, it is great on ecosytem processes, but 

has little on community ecology, and no 

section on biogeography. The coverage of 

uses of fungi is particularly extensive and 

informative, and also well-illustrated, but 

surprisingly there was no section devoted to 

biodeterioration and challenge-testing which 

are so important in manufacturing. Student 

appeal might be enhanced by some perhaps 

rather unexpected features, such as that 

on the origin of the universe and of Earth, 

detailed treatments of cheese manufacture 

and ripening, and headings like “Ten ways 

to make a mushroom”. A detailed discussion 

of a Clitocybe nebularis colony arising under 

paving slabs at David Moore’s home garden 

is novel approach to the teaching of fungal 

development and structure, but did it really 

merit 10 pages of colour plates? 

A major innovation and “plus” for this 

work is the CD. The imbedded hyperlinks 

are not just to an extraordinary number of 

websites, but to all cited original papers with 

DOI numbers. The CD uses Firefox and I 

was most impressed by the speed at which 

links were made. While not all papers will be 

open-access and available for free download, 

at least their abstracts can be found; and a 

click on a book title or chapter can take you 

directly to the publisher’s sales page. Those 

fortunate to be located at institutions with 

electronic subscriptions to journals that are 

not open access, however, will quickly reach 

the full-texts. This ability to link students 

directly from a textbook to primary research 

papers is really exciting and sure to enthuse. It 

will also be a great short-cut for mycologists 

in general who have access to the CD. I can 

imagine the CD being carried around in 

many a student’s bag, not least as even the 

paperback version of the book weighs just 

over 1.9 kg. 

I particularly liked the line drawings 

incorporating colour explaining 

ultrastructural and developmental features. 

The quality of the colour photographs on the 

CD is superb, but the versions in the volume 

would have benefitted from being printed 

to higher specifications. For the systematist 

there are inevitably some minor irritations, 

for instance the indication of Pneumocystis 

carinii and P. jirovecii as synonyms (p. 30) 

when they are actually distinct species, 

a Coprinus that did not get changed to 

Coprinopsis (Fig 11.2) through most were 

changed where appropriate, and use of the 

kingdom name Chromista over Straminipila 

on the grounds of priority of publication, 

a criterion that does not apply above the 

rank of family. However, such small points 

are more than compensated for by a second 

Appendix which provides a splendid account 

of the terminology of mycological structures 

from mycelia to sporophores, and including 

conidiogenesis patterns, and types of asci, 

basidia, hyphae, sporophores, and tissues. 

No two groups of authors are ever likely 

to concur about just what should go into 

an advanced student text, and what the 

balance between the various topics should 

be. There can be no doubt, however, that 

this will be great as a main text for mycology 

courses at advanced degree and masters 

levels, and also a valuable sourcebook for 

up-to-date information on diverse aspects 

for the subject. The authors can be proud of 

this achievement, which has the potential 

to enthuse and inspire a new generation of 

experimental mycologists. I cannot commend 

it too highly, and am recommending on the 

postgraduate courses to which I contribute. 

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Evolution of Fungi and Fungal-like Organisms. Edited by Stefanie Pöggeler & 

Johannes Wöstemeyer. 2011. ISBN 978-3-642-19973-8. Pp. xix + 345, figs 60, col. 10. 

Heidelberg, Germany: Springer. [The Mycota Vol. XIV. Edited by Karl Esser.] Price 

£ 180, 199.95 €, US$ 269. 

There have been so many insights into the 

evolution of fungi since the two Systematics 

and Evolution books in The Mycota (Vol. 

VII A & B, McLaughlin DJ, McLaughin 

EG, Lemke PA, eds, 2001), that a volume 

addressing this topic was a natural extension 

of the series. Essentially, this is a mixture of 

12 in-depth topical and scholarly reviews 

on different aspects of an enormous topic 

arranged in four groups. 

The first concern the ‘Evolutionary 

roots of fungi’, where there is a detailed 

and welcome discussion of the position 

of the Fungi within Opisthokonta (Carr & 

Baldaup) which they accept as including 

Rozella – which is now placed in phylum 

Cryptomycota (see IMA Fungus 2: 173–175, 

2011). Opisthokonts other than Fungi 

are referred to as Holozoa, and as sister 

to Fungi and also outside Holozoa are a 

group of amoeboid protists which were 

unfamiliar to me (Nucleariida) and are yet 

to be included in multigene phylogenies 

along with microsporidians and other 

Fungi. The situation with Microsporidia is 

lucidly explained by Williams & Keeling, 

who consider that these mitochondriondeficient 

organisms may have acquired 

an ADP/ATP transferase by horizontal 

gene transfer from bacteria which enables 

them to exploit ATP in animal hosts. The 

impact of environmental DNA analyses 

on the concept of the fungal kingdom is 

discussed by Jones & Richards; they explain 

gene-library and 454 amplicon sequencing 

approaches and report in particular on 

their studies of sequences from marine and 

freshwater habitats and the discovery and 

visualization of Cryptomycota. 

Three chapters are included under 

‘Evolution of signalling in fungi and fungallike 

organisms’. The phrase ‘fungal-like’ is 

particularly appropriate as the first concerns 

dictyostelids, which are now placed in 

the amoebozoans as a sister group to the 

opisthokonts. Dictyostelium discoideum has 

been the subject of penetrating studies since 

Kenneth B. Raper started to investigate 

it in the 1940s and these still make the 

pages of Nature today. Schaap provides a 

review which also covers the relationships 

of social amoebae, and a diagrammatic 

phylogenetic tree showing the evolution 

of 20 morphological features which many 

working on true fungi will wish they could 

emulate for ‘their’ model taxa. Studies 

on Saccharomyces cerevisae surely most 

closely approach those on Dictyostelium, 

and Pöggeler reviews the occurrence and 

functions of pheromones and pheromone 

receptors in both this yeast and diverse 

filamentous ascomycetes where pheromone 

genes have also been found in both homoand 

heterothallic species. A particularly 

detailed and welcome review of mating 

types and sexuality types in basidiomycetes 

by Kües, James & Heitman follows, ranging 

from rusts and smuts to different orders 

of tremelloid fungi and agarics; the new 

term ‘unipolar’ is coined for homothallic 

reproduction involving a single mating type 

producing meiotic progeny. 

The largest section concerns the 

‘Evolution of mutualistic systems and 

metabolism in fungi’. Schüßler & Walker, 

trace the origins of Glomeromycota from the 

earliest fossils > 460 Myr ago and discuss 

their role in the evolution of land plants 

as well as providing an overview of the 

taxonomy of the group. Schmitt addresses 

sporophore evolution in ascomycetes, 

including lichenized groups, and the 

now well-established development of 

similar ascomata in diverse orders and 

classes – but not the currently contentious 

issue of whether the earliest filamentous 

ascomycetes were lichenized and subsequent 

loss of the ability to form lichens. The results 

of genomic analysis in Dothideomycetes 

are reviewed by Hane, Williams & Oliver 

now data on three representatives are 

available, all plant pathogens (Leptosphaeria 

maculans, Mycosphaerella graminicola, 

and Phaeosphaeria nodorum); the extent 

of the data is impressive, and includes 

mitochondrial DNA and evidence of 

horizontal transfer of pathogenicity genes. 

The last two contributions in this section 

concern the evolution of particular groups 

of genes or gene families. Those involved 

in ‘secondary metabolism’ are treated 

by Teichert & Nowrousian, principally 

polyketide synthase (pks) genes, but also 

covered are peptides, alkaloids, terpenes and 

melanins – the latter being treated in more 

depth than I have noted elsewhere. Genes 

involved in carbonic anhydrase enzyme 

production in fungal-like as well as fungal 

organisms are reviewed by Elleuche; these 

encode five unrelated classes of enzymes, 

and plant-type β-carbonic anhydrases in 

filamentous ascomycetes is linked to gene 

duplication following separation from 

yeasts. 

The final section, ‘Evolutionary 

mechanisms and trends’, has just two 

chapters. The first, by Whittle & 

Johannesson, returns to the evolution of 

mating-type loci and chromosomes, but 

this time in Neurospora tetrasperma – and 

so might have been placed in the second 

section of the book. In a similar way, 

the second, on the evolution of special 

metabolisms by Schimek, could have been 

placed in the third group with that covering 

pks genes. It is, however, much more wideranging 

in the range of compounds covered 

and serves as a comprehensive introduction 

to this fascinating aspect of fungi. 

I can appreciate that the editors had 

difficult choices to make in deciding 

what to include in a volume of this title. 

I was excited at the prospect of the title, 

BOOK NEWS 


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BOOK NEWS 

and found some of the contributions 

illuminating, but was left feeling frustrated 

by what was not there. Examples include: 

the overall fossil record (including a 

discussion of the enigmatic gigantic 

Prototaxites now increasingly featured 

in fungal texts), the nature of the first 

filamentous fungi on land, the evolution of 

ectomycorrhizas and expansion of forests, 

convergent evolution in basidiomes, cospeciation 

with animals (including insects) 

and plants, biogeography and speciation 

through genetic drift, evolution in mitotic 

fungi, cryptic speciation, species concepts, 

etc. Perhaps some of these topics will be 

covered in future in the six additional 

volumes which Karl Esser indicates are to 

come in an addendum to the series Preface 

(p. xi)? Availability will remain a problem 

because of the cost, though an e-book 

version can also be purchased, However, 

I really must concur with the sentiments 

expressed by Frank Odds (2004) when 

reviewing Volume XII that “Perhaps 

The Mycota could form the embryo for a 

new review journal in mycology?” Surely 

that would be the best way to make such 

scholarly reviews more widely available. 

Odds F (2004) [Book review.] Medical mycology. The Mycota. XII. Human Fungal Pathogens. Mycological Research 108: 463–464. 

Metagenomics: current innovations and future trends. Edited by Diana Marco. 2011. 

ISBN 978-1-904455-87-5. Pp. xii + 296, col. pl. 1. Caister Academic Press, Norfolk, UK. 

Price £ 159, US$ 319. 

Metagenomics, the comparison of entire 

communities from the genomes of the 

constituent organisms, is exciting cuttingedge 

research with respect to the exploration 

of phylogenetic and functional genetic 

diversity in particular ecological niches. The 

approach is very much technique-driven, 

as possibilities expand as instrumentation 

and protocols develop. So far, the majority 

of studies have focussed on bacterial 

groups and viruses, but the approach is 

increasingly being taken up by fungal 

ecologists fortunate to have access to the 

necessary equipment – and generating some 

illuminating results, especially with respect 

to phylogenetic diversity. 

In entering a new field or using a new 

technology, topical syntheses can be viewed 

as equivalent to a crash-course. This text has 

15 chapters, only one developed to fungi 

(see below), with the rest centred on either 

techniques or bacterial groups or viruses 

in particular communities. The value of 

this text for mycologists is that in presents 

state-of.-the art information on the methods 

and their limitations, and has examples of 

actual applications in other groups that 

might be mirrored in future mycological 

investigations. 

The chapter on current approaches 

(Meiring et al., pp. 1–19) is especially 

informative, explaining the theory 

and practice of both sequence-driven 

and function-driven approaches and 

how they relate to the complementary 

metaproteomics and metabolomics. There 

is a separate chapter on next-generation 

sequencing and the use of 454 and other 

sophisticated machines (Walshaw et al., 

pp. 63–88) which I found to be a most 

illuminating introduction to the protocols 

and procedure of this much talked-about 

methodology. That on microarrays (van 

Norstrand et al., 265–288) was similarly 

most helpful, and includes a section on 

GeoChips (functional gene arrays) which 

were new to me. Other chapters cover 

topics such as bacterial genealogy, viruses, 

the human microbiome, sequencing from 

uncultured single cells (using flow cytometry 

for their separation), bioremediation, host 

engineering and enzyme discovery, nonfungal 

plant pathogens. 

The single fungal chapter concerns 

arbuscular mycorrhizal fungi, and has 

been prepared by Paola Bonfante´s group 

in Turin (Bianciotto et al., pp. 161–178). 

This includes an overview of all studies 

using metagenomic approaches to date, 

from the pioneering work by Alastair 

Fitter´s group in 1998–99). The practical 

relevance is clear in view of the large 

numbers of species that would otherwise 

have remained unrecognized by reliance 

on non-molecular approaches. By the end 

of September 2009, there was a staggering 

12 274 “uncultured” AM fungal genomes 

recognized for which there was no link 

to described morphospecies. The issue of 

overestimations due to artefacts arising from 

the fragmentation of genomes is flagged up 

here, and perhaps might have benefited from 

more discussion in some others as this is so 

critically important to estimates of actual 

organismal diversity derived. 

In summary, if you are a mycologist 

contemplating adopting, or even already 

using, metagenomic and next-generation 

sequencing technologies, this work 

should be consulted when designing work 

programmes or interpreting the mass of 

generated data. 

Los Hongos de Panamá: introducción a la identification de los macroscópicos. By 

Gastón Guzmán & Meike Piepenbring. 2011. ISBN 978-607-7579-21-2. Pp. xiv + 372, 

figs 710 (most col.), tables 3. Xalapa, Mexico: Instituto de Ecología A.C. Price: Not indicated. 

(64) ima fUNGUS

December 2010 was the centenary of the 

arrival of the first scientific expedition of 

the Smithsonian Institution to Panamá, 

and what better way to mark the event than 

by a splendidly illustrated work on fungi. 

Meike Piepenbring, who is based at the J. 

W. Goethe Universität in Frankfurt but 

also holds a position in the Universidad 

Autónoma de Chiriquí in Panamá, is 

well-known for her detailed and on-going 

investigations into the diversity of fungi of 

all kinds that occur in Panamá. Here she 

has joined forces with Gaston Guzmán, 

who has, and continues to, so energetically 

promote mycology in the region. 

It was pleasing to see a broad 

interpretation of macroscopic fungi 

adopted, encompassing not only larger 

basidiomycetes and discomycetes, but also 

a range of slime-moulds, pyrenomycetes, 

and lichens. In all, 226 species are treated in 

detail, with discussions of their microscopic 

as well as macroscopic features, differences 

from similar taxa, and references to 

pertinent literature; they are arranged 

alphabetically which facilitates their 

location. The colour photographs include 

some close-ups showing diagnostic features 

such as gill types, or slices through them 

to show the arrangement of perithecia in a 

stroma (that of Hypoxylon haematostroma 

on p. 136 is a striking example). According 

to the Abstract (p. ii), over 700 species are 

covered to some extent. There is a series 

of 13 keys to genera, and in some cases 

species, based on the gross morphology 

of the sporophores, an introduction 

including microscopic characters which 

is well-illustrated by clear line drawings, a 

glossary, taxonomic arrangement of taxa 

discussed, an appendix which includes 

further observations on 29 genera or groups 

of species (with especially informative 

discussions of several gasteroid groups), 

a taxonomic index which lists synonyms 

under treated species, and a main index 

including entries by species epithet. 

This lavishly illustrated book should 

do much to encourage both students and 

citizen scientists to take a deeper interest 

in fungi. While it is in Spanish, it is 

nevertheless easy to use by Anglophones 

with knowledge of a few key words and 

mycological terms. I just wish it had been 

available when I visited Barro Colorado 

Island in 1995, and was so fascinated by the 

array of Xylaria species sprouting from logs 

– 11 receive full treatment here, several of 

which I had not seen colour photographs of 

before. While the colour reproduction and 

quality of some of the photographs might 

have been better, and the taxonomy is in 

some cases conservative (e.g. the retention of 

Coprinus for C. cinereus and C. stercoreus), 

this production represents a tremendous 

achievement of which the authors can be 

justly proud. 

The production of this book was 

made possible through the support of the 

Smithsonian Tropical Research Institute 

(STRI) in Panamá and eight other bodies. 

Only 500 copies have been printed, so if you 

work on, or are interested in, Central and 

South American fungi, it would be advisable 

to endeavour to secure a copy soon as it is 

sure to prove very popular in the region. 

Champignons Comestibles des Forêts denses d’Afrique Centrale: taxonomie et identification. 

By Hugues E. Ndong, Jérôme Degreef & André De Kesel. 2011. ISSN 1784- 

1283 (hd copy), 1784-1291 (online PDF). Pp. viii+ 253, figs 151 (many col.), tables 1, 

backpocket. Brussels, Belgium: Royal Belgian Institute of Natural Sciences. [ABC Taxa 

Vol. 10.] Price: Free (developing countries), 15.45 € (other countries). 

BOOK NEWS 

This work is one of series aimed at 

accelerating taxonomic capacity building 

in developing countries, and the first on 

fungi. The aim is to provide sufficiently 

detailed state of the art treatments to enable 

recipients to embark on the taxonomy of 

the group treated. Consequently, almost one 

third of the book is devoted to background 

information: current knowledge, 

ethnomycology, preparation for a collecting 

trip, field and laboratory requisites, 

collection, documentation, photography, 

description, microscopic preparations, 

measurements, preservation, and herbarium 

formation. In order to facilitate detailed 

descriptions there is a detailed account of 

anatomical and morphological features 

illustrated by fine line drawings. A great 

deal of care has been taken to make sure 

a beginner would find all he or she needs 

to start to make contributions to the field, 

though a section on nomenclature could 

have been a useful addition. Inside the 

back cover, is a pocket including a sample 

recording card for descriptive information, 

where pertinent characters can be quickly 

circled to facilitate the rapid processing of 

specimens. 

Accounts of 62 edible species follow, 

most with a text page facing a figure which 

includes well-executed coloured illustrations 

of intact sporophores and vertical sections, 

and also drawings of key microscopic features. 

In some cases photographs of fresh specimens 


(65)

BOOK NEWS 

are also provided. The species are drawn 

from a wide range of genera, amongst which 

are Amanita, Auricularia, Cantharellus, 

Cookeina, Lactarius, Marasmius, Polyporus, 

Russula, Schizophyllum, and Termitomyes. 

The text has detailed macro- and microscopic 

descriptive data, information on ecology 

and distribution, and notes discussing 

the separation from similar taxa – but 

surprisingly not on preparation or taste. A 

comprehensive glossary is provided, and the 

reference list is extensive. 

The authors, all who have experience 

of working in the region, have clearly put 

an immense amount of thought into the 

volume and it is deserves to be widely 

distributed in central Africa. On the back 

cover, Bart Buyck states that the book 

should occupy prime position in the 

libraries of mycologists, particularly for the 

full introduction and practical approach; 

I totally concur with his sentiments. 

The concept of making this work freely 

available in developing countries can only 

be applauded and was made possible by 

the foresight of the Belgian Development 

Cooperation. That is an aspect of capacity 

building which is too often overlooked in 

aid programmes. My one sadness is that 

the text is entirely in French, as an English 

translation would be so valuable for use 

in the non-Francophone countries in the 

region; it would be tremendous if additional 

funds to do that could be found. 

Love, Sex and Mushrooms: adventures of a woman in science. By Cardy Raper. 2011. 

ISBN 978-0-615-43440-7. Pp. xii + 254, illustr. Burlington, VE: C. Raper. Price: US$ 

18.95. 

This is a very personal, and in parts emotive, 

account of aspects of both the personal and 

professional life of Cardy Raper, the wife 

of the renowned fungal geneticist John 

R. Raper (1911 –1974) 1 and well-known 

for his monograph on the genetics of 

sexuality in macromycetes (Raper 1966). 

She recounts the trials she has experienced 

in establishing herself as a respected 

fungal geneticist in her own right, in an 

academic climate which often seemed to 

conspire against female scientists. She also 

documents the tedious and often frustrating 

attempts to obtains samples of hormones 

involved in the sexual behaviour of Achlya, 

and to obtain isolates of elusive mating 

types before their work changed its focus 

to Schizophyllum commune – a change in 

course largely due to graduate student Haig 

Papazian arriving from London. There are 

insights into her experiences as a faculty 

wife in the USA and as a mother, and into 

her personal life and relationship problems 

that she had to contend with. There are also, 

perhaps sometimes tongue-in-cheek, asides 

about other mycological luminaries she 

encountered or who influenced her, such 

as Karl Esser and Dirk Wessels. The actual 

science is not described in detail, however, 

though there are tantalizing tid-bits here 

and there; not being a fungal geneticist, I 

would have found citations and discussions 

of actual papers illuminating (those by 

Cardy are, however, listed on her website, 

http://cardyraper.com). 

Cardy comes over as a person determined 

to succeed and full of enthusiasm for her 

chosen area of science. This autobiography 

demonstrates that a scientific path can be 

long and hard, and that is something as 

true now as it was during Cardy’s struggling 

years – especially when tenure is now so 

difficult to secure in many countries. The 

preliminary pages include comments from 

two distinguished fungal geneticists, Lorna 

Casselton and Peter Day. Lorna’s ends with 

the phrase “This is the personal account 

of an exceptional scientist”, and Peter’s 

with the remark that she lived up to the 

slogan of a Harvard band, “Illegitimum 

non carborundrum: don’t let the bastards 

grind you down”. It could be seen either as a 

cautionary tale or as an inspiration to aspiring 

researchers, and of course will also be of 

interest to those wishing to know more of 

both John and Cardy’s backgrounds. 

1 

Brother of Kenneth B. Raper (1908–1987). 

Raper JR (1966) Genetics of Sexuality in Higher Fungi. New York: Ronald Press. 

(66) ima fUNGUS

FORTHCOMING MEETINGS 

International and regional meetings which are entirely mycological or have a mycological content 

2012 

International Association for Lichenology (IAL7) – Lichens: from genome to ecosystems in a changing world 

9–13 January 2012 

Bangkok, Thailand 

Contact: Lichen Research Unit, Ramkhamhaeng University; e-mail: lichen.ial7@gmail.com 

 

Fungal Pathogens: from basic biology to drug discovery [A Keystone Symposium] 

15–20 January 2012 

Community Convention Center, Santa Fe, New Mexico, USA 

 


5 th Advances Against Aspergillosis 

26–28 January 2012 

Lutfi Kirdar Convention and Exhibition Centre, Istanbul, Turkey 

Contact: Hartley Taylor Medical Communications, Henderson House, New Road, Princess Risborough, Buckinghamshire HP27 0JN, UK; 

derry@hartleytaylor.co.uk 

 

International Conference on Mycology and Plant Pathology: Biotechnological Approaches 

27–29 February 2012 

Baranas Hindu University, Varanai, India 

Contact: Dr Ravindra N. Kharwar, Centre for Advanced Studies in Botany, Baranas Hindu University, Varanai, 221005 India; rnkharwar@ 

gmail.com or icmpb2012@gmail.com 

 

11 th European Congress of Fungal Genetics 

30 March–2 April 2012 

Phillips-Universität Marburg, Germany 

Contact: Congress Office, c/o Intelligent Events, 126 High Street, Dunblane, Perthsire FK15 0ER, UK; contact@ecfg.info 

 

CBS Symposium: One Fungus = Which Name? 

[In collaboration with the Nomenclature Committee for Fungi and the International Commission on the Taxonomy of Fungi] 

12–13 April 2012 

Amsterdam, The Netherlands 

Contact: Pedro Crous, CBS-KNAW Fungal Biodiversity Centre, PO Box 85167, 3508 AD Utrecht, The Netherlands; p.crous@cbs.knaw.nl 

 

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11–15 June 2012 

Berlin, Germany 

 

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30 July–1 August 2012 

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China; doris@bit-ibio.com 

 

2013 

10 th International Congress of Plant Pathology 

25–31 August 2013 

Beijing, China 

 

2014 

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3–8 August 2014 

Bangkok Convention Center, Bangkok, Thailand 

Contact: Lekha Manoch; e-mail: agrlkm@ku.ac.th 

IUMS XIV International Congress of Mycology 

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(68) ima fUNGUS

doi:10.5598/imafungus.2011.02.02.01 IMA Fungus · volume 2 · no 2: 113–120 

One Fungus = One Name: DNA and fungal nomenclature twenty years after 

PCR 


ARTICLE 

University of California Berkeley, 111 Koshland Hall, Berkeley, CA 94720-3102, USA; e-mail: jtaylor@berkeley.edu 

Abstract: Some fungi with pleomorphic life-cycles still bear two names despite more than 20 years of molecular 

phylogenetics that have shown how to merge the two systems of classification, the asexual “Deuteromycota” 

and the sexual “Eumycota”. Mycologists have begun to flout nomenclatorial regulations and use just one name 

for one fungus. The International Code of Botanical Nomenclature (ICBN) must change to accommodate 

current practice or become irrelevant. The fundamental difference in the size of fungi and plants had a role in 

the origin of dual nomenclature and continues to hinder the development of an ICBN that fully accommodates 

microscopic fungi. A nomenclatorial crisis also looms due to environmental sequencing, which suggests that 

most fungi will have to be named without a physical specimen. Mycology may need to break from the ICBN 

and create a MycoCode to account for fungi known only from environmental nucleic acid sequence (i.e. ENAS 

fungi). 

Key words: 

Amsterdam Declaration 

ENAS 

MycoCode 

nomenclature 

pleomorphic fungi 

Article info: Submitted: 8 June 2011; Accepted: 15 June 2011; Published: 12 July 2011. 

INTRODUCTION 

It has been a bit over two decades since the polymerase chain 

reaction (PCR) changed evolutionary biology in general and 

fungal systematics in particular. Even before PCR became 

generally available, mycologists realized that the evolutionary 

record contained in the nucleic acid sequence of every fungus 

could be used to merge two systems of nomenclature that 

had been employed in most fungi, i. e. one for the “Eumycota” 

based on sexual morphology and the “Deuteromycota” based 

on all other morphologies (Berbee & Taylor 1992, Bruns et al. 

1991, Guadet et al. 1989, Reynolds & Taylor 1992). Why, then, 

has it taken more than two decades for nomenclature to catch 

up with biology, and why is the possibility of nomenclatorial 

rapprochement now being taken seriously? These questions, 

and three others posed to the participants in this symposium 

will be the subject of this contribution: Does DNA sequencing 

make dual nomenclature superfluous? Can the International 

Code of Botanical Nomenclature (ICBN) (McNeill et al. 2006) 

be modified to enable this process, or would a MycoCode 

be more effective? How can the mycological community get 

rid of the legacy of dual nomenclature and Article 59 without 

nomenclatural chaos? 

Two examples illustrate the practical problems raised 

by dual nomenclature. First, this year, while serving as a 

member of a governmental committee researching the 

use of mycoherbicides to eradicate drug crops, it fell to me 

to explain the nomenclature of two poppy pathogens that 

are sister species, one named as a teleomorph Crivellia 

papaveracea and the other as an anamorph, Brachycladium 

papaveris (Inderbitzin et al. 2006) (Fig. 1). The fifteen other 

members of the committee, eleven academics and four very 

knowledgeable staff, stared at me in disbelief when I said that 

sister species could have different generic names. Second, 

together with Tom Bruns, I have been directing research 

about fungi that naturally decay plants proposed as sources 

of lignocellulose for the production of biofuels. In the course 

of this work, we have sequenced ITS using DNA isolated 

from the decaying grasses and compared the sequences to 

those deposited in GenBank. Often, a single sequence will be 

attached to two names; you guessed it, it’s the same fungus 

with some GenBank sequences having been deposited 

under the teleomorph name and others under the anamorph 

name. Perpetuation of dual nomenclature when we have the 

means to abandon it is hindering mycology, both scientifically 

and socially. 

Dual nomenclature has persisted for the past 20 years 

because few mycologists are deeply interested in both 

molecular phylogenetics and nomenclature. One Fungus 

= One Name has gained momentum, as evidenced by this 

conference, because mycologists who are studying the 

Dedication: Dedicated to Don Reynolds, mycological iconoclast, 

whose sabbatical visit to Berkeley from the Los Angeles 

County Museum of Natural History more than 20 years ago 

stimulated thought about One Fungus = One Name. 

© 2011 International Mycological Association 

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volume 2 · no. 2 113


ARTICLE 

Pleospora 

Alternaria 

Crivellia papaveracea/Brachycladium penicillatum 

Crivellia sp (unnamed)/Brachycladium papaveris 

Fig. 1. Phylogenetic relationships of the sister species Crivellia papaveracea 

and Brachycladium papaveris, the former named as teleomorphic 

and the latter as an anamorphic fungus. The Crivellia state 

of B. papaveris remains unnamed due to a lack of suitable material to 

serve as a nomenclatural type (Inderbitzen et al. 2006). 

molecular phylogenetics of economically important fungal 

groups have begun naming newly recognized genus-level 

clades with just one Ascomycota name, whether or not 

the fungus exhibits sexual reproduction. The first thorough 

exploration of this practice was provided by Crous et al. 

(2006), whose revision of the Botrysphaeriaceae includes 

this sentence, “Separate teleomorph and anamorph names 

are not provided for newly introduced genera, even where 

both morphs are known.” Where a teleomorph name was 

available, as in the case of Botryosphaeria, the authors used 

it. Where only anamorph names were available, they were 

used, e.g. Macrophomina or Neoscytalidium. Where a new 

clade was segregated from an existing teleomorph genus, 

and best distinguished by the anamorphic morphology, the 

new name reflected the anamorph, e.g. Neofusicoccum. 

Matters were taken further in a study of Penicillium species 

by Houbraken et al. (2010). As they put it, “Using this approach 

and applying the concept of one name for one fungus (Reynolds 

& Taylor 1992), we have chosen to describe these two 

species under [their] anamorphic name.” That is, Houbraken 

et al. described new species that have both anamorphic and 

teleomorphic states as species in the anamorph-typified genus 

Penicillium and ignored the existing teleomorphic generic 

name, Eupenicillium. These actions are clearly outside the 

ICBN and constitute a social rebellion. Though smaller and far 

less important than social rebellions concerning, for example, 

women’s rights, the rights of African Americans, or those of 

homosexuals, this mycological rebellion is similar to the others 

in that activism has outpaced the law and the law must now 

change or become irrelevant. 

Dual nomenclature has a long history. The choice made 

by Houbraken et al. ( 2010) to use the anamorph name 

Penicillium over the teleomorph name Eupenicillium for one 

of the most economically important fungi echoes the choice 

made more than 40 years earlier by Raper & Fennel (1965) 

when they applied the anamorphic name Aspergillus to all 

members of that genus whether or not the species also 

produced a sexual structure. Forty years are not enough to 

understand the origins of dual nomenclature, to do that we 

have to go all the way back to Linnaeus and the beginning 

of botanical nomenclature. In this tour back through time, our 

guides will be Weresub &Pirozynski through their excellent 

article on the history of fungi that produce both meiotic 

and mitotic spores, that is, pleomorphic fungi (Weresub 

& Pirozynski 1979) and the opening chapters of Selecta 

Fungorum Carpologia, the monumental work of Louis-René 

Tulasne and Charles Tulasne (Fig. 2) (Tulasne & Tulasne 

1861). 

The Tulasne’s point out that Linnaeus based his plant 

taxonomy on floral morphology and that he could demonstrate 

that each plant had but one type of flower. At a time when fungi 

were considered to be plants, and fungal spores were equated 

with seeds, Linnaeus extended his taxonomic concept to fungi. 

The Tulasne brothers then argue that Linnaeus had such an 

influence over his mycological contemporaries, Fries foremost 

among them, that these mycologists were in denial about 

pleomorphy, despite their being able to see more than one 

type of “seed” through their lenses. 

“In the Mucedinei [Fries] sees the conidia . . . but everywhere 

he flatly denies that there occur “two kinds of sporidia on the 

same plant”, exactly as if he had heard, sounding in his ears, 

the loud voice of Linnaeus, crying “ It would be a remarkable 

doctrine – that there could exist races differing in fructification, 

but possessing one and the same nature and power; that one 

and he same race could have different fructifications; for the 

basis of fructification, which is also the basis of all botanical 

science, would thereby be destroyed, and the natural classes 

of plants would be broken up” (Tulasne & Tulasne 1861: 48 1 ). 

The brothers go on to chide Linnaeus, adding “But since 

the illustrious author always completely abjured the use 

of magnifying glasses, and therefore scarcely ever tried to 

describe accurately either conidia or spores, we fear (may he 

pardon the statement) that he really knew very few seeds of 

either kind” (Tulasne & Tulasne 1861: 48-49). The influence 

that the size of an organism has on its systematics can be 

profound (Taylor et al. 2006). The fact that the overwhelming 

majority of plants are macroscopic while the overwhelming 

majority of fungi are microscopic still affects nomenclature and 

will be revisited near the end of this article. 

Louis René and Charles Tulasne went on to argue 

against mycological denial of pleomorphy when they wrote, 

“The fungus upon which we are now touching [Pleospora] is 

not only almost the commonest of all belonging to its order, 

but also affords a wonderful proof of our doctrine concerning 

the multiple nature of the seeds of species of fungi“ (Tulasne 

& Tulasne 1861: 248). One cannot help wondering if the 

brothers guessed not only that their work was controversial, 

but that the mycological world was heading toward dual 

nomenclature, when they wrote, “As today we have seen 

the various members of the same species now unwisely torn 

from one another against the laws of nature . . .” (Tulasne & 

Tulasne 1861: 189). 

Alas, when the most useful characters that could be used 

for classification were meiosporic, and when many fungi 

did not exhibit them, there were not many options and the 

one that prevailed was dual nomenclature. Fuckel, a retired 

1 

The English translations are from the 1931 Clarendon Press 

(Oxford) edition, and were prepared by W B Grove and edited by A H 

R Buller and C L Shear. 

114 

ima fUNGUS

One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR 

ARTICLE 

Fig. 2. Louis Renè Tulasne (l) and Charles Tulasne (r). Photo: courtesy of the National Museum of Natural History, Paris. 

pharmacist, got the ball rolling (Fuckel 1870) and Saccardo 

did the heavy lifting with his Sylloge Fungorum beginning in 

1882 (Saccardo 1882). By 1910, the International Rules of 

Botanical Nomenclature (Briquet 1912) contained a section 

of Article 49, Art 49 bis (the precursor of the current Article 59), 

that forbade “botanical” names for any but the sexual stage 

of pleomorphic fungi and that is where matters rest with the 

current ICBN. 

Saccardo’s use of mature anamorph morphology is 

wonderfully convenient for classification and identification 

but, obviously, it is not based on evolutionary relationships. 

The hope that study of mitospore development would lead to 

a separate systematics based on evolutionary relationships 

began with Vuillemin (1910a, b) and Mason (1933, 1937) and 

led to the work of Hughes (1953), Tubaki (1958) and Barron 

(1968). Elegant microscopic studies of mitospore development 

followed (Cole & Samson 1979) and the movement reached 

its zenith at the second Kananaskis conference (Kendrick 

1979). Just as these studies of development were peaking, 

two events occurred in the realms of evolution and systematics 

that promised the irresistible appeal of a new approach and 

a seemingly endless supply of characters – cladistic analysis 

(Hennig 1966) and access to nucleic acid variation. 

The first applications of nucleic acid variation to fungal 

systematics involved DNA-DNA hybridization of yeasts 

(Kurtzman 1980) and then sequencing of nucleic acids. 

Pioneering work with painfully difficult RNA sequencing 

modeled on the work of bacteriologists (Walker & Doolittle 

1982, 1983) was followed by DNA sequencing (Gottschalk 

& Blanz 1984, Guadet et al. 1989, Gueho et al. 1989). But 

it was the discovery of the polymerase chain reaction (PCR) 

(Rabinow 1996, Saiki et al. 1988) that made possible the 

broad studies we now take for granted. 

The first application of PCR amplified DNA sequence 

to fungal phylogenetics demonstrated the evolution of 

hypogeous fungi from mushroom ancestors (Bruns et 

al. 1989; Fig. 3). This work relied on the development of 

primers designed to amplify regions of both mitochondrial 

and nuclear rDNA including the nuclear small subunit, large 

subunit and internal transcribed spacer (ITS), which were 

published the following year and have been cited a bit more 

often than once-a-day since then (White et al. 1990; Fig. 4). 

Boletus 

Boletus 

Suillus 

Suillus 

Rhizopogon 

Rhizopogon 

Fig. 3. Phylogenetic analysis of PCR amplified rDNA showing the 

evolution of hypogeous Basidiomycota in the genus Rhizopogon, 

from mushroom ancestors in the genus Suillus (Bruns et al. 1989). 

Adapted from Bruns et al. (1989). 



ARTICLE 

Fig. 4. Authors of the publication of PCR primers for the amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. 

Left to right: Tom Bruns, Tom White, Steve Lee, and John Taylor. Photo: taken in 2010, 20 years after the publication of White et al. (1990). 

Sporothrix schenckii 

Ophiostoma stenoceras 

Ophiostoma ulmi 

Leucostoma persoonii 

Neurospora crassa 

Fig. 5. Phylogenetic analysis of PCR amplified rDNA showing the 

anamorphic Sporothrix schenckii nestled within the teleomorphic genus 

Ophiostoma (Berbee & Taylor 1992). 

Within a few years, analysis of PCR amplified rDNA showed 

that the anamorphic Sporothrix schenckii nested within the 

teleomorph genus Ophiostoma (Berbee & Taylor 1992; Fig. 

5). This work demonstrated the integration of anamorphic 

and teleomorphic fungi based on DNA variation, as had 

earlier work on Fusarium (Guadet et al. 1989). These studies 

showed a separate classification for “Deuteromycota” to be 

superfluous. 

That same year, Reynolds & Taylor (1992) addressed the 

nomenclatural implications of using DNA variation to assess 

the phylogenetic relationships of fungi, writing, “The use of 

nucleic acid sequence allows systematists to demonstrate 

the phylogenetic relatedness of fungi possessing and 

lacking meiotically produced spores. . . . This demonstration 

presents a serious challenge to the separate classification 

of these two types of fungi and undermines the elevated 

position that characters associated with sexual reproduction 

have held in the classification of higher fungi. . . . We believe 

that all fungi should be classified in one system and that 

characters associated with sexual reproduction should be 

given the same weight as other characters. . . . By the broad 

interpretation [of Article 59] in current use, the potential for 

pleomorphy is assumed of all fungi and the Article is applied 

to all fungi. . . . With an alternative and strict interpretation 

however, Article 59 would apply only to fungal species that 

have been actually demonstrated to be pleomorphic. Under 

the latter interpretation, sexual, asexual, and pleomorphic 

fungi would be classified together and form taxa would not 

be necessary.” 

Following the Fungal Holomorph Symposium in Newport 

(OR, USA) to discuss nucleic acid variation and the integration 

of anamorphic and teleomorphic classifications (Reynolds & 

Taylor 1993), there have been presentations and discussions 

on the topic at every International Mycological Congress from 

116 

ima fUNGUS


ARTICLE 

Environmental Nucleic Acid Sequence (ENAS) 

Specimen Based 

Both ENAS and Specimen Based 

Fig. 6. Graph of the Operational Taxonomic Units (OTUs) added to GenBank from 1991 to 2009 showing the increasing proportion of OTUs 

based only on environmental nucleic acid sequence (ENAS). Adapted from Hibbett et al. (2011). 

Vancouver (1994; Taylor 1995) to Edinburgh (2010; Norvell et 

al. 2010), leading up to the present One Fungus = One Name 

conference and the Amsterdam Declaration (Hawksworth et 

al. 2011). 

Nucleic acid variability has proved to be useful in other 

areas of fungal systematics and classification related to 

mitotic fungi. Beginning with the mitosporic human pathogen 

Coccidioides immitis, DNA variation has been used to show 

that anamorphic fungi recombine in nature (Burt et al. 1996), 

that they speciate (Koufopanou et al. 1997), and that, based 

only on DNA variation, they can be described in the system 

for Ascomycota (Fisher et al. 2002). As Fisher et al. wrote 

when they described a new Coccidioides species as an 

ascomycete, “Coccidioides posadasii is morphologically 

indistinguishable from Coccidioides immitis. C. posadasii 

is diagnosed by the following nucleotide characters (given 

as the gene, the nucleotide position in the gene, and, 

parenthetically, the nucleotide fixed in C. posadasii) showing 

reciprocal fixation between C. immitis and C. posadasii: 

Chitin synthase positions 192 (A), 288 (T); Dioxygenase 

positions 872 (C), 1005 (C), 1020 (G), 1179 (C), 1272 (T); 

etc.” Of course, description is not the same as acceptance. 

In the case of Coccidioides posadasii, acceptance for this 

“Select Agent” came from an unexpected quarter, the United 

States Congress (Federal Register 2005). 

Another point made soon after PCR became available 

was that DNA, or even a DNA sequence, could act as the 

type element in a species description (Reynolds & Taylor 

1991). This observation has gained importance due to the 

advent of environmental sequencing, where mycologists use 

PCR primers for rDNA to amplify variable regions from DNA 

isolated from soil or plants. Environmental sequencing has 

begun to produce large numbers of rDNA sequences that 

document the existence of fungi for which there is neither a 

specimen nor a culture. Most importantly, ecological studes 

have shown that the number of these DNA-only fungi, 

or “Environmental Nucleic Acid Sequences” (ENAS) can 

exceed the number of fungi for which there is a culture or 

specimen (Jumpponen & Jones 2009, 2010). This imbalance 

poses a challenge to fungal classification and nomenclature 

that may dwarf the challenge of integrating anamorphic and 

teleomorphic fungi. 

David Hibbett, in his plenary presentation at IMC9 

(Hibbett et al. 2011), noted that the number of fungal OTUs 

added each year to GenBank that are based only on rDNA 

sequences (ENAS fungi) is now exceeding the number from 

fungi with cultures or specimens (Fig. 6). Ecologists face 

the prospect that most of the fungal species dwelling in their 

favourite environment can neither be cultivated nor collected; 

as a result they are going to have to rely on ENAS to assess 

the true fungal diversity. Each of these ecological studies may 

add hundreds or thousands of ENAS to GenBank. Already, 

searches of GenBank using a new ENAS mostly recover 

previously deposited ENASs, which are identified not by 

names but by numbers. Imagine two ecological studies, one 

where each new ENAS in tables or figures is associated with 

a numbered, existing ENAS and the other where the existing 

ENASs have been named – the reader would come away with 

ignorance on the one hand and understanding on the other. 

Fungal classification and nomenclature must respond to this 

challenge by developing a means of associating ENASs with 

names and the response must be timely. 

As discussed by Hibbett etal. (2011), fungi known only as 

ENAS can be named by comparison to named fungi already 

in GenBank. It seems important that this name be identified 

as attached to an ENAS rather than a culture or specimen, 



ARTICLE 

perhaps by appending ENAS as a suffix. Several essential 

issues will have to addressed before ENAS naming can begin, 

among them the problems of sequencing errors, variation in 

rDNA sequence within an individual, and accommodation of 

all these new ENAS fungi in MycoBank (Hawksworth et al. 

2010). Perhaps most unsettlingly, the naming will have to be 

automated in some way because no one can possibly name 

the thousands of new sequences that will arise in each new 

environmental study. 

At this point, a reader might fairly ask, if separate 

“Deuteromycota” and “Eumycota” nomenclatural systems 

still remain separate 20 years after their merger became 

intellectually obvious, how could anyone possibly entertain 

thoughts about the acceptance of the automated description 

of fungi based only on DNA sequence? I see two steps 

to acceptance of ENAS fungi. The first step would be a 

published demonstration of the naming of ENAS fungi, 

echoing the aforementioned social activism already in play 

for One Fungus = One Name (Crous et al. 2006, Houbraken 

et al. 2010). The second step, acceptance of named ENAS 

fungi by the ICBN, is the tougher problem and is unlikely 

to occur quickly enough to satisfy the pressing needs of 

fungal ecologists. Here, social activism alone is not going to 

be sufficient largely due to the problem of organismal size, 

mentioned above, which is as old as Linnaeus. Mycologists 

cannot expect botanists to fully appreciate the problems 

created by working with microscopic organisms that can 

neither be routinely collected nor cultured. Mycology, to free 

itself from the legacy of botanical nomenclature, needs a 

nomenclatorial revolution. 

It is time for mycologists, who best understand the 

nomenclatorial needs peculiar to fungi, to design a 

nomenclatorial code for fungi. The timing could not be better 

because over the past two decades one of our own, David 

Hawksworth, has been helping to guide the development 

of the BioCode (Greuter et al. 2011, Hawksworth 2011). 

Modification of the draft BioCode to enable One Fungus = 

One Name and to accommodate ENAS fungi could produce 

a MycoCode that would be fully compatible with the BioCode. 

In considering microscopic organisms, a newly created 

MycoCode could also inspire those working on Bacteria, 

Archaea and other microscopic Eukarya. We mycologists 

have the need and, in the nomenclatorial committees of the 

International Mycological Association 2 and the Mycological 

Section of the International Union of Microbiological Societies, 

the means to accomplish this task. All that mycologists now 

lack is an excuse to do nothing. 

2 

Including the Nomenclature Committee for Fungi, which it is 

proposed be elected at International Mycological Congresses rather 

than at International Botanical Congresses as at present (Hawksworth 

et al. 2009, Norvell et al. 2010), and the International Commission on 

the Taxonomy of Fungi (a joint Commission with IUMS). 

ACKNOWLEDGEMENTS 

Thanks are due to Pedro Crous and Robert Samson of the CBS, 

Utrecht, who conceived of and hosted the One Fungus = One 

Name Conference, on 19–20 April 2011 in Amsterdam. JWT also 

acknowledges support from NSF DEB-0516511 

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ARTICLE 



ARTICLE 

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doi:10.5598/imafungus.2011.02.02.02 

IMA Fungus · volume 2 · no 2: 121–125 

Penicillium menonorum, a new species related to P. pimiteouiense 

Stephen W. Peterson 1 , Samantha S. Orchard 2 , and Suresh Menon 2 

1 

USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Bacterial Foodborne Pathogens and Mycology 

Research Unit, 1815 North University Street, Peoria, Illinois 61604 USA; corresponding author e-mail: Stephen.Peterson@ARS.USDA.GOV 

2 

Menon & Associates, Inc., P.O. Box 910033, San Diego, California 92191-0033 USA 

ARTICLE 

Abstract: Penicillium menonorum is described as a new monoverticillate, non-vesiculate species that resembles 

P. restrictum and P. pimiteouiense. On the basis of phylogenetic analysis of DNA sequences from four loci, P. 

menonorum occurs in a clade with P. pimiteouiense, P. vinaceum, P. guttulosum, P. rubidurum, and P. parvum. 

Genealogical concordance analysis was applied to P. pimiteouiense and P. parvum, substantiating the phenotypically 

defined species. The species P. rubidurum, P. guttulosum, and P. menonorum were on distinct branches statistically 

excluded from inclusion in other species and have distinct phenotypes. 

Key words: 

monoverticillate 

fungal systematics 

congruence analysis 

Penicillium 

Article info: Submitted: 13 April 2011; Accepted: 15 June 2011; Published: 29 September 2011. 

INTRODUCTION 

In the course of a screening program to find useful fungi for 

conversion of organic matter into high-value products such 

as lipid precursors to biofuels and animal feed formulations, 

a Penicillium isolated from garden soil in southern California 

was obtained that could not be placed with confidence 

in any described species. Sequencing of the ITS region 

was performed, with sequence analysis showing that this 

isolate is phylogenetically related to P. pimiteouiense. DNA 

distance from P. pimiteouiense suggested that it might be an 

undescribed species. 

Additional gene loci (β-tubulin, calmodulin, and DNA 

replication licensing factor Mcm7) were amplified and 

sequenced for this isolate and for phylogenetically and 

phenotypically similar species. On the basis of the phenotypic 

and phylogenetic distinctions, this isolate is described as a 

new species. 

MATERIALS AND METHODS 

Cultures (Table 1) may be obtained from the Agricultural 

Research Service Culture Collection (NRRL), Peoria, IL 

(http://nrrl.ncaur.usda.gov). The P. menonorum culture 

ex-type is available from the Agricultural Research Service 

Patent Culture Collection (http://nrrl.ncaur.usda.gov). 

Cultures were maintained on potato-dextrose agar (PDA) 

during the course of this study. Colony descriptions were 

based on 7 d growth of cultures on Czapek’s yeast autolysate 

agar (CYA), malt extract agar (MEA), and glycerol nitrate agar 

(G25N) at 25 °C, and on CYA at 5 °C and 37 °C as detailed 

by Pitt (1980). Some color names are taken from Ridgway 

(1912) and are designated with an upper case R and a plate 

number. 

Microscope slides were made by teasing apart bits 

of mycelium in a drop of lactic acid with cotton blue. A 

Zeiss axioscope with DIC optics was used for microscopic 

observations. Photomicrographs were taken with a Kodak 

14n digital camera attached to the microscope. Micro- and 

macro-photographs were sized and placed in a plate using 

Adobe Photoshop v. 6.0.1. 

Biomass for DNA extraction was grown in 125 mL flasks 

containing 25 mL malt extract (ME) broth incubated at 25 

°C on a rotary platform (200 rpm). Biomass ca. 0.5 g wet 

weight was collected by vacuum filtration, placed in micro 

centrifuge tubes, and freeze-dried. Freeze-dried mycelium 

was ground to a powder with a sterile pipette tip and DNA 

was extracted from the powdered biomass using the 

CTAB method. Purified DNA was stored in TE buffer (Tris 

10 mM, EDTA 1 mM, pH 8.0) at -20 °C until needed. DNA 

was amplified using the primers and conditions detailed 

in Peterson et al. (2010). Amplified DNA was prepared for 

sequencing using ExoSAP-IT (www.usbweb.com). DNA 

sequences were produced using DyeDeoxy v. 3.1 reagents 

and an ABI 3730 DNA sequencer (www.appliedbiosystems. 

com). Complementary strand sequences were assembled 

and corrected using Sequencher (www.genecodes.com). 

Finished sequences were aligned using CLUSTALW 

(Chenna et al. 2003), and maximum parsimony trees and 

bootstrap proportions were calculated using PAUP v. 4.0b10 

(Swofford 2003). MrBayes v. 3.12 (Huelsenbeck & Ronquist 

2001, Ronquist & Huelsenbeck 2003) was used to calculate 

Bayesian posterior probabilities. DNA sequences used in this 



Attribution: 







Peterson, Orchard & Menon 

ARTICLE 

Table 1. Provenance of isolates used in this study. 

Species NRRL Accession No. Origin 

Penicillium erubescens MB335726 a (syn. Eupenicillium 

erubescens) 

6223 South Africa: Pretoria: isolated from nursery soil, 

1967, culture ex-type 

Penicillium guttulosum MB266689 907 USA: Utah: isolated from soil, 1927, culture ex-type 

Penicillium menonorum MB519297 50410 USA: California: isolated from garden soil, 2009, 

culture ex-type 

Penicillium parvum MB289101 (syn. Eupenicillium parvum) 2095 

Nicaragua: isolated from soil, July 1945, A.G. 

Kevorkian, culture ex-type 

6032 Papua-New Guinea: isolated from soil, ca. 1973, S. 

Udagawa, culture ex-type of P. papuanum MB319290 

35488 Ghana: Tafo: isolated from soil, ca. 1949 

35492 Venezuela: isolated from soil, ca. 1976, D.T. Wicklow 

Penicillium pimiteouiense MB460126 2063 New Guinea: isolated from tent cloth, ca. 1944, G.W. 

Martin 

25542 USA: Illinois: Peoria: isolated from human kidney cell 

culture plate, April 1996, J.T. Hjelle, culture ex-type 


culture plate, November 1997, M.A. Miller-Hjelle 


culture plate, November 1997, M.A. Miller-Hjelle 


culture plate, July 1998, J.T. Hjelle 

Penicillium rubidurum MB319295 (syn. Eupenicillium 

rubidurum) 

6033 Papua-New Guinea: isolated from soil, 1975, culture 

ex-type 

Penicillium vinaceum MB281754 739 USA: Utah: isolated from soil, 1927, culture ex-type 

740 Unknown: obtained from M.B. Morrow, 1936 

a 

MB=MycoBank (http://www.mycobank.org/). 

study are deposited in GenBank (www.ncbi.nlm.nih.gov) 

with accession numbers HQ646566–HQ646603, AF033460– 

AF033462, AF033464, AF037431, and AF037434. Data 

sets and tree diagrams are deposited at TREEBASE (www. 

treebase.org). 

The initial search to find phylogenetically related species 

was performed by BLAST searches of GenBank using the 

ITS sequence from the new species. 

Results 

Penicillium menonorum S.W. Peterson sp. nov. 

MycoBank MB519297 

(Fig. 1A–D) 

Etymology: Named for Menon & Associates whose scientists 

isolated the fungus. 

A speciebus aliis conidiophoris brevibus, conidiis scaberulis, 

colore in substrato nutritorio CYA pallide caesio atque augmento in 

temperatura 37 °C distinguendum. 

Typus: USA: California: isolated from garden soil, 2009 (BPI 

881018 – holotypus; culture ex-holotype NRRL 50410). 

Colonies on CYA (Fig. 1A) attaining 17–20 mm diam after 7 d 

growth at 25 °C, velutinous-silky, radially sulcate peripherally, 

centrally raised ca. 2–3 mm, sporulation moderate, central 

region pale bluish gray (court gray R-47), peripheral area white; 

no exudate or soluble pigments; no sclerotia or ascomata; 

reverse yellowish brown centrally (buckthorn brown R-15) 

to pale brownish-yellow (warm buff, R-15) peripherally. On 

MEA (Fig. 1B) attaining 17–19 mm diam after 7 d growth at 

25 °C, mycelium loosely woven, wooly, umbonate 3–4 mm 

deep centrally, sporulation moderate, white peripherally, 

court gray (R-47) centrally; no exudate or soluble pigments; 

no sclerotia or ascomata; reverse yellowish brown centrally 

to brownish yellow peripherally. On G25N attaining 8–10 mm 

diam after 7 d growth at 25 °C, umbonate, wooly 1–2 mm 

deep, white to court gray; no exudate or soluble pigment; no 

sclerotia or ascomata; reverse white to buff. Incubation for 

7 d on CYA at 5 °C produced no growth or germination of 

conidia. Incubation for 7 d on CYA at 37 °C produced colonies 

of 29–32 mm diam, resembling growth on CYA at 25 °C, but 

clear exudate moderately abundant, the reverse color is a 

darker, more uniform shade of brown. Conidiophores (Fig. 

1C) smooth-walled, hyaline, 5–15(–20) × 1.5–2.0 µm, nonvesiculate, 

with an apical whorl of (1–)2–5 phialides 5–7(–9) 

× 2.5–3.5 µm, conidia spherical to subspherical, (2–)2.5–3.5 

µm (Fig. 1D), with roughened to rugose surface. 

122 ima fUNGUS

Penicillium menonorum sp. nov. 

ARTICLE 

A B C D 

Fig. 1. Penicillium menonorum NRRL 50410. A. Colonies grown 7 d at 25 °C on CYA showing the radial sulcation and faint blue-gray central color 

characteristic of the species. Bar = 1 cm. B. Colonies grown 7 d at 25 °C on MEA having wooly consistency and darkened central area where the 

fungus is sporulating. Bar = 1 cm. C. Conidiophores, phialides and conidia. Bar = 10 µm. D. Roughened conidia. Bar = 10 µm. 

DNA sequences from the β-tubulin locus included all 

or part of 4 exon and 4 intron regions. After alignment the 

data set included 703 base positions. The calmodulin data 

included all or part of 4 exon and 3 intron regions and aligned 

with 726 base positions. The ID regions included the ITS1, 

ITS2, 5.8S rDNA, and ca. 650 bases from the 28S rDNA in 

an alignment of 1141 bases. DNA replication licensing protein 

(Mcm7) was composed of an amino acid coding region of 616 

bp length. Penicillium erubescens was chosen as the outgroup 

on the basis of phylogenetic trees previously published 

(Peterson et al. 1999, Peterson 2000). 

The most parsimonious trees, bootstrap proportion and 

Bayesian posterior probabilities for individual data sets 

were determined and the trees were compared for strongly 

supported contradictory branch points. Strongly supported 

nodes are those with > 90 % of the bootstrap sample and a 

Bayesian posterior probability of > 0.90. The individual locus 

trees contained no strongly supported contradictions that 

would preclude combining the data. The data from the four loci 

were combined to calculate a single phylogenetic tree (Fig. 2). 

The five isolates of P. pimiteouiense occur on a single 

strongly supported branch; three isolates of P. parvum 

and the single isolate of P. papuanum occur on a different 

strongly supported branch, and the two P. vinaceum isolates 

occur on another strongly supported branch. Penicillium 

rubidurum and P. guttulosum are most closely related to 

each other and form a sibling group to P. pimiteouiense, 

while P. menonorum is positioned basal in the tree to this 

three species branch. 

DISCUSSION 

Penicillium menonorum is similar phenotypically to P. 

pimiteouiense, P. restrictum, P. striatisporum, P. vinaceum, 

P. rubidurum, P. erubescens, and P. parvum. Penicillium 

restrictum, P. malacaense, P. kurssanovii, P. griseolum, and P. 

striatisporum, which phenotypically resemble P. menonorum, 

are phylogenetically positioned in different clades (Peterson 

& Horn 2009). Other species bearing some resemblance 

to P. menonorum are either not represented by extant extype 

cultures or the type cultures are not readily available. 

Penicillium menonorum differs from P. pimiteouiense by 

producing conidiophores in a basal layer rather than from 

aerial hyphae and a bluish gray (Court gray R-47) color 

on CYA versus white in P. pimiteouiense. Additionally, P. 

pimiteouiense produces yellow exudate and a brown soluble 

pigment, neither of which appear in P. menonorum after 7 d 

incubation. On different media (e.g., yeast extract malt agar 

incubated at 25 °C) or after extended incubation, a clear to 

rosy exudate often appears in P. menonorum. Penicillium 

restrictum produces somewhat longer conidiophores (up to 

60 µm) and has smaller colonies (< 10 mm diam) at 37 °C than 

P. menonorum (29–32 mm diam). Penicillium striatisporum 

produces rosy colored colonies on Czapek’s agar and has 

striate conidia. Penicillium vinaceum produces copious 

exudate in yellow to vinaceous colors, yellow to brown 

soluble pigments, and a dark brown colony reverse on CYA, 

and colonies grown at 37 °C are somewhat smaller (8–20 

mm diam) than those of P. menonorum. Penicillium parvum 

typically has mycelium that varies from white to yellow to red 

in color, while the P. menonorum mycelium is uniformly white. 

Penicillium parvum usually makes brown or purple-brown 

exudate, a brown soluble pigment, and has a colony reverse 

that is deep reddish-brown versus P. menonorum, which 

has no exudate or soluble pigments and a yellow brown 

colony reverse after 7 d incubation. Penicillium rubidurum 

produces white to orange or rosy-buff mycelium, red-brown 

exudate, a dark brown colony reverse, and produces conidia 

on M40Y medium but not on CYA. Penicillium menonorum 

produces no exudate or soluble pigment and has a yellow 

brown reverse and has abundant conidiogenesis on CYA. 

Penicillium erubescens produces white, pink or flesh color 

mycelium, reddish-brown exudate, and gray-red to magenta 

to vinaceous purple soluble pigments, with colony reverse 

either similarly colored or brown. Each of these species is 


123

Peterson, Orchard & Menon 

ARTICLE 

Combined data from BT2, CF, ID and Mcm7 loci, 

3186 total characters, 2798 are constant, 204 are 

variable not parsimony informaKve, 200 are parsimony 

InformaKve; 1 mpt, CI=0.8348, RC=0.7190 

NRRL 2063 

NRRL 28602 

100/1.00 

NRRL 26933 

P. pimitiouiense 

64/0.94 

NRRL 26932 

81/1.00 

NRRL 25542 T 

98/1.00 P. rubidurum NRRL 6033 

P. gu+ulosum NRRL 907 

P. menonorum NRRL 50410 T 

90/1.00 

NRRL 35488 

100/1.00 

NRRL 35492 

NRRL 2095 T 

P. papuanum NRRL 6032 T P. parvum 

100/1.00 

P. vinaceum NRRL 739 T 

P. vinaceum NRRL 740 

10 

P. erubescens NRRL 6223 T 

Fig. 2. Phylogenetic tree calculated using maximum parsimony criterion for the concatenated data set composed of beta-tubulin, calmodulin, ITS 

and 28S rDNA, and DNA replication licensing protein (Mcm7). Bootstrap proportions/Bayesian posterior probabilities are placed on internodes. 

easily distinguished from P. menonorum on these bases. 

Raper & Thom (1949) regarded P. guttulosum to be a 

synonym of P. janthinellum, differing primarily by the production 

of copious amounts of exudate. Penicillium guttulosum as 

represented by Gilman & Abbott’s ex-type strain is distinct 

from P. janthinellum as well as the species studied here. 

Penicillium guttulosum cultures on CYA resemble the cultures 

of P. vinaceum, differing most noticeably in the production of 

dark purple exudate in large quantities, while P. vinaceum 

exudate is more red in color. Penicillium rubidurum colonies 

also resemble P. vinaceum and P. guttulosum but produce 

pale yellow exudate. Pitt (1980) treated P. papuanum as a 

124 ima fUNGUS

Penicillium menonorum sp. nov. 

synonym of P. parvum and they are in the same strongly 

supported clade (Fig. 2). Phenotypically, they are very similar 

to each other. Additional isolates of each species are needed 

to further assess the phylogenetic and phenotypic distinctions 

of these species. 

Phylogenetic systematics (Hennig 1966) is based on the 

principle that species must be monophyletic. Taylor et al. (2000) 

presented the genealogical concordance phylogenetic species 

recognition (GCPSR) concept as a means of determining the 

boundaries of species in fungi. Dettman et al. (2006) showed 

experimentally that GCPSR is effective in recognizing species 

boundaries in the genus Neurospora. GCPSR can be applied 

to P. pimiteouiense and P. parvum in this study and the species 

are supported by the GCPSR principles. Penicillium vinaceum, 

P. guttulosum, P. rubidurum, and P. menonorum are each on 

distinct branches, but the boundaries of the species cannot be 

determined from the single isolates available here. Phenotypic 

distinctions make each of these species recognizable and the 

phylogenetic placement of the species is consistent with the 

phenotypic descriptions of the species. 

Peterson SW, Jurjevic Z, Bills GF, Stchigel AM, Guarro J, Vega FE 

(2010) The genus Hamigera, six new species and multilocus 

DNA sequence based phylogeny. Mycologia 102: 847–864. 

Pitt JI (1980) ['1977'] The genus Penicillium and its teleomorphic 

states Eupenicillium and Talaromyces. Academic Press, UK. 

Raper KB, Thom C (1949) The genus Penicillium. Williams and 

Wilkins, USA. 

Ridgway R (1912) Color standards and color nomenclature. 

Published by the author, USA. 

Ronquist F, Huelsenbeck JP (2003) MrBayes3: Bayesian phylogenetic 

inference under mixed models. Bioinformatics 19: 1572–1574. 

Swofford DL (2003) PAUP*. Phylogenetic Analysis Using Parsimony 

(*and other methods). Version 4. Sinauer Associates, USA. 

Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett 

DS, Fisher MC (2000) Phylogenetic species recognition and 

species concepts in fungi. Fungal Genetics and Biology 31: 

21–32. 

ARTICLE 


Amy McGovern provided highly skilled technical support that is 

greatly appreciated. Patricia Eckel kindly translated the diagnosis 

into Latin. Mention of trade names or commercial products in this 

publication is solely for the purpose of providing specific information 

and does not imply recommendation or endorsement by the U.S. 

Department of Agriculture. USDA is an equal opportunity provider 

and employer. 

REFERENCES 

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, 

Thompson JD (2003) Multiple sequence alignment with the 

Clustal series of programs. Nucleic Acids Research 31: 3497– 

3500. 

Dettman JR, Jacobson DJ, Taylor JW (2006) Multilocus sequence 

data reveal extensive phylogenetic species diversity within the 

Neurospora discreta complex. Mycologia 98: 436–446. 

Hennig W (1966) Phylogenetic Systematics. (English Translation). 

Urbana: University of Illinois Press. 

Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference 

of phylogenetic trees. Bioinformatics 17: 754–755. 

Peterson SW, Corneli S, Hjelle JT, Miller-Hjelle MA, Nowak DM, 

Bonneau PA (1999) Penicillium pimiteouiense: a new species 

isolated from polycystic kidney cell cultures. Mycologia 91: 269– 

277. 

Peterson SW (2000) Phylogenetic analysis of Penicillium based on 

ITS and LSU-rDNA sequences. In: RA Samson & JI Pitt (eds), 

Classification of Penicillium and Aspergillus: Integration of 

modern taxonomic methods: 163–178. Harwood Publishers, UK. 

Peterson SW, Horn BW (2009) Penicillium parvulum and Penicillium 

georgiense, sp. nov. isolated from the conidial heads of 

Aspergillus species. Mycologia 101: 71–83. 


125

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ima fUNGUS


What is Scirrhia? 

Pedro W. Crous 1 , Andrew M. Minnis 2 , Olinto L. Pereira 3 , Acelino C. Alfenas 3 , Rafael F. Alfenas 3 , Amy Y. Rossman 2 , and Johannes 

Z. Groenewald 1 

1 

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; corresponding author e-mail: p.crous@cbs.knaw.nl 

2 

Systematic Mycology & Microbiology Laboratory, USDA-ARS, Rm. 246, B010A, 10300 Baltimore Ave., Beltsville, MD 20705, USA 

3 

Departemento de Fitopatologia, Universidade Federal de Viçosa, 36.570 Viçosa, MG, Brazil 

ARTICLE 

Abstract: The ascomycetous genus Scirrhia is presently treated as a member of Dothideomycetidae, though 

uncertainty remains as to which family it belongs in Capnodiales, Ascomycota. Recent collections on stems of a 

fern, Pteridium aquilinum (Dennstaedtiaceae) in Brazil, led to the discovery of a new species of Scirrhia, described 

here as S. brasiliensis. Based on DNA sequence data of the nuclear ribosomal DNA (LSU), Scirrhia is revealed 

to represent a member of Dothideomycetes, Capnodiales, Mycosphaerellaceae. Scirrhia is the first confirmed 

genus in Mycosphaerellaceae to have well developed pseudoparaphyses and a prominent hypostroma in which 

ascomata are arranged in parallel rows. Given the extremely slow growth rate and difficulty in obtaining cultures 

of S. brasiliensis on various growth media, it appears that Scirrhia represents a genus of potentially obligate plant 

pathogens within Mycosphaerellaceae. 

Key words: 

Brazil 

Capnodiales 

Dothideomycetes 

ITS 

LSU 

Mycosphaerellaceae 

Pteridium 

systematics 

Article info: Submitted: 19 August 2011; Accepted: 25 September 2011; Published: 3 October 2011. 

Introduction 

The genus Scirrhia was originally known from four species 

(Fuckel 1870), and later lectotypified based on S. rimosa, 

a species known from stems of Phragmites australis 

(Poaceae) collected in Europe (Saccardo 1883). Based on 

its ascomata arranged in linear rows in a hypostroma of 

pseudoparenchymatal cells, bitunicate asci, hyaline, 1-septate 

ascospores, and the presence of pseudoparaphyses, 

Müller & von Arx (1962) placed the genus in Dothiorales, 

Mycosphaerellaceae, listing Scirrhodothis (Theissen & 

Sydow 1915), Scirrhophragma (Theissen & Sydow 1915) 

and Metameris (Theissen & Sydow 1915) as possible generic 

synonyms. All three genera have bitunicate asci, hyaline, 

1-septate ascospores, pseudoparaphyses, and stromata 

with immersed, longitudinally arranged ascomata, appearing 

to justify this opinion. 

In a later study, von Arx & Müller (1975) again placed 

Scirrhia in Dothideaceae, suborder Dothideineae in 

Dothideales. Barr (1972) questioned the synonymy 

of Scirrhodothis (lectotype species S. confluens), 

Scirrhophragma (type species S. regalis) and Metameris 

(type species M. japonica) under Scirrhia, and Sivanesan 

(1984) also chose not to list them as such, but included 

species that occurred on Gymospermae, namely S. acicola 

and S. pini. Barr (1987) chose to reinstate these generic 

synonyms, and placed Scirrhia together with Mycosphaerella 

in Dothideaceae, Dothideales. Although little is known about 

the three generic synonyms listed by Müller & von Arx 

(1962), the species on Gymnospermae are presently treated 

as separate genera, namely Lecanosticta (L. acicola) and 

Dothistroma (D. pini) (Crous et al. 2009a). Presently, the 

taxonomic position of Scirrhia remains obscure. 

During a recent visit to Brazil, we collected fresh material 

of a species of Scirrhia on stems of a fern. The aims of 

the present study are, therefore, to identify the species of 

Scirrhia, and to see if the taxonomic position of the genus 

could be resolved. 

Materials and methods 

Isolates 

Stems bearing ascomata were soaked in water for 

approximately 2 h, after which they were placed in the bottom 

of Petri dish lids, with the top half of the dish containing 

2 % malt extract agar (MEA), or potato-dextrose agar (PDA; 

Crous et al. 2009b). Ascospore germination patterns were 

examined after 24 h, and single ascospore cultures were 

established as described earlier (Crous et al. 1991, Crous 

1998). Colonies were subcultured onto PDA and oatmeal 

agar (OA) (Crous et al. 2009b) and incubated at 25 °C under 

continuous near-ultraviolet light to promote sporulation. 

Germinating ascospores died on MEA. Reference strains 

are maintained in the CBS-KNAW Fungal Biodiversity Centre 

(CBS), Utrecht, The Netherlands. 



Attribution: 







Crous et al. 

ARTICLE 

Teratosphaeria fibrillosa GU214506 

Johansonia chapadiensis HQ423450 

98 

Zygophiala cryptogama FJ147157 

Zygophiala wisconsinensis FJ147158 

Schizothyrium pomi EF134948 

100 77 Schizothyrium pomi EF134949 

98 Mycosphaerella intermedia DQ246248 

71 Mycosphaerella marksii GQ852614 

92 Microcyclosporella mali GU570547 

Mycosphaerella madeirae DQ204756 

56 

57 Pseudocercosporella sp. FJ031991 

Mycosphaerella punctiformis EU167569 

Ramularia proteae EU707899 

20 changes 

88 Ramularia coleosporii GU214692 

Ramularia uredinicola GU214694 

Ramularia lamii JF700950 

Ramularia miae DQ885902 

94 54 Ramularia eucalypti JF700949 

Ramularia pratensis var. pratensis EU019284 

100 

Mycosphaerella endophytica DQ246255 

Mycosphaerella endophytica GQ852603 

62 Mycosphaerella pseudoendophytica DQ246253 

98 

Passalora daleae EU040236 

Mycosphaerella pini GQ852597 

60 Dothistroma pini GQ852596 

Passalora fulva DQ008163 

Legend to families: 

Pseudocercosporella bakeri GU570553 

79 

Incertae sedis 

72 Mycosphaerella microsora EU167599 

Schizothyriaceae 

57 

Passalora bellynckii GQ852618 

Passalora brachycarpa GQ852619 

Mycosphaerellaceae 

Mycosphaerella buckinghamiae EU707856 

62 Mycosphaerella africana DQ246258 

95 Mycosphaerella aurantia DQ246256 

Mycosphaerella ellipsoidea GQ852602 

100 Pseudocercospora vitis GU214483 

Pseudocercospora paraguayensis GQ852634 

66 59 Pseudocercospora natalensis DQ267576 

Cercosporella virgaureae GQ852585 

87 Ramulispora sorghi GQ852653 

Scirrhia brasiliensis CPC 18733 

53 Mycosphaerella podagrariae EU386700 

97 Mycosphaerella brassicicola EU167607 

Pseudocercosporella capsellae GU214662 

Septoria obesa GU214493 

82 

Mycosphaerella latebrosa GU214444 

Mycosphaerella berberidis EU167603 

54 Mycosphaerella harthensis EU167602 

Mycosphaerella flageoletiana EU167597 

74 Pseudocercosporella sp. GU214683 

Septoria apiicola GQ852674 

Mycosphaerella rubi EU167589 

Septoria convolvuli GQ852675 

Septoria senecionis GQ852678 

Septoria leucanthemi GQ852677 

Pseudocercosporella sp. GU214684 


Passalora dioscoreae GU214665 

Septoria lactucae GU214491 

68 

Cercospora janseana GU214405 

Cercospora sojina GU214655 

87 Cercospora zebrinae GU214657 


Pseudocercospora eucommiae GU214674 

Mycosphaerella linorum EU167590 

Septoria cucubali GU214698 

91 

Mycosphaerella coacervata EU167596 

Fig. 1. The first of 1000 equally most parsimonious trees obtained from a heuristic search with 100 random taxon additions of the LSU sequence 

alignment. The scale bar shows 10 changes, and bootstrap support values from 1000 replicates are shown at the nodes. The novel sequence 

generated for this study is shown in bold. Branches present in the strict consensus tree are thickened and the tree was rooted to a sequence of 

Teratosphaeria fibrillosa (GenBank accession GU214506). 

128 ima fUNGUS


DNA isolation, amplification and analyses 

Genomic DNA was isolated from fungal mycelium grown on 

MEA, using the UltraCleanTM Microbial DNA Isolation Kit 

(MoBio Laboratories, Solana Beach, CA, USA) according 

to the manufacturer’s protocols. The primers V9G (de Hoog 

& Gerrits van den Ende 1998) and LR5 (Vilgalys & Hester 

1990) were used to amplify part of the nuclear rDNA operon 

spanning the 3’ end of the 18S rRNA gene (SSU), ITS 1, the 

5.8S rRNA gene, ITS 2 and the first 900 bases at the 5’ end 

of the 28S rRNA gene (LSU). The primers ITS4 (White et al. 

1990) and LSU1Fd (Crous et al. 2009c) were used as internal 

sequence primers to ensure good quality sequences over the 

entire length of the amplicon. The PCR conditions, sequence 

alignment, and subsequent phylogenetic analysis followed 

the methods of Crous et al. (2006, 2009d). Sequences were 

compared with the sequences available in NCBI’s GenBank 

nucleotide (nr) database using a megablast search and results 

are discussed in the relevant species notes where applicable. 

Based on the Blast results, the novel sequence was added to 

the alignment of Crous et al. 2010 (TreeBASE study S10980). 

Alignment gaps were treated as new character states. 

Sequences derived in this study were lodged at GenBank, 

the alignment in TreeBASE (www.treebase.org/treebase/ 

index.html), and taxonomic novelties in MycoBank (www. 

MycoBank.org; Crous et al. 2004). 

Morphology 

Morphological descriptions are based on preparations made 

from host material in clear lactic acid, with 30 measurements 

determined per structure, and observations made with a Nikon 

SMZ1500 dissecting microscope, and with a Zeiss Axioscope 

2 microscope using differential interference contrast (DIC) 

illumination. Colony characters and pigment production were 

noted after 3 mo of growth on PDA and OA (Crous et al. 2009b) 

incubated at 25 ºC. Colony colours (surface and reverse) were 

rated according to the colour charts of Rayner (1970). 

RESULTS 

Phylogeny 

Approximately 1700 bases, spanning the ITS and LSU 

regions, were obtained from the sequenced culture. The 

LSU region was used in the phylogenetic analysis for the 

generic placement (Fig. 1) and ITS to determine speciesrank 

relationships (see notes under the species description). 

The manually adjusted LSU alignment contained 66 taxa 

including the outgroup sequence and, of the 749 characters 

used in the phylogenetic analysis, 104 were parsimonyinformative, 

51 were variable and parsimony-uninformative, 

and 594 were constant. Only the first 1000 equally most 

parsimonious trees were retained from the heuristic search, 

the first of which is shown in Fig. 1 (TL = 415, CI = 0.494, RI = 

0.851, RC = 0.421). The phylogenetic tree of the LSU region 

(Fig. 1) show that the obtained sequence clusters together 

with species belonging to Cercospora, Pseudocercospora, 

Pseudocercosporella and Septoria in Mycosphaerellaceae. 

Taxonomy 

Scirrhia rimosa (Alb. & Schwein.) Fuckel, Jb. nassau. 

Ver. Naturk. 23–24: 221 (1870). 

Basionym: Sphaeria rimosa Alb. & Schwein., Consp. 

Fung.: 13 (1805). 

(Fig. 2) 

Specimen examined: Czech Republic: Lipnik, on culms (stems) of 

Phragmites australis, June 1942 (Reliquiae Petrakianae Institut für 

Systematische Botanik Graz, exsiccati no. 1871, BPI 1111233). 

Hypostroma on upper leaf surfaces, dark brown to black, 

immersed beneath epidermis, becoming raised, irregularly 

ellipsoid, to 20 mm long, 5 mm wide. Ascomata immersed in 

brown stroma of textura angularis; arranged in parallel rows, 

opening by a 10–15 µm diam central ostiole; ascomata to 

250 µm diam, wall 10–20 µm wide. Asci 80–130 × 13–18 

µm, hyaline, smooth, cylindrical, sessile in fascicles, shortstipitate, 

bitunicate with ocular chamber, 3–4 µm diam. 

Pseudoparaphyses hyaline, cellular, smooth, distributed 

among asci, septate, branched, prominently constricted 

at septa, 5–8 µm diam, extending above asci. Ascospores 

hyaline, smooth, biseriate in asci, guttulate, fusoid-ellipsoidal, 

widest just above septum, tapering towards both ends, but 

more prominently towards lower end, prominently constricted 

at the median septum, thin-walled, (20–)21–23(–26) × 6–7(– 

7.5) µm; ascospores germinating on host with germ tubes at 

right angles to the long axis of spore, but remaining hyaline, 

not distorting. 

Notes: Despite several attempts, we have thus far been 

unable to recollect fresh material of this species on 

Phragmites, and thus no DNA sequence data are available. 

The nature of the hypostroma, ascomatal arrangement, asci, 

ascospores, and pseudoparaphyses, closely match that of 

the species described below. The specimen described and 

illustrated here agrees with the original description as well as 

locality and host of this species, occurring on stems. A later 

Schweinitz collection on Zizania (Poaceae) from the USA 

proved to be a misidentified Leptosphaeria zizaniicola (Ellis 

& Everhart 1892). We are unaware of any confirmed reports 

of Scirrhia rimosa from North America. 

Scirrhia brasiliensis Crous, O.L. Pereira, Alfenas & 

R.F. Alfenas, sp. nov. 


(Fig. 3) 

Etymology: Named after the country where the holotype was 

collected, Brazil. 

Scirrhiae rimosae morphologice similis, sed asco saepe minus quam 

octosporo et ascosporis dissimiliter contractis. 

Typus: Brazil: Minas Gerais: Viçosa, Serra do Brigadeiro, S20°41.487, 

W42°29.875, on stems of Pteridium aquilinum (Dennstaedtiaceae), 

22 Aug. 2010, P.W. Crous, O.L. Pereira, A.C. Alfenas & R.F. Alfenas, 

ARTICLE 


129

Crous et al. 

ARTICLE 

Fig. 2. Scirrhia rimosa (BPI 1111233). A. Hypostroma on leaf of Phragmites australis. B. Horizontal section through ascomata. C–F. Asci 

intermingled among pseudoparaphyses. G. Ascus with basal stalk. H. Ascospores inside disintegrated ascus. Bars: A = 5 mm; B = 250 µm, all 

others = 10 µm. 

(CBS H-20538 – holotypus; cultures ex-holotype CPC 18734, 18735, 

18733 = CBS 128762). (GenBank accession numbers: CPC 18733, 

ITS JN197292, LSU JN197293). 

Stem cankers narrowly fusoid, brown, at times with redpurple 

margin, visible on shoots and stems of host, up to 

5 mm wide, 3 cm long; raised areas forming longitudinal 

cracks in the host epidermis through which erumpent 

ascomata protrude. Ascomata to 160 µm diam, 200 µm 

high, subepidermal, situated in rows in a brown hypostroma 

of textura angularis; wall consisting of to 6 layers of textura 

angularis, to 60 µm diam; cells brown, becoming flattened 

between ascomata, to 20 µm diam; ostioles ellipsoid, single, 

central, to 20 µm diam, situated on a dark brown, depressed 

neck, to 50 µm wide, 15 µm high; ostiole lined with hyaline, 

cylindrical periphyses with rounded ends, to 25 µm long, 3 

µm wide. Asci 90–130 × 8–11 µm, fasciculate, intermingled 

between pseudoparaphyses, subcylindrical, with thick wall, 

2–4 µm diam, inconspicuous apical chamber, 2–3 µm diam; 

wall appearing multi-layered with fissitunicate dehiscense, 

widest in middle of ascus, tapering to a long, thin, basal part 

and lobed base, to 9 µm wide; asci initially with 8 immature 

ascospores, of which some dissolve, leaving 4–6 mature 

ascospores per ascus. Pseudoparaphyses hyaline, cellular, 

smooth, septate, anastomosing, extending above asci, 3–5 

µm wide. Ascospores fusoid-ellipsoidal, hyaline, smooth, 

guttulate, obliquely uniseriate in asci, medianly 1-septate, at 

times constricted at the septum, widest in the middle of apical 

cell, tapering towards both ends, (17–)20–23(–27) × (5–) 

6–7(–8) µm; germinating from both ends, with germ tubes 

generally parallel to the long axis; spores neither darkening 

nor distorting. 

Culture characteristics: Colonies after 3 mo on PDA 

and OA with sparse aerial mycelium and even margins, 

olivaceous-grey (surface and reverse), reaching to 6 mm 

diam, extremely slow growing, with brown, diffuse pigment 

visible in agar surrounding colony; colonies sterile. Most 

ascospores died upon germination, and only a few of the 

germinated spores on PDA survived to form extremely slowgrowing 

colonies, suggesting this pathogen to be highly 

obligate in nature. 

Notes: The only culture of a species of Scirrhia presently 

available in the CBS culture collection, S. aspidiorum (CBS 

204.66, on Pteridium aquilinum, UK; GenBank accession 

number: ITS, JN197294) turned out to be related to Phoma 

herbarum (Didymellaceae, Pleosporales; de Gruyter et al. 

2010), and thus unrelated to S. brasiliensis. Although the 

specimen from which this culture was derived (ETH 2662) 

was not examined, examination of another collection under 

this name (The Netherlands, Baarn, Groenevelt, Pteridium 

130 ima fUNGUS


ARTICLE 

Fig. 3. Scirrhia brasiliensis (ex-type CPC 18733). A. Fronds of Pteridium aquilinum. B, C. Stems with cankers extending into inner tissue. D. 

Hypostroma viewed from above. E–G, K. Sections through ascomata. H–J. Ostiolar area of ascomata, showing depressed neck. L–N. Bitunicate 

asci (arrow denotes apical chamber). O, P. Germinating ascospores. Q. Ascospores. Bars: B, C = 5 mm; D = 1 mm; E–H = 160 µm, all others 

= 10 µm. 

aquilinum, May 1962, J.A. von Arx, CBS H-17938), revealed 

a typical species of Scirrhia to be present on this fern, but no 

culture is presently available to confirm that it is the same 

taxon represented by CBS 204.66. Müller & von Arx (1962) 

treat S. aspidiorum in detail, citing ascospores as being 10– 

15 × 3–4 µm, thus being significantly smaller than those of 

S. brasiliensis. The ITS sequence of S. brasiliensis did not 

retrieve any highly identical hits with a megablast search of 

the NCBI’s GenBank nucleotide database; the closest hits 

represent species of Septoria, e.g. Septoria digitalis GenBank 


131

Crous et al. 

ARTICLE 

Fig. 4. Scirrhodothis confluens (isotype specimen CBS H-4806). A, B. Superficial view of stromata with imbedded ascomata. C. Asci. D. Broken 

asci with Didymella-like ascospores. Bars: A, B = 2 mm; C, D = 10 µm. 

FJ557246; Identities = 507/534 (95 %), Gaps = 8/534 

(1 %), and Cercospora, e.g. Cercospora piaropi GenBank 

HQ902254; Identities = 514/547 (94 %), Gaps = 9/547 (2 %) 

(data not shown). 

Discussion 

Persoon (1796) was the first to use the term “stroma” to 

define structures on or in which ascomata of the genus 

Sphaeria were borne. Fruisting (1867) introduced the terms 

“epistroma” for the hyaline pseudoparenchymatous crust 

formed in the outer layers of the host cortex, in which conidia 

were produced, and under which a “hypostroma” was formed 

in which ascomata developed. Based on the concepts of 

Fruisting, Ruhland (1900) introduced the terms “ectostroma” 

and “entostroma”. Blain (1927) subsequently defined Scirrhia 

rimosa as having a dothideoid epistroma and a hypostroma 

of compressed pseudoprosenchyma. The same hypostroma 

anatomy observed in S. rimosa was also found in S. 

aspidiorum and S. brasiliensis, and appears to be typical for 

the genus. 

Although the type species of Hadrotrichum, H. phragmitis, 

has been linked to S. rimosa as a possible anamorph of the 

genus Scirrhia (Fuckel 1870), this relationship has never 

been proven and has been disputed (von Arx & Müller 1975). 

The phylogenetic position of Hadrotrichum presently remains 

unknown, and this genus will have to be recollected to 

resolve this issue. Presently, no anamorph connections have 

been confirmed for Scirrhia, and none formed in culture for 

S. brasiliensis. 

Von Arx & Müller (1975) considered Scirrhodothis, 

Scirrhophragma, and Metameris to be synonyms of 

Scirrhia. Holm & Holm (1978) mentioned that although the 

taxa were closely related, the synonymy was controversial 

given different types of centrum development in some of the 

species. Barr (1992) regarded Scirrhia to represent a genus 

in Dothideales, while members of Metameris were found 

to have pseudoparaphyses and 1–2-septate, Didymellalike 

ascospores (Pleosporales). Furthermore, based on 

its small ascomata, broadly cylindrical to slightly obclavate 

asci with a short, thick, knob-like pedicels, as well as its 

monocotyledonous host preference, Zhang et al. (2012) 

suggested Metameris to belong to Phaeosphaeriaceae, 

though molecular data are still lacking to resolve its final 

placement. 

Lumbsch & Huhndorf (2010) list Scirrhia under 

Dothideaceae and Metameris under Phaeosphaeriaceae. 

The lectotype species of the genus Scirrhodothis, S. confluens 

(isotype CBS H-4806; Fig. 4), was examined in the present 

study and found to differ from Scirrhia in that the ascomata 

were locules formed in a stroma, not in linear rows in a 

hypostroma as in Scirrhia, and ascospores were Didymellalike. 

Although Scirrhodothis is clearly not a synonym of 

Scirrhia, the synonymy of these genera cannot be resolved 

in the absence of cultures, and they are best retained as 

separate entities until more data become available. 

Kirschner & Chen (2010) stated that the systematic 

position of Scirrhia was also in need of re-examination, and 

referred to a paper by Suetrong et al. (2009), who placed 

S. annulata (Juncaceae) within Mycosphaerellaceae. 

The clustering of S. brasiliensis in this family in the 

present study supports this finding and confirms 

Scirrhia as the first genus within Mycosphaerellaceae 

(Capnodiales, Dothideomycetes) with well developed 

pseudoparaphyses and an epi- and hypostroma. Other 

ascomycetous genera that have recently been shown to 

cluster in Mycosphaerellaceae include Phaeocryptopus 

and Rosenscheldiella (Winton et al. 2007, Sultan 

et al. 2011). Further collections are now required to 

resolve the questions: does S. rimosa cluster with 

S. brasiliensis, and what is the status of its reported 

synonyms, Scirrhodothis, Scirrhophragma and Metameris? 

132 ima fUNGUS


Acknowledgements 

We thank the technical staff, Arien van Iperen (cultures), Marjan 

Vermaas (photo plates), and Mieke Starink-Willemse (DNA isolation, 

amplification and sequencing) for their invaluable assistance. 

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ARTICLE 


133

ARTICLE 

 

ima fUNGUS


A new species of Antherospora supports the systematic placement of its 

host plant 

Marcin Piątek 1 , Matthias Lutz 2 , Paul A. Smith 3 , and Arthur O. Chater 4 

ARTICLE 

1 

Department of Mycology, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, Poland; corresponding 

author e-mail: m.piatek@botany.pl 

2 

Organismische Botanik, Institut für Evolution und Ökologie, Universität Tübingen, Auf der Morgenstelle 1, D-72076 Tübingen, Germany 

3 

128 Llancayo Street, Bargoed, Mid Glamorgan, CF81 8TP, UK 

4 

Windover, Penyrangor, Aberystwyth, SY23 1BJ, UK 

Key words: 

Abstract: The morphology and phylogeny of anther smut specimens on Tractema verna collected in the United Molecular Analysis 

Kingdom were investigated using light microscopy, scanning electron microscopy and partial rDNA sequence Phylogeny 

analyses. The anther smut of Tractema verna shows similarity to Antherospora eucomis, A. scillae, A. tourneuxii, A. Plant Pathogens 

urgineae, A. vaillantii, and A. vindobonensis but differs in spore size range, spore wall thickness, host plant genera Scilla verna 

and considerable divergences of ITS and LSU sequences. Consequently, the smut is described here as a new Smut Fungi 

species, Antherospora tractemae. The host plant was formerly included in the genus Scilla (S. verna), but recently Tractema verna 

moved to a distinct genus Tractema. Molecular phylogenetic analyses reveal that Antherospora tractemae is sister Coevolution 

to the lineage of Muscari-parasitizing Antherospora and only distantly related to the Scilla-parasitizing Antherospora Ustilaginomycotina 

species. Thus, the phylogenetic placement of the smut fungus supports the systematic placement of its host plant. 

Article info: Submitted: 28 July 2011; Accepted: 30 September 2011; Published: 11 October 2011. 

INTRODUCTION 

The smut fungi sporulating in the anthers and on the 

surface of the inner floral organs of different Hyacinthaceae 

have recently been accommodated in a separate genus 

Antherospora (Bauer et al. 2008). Antherospora resides 

in the family Floromycetaceae (Urocystidales), together 

with the genus Floromyces, which produces sori in the 

inner floral organs of Anemarrhena asphodeloides 

(Agavaceae) (Vánky et al. 2008). Antherospora includes 

eight species, parasitic on hosts in seven different 

plant genera (Bauer et al. 2008, Vánky 2009). Despite 

phenotypic similarity, molecular phylogenetic analyses of 

Antherospora specimens parasitic on species of Muscari 

and Scilla have revealed significant genetic divergence 

between accessions from different host species (Bauer 

et al. 2008). For example, two closely related Central 

European Scilla species, S. bifolia and S. vindobonensis, 

harbour two morphologically similar but phylogenetically 

different Antherospora species. On the other hand, the 

phylogenetic results demonstrated that Antherospora 

vaillantii s. str. could infect two different hosts, Muscari 

comosum and M. neglectum (Bauer et al. 2008), indicating 

that some Antherospora spp. infect more than one host 

species. It is probable that host specificity is a widespread 

phenomenon and evolutionary driver in the genus 

Antherospora, similar, for example, to the anther smuts 

classified in the genus Microbotryum (Lutz et al. 2005, 

2008, Le Gac et al. 2007, Refrégier et al. 2008, Denchev 

et al. 2009, Kemler et al. 2009, Piątek et al. unpubl. data). 

Nevertheless, the DNA sequence data for Antherospora 

available in the NCBI’s GenBank nucleotide database 

is scant due, in part, to the inaccessibility of recently 

collected material. Much collecting and sequencing effort 

is necessary to understand the level of host specificity 

and the phylogenetic relationships within the genus. 

Infected specimens of Tractema verna were collected 

recently in Wales and the Outer Hebrides (United Kingdom). 

The host plant is commonly known by its synonym, Scilla 

verna, while its anther smut has been referred to as Ustilago 

vaillantii (Vánky 1994, Legon et al. 2005). This study aimed 

to clarify whether the collected specimens could be assigned 

to any of the described Antherospora species, especially to 

A. vaillantii or one of the recognized species sporulating in 

anthers of Scilla, or whether it represented a distinct species. 

A further aim was to check the phylogenetic affinity within 

the genus Antherospora and to expand the sampling of 

Antherospora species for which DNA sequence data are 

available. 



Attribution: 







Piątek, Lutz, Smith & Chater 

ARTICLE 

MATERIALS AND METHODS 

Specimen sampling and documentation 

The specimens examined during the present work are listed in 

Table 1. The voucher specimens are deposited in KR, KRAM 

F and H.U.V. The latter abbreviation refers to the personal 

collection of Kálmán Vánky named as Herbarium Ustilaginales 

Vánky (Gabriel-Biel-Str. 5, D-72076 Tübingen, Germany). The 

nomenclatural novelty was registered in MycoBank (www. 

MycoBank.org, Crous et al. 2004). 

Nomenclature of anther smuts on 

Hyacinthaceae 

The nomenclature of anther smuts on Hyacinthaceae follows 

Bauer et al. (2008) and Vánky (2009). The collective name 

Ustilago vaillantii (syn. Vankya vaillantii) refers to all anther 

smuts on hyacinthaceous genera and species. The name 

Antherospora vaillantii refers to a species complex on 

Muscari spp., while Antherospora vaillantii s. str. refers to the 

species in its narrow sense (Bauer et al. 2008). 

Morphological examination 

Dried fungal teliospores of the investigated specimens were 

mounted in lactic acid, heated to boiling point and cooled, and 

then examined under a Nikon Eclipse 80i light microscope at a 

magnification of ×1000, using Nomarski optics (DIC). Spores 

were measured using NIS-Elements BR 3.0 imaging software. 

Spore size range, and the mean and standard deviation of 

the size of 50 measured spores were calculated for each 

investigated specimen (Table 1). The species description 

includes the combined values from all measured specimens. 

LM micrographs were taken with a Nikon DS-Fi1 camera.The 

ornamentation of the spore surface was studied using scanning 

electron microscopy (SEM). For this purpose, dry spores were 

mounted on carbon tabs and fixed to an aluminium stub with 

double-sided transparent tape. The tabs were sputter-coated 

with carbon using a Cressington sputter-coater and viewed 

with a Hitachi S-4700 scanning electron microscope, with a 

working distance of ca. 12−13 mm. SEM micrographs were 

taken in the Laboratory of Field Emission Scanning Electron 

Microscopy and Microanalysis at the Institute of Geological 

Sciences, Jagiellonian University, Kraków (Poland). 

Table 1. List of specimens, with host plants, GenBank accession numbers, spore size range, mean spore sizes with standard deviation, and 

reference specimens, newly examined in the course of this study. 

Smut species Host species GenBank 

acc. no. (ITS/ 

LSU) 

Spore size 

range (µm) 

Average spore 

size with standard 

deviation (µm) 

Reference specimens 1 

Antherospora 

tractemae 

Antherospora 

tractemae 

Antherospora 

tractemae 

Antherospora 

tractemae 

Antherospora 

tractemae 

Floromyces 

anemarrhenae 

Tractema verna 





Anemarrhena 

asphodeloides 

JN104589/ 

JN104590 

JN204283/ 

JN204279 

JN204284/ 

JN204280 

JN204285/ 

JN204281 

JN204286/ 

JN204282 

7.0–12.0 × 

6.5–9.5 

7.5–14.5(–16.5) 

× 7.0–9.5(–10.5) 

6.5–12.5(–16.0) 

× (5.5–)6.0– 

9.5(–10.0) 

7.0–11.5(–15.0) 

× 6.0–10.5 

(7.0–)8.0– 

13.0(–14.0) × 

6.0–10.5(–11.5) 

9.3 ± 1.3 × 7.8 ± 0.7 UK, Scotland, Outer Hebrides, 

Sgeir Ghlas Leac an Aiseig, Lewis, 

NA–993–215 [grid reference on 

UK national grid], 6 May 2010, P.A. 

Smith, KR 28182 

10.5 ± 2.1 × 8.5 

± 0.8 

UK, Wales, Ceredigion, Llangranog 

Head, SN–312–551 [grid reference 

on UK national grid], 19 April 2011, 

A.O. Chater, KRAM F-48879 – 

holotype 

9.3 ± 1.8 × 7.7 ± 0.9 UK, Wales, Ceredigion, 100 m SW 

of mouth of Cwm Soden, SN–361– 

582 [grid reference on UK national 

grid], 29 April 2011, A.O. Chater, 

KRAM F-48878 

9.6 ± 1.7 × 8.2 ± 1.1 UK, Wales, Ceredigion, 200 m NE 

of Mwnt church, SN–196–521 [grid 

reference on UK national grid], 6 

May 2011, A.O. Chater, KRAM 

F-48877 

10.1 ± 1.6 × 8.6 

± 1.2 

UK, Wales, Ceredigion, 500 m E 

of Mwnt church, SN–200–521 [grid 

reference on UK national grid], 6 

May 2011, A.O. Chater, KRAM 

F-48876 

JN104591/- not analysed not analysed China, Inner Mongolia, Chifeng 

city (Ulanhad), Hongshan Distr., 

Hongshan, 15 July 2007, T.Z. Liu, 

H.U.V. 21482 

1 

H.U.V. – Herbarium Ustilaginales Vánky, Gabriel-Biel-Str. 5, D-72076 Tübingen, Germany; KR – Herbarium of the Staatliches Museum 

für Naturkunde, Karlsruhe, Germany; KRAM F – Mycological Herbarium of the W. Szafer Institute of Botany, Polish Academy of Sciences, 

Kraków, Poland. 

136 ima fUNGUS

Antherospora tractemae sp. nov. 

A. vindobonensis EF653990/EF653972 on S. vindobonensis 



85/97/94 


ssp. borhidiana 


ARTICLE 

100/100/99 


A. scillae EF653983/EF653965 on S. bifolia 

87/100/91 


84/70/93 


100/100/100 

100/100/100 

77/99/96 

87/100/68 

91/100/93 

70/59/80 

81/-/- 

81/97/83 



A. vaillantii EF653986/EF653968 on M. tenuiflorum 



A. vaillantii EF653982/EF653964 on M. neglectum 

A. vaillantii EF653997/EF653979 on M. comosum 

A. vaillantii EF653998/EF653980 on M. neglectum 

A. tractemae JN104589/JN104590 on T. verna 

Floromycetaceae 


99/100/98 




Floromyces anemarrhenae JN104591/EU221284 

76/-/- 

Melanustilospora ari EF635904/EF517924 

-/59/73 Vankya ornithogali EF635910/EF210712 

-/-/56 

Ustacystis waldsteiniae DQ875356/AF009880 

60/100/99 

Melanoxa oxalidis EF635907/EF635908 

95/100/84 

Urocystis colchici DQ875355/DQ838576 

Flamingomyces ruppiae EF635909/DQ185436 

Mundkurella kalopanacis DQ875351/AF009869 

0.005 substitutions/site 

Fig. 1. Hypothesis on phylogenetic relationships within the sampled Urocystidales based on neighbour-joining analysis of an alignment of 

concatenated ITS + LSU base sequences using the TrN + G model of DNA substitution. The topology was rooted with the urocystidacean 

species. NJ bootstrap values of 1000 replicates are indicated before slashes, numbers on branches between slashes are estimates for a 

posteriori probabilities, numbers on branches after slashes are ML bootstrap support values. A. = Antherospora, M. = Muscari, S. = Scilla, T. = 

Tractema. 

Urocystidaceae 

DNA extraction, PCR, and sequencing 

Genomic DNA was isolated directly from the herbarium 

specimens. For methods of isolation and crushing of fungal 

material, DNA extraction, amplification, purification of PCR 

products, sequencing, and processing of the raw data see 

Lutz et al. (2004). ITS 1 and ITS 2 regions of the rDNA 

including the 5.8S rDNA (ITS) were amplified using the 

primer pair ITS1-F (Gardes & Bruns 1993) and ITS4 (White et 

al. 1990). The 5´-end of the nuclear large subunit ribosomal 

DNA (LSU) was amplified using the primer pairs LR0R and 

LR5 or NL1 and NL4, respectively (O´Donnell 1992, 1993, 

White et al. 1990). Primers were used for both PCR and cycle 

sequencing. For amplification the annealing temperature was 

adjusted to 45 °C. DNA sequences determined in this study 

were deposited in GenBank. GenBank accession numbers 

are given in Fig. 1 and Table 1. 

Phylogenetic analyses 

In addition to the sequences of Antherospora sp. on Tractema 

verna (ITS and LSU) and Floromyces anemarrhenae (ITS) 

newly obtained in this study, sequences from GenBank of 

the following species were used for molecular phylogenetic 

analyses (Begerow et al. 1997, 2006, Bauer et al. 2007, 

2008, Vánky et al. 2008, Lutz et al. in press): Antherospora 


137


ARTICLE 

Table 2. ITS and LSU sequence divergences of Antherospora species used in phylogenetic analyses. 

Smut species Antherospora scillae Antherospora vaillantii Antherospora 

vindobonensis 

Host Scilla bifolia Muscari 

comosum 

Muscari 

neglectum 

Muscari 

tenuiflorum 

Scilla 

vindobonensis 

Antherospora tractemae ITS (653 a ) 3.4–3.5 % (22–23 b ) 1.8–2.0 % 1.4–2.0 % (9–13) 5.7–6.0 % (37–39) 3.5–3.7 % (23–24) 

on Tractema verna 

(no. of characters) LSU (658) 1.5–1.7 % (10–11) 

(12–13) 

0.9 % (6) 0.9–1.2 % (6–8) 1.2–1.4 % (8–9) 1.7–1.8 % (11–12) 

a 

A total number of nucleotide characters. 

b 

The number of different nucleotide characters. 

scillae, A. vaillantii, A. vindobonensis, Flamingomyces 

ruppiae, Floromyces anemarrhenae, Melanoxa oxalidis, 

Melanustilospora ari, Mundkurella kalopanacis, Urocystis 

colchici, Ustacystis waldsteiniae, and Vankya ornithogali 

(GenBank accession numbers included in Fig. 1). 

To elucidate the phylogenetic position of the Antherospora 

specimens from Tractema verna their concatenated ITS + 

LSU sequences were analysed within a dataset covering all 

sequences of Floromycetaceae available in GenBank and 

representatives of all genera of Urocystidaceae. If present in 

GenBank, the respective type species were used. 

Sequence alignment was obtained using MAFFT v. 6.853 

(Katoh et al. 2002, 2005, Katoh & Toh 2008) using the L-INS-i 

option. To obtain reproducible results, manipulation of the 

alignment by hand as well as manual exclusion of ambiguous 

sites were avoided as suggested by Giribet & Wheeler (1999) 

and Gatesy et al. (1993), respectively. Highly divergent 

portions of the alignment were omitted using GBlocks 0.91b 

(Castresana 2000) with the following options: “Minimum 

Number of Sequences for a Conserved Position” to 16, 

“Minimum Number of Sequences for a Flank Position” to 16, 

“Maximum Number of Contiguous Non-conserved Positions” 

to 8, “Minimum Length of a Block” to 5 and “Allowed Gap 

Positions” to “With half”. 

The resulting alignment [new number of positions: 1308 

(65 % of the original 1990 positions) number of variable 

sites: 300] was used for phylogenetic analyses using 

Neighbour-Joining (NJ), a Bayesian Approach (BA) and 

Maximum Likelihood (ML). For NJ analysis the data were 

first analysed with Modeltest 3.7 (Posada & Crandall 1998) 

to find the most appropriate model of DNA substitution. The 

hierarchical likelihood ratio test proposed the TrN + G DNA 

substitution model. Bootstrap values were calculated from 

1000 replicates. NJ analyses were carried out using PAUP 

v. 4.0b10 (Swofford 2001). For BA a Bayesian approach to 

phylogenetic inference using a Markov chain Monte Carlo 

technique was used as implemented in the computer program 

MrBayes v. 3.1.2 (Huelsenbeck & Ronquist 2001, Ronquist & 

Huelsenbeck 2003). Four incrementally heated simultaneous 

Markov chains were run over 5 000 000 generations using 

the general time reversible model of DNA substitution with 

gamma distributed substitution rates and estimation of 

invariant sites, random starting trees and default starting 

parameters of the DNA substitution model as recommended 

by Huelsenbeck & Rannala (2004). Trees were sampled 

every 100th generation, resulting in an overall sampling of 

50 001 trees. From these, the first 5 001 trees were discarded 

(burnin = 5 001). The trees sampled after the process had 

reached stationarity (45 000 trees) were used to compute a 

50 % majority rule consensus tree to obtain estimates for the 

a posteriori probabilities of groups of species. This Bayesian 

approach to phylogenetic analysis was repeated five times to 

test the independence of the results from topological priors 

(Huelsenbeck et al. 2002). 

ML analysis (Felsenstein 1981) was conducted with the 

RAxML v. 7.2.6 software (Stamatakis 2006), using raxmlGUI 

(Silvestro & Michalak 2010), invoking the GTRCAT and the 

rapid bootstrap option (Stamatakis et al. 2008) with 1000 

replicates. 

In line with Vánky et al. (2008), trees were rooted with the 

urocystidacean species Flamingomyces ruppiae, Melanoxa 

oxalidis, Melanustilospora ari, Mundkurella kalopanacis, 

Urocystis colchici, Ustacystis waldsteiniae, and Vankya 

ornithogali. 

RESULTS 

Morphological analyses 

The examined specimens on Tractema verna produced 

olivaceous sori with teliospores in all anthers of the 

inflorescences. The spores in all specimens were verruculose, 

variable in shape and size within particular collections, and 

variable in spore size range and mean spore size between 

different collections (Table 1). The spore wall was twolayered, 

although the layers were not always clearly visible 

in some spores. The detailed morphological characteristics 

of anther smut on Tractema verna are included in the species 

description and depicted in Fig. 2. 

Phylogenetic analyses 

The ITS sequences of the five Tractema verna anther smut 

specimens analysed differed in one base pair (0.15 %) from 

each other or were identical, LSU sequences were identical. 

ITS and LSU sequence divergences of Antherospora species 

used in phylogenetic analyses are included in Table 2. 

The different runs of BA that were performed and the ML 

analyses yielded consistent topologies which were congruent 

138 ima fUNGUS


to the results of the NJ analysis in respect to well supported 

branchings (a posteriori probability greater than 54, ML 

bootstrap support values greater than 29). To illustrate the 

results, the phylogenetic hypothesis resulting from the NJ 

analysis is presented in Fig. 1. Bootstrap values from the NJ 

analysis are indicated on branches before slashes, estimates 

for a posteriori probabilities are indicated between slashes, 

numbers on branches after slashes are ML bootstrap support 

values. 

In all analyses the Antherospora species included in 

previous work (Bauer et al. 2008) were inferred with high 

support values, and phylogenetic relationships between 

floromycetacean species were as in Bauer et al. (2008) 

and Vánky et al. (2008). The Antherospora specimens from 

Tractema verna formed a well supported clade that clustered 

as a sister group of Antherospora vaillantii with high (NJ, BA) 

to moderate (ML) support values. Thus, the Antherospora 

specimens from Tractema verna were well separated from 

the Antherospora species growing on Scilla species, A. 

scillae and A. vindobonensis. 

on Tractema verna, 6 May 2011, A.O. Chater (KRAM F-48877); 

Ceredigion, 500 m E of Mwnt church, on Tractema verna, 6 May 

2011, A.O. Chater (KRAM F-48876). 

Ecology: The infected plants were found in April and May, 

peak flowering time for Tractema verna. The habitats for all 

the collections are broadly similar, consisting of short coastal 

turf on shallow soils. The Outer Hebrides locality is on pockets 

of maritime peat on a rocky substrate, referable to the MC10 

Festuca rubra–Plantago spp. maritime grassland community 

(plant community nomenclature follows Rodwell et al. 1991– 

2000). The Welsh sites are in coastal heath vegetation 

referable to the H7 Calluna vulgaris–Scilla verna heath and 

H8d Scilla verna subcommunity of Calluna vulgaris–Ulex 

gallii heath, as well as in the Armeria subcommunity of the 

MC10 community. Tractema verna is locally common around 

the rocky western coasts of Britain, and occurs in a number of 

maritime communities. The smut often infects large numbers 

of individuals within a population, and its incidence varies 

greatly from year to year. 

ARTICLE 

Taxonomy 

Antherospora tractemae M. Piątek & M. Lutz, sp. nov. 


(Fig. 2) 

Etymology: Named after the host plant genus. 

Sori in antheris Tractemae vernae. Massa sporarum pulverulenta, 

olivaceo-brunnea. Sporae globosae, subglobosae, late ellipsoideae, 

late ovales, nonnumquam elongatae, pyriformae vel asymmetricae, 

6.5–14.5(–16.5) × (5.5–)6.0–10.5(–11.5) µm, olivaceae vel flavidobrunneae, 

parietibus 0.5–1.3 µm crassis, dense verruculosis, a 

latere visae fere levigatae vel subtiliter sinuatae. 

Typus: UK: Wales: Ceredigion, Llangranog Head, on Tractema verna 

(syn. Scilla verna), 19 Apr. 2011, A.O. Chater (KRAM F-48879 – 

holotypus; ITS/LSU sequences GenBank accession nos JN204283 

and JN204279). 

Parasitic on Tractema verna. Sori in the anthers, producing 

olive-brown, powdery mass of spores inside the pollen sacs. 

Infection systemic, all anthers of a plant infected. Spores 

globose, subglobose, broadly ellipsoidal, broadly ovoid, 

sometimes elongated, pyriform or asymmetrical, 6.5–14.5(– 

16.5) × (5.5–)6.0–10.5(–11.5) µm [av. ± SD, 9.8 ± 1.8 × 8.2 ± 

1.0 µm, n = 250/5], olivaceous or yellowish-brown, sometimes 

lighter coloured on one side; wall two-layered, ca. 0.5–1.3 µm 

thick, thinner on the lighter side, finely, densely verruculose, 

spore profile almost smooth or finely wavy. 

Additional specimens examined (paratypes): UK: Scotland: Outer 

Hebrides, Sgeir Ghlas Leac an Aiseig, Lewis, on Tractema verna, 

6 May 2010, P.A. Smith (KR 28182); Wales: Ceredigion, 100 m SW 

of mouth of Cwm Soden, on Tractema verna, 29 Apr. 2011, A.O. 

Chater (KRAM F-48878); Ceredigion, 200 m NE of Mwnt church, 

DISCUSSION 

The anther smuts of the genus Antherospora offer few 

morphological characteristics for inter-specific differentiation. 

This is the reason why they were formerly identified as a 

single species, Ustilago vaillantii (syn. Vankya vaillantii) 

(e.g. Vánky 1994). It appears that only a few species could 

be differentiated based on differences in spore sizes, and 

to a lesser extent also the spore wall thickness and the 

localization of the sori which is limited to the anthers or to the 

anthers and the surface of the inner floral organs (Bauer et 

al. 2008, Vánky et al. 2008, Vánky 2009). The recognition of 

Antherospora species that lack morphological differences is 

difficult or impossible without the support of molecular data. 

The variation of spore sizes between different collections 

of the same species (Bauer et al. 2008) may additionally 

complicate the situation with species delimitation. The 

differences in spore size range and mean spore size between 

different collections on Tractema verna (Table 1) confirm the 

variability of this character in Antherospora species, and it 

seems that whenever possible the morphology should be 

characterized based on collections from different populations. 

In spore size range (assessed from five specimens), 

the anther smut of Tractema verna is intermediate between 

Antherospora tourneuxii and A. urgineae on the one side 

and A. eucomis, A. scillae, A. vaillantii, and A. vindobonensis 

on the other side. Molecular data are not available for 

Antherospora eucomis, A. tourneuxii and A. urgineae. 

Other than infecting different host plant genera (Eucomis, 

Bellevalia and Charybdis respectively), A. eucomis can be 

separated by having smaller spores and a thinner spore 

wall, while the two remaining species have somewhat larger 

spores and thinner spore walls (Bauer et al. 2008, Vánky 

2009, Vánky et al. 2010). The spores of Antherospora 

scillae, A. vindobonensis (on Scilla) and A. vaillantii (on 


139


ARTICLE 

Fig. 2. Antherospora tractemae (KRAM F-48879 – holotype). A. Type locality on Llangranog Head, Wales, United Kingdom. B. Flower of 

Tractema verna with infected anthers. C–I. Spores seen by LM, median and superficial views. Note somewhat lighter coloured and thinner one 

side of spores indicated by arrows on pictures F and H, and two-layered spore wall visible on picture E. J–M. Ornamentation of spores seen by 

SEM. Bars: B = 1 mm; C–J = 10 µm; K–M = 5 µm. 

Muscari) are smaller than those of the anther smut of 

Tractema verna, and the spore wall is additionally thinner 

in A. vaillantii. The spore wall thickness of Antherospora 

scillae and A. vindobonensis (0.8–1.5 µm, according to the 

key to Antherospora species by Vánky 2009) is comparable 

to those of the anther smut of Tractema verna, and different 

from all remaining Antherospora species that have spore 

walls of 0.5–0.8 µm thick. The molecular phylogenetic 

analyses separate the specimens on Tractema verna from 

these three Antherospora spp. (Fig. 1) and both ITS and 

LSU sequences differ significantly (Table 2). In conclusion, 

the morphology, the genetic difference, the results of 

the molecular phylogenetic analyses and different host 

plant genera support the recognition of the anther smut 

of Tractema verna as a new species, for which the name 

Antherospora tractemae is proposed in this study. 

140 ima fUNGUS


The host plant was at first assigned to the genus Scilla (S. 

verna) according to most taxonomic treatments (e.g. McNeill 

1980), and thus it was initially assumed that its anther smut 

could be related to the two Antherospora species on Scilla 

already described. The molecular phylogenetic analyses 

revealed that the smut sporulating in anthers of Tractema 

verna occupies a position basal to the lineage of Muscariparasitizing 

Antherospora. A subsequent survey of the 

botanical literature revealed that Scilla is a polyphyletic genus 

and that Scilla verna actually belongs to the distinct genus 

Tractema (Speta 1998). Tractema verna has not as yet been 

included in phylogenetic analyses, but the related species 

Tractema monophyllos, the type of the genus Tractema, 

clusters distantly from the lineage attributed to Scilla s. str. 

(Pfosser & Speta 1999). Thus, the phylogenetic position of 

Antherospora tractemae supports the disentanglement of 

Scilla verna from Scilla s. str. This emphasizes the importance 

of the assignment of host species to the correct genus in 

order to promote the understanding of the evolutionary 

relationships between smut fungi and their host plants. 

Furthermore, it supports the long known hypothesis that 

plant parasitic fungi, especially rusts and smuts, can indicate 

relationships between their host plants (e.g. Savile 1954, 

1979, Nannfeldt 1968, Hijwegen 1979, 1988, Kukkonen & 

Timonen 1979). 

The large number of host plants reported for Ustilago 

vaillantii (syn. Vankya vaillantii) (Zundel 1953, Vánky 

1994) suggested that further species of Antherospora 

are likely to emerge. The descriptions of new species that 

lack morphological characteristics or have very subtle 

morphological differences needs to be supported by molecular 

data. The introduction of new species names based solely on 

supposed host specificity may be risky, because it is probable 

that within Antherospora there are species that have more 

than one host species as was evidenced for Antherospora 

vaillantii s. str. which is able to infect both Muscari comosum 

and M. neglectum (Bauer et al. 2008). 


We thank Krzysztof Pawłowski (Kraków, Poland) and Michael Weiß 

(Tübingen, Germany) for translating the Latin description, Michael 

Weiß, Sigisfredo Garnica and Robert Bauer (Tübingen, Germany) 

for providing the molecular lab, Anna Łatkiewicz (Kraków, Poland) 

for help with the SEM pictures, and Roger G. Shivas (Indooroopilly, 

Australia) for helpful comments on the manuscript. 

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142 

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Ascospore discharge, germination and culture of fungal partners of tropical 

lichens, including the use of a novel culture technique 

Ek Sangvichien 1 , David L. Hawksworth 2 , and Anthony J.S. Whalley 3 

ARTICLE 

1 

Faculty of Science, Ramkhamhaeng University, Hua Mark, Bangkok 10240, Thailand; corresponding author e-mail: bmsesang@yahoo.com 

2 

Departmento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, Ciudad Universitaria, 

ES-28040 Madrid, Spain; and Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, UK 

3 

School of Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK 

Abstract: A total of 292 lichen samples, representing over 200 species and at least 65 genera and 26 families, 

were collected, mainly in Thailand; 170 of the specimens discharged ascospores in the laboratory. Generally, 

crustose lichens exhibited the highest discharge rates and percentage germination. In contrast, foliose lichen 

samples, although having a high discharge rate, had a lower percentage germination than crustose species 

tested. A correlation with season was indicated for a number of species. Continued development of germinated 

ascospores into recognizable colonies in pure culture was followed for a selection of species. The most successful 

medium tried was 2 % Malt-Yeast extract agar (MYA), and under static conditions using a liquid culture medium, a 

sponge proved to be the best of several physical carriers tested; this novel method has considerable potential for 

experimental work with lichen mycobionts. 

Key words: 

Ascomycota 

colony development 

mycobiont 

seasonality 

Thailand 

Article info: Submitted 30 September 2011; Accepted 17 October 2011; Published 11 November 2011. 

Introduction 

The highest species diversity for most groups of organisms 

lies in the tropics. Lichenized fungi do not appear to be 

an exception, as Sipman & Aptroot (2001) estimated that 

between one-third and one-half of the world’s lichen diversity 

occurs there, and suggested that 50 % of the tropical 

lichen biota remained unknown. Yet there have been few 

experimental studies on ascospore discharge, germination, 

development of mycelia, and physiology of the fungal partners 

(mycobionts) of tropical lichens compared with those on 

temperate species. This is a major gap in our understanding 

of even basic aspects of the biology of tropical lichens. 

The first cited studies on the isolation of lichen-forming 

fungi are generally those of Töbler (1909) and Thomas 

(1939), although Töbler was primarily interested in the resynthesis 

of lichens from their individual symbionts (Turbin 

1996). However, Werner (1927), innovatively examined 

the effect of different media and additions on the growth of 

selected mycobionts from a range of lichens. Subsequent 

workers have concentrated on the development of methods 

for lichen re-synthesis (Ahmadjian 1964), and later Ahmadjian 

et al. (1980) and Ahmadjian & Jacobs (1981) produced the 

two most successful protocols (Bubrick 1988). Crittenden 

et al. (1995) were the first to attempt the isolation of a wide 

range of fungal partners of lichens, and also lichenicolous 

fungi, on a worldwide basis, although their material was 

predominantly from non-tropical regions. More recently, 

Yoshimura et al. (2002) reviewed the protocols available 

for isolation and cultivation of fungal and algal partners of 

lichens, emphasising studies by Japanese researchers, but 

again based largely on non-tropical material. A brief synopsis 

of methods used is provided by Stocker-Wörgötter & Hager 

(2008), with an emphasis on the production of extrolites 

(“lichen substances” or “secondary metabolites”). 

The lack of basic information on the isolation and 

growth of the fungal partners of tropical lichens provided the 

rationale for the present study. We investigated ascospore 

discharge from a wide range of tropical lichens in order to 

make a preliminary assessment of the conditions under 

which discharge occurred, and whether there could be any 

seasonal correlations. Observations on factors affecting 

germination and subsequent development on solid, or in 

liquid, growth media are also reported, since these are 

virtually undocumented for the fungal partners of tropical 

lichens. Our studies were carried out to identify apparent 

trends and issues that merited in-depth investigations, as 

well as testing the efficacy of alternative culture methods. 



Attribution: 







Sangvichien, Hawksworth & Whalley 

ARTICLE 

Table 1. Lichen collections according to locality and growth form type. 

Location Code Number of samples Crustose Foliose Erect shrubby or pendent 

Thailand 

Chiang Mai Province CM 27 15 11 1 

Chiang Rai Province CR 5 5 – – 

Kanjanaburi Province KJB 8 8 – – 

Nakon Sithammarat Province TS, RPB 6 6 – – 

Ratchaburi Province SP 7 7 – – 

Khao Yai National Park KY 208 140 60 8 

Phu Kradueng National Park PKD 5 4 – 1 

Sakaeraj Research Station SKR 2 2 – – 

Huai Kha Khaeng Wildlife Sanctuary HKK 4 4 – – 

Cambodia CAM 5 4 1 – 

Vietnam VN 15 15 – – 

Total 292 210 72 10 

Materials and Methods 

Taxon sampling 

The collection of samples began in 1998, and concentrated 

on Khao Yai National Park (KY), central Thailand. The 

remainder were collected during field surveys to Doi Suthep 

(18°49' N, 99°53' E) and Chiang Dao (l9°40' N, 99° E) in 

Chiang Mai Province (CM), Mae Fah Luang Arboretum (20° 

N, 99.5° E) Chiang Rai Province (CR), Sai Yok District (14° 

N, 99° E) Kanjanaburi Province (KJB), Khao Sok National 

Park (8° N, 99.5° E) Nakon Srithammarat Province (TS and 

RPB respectively), Phu Kradueng National Park, (16.8° N, 

101.8° E) Loei Province (PKD), Suan Phueng District (13.5° 

N, 99° E) Ratchaburi Province (SP), and Sakaeraj Research 

Station (14° N, 102° E) Nakhon Ratchasima Province (SKR). 

Some collections from Huai Kha Khaeng Wildlife Sanctuary 

Kanjanaburi Province, Vietnam (VN) and Cambodia (CAM) 

were donated by colleagues and friends. Khao Yai National 

Park was visited monthly during one year (1999–2000) for 

seasonal observations and experiments to explore the 

development of thalli, and also to ascertain if there were 

seasonal differences in ascospore discharge and spore 

viability 

Samples were cut into pieces, wrapped in tissue paper, 

and placed in individual strong brown paper bags. These 

were then returned to a survey house workroom and cleaned 

of attached soil or other extraneous material. Each sample 

was given a collection number, and information on the locality, 

substratum, and collection details were recorded. Then. if 

the specimens could not be immediately transferred to the 

laboratory for pre-isolation treatment, they were either kept 

in a cool place, or (where available) a domestic refrigerator, 

until they could be transferred. In the laboratory, samples 

were air-dried at room temperature (30 °C) overnight, and 

then transferred to new paper envelopes with identification 

labels and stored in a domestic refrigerator at 4 °C until the 

isolation protocol had been completed. 

Specimens were identified as precisely as possible on the 

basis of their morphology, anatomy, and chemical constituents 

(determined by standard thin-layer chromatographic methods; 

Orange et al. 2001). In many cases it was not possible to fully 

determine the samples to species as identification remains a 

major problem in tropical lichenology. The basic monographic 

treatments required to provide a sound taxonomic basis 

for studies of lichen distribution, ecology, and physiology 

are still lacking for most lichen families and genera in the 

tropics. Species that have not previously been described 

are also likely to be found; Homchantara & Coppins (2002) 

described 26 species of Thelotremataceae as new to science 

from Thailand 1 , and Aptroot et al. (2007) added 300 tropical 

species to the national list, of which 12 were new to science. 

The number of collections made for each morphological 

type of lichen, together with their geographical locations, are 

summarized in Table 1, while full details of selected collections 

for which positive results were obtained are given in Table 2. 

A list of the material collected is included as Supplementary 

Information (Table S1, online only) and in Sangvichien (2005). 

Voucher specimens are maintained in The Lichen Herbarium, 

Ramkhamhaeng University, Bangkok (RAMK). 

Spore discharge and germination 

The specimens were removed from storage, and surfacecleaned 

with air from an aerosol camera blower to remove 

any remaining soil and debris. A sterile surgical blade 

(Gowlands No. 11) was used to dissect specimens to obtain 

small portions with ascomata, and the remainder of the 

samples were then returned to storage. The process was 

repeated if the first isolation attempts were unsuccessful. The 

portions of lichen with ascomata, or occasionally only a single 

ascoma, were attached with a small quantity of petroleum 

jelly onto the inverted lid of a 9 cm diam Petri dish (Sterilin). 

The spores were allowed to shoot upwards onto an overlying 

layer of Tap Water Agar (WA; Booth 1971). The agar surface 

was examined daily with a stereozoom binocular microscope 

(Olympus SZ11), and once ascospores had been discharged, 

1 

Eleven of these have since proved to be synonyms of previously 

described species (Papong et al. 2010). 

144 ima fUNGUS

Tropical lichen fungi: ascospore discharge and culture 

small agar blocks (3–5 mm 2 ) with ascospores on the surface 

were excised and transferred to Malt-Yeast extract Agar 

(MYA; Merck or Oxoid). Germination of ascospores was 

assessed under the stereozoom microscope; observations 

were made daily for 7 d, and subsequently twice weekly. 

If no germ tubes had been observed after six weeks, then 

“no-germination” in that collection was recorded. Germinated 

ascospores were maintained at room temperature for further 

studies on growth and colony morphology, or were used as 

inoculum for liquid media. 

In order to investigate the seasonality and discharge of 

ascospores, thalli were collected each month from the same 

trees in Khao Yai National Park over a one year period, 

and their discharge patterns and rates of germination were 

determined for each monthly sample following the protocol 

described above. 

The distance to which ascospores were discharged was 

studied in a representative sample of 15 species. Clear 

plastic boxes 18 x 7.5 x 5 cm were used with a layer of tap 

water agar in the lid of the box. Ascomata samples, approx. 

0.3 mm diam, were attached to one vertical microscope 

slide (2 x 4 cm) which was shallowly immersed in the agar 

layer. The box was then incubated on the laboratory bench 

at an ambient temperature of 25–30 °C, with approximately 

12 h of daylight. The agar surface was examined under an 

Olympus stereozoom microscope (Model SZ 11) daily for 5 d. 

If no spores were discharged within 3 d, the procedure was 

repeated, and then, if after a second 3 d period no discharge 

was observed, the protocol was repeated for a third and final 

time. 

We also investigated the effects of relative humidity by 

incubating Petri dishes in plastic moist chambers containing 

different saturated solutions to maintain the relative humidity 

at particular levels, following Kaye & Laby (1966): potassium 

nitrate (92 %), ammonium sulphate (80 %), and sodium 

nitrate (65 %). 

We tried, but did not adopt, the surface sterilization 

protocol of Crittenden et al. (1995) as we found it to be 

detrimental to ascospore discharge in the tropical lichens 

tested; in consequence, untreated lichen samples were used 

throughout. 

pieces of the fungal cultures into the liquid medium, different 

types of physical support for the fungi on the surface of the 

liquid were tested. 

Four types of material were evaluated: (1) Stacked 

Membrane filters (pores 0.22 μm diam; polyvinylidene 

fluoride, PVDF) were promising when tested first, but the 

slippery surface when floating on the liquid rendered them 

difficult to inoculate. (2) Whatman No.1 filter papers were 

tested in order to overcome the problem of stacked layers. (3) 

Kraft paper was tried as an alternative to Whatman No.1. And 

(4), synthetic sponge (polystyrene) pieces 2.5 x 2.5 x 0.3 cm, 

together with pieces of fungal colonies cut from solid media 

of 0.4 x 0.4 cm, placed on the surface of these materials, and 

floated on the surface of 50 ml MYB in 250 mL Erlenmeyer 

flasks. Observations were made twice daily and, at the same 

time, the flasks were gently swirled for 10–15 s to circulate 

the medium. 

Since poor aeration could be a factor limiting growth, the 

effect of increased aeration was tested in two ways. First, air 

was supplied by an aquarium air pump and passed through 

a sterile filter (Sartorious, Sartofluor ® ; pores 0.2 µm diam) to 

prevent contamination. Second, flasks were placed on an 

orbital shaker (Innova 4230, New Brunswick). Shake cultures 

were prepared using inocula produced in the same way as for 

static cultures, and transferred to 250 mL Erlenmeyer flasks 

containing 50 mL of MYB. The orbital shaking incubator was 

set at a speed of 200 rpm, and at a temperature of 30 ± 0.5 

°C. 

Scanning electron microscopy 

Specimens for scanning electron microscopy (SEM), either 

intact ascomata or cultures of the isolated fungal partners, 

were fixed in 5 % glutaraldehyde and dehydrated in a graded 

ethyl alcohol series. The specimens were then attached to 

aluminium stubs using either Dag metallic paint or adhesive 

carbon pads to prevent electron charging of the specimens. 

The samples were gold-coated using a Sputter Coating Unit 

(Polaron RU-SC7620) and examined either with a Jeol 840 

SEM, a Jeol SEM5410LV, or a Leo 1455VP scanning electron 

microscope. Digital images were produced using an imagecapture 

system (Röentec) or with accessories of Leo 1455 VP. 

ARTICLE 

Fungal culture on solid media 

MYA (see above) was the medium of choice for all cultures 

of the fungal partners, but Potato Dextrose Agar (PDA), 

Corn Meal Agar (CMA), Oatmeal Agar (OMA), and Czapek- 

Dox Agar (CDA), were also used to determine the optimum 

medium for growth. For recipes see Booth (1971). 

Fungal culture in liquid media 

Malt Yeast Extract Broth (MYB) was selected as the standard 

medium for studies of the isolated fungi in liquid culture, 

since good growth rates of several fungal partners had been 

observed on solid MYA. MYB has also been favoured by 

previous researchers (e.g. Hamada 1989, Honegger 1990, 

Yamamoto et al. 1998). Static culture was most frequently 

used, and following initial trials with direct inoculation of 

Results and Discussion 

This study employed a large number of samples in order to 

gain an impression of possible general features of ascospore 

discharge and development in tropical lichens to provide a 

basis on which to determine directions future investigations 

might take. As replicates were not used for most of the 

species, the conclusions must be viewed as preliminary 

and treated with caution. Nevertheless, some indications of 

trends emerged, although we recognize that further work may 

require their modification or refinement. This caveat must be 

borne in mind with respect to this discussion of our results. 

The number of crustose lichen collections made was 

much larger than that of foliose lichens (Table 1). Crustose 


145


ARTICLE 

Table 2. Lichen collections, ascospores discharged, germination (%), and colony development in selected species. The classification follows 

Lumbsch & Huhndorf (2010). 

Taxon Collection number Ascospores discharged Germination (%) Colony development 

ARTHONIALES 

Arthoniaceae 

Arthothelium sp. KY175 11 100 2 

LECANORALES 

Cladoniaceae 

Cladonia submultiformis KY117,118,119 > 500 100 1 

Haematommataceae 

Haematomma puniceum KY107 NA ND 0 

Haematomma sp. VN3 NA ND 0 

Lecanoraceae 

Lecanora cenisia SP4 47 0 0 

Lecanora intumescens CM27 NA ND + 

Lecanora leprosa SP6 310 0 0 

Lecanora polytropa KY177 47 92 0 

Pyrrhospora sp. 1 CR8 NA ND + 

Parmeliaceae 

Parmelina sp. CM33 50 0 0 

Relicinopsis sp. KY81 NA ND 0 

Relicinopsis sp. CM32 191 0 0 

Usnea complanata CM12 > 500 0 0 

Pilocarpaceae 

Sporopodium argillaceum VN16 2 50 + 

Ramalinaceae 

Bacidia subannexa SP10 > 900 89 0 

Bacidia sp. 1 SP12 190 21 0 

OSTROPALES 

Graphidaceae 

Cyclographina sp. 2 KY390 23 57 0 

Glyphis cicatricosa SP7 12 100 3 

Glyphis cicatricose KY231 NA ND + 

Graphina cleistoblephara KY129 96 98 + 

Graphina hiascens KY160 69 99 3 

Graphina sp. 2 KY104 NA ND + 

Graphina sp. 5 KY157 124 91 + 

Graphina sp. 9 KY124 10 90 + 

Graphina sp.18 KY171 28 100 3 

Graphina sp. 19 KY91 NA ND + 

Graphina sp. 20 KY180 186 90 + 

Graphis afzelii CR5 NA ND + 

Graphis albocolpata KY147 NA ND + 

Graphis analoga HKK7 > 1000 100 0 

Graphis apertella HKK4 255 100 0 

Graphis apertella SP2 307 259 0 

Graphis elegans KY162 73 99 3 

Graphis kakaduensis TS3 435 100 0 

Graphis librata RPB1 760 100 0 

146 ima fUNGUS


Table 2. (Continued). 


Graphis rigidula KY165 > 500 100 3 

Graphis rimulosa CR3 5 100 3 

Graphis xanthospora TS2 56 100 0 

Graphis sp. 10 KY148 111 94 3 

Graphis sp. KY133 5 0 0 

Graphis rimulosa SP1 180 100 0 

Graphis rimulosa KY133 NA ND + 

Graphis sp. SP9 > 1000 100 3 

Gyrostromum sp. KY161 26 96 + 

Ocellularia s. lat. sp. KY173 129 89 3 

Phaeographina caesioradians HKK1 450 100 0 

Phaeographina quassiaecola VN6 1 100 3 

Phaeographina sp. CAM5 1 100 3 

Phaeographina sp. 4 HKK2 > 1000 100 3 

Pheopgraphis melanostalazans KY144 113 88 3 

Phaeographis melanostalazans KY121 NA ND + 

Phaeographis pyrhochora PKD4 42 100 3 

Phaeographis sp. 27 KY229 NA ND + 

Sarcographa actinobola KY205 NA ND + 

Sarcographa labyrinthica KY240 NA ND + 

Thelotrema s. lat. sp. 3 KY233 NA ND + 

Thelotrema sp. 4 VN9 1 0 0 

Thelotrema s. lat. sp. 5 KY245 NA ND + 

Thelotrema sp. 6 VN10 1 100 + 

ARTICLE 

PELTIGERALES 

Nephromataceae 

Nephroma sp. CM30 15 67 0 

PERTUSARIALES 

Pertusariaceae 

Pertusaria sp. 4 PKD2 18 100 2 

PYRENULALES 

Pyrenulaceae 

Pyrenula sp. KY208 NA ND + 




TELOSCHISTALES 

Physciaceae 

Rinodina sp. KY169 NA ND + 

Teloschistaceae 

Caloplaca sp. CR6 2 0 0 

TRYPETHELIALES 

Trypetheliaceae 

Campylothelium sp. SKR2 NA NA + 


147


ARTICLE 

Table 2. (Continued). 


Laurera benguelensis KY61 197 99 3 

Laurera madreporiformis KY14 NA ND + 

Laurera megasperma KY238 NA NA 3 

Laurera meristospora KY195 NA NA 3 

Laurera subdiscreta SKR1 NA NA + 

Pseudopyrenula diluta KY113 NA ND + 

Trypetheliaceae sp. KY135 39 100 3 

Trypetheliaceae sp. KY131 63 87 + 

Trypethelium eluteriae KY66 82 100 3 

Trypethelium ochroleucum KY235 NA ND + 

INCERTAE SEDIS 

Unidentified KY141 46 83 + 

Unidentified KY143 6 50 + 

NA = not available, ND = not detected. 

Colony development : 0 = none, 1 = poor, 2 = moderate, 3 = good , + = germination but with premature cessation of growth. 

Fig. 1. Ascospore germination in selected species. A. Glyphis 

cicatricosa (KY231). B. Phaeographina montagnei (KY263). C–D. 

Pyrenula sp. (KY95 and 208). E–F. Trypethelium eluteriae (KY66). 

G-H. Trypethelium tropicum (KY131). 

lichens were preferentially selected for experimentation 

as preliminary studies suggested that their ascospores 

germinated more readily on artificial media. Ascomata of 

erect shrubby (fruticose) and pendent lichens were much less 

common than crustose or foliose ones, especially at Khao Yai 

National Park, and so could not be investigated further. 

Of the 292 lichen samples collected (Table 1), 170 

samples liberated ascospores in the laboratory, and in several 

instances successive samples of the same lichen exhibited 

high percentage germination rates (Table 2, Fig.1). Crustose 

lichens exhibited the highest rate of spore discharge, and also 

subsequent germination. In contrast, foliose lichen species 

(e.g. Heterodermia diademata) exhibited a high discharge 

rate, but only a low percentage of ascospores germinated. 

Seasonal influences on ascospore discharge and 

germination were explored in selected species (Fig. 2). In 

Trypethelium eluteriae (KY 66), Graphis elegans (KY162),and 

G. rigidula (KY165), ascospores were discharged readily 

each month, and spores from each monthly sample also 

germinated. However, in contrast, Cladonia submultiformis 

(KY117) discharged ascospores only towards the end of the 

winter (January-February), and in the summer (April-June) 

none were discharged (Fig. 2). 

Following germination, the ability of the isolated fungi to 

continue to develop and form colonies was investigated. In 

some common crustose lichen species, the fungal partners 

grew well and produced small colonies within a few months 

(Fig. 3). Species of Trypethelium and Laurera developed 

colonies readily, while in Haematomma wattii and Lecanora 

intumescens the spores germinated but growth was either 

very slow or soon ceased. In addition to growth on solid 

media, liquid culture under static growth conditions was 

tried, but generally growth was slow. Further, when the 

fungi were inoculated onto the surface of membrane filters 

floating on the surface of MYB, this was not satisfactory as 

148 ima fUNGUS

Janu 

Febua 

Mar 

A 

M 

Ju 

J 

Augu 

Septemb 

Octob 

Novem 

Decemb 

% 

Janua 

January 

Febua 

Febuary Febua 

March 

Mar 

Mar 

Ap 

April A 

M 

May 

Ju 

June Ju 

July 

J 


Months 

0 

Months 

August 

Augu 

Augu 

September 

Septemb 

Octob 

October Octob 

November 

Novem 

December 

Decemb 

0 

January Janua 

Febuary Febua 

March Mar 

A 

April 

Months 

% spore % spore germination 

100 

100 80 

80 60 

60 40 

40 20 

200 

0 

January January 

Febuary Febuary 

March March 

April 

April 

B 

A 

May 

June 

July 

May 

June 

July 

Months 

August August 

September September 

October October 

November November 

December December 

% spore spore % spore 

% 

germination 

spore germination 

100 

100 80 

100 

80 

100 60 80 

60 60 

40 80 

60 40 

40 

20 

40 20 

20 

20 00 

00 

January 

January 

January 

January 

Febuary 

Febuary 

Febuary 

Febuary 

March 

March March 

March 

April 

April 

April 

April 

May 

May 

May 

May 

C 

B 

June 

June 

June 

June 

July 

July 

July 

July 

Months 

August 

August August 

August 

September 


September 



November 

November 

November 

November 

December 

December 

December 

December 


100 

100 

80 

80 

60 

60 

40 

40 

20 

20 

0 

0 



ARTICLE 

March March 

April April 

Months 

Months 


100 

100 80 

80 60 

60 40 

40 20 

200 

0 



March March 

April 

Fig. 2. Apparent seasonal effect on ascospore D discharge and germination on 100 selected species. A. Cladonia submultiformis (KY117). B. Graphis 

elegans (KY162). C. G. rigidula (KY165). C D. Trypethelium eluteriae (KY66). 100 80 

D 

100 


100 80 

80 60 

the membranes 60 40 

often sank following inoculation, or tended to 

40 20 

collapse after a period of growth. Amongst the other physical 

200 

carriers tested, were segments of unbleached Kraft paper or 

0 

Whatman filter paper several layers thick. Growth occurred 

on the surface of these, but it was only possible to assess 

Months 

this visually as it proved impossible to physically separate 

Months 

all the fungal material from their surfaces. In contrast, the 

sponge pieces tested as alternative carriers facilitated growth 

after incubation in the fungal partners D tested; in most cases, 

sponge proved to be superior to the other carriers tried 

(Fig. 3). 

Trypethelium 100 eluteriae (KY66). 

80 

No contamination by spores from other fungi during 

60 

discharge were 40 encountered; the distinctive ascospores 

from the lichens 20 were deposited, either as small packets of 

0 

spores or as single spores, and could easily be recognized 

for subculturing using a stereozoom microscope. 

Our results suggest that high spore discharge rates are 

Months 

correlated with the freshness of the samples and season of 

collection, as well as the state of maturity of the ascomata. 

Spore germination also appeared to be correlated with 

species distributions. Widely distributed species, such as 

Trypethelium eluteriae, Laurea bengualensis, and most 

Graphidaceae Trypethelium studied, eluteriae exhibited (KY66). relatively high rates of 

germination. 

There was, however, considerable variation in ascospore 

discharge between the species tested, and, also between 

different collections of the same species. In Laurera 

bengualensis and L. madreporiformis, spores were readily 

discharged in all of the collections examined, but in L. 

meristospora, although discharge occurred, it was at a much 

lower rate. In Trypethelium eluteriae, spore discharge occurred 

% spore germination 

100 


January 


Febuary 

March March 

March 

April 

April 

April 

April 

May 

May 

May 

May 

May 

C 

B 

June 

June 

July 

Months 

June 

June 

July 

Months 

June 

July 

July 

July 

August August 

August August 

August 



September 



October 



November 



December 

% spore % 

spore 

spore 

% 

germination 


% spore 

% spore % 

germination 


100 80 

100 

80 

100 60 80 

60 60 

40 80 

60 40 

40 

20 

40 20 

20 

20 00 

00 

60 40 80 

January 

January 

January 

January 

Febuary 

Febuary 

Febuary 

Febuary 

March 

March 

March 

March 

April 

April 

May 

May 

June 

June 

July 

July 

Months 

throughout 60 

40 the year, but in Cladonia submultiformis, although 

20 

40 

40 

ascospores were also readily discharged, only those from the 

20 

20 0 

20 

end of the winter season (February) germinated. This suggests 

00 

0 

that in some lichen-fungi, seasonality is important even in the 

tropics. These observations of differences in spore discharge 

Months 

between species are in agreement with those of Crittenden et 

Months 

al. (1995), based mainly on samples from non-tropical regions. 

The distance of discharge of ascospores is important for 

the dissemination of the species (Table 3). Of the 15 species 

100 

tested, those of Graphina sp. 9 (KY104) were discharged the 

80 

furthest, to 63 mm. This figure compares with the maximum of 

60 

45 mm obtained for the temperate Rhizocarpon umbilicatum 

40 

(Bailey & Garrett 1968). However, in that study no information 

20 

was given as to the distance attained by the majority of spores, 

0 

which is perhaps the most pertinent parameter in relation to 

effective dispersal and establishment in nature. There was a 

wide variation even within the 75 % ranges of projection in 

Months 

many cases, and we speculate that this could be an adaptation 

to increase the probability of contact with a suitable new 

substrate. In nature, air turbulence currents and wind would 

also be expected to influence the final distance travelled. 

Environmental conditions also appeared to influence 

ascospore discharge. At 15 °C any discharge was rare, 

occurring only in Arthopyrenia sp. (PKD3) and Laurera 

subdiscreta (SKR1), while at 45 °C no discharge was 

observed in any species tested (Table 4). As might have been 

expected for tropical species, most species discharged at 30 

°C and 35 °C, but the mean optimum discharge temperature 

for all species was close to 25 °C. Relative humidity also 

appears to be important, with three of the four species 

investigated discharging at relative humidities from 65 % 

August 

August 

August 

August 

80 

Trypethelium 100 60 eluteriae (KY66). 

Fig. 2. Apparent seasonal effect on ascospore discharge and germination on selected species. A. 

Cladonia submultiformis (KY117). B. Graphis elegans (KY162). C. G. rigidula (KY165). D. 


100 

January 

January 

January 

January 

Febuary 

Febuary 

Febuary 

Febuary 

March 

March 

March 

March 

April 

April 

April 

April 

April 

May 

May 

May 

May 

May 

D 

C 

June 

June 

June 

June 

June 

July 

July 

Months 

July 

July 

July 

August 

August 

August 

August 

September 

September 

September 

September 

Fig. 2. Apparent seasonal effect on ascospore discharge and germi 

Cladonia submultiformis (KY117). B. Graphis elegans (KY162). C 

Fig. 2. Apparent seasonal effect on ascospore discharge and germination on selected species. A. 

Fig. 2. Apparent seasonal effect on ascospore discharge and germi 

Cladonia submultiformis (KY117). B. Graphis elegans (KY162). C. G. rigidula (KY165). D. 

Cladonia submultiformis (KY117). B. Graphis elegans (KY162). C 

Trypethelium eluteriae (KY66). 

April 

May 

June 

July 

September 

September 

September 

September 




October 

October 

November 

November 

November 

November 

November 

November 

November 

November 

December 

December 

December 

December 

December 

December 

December 

December 



100 

100 80 

80 

60 

60 40 

40 

20 

200 

0 

80 

60 


January 


Febuary 

March March 

March 

April 

April 

April 


149


ARTICLE 

Fig. 3. Development and growth of selected species. A. SEM of germinating ascospore of Cyclographina platyleuca (KY390). B. SEM of 

germinating ascospore of Phaeographina chapadana (KY474). C. Colony development of Thelotrema sp. on 2 % MYA agar (VN10). D. Colony 

development of Sarcographa labyrinthica (KY240). E. 2 % MYB broth showing colony development of Trypethelium eluteriae (KY131) under 

static conditions. F–H. Colony of T. eluteriae (KY131) developing on sponge in 2 % MYB broth under static conditions. Bars: A = 10 µm; E = 3 

cm; F, H = 1 cm. 

150 ima fUNGUS


Table 3. Ascospore discharge and distance of projection from selected lichens studied (arranged in descending order). 

Species 

Collection 

number 

Number of ascopores 

discharged 

Distance ascospores projected Minimum – (average 

range of 75 % spores) – Maximum (mm) 

Graphina sp. 2 KY104 52 5–(10–50)–63 

Thelotrema s. lat. sp. 3 KY233 114 7.5–(10–29)–40 

Graphina sp. 20 KY180 78 2.5–(3.5–20)–38 

Graphina hiascens KY160 38 14.5–(15–21.5)–36 

Graphina sp. 10 KY217 57 15–(15–31)–34.5 

Sarcographa actinobola KY205 62 2.5–(5–25)–26 

Graphis elegans KY162 154 3–(6–15)–24.5 

Glyphis cicatricosa KY231 183 3.5–(7.5–21)–24 

Pyrenula sp. 6 KY206 81 8–(10–15)–21.5 

Pheographis sp. 27 KY229 67 5–(9–15)–21.5 

Graphina sp. 9 KY124 4 12.5–20 

Trypethelium ochrolecum KY235 19 4–(4–10)–18 

Sarcographa labyrinthica KY240 102 3.5–(3–15)–18 

Graphis albocolpata KY147 95 5–(5–9.5)–14.5 

Buellia sp. 5 KY220 31 1–(1–9.5)–12.5 

ARTICLE 

Table 4. Ascospore discharge from selected species over the temperature range 15–45 °C. 

Species 

Collection 15 °C 20 °C 25 °C 30 °C 35 °C 45 °C 

number 

Arthopyrenia sp. PKD3 + + + + + – 

Graphina sp. 9 KY124 – + + + – – 

Graphis albocolpata KY147 – – + + + – 

Haematomma puniceum KY108 – + + – + – 

Laurera subdiscreta SKR1 + + + + – – 

Pertusaria sp. 4 PKD2 – + + – + – 

Phaeographina pyrrhochroa PKD4 – + + – + – 

Phaeographina sp. CAM5 – + + + – – 

Pyrrhospora sp. 1 PKD1 – + + + + – 

Trypethelium eluteriae KY79 – + + + – – 

to 100 % (Fig. 4). However, Laurera subdiscreta (SKR1), 

L. benguelensis (KY 61), Pyrenula sp. (KY95), and Graphis 

sp. 3 (KY260), discharged only at 100 % relative humidity. 

These results suggest that both temperature and relative 

humidity, which will vary with habitat and season, influence 

ascospore discharge in tropical lichens to different degrees, 

something that would be a major factor in their performance 

and occurrence in nature. 

Ascospore germination appeared also to be linked to 

species distributions. Widely distributed species such as 

Trypetheium eluteriae and Laurera bengualensis, together 

with most Graphidaceae tested, exhibited relatively high rates 

of ascospore germination. Ascospores of crustose lichens 

generally germinated readily, whilst those from shrubby and 

pendent species were much more difficult, or failed to germinate. 

Ascospores of the different fungi exhibited several 

distinctive germination patterns (Fig.1A–H): (1) multiple 

germination tubes developing from different regions of the 

spore (e.g. Pyrenula and Arthopyrenia species, Graphis 

cicatricosa, Laurera benguelensis, Graphina irabensis; (2) 

bipolar germination (e.g. Trypethelium tropicum); and (3) 

multiple germination tubes developing all over the spore from 

individual segments within them (e.g. Thelotremataceae, 

Cyclographina platyleuca KY390/RPB3). 

When germination was successful, fungal partners of 

most crustose species tested grew well on solid media, with 

small colonies developing within a few months. Trypethelium 

and Laurera species generally grew well, but Haematomma 

wattii and Lecanora intumescens developed very slowly 

and growth often ceased – even though the ascospores 

germinated readily. Growth in liquid culture was generally 

very slow, and static culture was found to be superior to 

shake culture for all species tested. However, growth on static 

liquid culture was much enhanced by the use of a physical 

carrier. While segments of Kraft paper or Whatman filter 

paper proved to be successful carriers, sponge pieces were 

superior in relation to visible enhanced growth. We consider 

that sponge pieces used as a carrier have a wide potential 

for studies on the physiology and development of lichen 

fungi as the colonies can be transferred without disruption 


151


ARTICLE 

Spore germination (%) 

100 

80 

60 

40 

20 

A 


100 

80 

60 

40 

20 

B 

0 

1 2 3 4 5 

Days 

0 

1 2 3 4 5 

Days 

C 

D 

100 

100 

Spore germination 

80 

60 

40 

20 


80 

60 

40 

20 

0 

1 2 3 4 5 

Days 

0 

1 2 3 4 5 

Days 

Fig. 4. Ascospore discharge and germination in selected species as influenced by percentage humidity in the experiments. A. Laurera subdiscreta 

(SKR1). B. L. benguelensis (KY61). C. Graphis sp. 3 (KY 260). D. Pyrenula sp. (KY95). 

to different liquid media. This means that, for example, the 

effect of different nutrients in the medium on the production 

of extrolites could be explored. Culberson & Armaleo 

(1992), in their investigation of Cladonia grayi, previously 

concluded that the production of compounds concentrated 

in the naturally occurring lichen was linked to the aerial 

growth habit. Their conclusion was based on the finding that, 

following the transfer of lightly fragmented mycelia from liquid 

to solid media, there was a subsequent proliferation of aerial 

hyphae and extrolite production. Although only a limited 

investigation of the chemical products of the isolated fungal 

partners of the tropical lichens was undertaken in our study, 

comparison of extrolites from the whole lichen thallus with 

those produced by the fungal partner alone indicated that in 

some cases more compounds were produced by the whole 

thallus than in the isolated fungal cultures. This conforms to 

the findings of a previous investigation (Leuckert et al. 1990). 

However, in Graphidaceae little difference between the two 

was observed. There were also few differences between the 

compounds produced by the fungus cultured under static 

conditions compared to those grown in shake culture. In a few 

cases, however, some additional compounds were detected 

in the shake culture extracts. 

Our results, and those of Crittenden et al. (1995) in 

particular, demonstrate that, contrary to a general belief 

of recalcitrance to grow on artificial media, it is possible 

to obtain many lichen-forming fungi in isolated culture – 

provided that recently collected material is used. Further, 

our results on ascospore discharge show that the seasonal 

behaviour and discharge distances of the ascospores of 

tropical lichens recalls that of those in temperate regions. We 

also suspect that the short distances over which ascospores 

are discharged, especially where these are multicelled and 

large, contributes to the inability of many to spread into 

secondary environments from old-growth native forests and 

so facilitates their utility as bioindicators of ecological stability 

(Wolesley et al. 1994). 

We hope that this preliminary study will encourage more 

experimental work on the factors affecting the reproductive 

biology of tropical lichens, which are crucial to an 

understanding of their ecology and distribution – especially 

at local scales. 


We thank the Royal Forest Department of Thailand for permission 

to collect samples and for provision of facilities during the surveys 

in the national parks of Thailand. We also thank Kansri Boonpragob 

(Ramkhamhaeng University), Prakitsin Sihanonth (Chulalongkorn 

University), and George P. Sharples (Liverpool John Moores 

University) for their valuable comments and laboratory support. This 

manuscript was completed while D.L.H. was in receipt of a research 

grant from the Ministerio de Ciencia e Innovación in Spain (project 

CGL 2008-01600). 

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Letters 4: 116–123. 

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in liquid culture? Lichen, News Bulletin of the Lichenological 

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Yoshimura I, Yamamoto Y, Nakano T, Finnie J (2002) Isolation and 

culture of lichen photobionts and mycobionts. In: Protocols in 

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A new dawn for the naming of fungi: impacts of decisions made in Melbourne 

in July 2011 on the future publication and regulation of fungal names 1 

David L. Hawksworth 

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal, Madrid 28040, Spain; 

and Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, UK; corresponding author e-mail: d.hawksworth@nhm. 

ac.uk 

ARTICLE 

Abstract: A personal synopsis of the decisions made at the Nomenclature Section meeting of the 

International Botanical Congress in Melbourne in July 2011 is provided, with an emphasis on those which 

will affect the working practices of, or will otherwise be of interest to, mycologists. The topics covered include 

the re-naming of the Code, the acceptance of English as an alternative to Latin for validating diagnoses, 

conditions for permitting electronic publication of names, mandatory deposit of key nomenclatural information 

in a recognized repository for the valid publication of fungal names, the discontinuance of dual nomenclature 

for pleomorphic fungi, clarification of the typification of sanctioned names, and acceptability of names 

originally published under the zoological code. Collectively, these changes are the most fundamental to have 

been enacted at a single Congress since the 1950s, and herald the dawn of a new era in the practice of fungal 

nomenclature. 

Key words: 

Amsterdam Declaration 

Code of Nomenclature 

electronic publication 

MycoBank 

nomenclature 

pleomorphic fungi 

registration 

sanctioned names 

taxonomy 

Article info: Submitted 12 September 2011; Accepted 20 September 2011; Published 11 November 2011. 

Introduction 

The internationally agreed rules that regulate how fungi 

are named are examined and revised at each International 

Botanical Congress, the last published being those resulting 

from the Vienna Congress in 2005 (McNeill et al. 2006). 

These Congresses are now held every six years, and the 

subsequent one in Melbourne in July 2011 was faced with a 

staggering 338 proposals made to modify the Vienna edition 

of the International Code of Botanical Nomenclature (McNeill 

& Turland 2011). This was the largest number to have 

confronted any Congress since that held in Paris in 1954. 

The issues that the Melbourne Congress had to address 

included topics as fundamental as the language required for 

the valid publication of names, the acceptability of electronic 

publication, and the unease amongst mycologists on how 

decisions were made. 

It may seem weird to 21 st century biological science 

students that fungi are embraced in a Code with just 

“botanical” in the title. However, the actual remit was all 

organisms traditionally studied in departments of botany 

in museums and universities, regardless of their current 

classification in the kingdoms of Life – even all bacteria 

were covered until the Montreal Congress of 1959. Some 

rules are, nevertheless, applicable only to particular 

systematic groups or categories, and since the Brussels 

Congress of 1910 there have been special regulations 

which only apply to the names of fungi. Foremost amongst 

these have been issues related to: (1) the date at which 

the nomenclature of fungi was deemed to commence; (2) 

the status of living cultures as name-bearing types; and (3) 

the separate naming of morphs in pleomorphic fungi. Any 

proposed changes in the rules relating to particular groups 

or categories (e.g. fossils) are discussed by a series of 

permanent committees, the members of which are elected 

at the end of each Congress and serve to the next. In the 

case of the fungi, the permanent committee is now called 

the Nomenclature Committee for Fungi (NCF). A valuable 

synopsis of how the current system operates is given by 

McNeill & Greuter (1986), while Nicolson (1991) provides 

an authoritative historical account of the development of the 

Code. 

During recent decades, and especially in the 2000s, 

many mycologists had become increasingly dissatisfied 

with various aspects of the rules concerning the naming 

of fungi. This was reflected in sessions and debates at 

various national, regional, and international meetings, 

culminating in three Nomenclature Sessions held as a part 

of the IXth International Mycological Congress (IMC9) in 

Edinburgh in August 2010. During those sessions, various 

1 

This article was first published in MycoKeys 1: 7–20 (2011), doi: 

10.3897/mycokeys.1.2062, and is reproduced here with minor 

corrections and with the permission of Pensoft Publishers. 



Attribution: 







Hawksworth 

ARTICLE 

already published proposals for change were discussed, 

and in addition all delegates to the Congress were invited 

to complete a questionnaire to canvass their views on key 

issues and possible ways forward; a report of those Sessions 

and the results of the questionnaires are provided by Norvell 

et al. (2010). 

The decisions taken at the Melbourne Congress 

were so fundamental, with respect to both “botanical” 

nomenclature as a whole, and especially with specific 

topics that concerned fungi, that these need to be widely 

promulgated. A formal report of those decisions is provided 

by McNeill et al. (2011), and more detailed information of 

those pertaining to fungi is presented by Norvell (2011). 

Those reports include the new approved wordings, though 

they may still undergo some fine-tuning by the Editorial 

Committee appointed by the Congress. The Editorial 

Committee is to meet in London in December 2011, and it is 

anticipated that the finalized Melbourne Code will be printed 

in mid-2012. However, changes effected at an International 

Botanical Congress come into effect immediately they are 

approved by the Plenary Session of the Congress unless 

specifically limited by date. It is, therefore, essential that all 

mycologists involved in the naming of fungi are made aware 

of both the changes made that come into force before the 

Code is printed, and those that are to be anticipated from 1 

January 2013. 

The purpose of the present article is to alert mycologists as 

a whole to the fundamental changes made at the Melbourne 

Congress, a package which represents a paradigm shift in how 

fungi are now to be named, and to indicate the implications 

of those changes for working practices. It is not, however, 

to be considered authoritative, and the final version of the 

Melbourne Code should be consulted as soon as it becomes 

available. 

Principle changes and their impacts 

Name of the Code changed 

Mycologists, tired of appearing subservient to botanists, and 

for mycology to be treated as a part of botany (Hawksworth 

1997, Minter 2011), made proposals for the name of the Code 

to be changed to reflect their independence (Hawksworth et 

al. 2009). This view had been supported at IMC9 (Norvell 

et al. 2010), and the Melbourne Congress agreed that 

the new Code should be called the International Code of 

Nomenclature for algae, fungi, and plants. The lower case 

letters used for the words “algae”, “fungi”, and “plants” are 

employed to make clear these terms are being used in a 

colloquial sense, for instance the inclusion of cyanobacteria 

in algae, and chromistan fungal analogues and slime moulds 

in “fungi”. 

The Congress further agreed that editorial changes should 

be made throughout the text so that it referred to “organisms” 

governed by the Code, and no longer used “plants” where 

fungi were included in the concept. 

Governance of fungal nomenclature to be 

considered 

Proposals to transfer decision-making on issues concerning 

fungi from International Botanical to International Mycological 

Congresses (Hawksworth et al. 2009), and which had been 

strongly supported at IMC9 (Norvell et al. 2009) were not 

accepted. However, a Subcommittee on governance of the 

Code with respect to fungi was established under a Special 

Committee mandated with examining how the Nomenclature 

Section operated. That Committee (and Subcommittee) 

are to report to the next International Botanical Congress 

in 2017. In view of this move, mycologists will now have to 

consider whether to put on hold the question of the need 

for an independent Code for fungi (see below) pending that 

report. The matter needs to be placed on the agenda for 

Nomenclature Sessions to be convened during IMC10 in 

2014. 

English or Latin validating diagnoses permitted 

The issue of whether to discontinue the requirement for 

validating diagnoses or descriptions in Latin has been raised 

at almost all International Botanical Congresses since this 

requirement was first introduced in 1935. The Melbourne 

Congress was presented with proposals from botanists to 

allow any language, as is the practice in zoology, and some 

alternative ones, including one by mycologists to require 

Latin or English for fungi (Norvell et al. 2010, Demoulin 

2010). There was a precedent in that the alternative of Latin 

or English was already allowed for fossils in the Vienna Code. 

The Congress not only supported the mycological proposal, 

but also decided that it should apply not just to fungi but to all 

organisms treated under the Code. Further, so enthusiastic 

was the meeting, that it was agreed that this provision 

should operate from 1 January 2012, not 1 January 2013. 

Consequently, mycologists no longer need to struggle with 

coining a few sentences of pseudo-Latin when describing 

new fungi. However, in consequence, I personally see 

value in presenting both a diagnosis (i.e. a short statement 

of how the fungus differs from others) and a separate 

description (i.e. a detailed account of all the features of the 

fungus) when describing a new fungus. If a diagnosis were 

in Latin or English, the description could then continue to 

be in any language of the author’s choice. A diagnosis has 

been required for the introduction of new scientific names in 

zoology since 1930 (International Commission on Zoological 

Nomenclature 1999: Art. 13), and the practice has much to 

commend it. 

Electronic publication permitted (but with 

restrictions) 

The issue of the acceptability of works published only 

electronically as a vehicle for the effective publication of 

scientific names has been the subject of a series of Special 

Committees established by successive International Botanical 

Congresses since that held in Tokyo in 1993, and is also an 

issue currently being actively debated by zoologists (Michel et 

al. 2009). With the increasing proliferation of new electronic 

156 ima fUNGUS

A new dawn for the naming of fungi 

journals, and established journals also increasingly being 

available in both electronic and hard-copy forms, the issue 

was becoming increasingly urgent. A Special Committee 

established by the Vienna Congress in 2005, considered the 

matter in depth (Chapman et al. 2010) and prepared detailed 

proposals for consideration by the Melbourne Congress 

(Special Committee on Electronic Publication 2010). The 

Melbourne Congress accepted many of these proposals, and 

the pertinent revised texts and guidelines as to best practice 

are given by Knapp et al. (2011). The key points agreed were 

that from 1 January 2012, works published in electronic form 

on the worldwide web in an unchangeable Portable Document 

Format (PDF) are to be treated as effectively published, 

provided that they have either an International Standard Serial 

Number (ISSN) or an International Standard Book Number 

(ISBN). However, non-final versions made available online 

in advance of a definitive version (e.g. accepted papers as 

yet unedited or proof-read) are not treated as effectively 

published. Where both electronic and hard-copy versions of 

a work are made available, the date of effective publication of 

both is treated as being the same. Guidance as to how copies 

can be differentiated is included in Knapp et al. (2011). 

It is important to appreciate that the new provisions do not 

mean that material placed on or available through websites 

and lacking ISSN or ISBN numbers constitutes effective 

publication. Authors considering submitting to an electronic 

journal, should therefore first check that it has an ISSN 

number. It is also recommended that electronic-only works 

containing new taxa are drawn to the attention of appropriate 

indexing centres, and mycologists should endeavour to do that 

until the requirement for the prior deposit of key nomenclatural 

information becomes mandatory on 1 January 2013. 

Deposit of key nomenclatural information 

made mandatory for fungi 

The concept of some form of obligatory registration of newly 

proposed scientific names for fungi goes back to the 1950s 

(Ainsworth & Ciferri 1955). Following the establishment of a 

Special Committee on Registration at the Berlin Congress in 

1987, and a series of subsequent workshops, a provision to 

make this a requirement for all groups of organisms covered 

by the Code was accepted by the Tokyo Congress in 1993 – 

but then rejected at the St Louis Congress in 1999 despite 

successful trials (Greuter 2009). The development of the 

worldwide web, however, has made it possible to devise 

much-improved systems from those that were possible in 

the 1980s and early 1990s. Following informal discussions 

during the 2002 International Mycological Congress (IMC7) 

in Oslo, in 2004 the CBS-KNAW Fungal Biodiversity Centre 

in Utrecht established an online system for the deposit of key 

information on newly proposed names of fungi – MycoBank. 

This voluntary system proved popular with mycologists, 

and also with mycological journals, as a way of rapidly 

expediting information on nomenclatural novelties. Since 

2007 Mycobank has operated under the auspices of the 

International Mycological Association (IMA) which now has 

long-term responsibility for its continuance. 

Formal proposals to make the deposit of key nomenclatural 

information in a recognized online repository a mandatory 

requirement for valid publication of new scientific names in 

fungi at all taxonomic ranks (including new combinations and 

replacement names) were then developed (Hawksworth et 

al. 2010). Those proposals were overwhelming endorsed 

by the International Mycological Congress in Edinburgh 

later in the same year (Norvell et al. 2010). The Melbourne 

Congress approved the formal proposals with some “friendly” 

amendments, mainly based on suggestions for avoiding 

unnecessary inflation of names in the repositories (Morris 

et al. 2011). In addition a recommendation that information 

on choices made between competing names or homonyms, 

spelling or gender also be deposited (Gams 2010) was 

approved. 

The new requirement comes into force on 1 January 2013, 

after which date scientific names of fungi which are published 

without a unique identifier by a recognized repository will not 

be considered as validly published; i.e. they will not exist for 

nomenclatural purposes and need not be considered when 

determining the correct name for a taxon under the Code. 

While the requirement is only for information required by the 

rules of the Code, such as the diagnosis and information as 

to the nomenclatural type or a basionym, as appropriate, 

there is no objection to databases also including additional 

information and the prospects are enormously exciting 

(Lumbsch et al. 2011). 

The responsibility of appointing online depositories was 

given to the Nomenclature Committee for Fungi, which will 

need to advise mycologists as to which are approved. No 

single repository was specified in the proposals, thus leaving 

the possibilities open in the rapidly-moving electronic age. At 

present it is deposit in MycoBank which is now required by 

almost all mycological journals. 

Mycologists should note that the prudent way to proceed 

is to make the online deposit of the required data, and 

obtain the numerical identifier, only after their work has been 

accepted for publication. This is to ensure that the information 

included agrees in every detail that which will appear in the 

publication which establishes the name. This will not affect 

the priority of the name as the effective date of publication 

will be that of the electronic or hard-copy publication and not 

the date information is deposited. The lodging of a name and 

associated details in a repository such as MycoBank will not 

in itself establish a name. 

This exciting move means that, for the first time ever, 

mycologists will have immediate and free online access to 

the key nomenclatural and diagnostic information on newly 

proposed fungal names. It also means that it is the authors of 

new names which will now have the responsibility of ensuring 

that names they propose are incorporated into international 

indexing repositories. 

Dual nomenclature of pleomorphic fungi 

discontinued 

The concept of permitting separate names for anamorphs 

of fungi with a pleomorphic life-cycle has been an issue of 

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debate since the phenomenon was recognized in the mid- 

19 th century. This was even before the first international rules 

for “botanical” nomenclature were issued in 1867 (Weresub 

& Pirozynski 1979, Taylor 2011). Special provisions are to 

be found in the earliest Codes, which were then modified 

several times, and often substantially (Weresub & Pirozynski 

1979). The rules became increasingly complex, and by the 

mid-1970s they were being interpreted in different ways 

by different mycologists – even ones working on the same 

genus. Following intensive discussions under the auspices 

of the International Mycological Association (IMA), drastic 

changes were made at the Sydney Congress in 1981 to clarify 

and simplify the procedures – and the now familiar terms 

anamorph, teleomorph, and holomorph entered general use. 

An unfortunate effect of the simplification was that many name 

changes had to be made as a consequence, including ones 

of some well-known and economically important species; at 

that date, the conservation of species names was not allowed 

under the Code. 

Unforeseen in the 1970s, when the 1981 provisions were 

crafted, was the impact of molecular systematics. A decade 

later, it was starting to become obvious that fungi with no 

known sexual stage could confidently be placed in genera 

which were typified by species in which the sexual stage 

was known (Reynolds & Taylor 1991), and the issue of the 

abandonment of the dual nomenclatural system was posited 

(Reynolds & Taylor 1992). This possibility was debated at 

subsequent International Mycological Congresses, and on 

other occasions (e.g. Seifert et al. 2000, Seifert 2003), and 

the need for change was increasingly recognized. Cannon 

& Kirk (2000) regarded deletion as inevitable in the longterm, 

and further calls for deleting the provision followed (e.g. 

Rossman & Samuels 2005). At the International Botanical 

Congress in Vienna in 2005, some minor modifications 

were made which allowed anamorph-typified names to be 

epitypified by material showing the sexual stage when it was 

discovered, and for that name or epithet to continue to be 

used where there was no previously sexually-typified name 

available. 

More importantly, the Vienna Congress established 

a Special Committee to investigate the issue further, but 

unfortunately it was unable to reach a consensus (Redhead 

2010). Matters were becoming increasingly desperate as 

mycologists using molecular phylogenetic approaches 

started to ignore the provisions, or interpret them in different 

ways (Rossman & Seifert 2010). The view that emerged 

from the International Mycological Congress in Edinburgh 

the same year, was that mycologists, as a whole, favoured 

gradual progress towards a single nomenclature (Norvell et 

al. 2010). In the meantime, various proposals were made 

to improve the situation, but the situation was becoming so 

complex that few mycologists were likely to take the time to 

understand them fully and implement them correctly. In order 

to progress the matter, an international symposium was 

held in Amsterdam in April 2011, under the auspices of the 

International Commission on the Taxonomy of Fungi (ICTF), 

to explore ways to obtain a solution. If a solution could not 

be reached at the Melbourne Congress, the prospect was 

for no substantive change to be made until after the 2017 

International Botanical Congress. This situation would then 

have become intolerable as mycologists increasingly ignore 

the rules. 

The Amsterdam symposium prepared a declaration of 

principles which, it was hoped, would be accommodated in 

any change made to Article 59 (Hawksworth et al. 2011). In 

effect these amounted to the ending of dual nomenclature, 

but with safeguards to minimize changes in familiar names. 

The “Amsterdam Declaration” prompted a critical response 

from some other mycologists who perceived difficulties in 

aspects of the declaration, and wished to continue allowing 

dual nomenclature (Gams et al. 2011). Both these documents 

were made available to delegates at the Melbourne Congress. 

In order to ensure some resolution of the issue, proposals 

for three possible options were developed by Redhead, in 

consultation with various mycologists, for presentation at the 

meeting. Following extensive discussions at the Congress, 

the option to discontinue the dual nomenclature system 

was approved, but with some safeguards to limit resultant 

instability (Norvell 2011, McNeill et al. 2011). 

After 1 January 2013, one fungus can only have one 

name; the system of permitting separate names to be used 

for anamorphs then ends. This means that all legitimate 

names proposed for a species, regardless of what stage 

they are typified by, can serve as the correct name for that 

species. All names now compete on an equal footing for 

priority regardless of the stage represented by the namebearing 

type. In order not to render names that had been 

introduced in the past for separate morphs as illegitimate, it 

was agreed that these should not be treated as superfluous 

alternative names in the sense of the Code. It was further 

decided that anamorph-typified names should not be taken 

up to displace widely used teleomorph-typified names until 

the case has been considered by the General Committee 

established by the Congress 2 . 

Recognizing that there were cases in some groups of 

fungi where there could be many names that might merit 

formal retention or rejection, a new provision was introduced. 

It was decided that lists of names can be submitted to the 

General Committee and, after due scrutiny, names accepted 

on those lists are to be treated as conserved over competing 

synonyms (and listed as Appendices to the Code). Lichenforming 

fungi (but not lichenicolous fungi) were always 

excluded from the provisions permitting dual nomenclature; 

the new Code will include a paragraph to make it explicit that 

lichen-forming fungi are excluded from the newly accepted 

provisions. 

Mycologists need now to work to implement this major 

change. In cases where a later teleomorph-typified name is 

2 

The General Committee is elected at each International Botanical 

Congress, and is responsible for receiving, considering, and 

approving reports from the various permanent nomenclature 

committees, such as the Nomenclature Committee for Fungi, for the 

period up to the next Congress. 

158 ima fUNGUS


not widely used, it can be anticipated that mycologists will 

now simply adopt the earlier anamorph-typified name. If 

others consider a decision inappropriate, a proposal for the 

conservation of the teleomorph-typified name over the earlier 

anamorph-typified name can be made to the Nomenclature 

Committee for Fungi (NCF). Although no detailed arrangements 

were made at the Congress, it is anticipated that, where 

specialist working groups on particular fungal genera or 

families exist, as is the case for subcommissions of the 

International Commission on the Taxonomy of Fungi (ICTF), 

draft lists of names for possible approval will be prepared 

by them. In my personal view, there could also be some 

advantage in endeavouring to have one list covering all 

potentially affected generic names, if mechanisms to achieve 

that could be put in place. In the early part of 2012, the NCF 

is to work closely with the ICTF and other groups where they 

exist (e.g. within the International Union of Microbiological 

Societies, IUMS) to develop processes for the preparation 

of lists on particular groups. Draft lists will need to be made 

available for comment by mycologists at large (e.g. through 

the IMA and ICTF web sites), and they will then require 

revising in the light of comments received. Lists received by 

the NCF would, after due consideration by that Committee, 

then be forwarded to the General Committee for approval. 

Where mycologists wish still to refer to anamorphs 

separately, the new provisions do not prohibit informal 

usages, such as “acremonium-state” or “acremonium-like”, 

ideally with a small initial letter and normal not italic type as 

suggested by Cannon & Kirk (2000). This form of typography 

makes clear that the designations are not scientific names 

governed by the Code. 

Typification of sanctioned names clarified 

The dates on which the nomenclature of fungi was deemed 

to start were changed from 1801 or 1821 to 1753 by the 

International Botanical Congress in Sydney in 1981. This 

change was made because the later-starting point system 

had come to be interpreted in different ways, and because 

of difficulties in ascertaining the first usages of already 

proposed names after the proscribed dates (Demoulin et 

al. 1981). In order to minimize the resultant name changes, 

the concept of “sanctioning” was introduced. Sanctioning 

permitted the continued use of names that had been adopted 

in the 1801 Synopsis Methodica Fungorum of Persoon, or 

the 1821-32 Systema Mycologicum of Fries over names that 

otherwise would have to be taken up under the normal rules 

of priority, homonymy, etc. However, the wording of the rule 

in the Sydney Code was somewhat ambiguous and, although 

modified slightly at the Berlin Congress in 1987, it could still 

be interpreted as meaning either that the typification of a 

sanctioned name should be made only on materials cited in 

the sanctioning work, or that it could be based on materials 

cited in the original pre-sanctioning place of publication. 

Proposals to address this issue were published before the 

Melbourne Congress (Perry 2010, Redhead et al. 2010), but 

there were concerns over these. In consequence, a series of 

informal discussions was held in Melbourne, which involved 

the proposers and other concerned mycologists. Those 

meetings led to the formulation of a series of proposals 

which were adopted by the Congress (McNeill et al. 2011, 

Norvell 2011). The net effect of the changes made is that a 

name that has been sanctioned can now be lectotypified (not 

neotypified) by material from among the elements associated 

with either the original protologue of the name, the sanctioning 

treatment, or both. A further and welcome clarification is that 

in cases where in the sanctioning work elements associated 

with the original protologue did not include a subsequently 

designated type selected for the sanctioned name, the 

sanctioning author is considered to have introduced a later 

homonym that is to be retained because of its sanctioned 

status. 

No particular date was mentioned in the adopted 

proposals, which means that they became operative when 

approved by the Melbourne Congress. They are also 

retroactive, and so safeguard many typifications made since 

the 1981 Congress which were based on material cited in the 

original protologue, or on material of the sanctioning author 

where that differed. The adoption of these clarifications is 

most welcome as it removes the need for many typifications 

made since 1981 to be revisited, something that could 

have had unfortunate implications for the stability of many 

sanctioned names. 

Names of fungi first described as animals are 

validly published 

The revelation that Microsporidia, a group traditionally studied 

by zoologists, belonged to kingdom Fungi posed a threat to 

numerous names in use in the phylum. This situation arose 

as, while those names had been correctly published and were 

available for use under the provisions of the International 

Code of Zoological Nomenclature, many did not meet the 

requirements of the botanical Code. At the Vienna Congress 

in 2005, it was agreed that names within Microsporidia, and 

other organisms that had originally been published under 

the zoological code, were to be treated as validly published 

under the botanical Code. However, in accordance with the 

wishes of workers on these fungi, the Melbourne Congress 

accepted proposals made by Redhead et al. (2009) that 

these organisms should be excluded from governance by the 

botanical Code and continue to be covered by the zoological 

one, despite their phylogenetic position. It was further agreed 

that this principle should be adopted for other groups of 

organisms traditionally treated under other codes. 

Explicitly indicate the physiological state of 

type cultures 

A rule in the current Code allows cultures of algae and fungi 

to serve as name-bearing types, provided that they are 

“preserved in a metabolically inactive state”. In practice, the 

physiological state of cultures designated as types is often not 

stated by describing authors. In order make this explicit, it is 

now recommended that the phrase “permanently preserved 

in a metabolically inactive state”, or equivalent, be used when 

cultures are designated as types. 

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Names based on fossil parts loose special 

provisions 

In recent years there have been extensive debates in the 

palaeobotanical community on how to revise the provisions 

relating to the naming of parts of fossil organisms treated 

under the Code – and which applied to fungi as well as 

plants. Competing sets of proposals were submitted to the 

Melbourne Congress. As in the case of ending the separate 

naming of anamorphs in pleomorphic fungi, the Congress 

decided to abandon the practice of separately naming parts 

of fossils. Consequently, names of fossils which prove to be 

parts of a single species will now compete with each other 

for priority, in the same way as occurs for names not based 

on fossils. 

The Draft BioCode and MycoCode need to be 

revisited 

Moves towards increased harmonization between the various 

codes of nomenclature were initiated in 1985. However, the 

prospect, in the long-term, of having a set of rules governing 

the future nomenclature of all organisms was developed 

in the early 1990s (Hawksworth 1995). This culminated in 

the publication of a Draft BioCode in 1996 which had been 

prepared by the IUBS 3 /IUMS International Committee on 

Bionomenclature (ICB) 4 . Little progress was made in taking 

the initiative further as the mechanisms and resources to 

develop the prerequisite lists of names to be considered 

available were not forthcoming. The project was subsequently 

revived as a scientific programme of IUBS in 2009, and an 

updated Draft BioCode was prepared and released for further 

discussion in January 2011 (Greuter et al. 2011). That draft 

was the subject of a session and debate at Biosystematics 

2011 (which incorporated the International Congress of 

Systematic and Evolutionary Biology) in Berlin in February 

2011. This initiative was mentioned briefly in the final session 

of the Nomenclature Section meetings in Melbourne, but was 

not considered in any depth. A suggestion that the Section 

establish a Special Committee to liaise with those involved in 

the revision of the draft was not approved. 

The possibility of having an independent code for 

mycology was raised and received considerable vocal 

support at the International Mycological Congress (IMC8) in 

Cairns in 2006. However, the option of renaming and revising 

the botanical Code was the one favoured at the subsequent 

Congress in Edinburgh in 2010 (Norvell et al. 2010). The 

issue was also raised at the Amsterdam symposium in April 

2011 which was primarily convened to address the issue 

of dual nomenclature. At that symposium it was suggested 

that the BioCode model could provide a framework for the 

3 

The International Union of Biological Sciences, in which the 

International Mycological Association represents general mycology. 

future regulation of the nomenclature of fungi (Hawksworth et 

al. 2011). Key to any movement in this direction, was seen 

as the extent to which the botanical Code would change 

to meet the needs of mycologists (Taylor 2011). In view of 

the major changes made at the Melbourne Congress, the 

issue of whether an independent MycoCode is really now 

required needs to be debated at the International Mycological 

Congress (IMC10) in Bangkok in 2014. 

Discussion 

I have participated in all International Botanical Congresses 

since that held in St Petersburg in 1975, and served on the 

Editorial Committee of the botanical Code since 1987. The 

progress made in adapting the rules to the needs of both 

user and practitioner mycologists over that period has been 

considerable. These have included, for example, the change 

in starting point, the conservation and rejection of species 

names, the designation of interpretive types (“epitypes”), 

and allowing living metabolically inactive cultures to 

be nomenclatural types. The powers of the permanent 

Nomenclature Committees have also been enhanced over 

the years, so that they can now recommend rejection of any 

name whose adoption is regarded as disadvantageous. 

Even against this background of increasing adaptation, 

the raft of changes effected at the Melbourne Congress in 

2011, has to be seen as the dawn of a new era for botanical 

and mycological nomenclature, truly bringing it into the 

modern age. The decisions made with respect to the name 

of the Code, its coverage, electronic publication, and the 

requirement for the deposition of key information in a 

recognized depositary as a requirement for the publication 

of fungal names, place the Melbourne Code ahead of what 

zoologists are currently endeavouring to do. 

There is still much to be achieved by mycologists, especially 

with respect to the implementation of the consequences of 

the end of dual nomenclature for pleomorphic fungi, although 

the regulatory mechanisms are now in place. A major issue 

that remains is how best to designate taxa only known from 

molecular studies of environmental samples, and to consider 

whether that requires any changes in the Code (Hawksworth 

et al. 2011, Hibbett et al. 2011, Taylor 2011). 

Finally, I must stress that the views and interpretations 

presented in this overview are personal, and that mycologists 

should check the decisions and verify actual wordings agreed 

in Melbourne for themselves, especially in the official report 

of the Nomenclature Section meetings (McNeill et al. 2011), 

and then the edited published version of the International 

Code of Nomenclature for algae, fungi, and plants when it 

becomes available in mid-2012. 

4 

The IUBS/IUMS International Committee on Bionomenclature 

comprises representatives of the five internationally mandated 

organismal codes of nomenclature: botanical, cultivated plant, 

prokaryote, viral, and zoological; it was formally established in 1994. 


My participation in the Melbourne Congress was supported 

through a research grant from the Ministerio de Educación 

160 ima fUNGUS


y Ciencia of Spain (Proyectos I+D CGL 2008-01600), with 

a contribution from the International Union of Biological 

Sciences (IUBS). 

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162 

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The inclusion of downy mildews in a multi-locus-dataset and its reanalysis 

reveals a high degree of paraphyly in Phytophthora 

Fabian Runge 1 , Sabine Telle 2,3 , Sebastian Ploch 2,3 , Elizabeth Savory 4 , Brad Day 4 , Rahul Sharma 2,3,5 , and Marco Thines 2,3,5 

1 

University of Hohenheim, Institute of Botany 210, D-70593 Stuttgart, Germany 

2 

Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany; corresponding author e-mail: 

marco.thines@senckenberg.de 

3 

Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany 

4 

Michigan State University, Department of Plant Pathology, 104 Center for Integrated Plant Systems, East Lansing, MI 48824, USA 

5 

Goethe University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Siesmayerstr. 70, 

D-60323 Frankfurt (Main), Germany 

ARTICLE 

Abstract: Pathogens belonging to the Oomycota, a group of heterokont, fungal-like organisms, are amongst the 

most notorious pathogens in agriculture. In particular, the obligate biotrophic downy mildews and the hemibiotrophic 

members of the genus Phytophthora are responsible for a huge variety of destructive diseases, including sudden 

oak death caused by P. ramorum, potato late blight caused by P. infestans, cucurbit downy mildew caused by 

Pseudoperonospora cubensis, and grape downy mildew caused by Plasmopara viticola. About 800 species of 

downy mildews and roughly 100 species of Phytophthora are currently accepted, and recent studies have revealed 

that these groups are closely related. However, the degree to which Phytophthora is paraphyletic and where 

exactly the downy mildews insert into this genus in relation to other clades could not be inferred with certainty to 

date. Here we present a molecular phylogeny encompassing all clades of Phytophthora as represented in a multilocus 

dataset and two representatives of the monophyletic downy mildews from divergent genera. Our results 

demonstrate that Phytophthora is at least six times paraphyletic with respect to the downy mildews. The downy 

mildew representatives are consistently nested within clade 4 (contains Phytophthora palmivora), which is placed 

sister to clade 1 (contains Phytophthora infestans). This finding would either necessitate placing all downy mildews 

and Phytopthora species in a single genus, either under the oldest generic name Peronospora or by conservation 

the later name Phytophthora, or the description of at least six new genera within Phytophthora. The complications 

of both options are discussed, and it is concluded that the latter is preferable, as it warrants fewer name changes 

and is more practical. 

Key words: 

AU test 

downy mildews 

multigene phylogeny 

Peronosporaceae 

Phytophthora 

taxonomy 

Article info: Submitted 21 September 2011; Accepted 20 October 2011; Published 11 November 2011. 

Introduction 

Oomycetes are a group of organisms that superficially 

resemble fungi in their hyphal growth and absorptive way of 

nutrition. However, they are not closely related to Mycota, 

but belong to a group of heterokont organisms, Straminipila 

(Dick 2001), which also includes diatoms and sea-weeds. 

Oomycetes have adapted to parasitism of plants at least three 

times, once in the Saprolegniales in the genera Aphanomyces 

and Pachymetra (Riethmüller et al. 1999, Diéguez-Uribeondo 

et al. 2009), and separately in Albuginales and Peronosporales 

(Riethmüller et al. 2002, Hudspeth et al. 2003, Thines et al. 

2008). While the evolution of obligate biotrophy seems to be 

an ancient occurrence for the white blister rusts (Thines & 

Kamoun 2010), the downy mildews have more recently arisen 

from Phytophthora-like ancestors (Riethmüller et al. 2002, 

Göker et al. 2003, 2007, Thines et al. 2008, 2009, Thines 

2009). The close relationship of the downy mildews and 

Phytophthora revealed by these studies is in contrast to the 

widely used taxonomic classifications of Waterhouse (1973) 

and Dick (1984, 2001), in which Phytophthora and Pythium 

were grouped together in the family Pythiaceae. Although 

Cooke et al. (2000) inferred a position of Peronospora sparsa 

as a sister group of clade 4 (as defined in that study) based on 

ITS sequences alone, no substantial phylogenetic resolution 

was present on the phylogenetic backbone, thus failing to 

position this group within the genus Phytophthora. Other 

studies (including multi-locus studies) that included both downy 

mildew and Phytophthora species have so far not resolved the 

placement of downy mildews in relation to the different clades 

of Phytophthora (Riethmüller et al. 2002, Göker et al. 2007, 

Thines et al. 2009, Giresse et al. 2010). Additionally, Thines et 



Attribution: 







Runge et al. 

ARTICLE 

al. (2009) demonstrated that the support for the sister-group 

relationship of Peronospora and clade 4 inferred by Cooke et 

al. (2000) could have been the result of an alignment artefact. 

Conversely, a recent study by Blair et al. (2008) addressed the 

phylogenetic relationships of Phytophthora species with good 

resolution, but no downy mildew was included in that study, 

leaving their placement to speculation. Downy mildews have 

been shown to be a monophyletic assemblage by Göker et 

al. (2007). However, Göker & Stamatakis (2006) later (in spite 

of being published earlier than Göker et al. 2007) came to the 

conclusion that a placement of Phytophthora clade 1 within the 

downy mildews would also be possible, although no support 

could be obtained for this scenario. The question of which 

is the sister clade of the downy mildews, and how this clade 

is embedded among the different lineages of Phytophthora 

therefore continues to be controversial, but is fundamental for 

understanding the evolution of this group of important plant 

pathogens, especially with respect to the evolution of biotrophy. 

In addition, the taxonomic status of many Phytophthora 

species depends on the degree of paraphyly of the genus. At 

least with two clades, 9 and 10, Phytophthora is paraphyletic 

with respect to downy mildews (Cooke et al. 2000, Göker et al. 

2007, Thines et al. 2009), but so far, the degree of paraphyly 

of Phytophthora could not be resolved. Therefore, it was 

the aim of this study to resolve the phylogenetic placement 

of the monophyletic downy mildews (represented by the two 

divergent downy mildew genera for which genome data are 

currently available) among Phytophthora and to test this 

placement statistically, to further clarify the relationships within 

this group of important plant pathogens. 


All sequences of Phytophthora and Pythium were obtained 

from the study of Blair et al. (2008) available in the National 

Center for Biotechnology Information (NCBI) nucleotide 

database, GenBank. The dataset includes sequences of 

seven different loci, and all species for which all seven loci 

were not available were discarded, except for two Pythium 

species for which only six of the seven loci could be obtained. 

This resulted in an overall dataset of 121 species sampled. 

The sequences of Phytophthora infestans were used to obtain 

homologous sequences from the genome of Hyaloperonspora 

arabidopsidis from the NCBI database using BLAST (Altschul 

et al. 1997) and from the genome of Pseudoperonospora 

cubensis (Tian et al. 2011) using the annotated EST 

sequence information. Because no sequence information for 

the 28S nuclear ribosomal DNA locus of Pseudoperonospora 

cubensis could be obtained from the EST library, which was 

enriched for protein-coding genes, sequence information was 

obtained from the NCBI database, using a sequence from 

the study of Riethmüller et al. (2002). GenBank accession 

numbers for all sequences included in the analyses are given 

in Table S1 (Supplementary Information, online only). 

Each of the seven sets of sequences was edited (i.e. 

leading and trailing gaps were removed) using the DNASTAR 

computer package v. 8 (Lasergene, Madison, WI), and were 

aligned separately using MAFFT v. 6.240 (Katoh et al. 2005) 

using a webserver interface (http://www.genome.jp/tools/ 

mafft/). The G-INS-i algorithm was chosen for all alignments. 

Subsequently, the aligned sequences were concatenated 

for phylogenetic analyses and no further editing was done 

on the alignment to ensure reproducibility and to prevent 

introduction of bias. After the removal of leading and trailing 

gaps 6282 nucleotide sites were included in the phylogenetic 

analyses. These comprised seven loci: 1119 bp of the betatubulin 

gene, 493 bp of the 60S ribosomal protein L10 gene, 

873 bp of the translation elongation factor 1-alpha gene, 720 

bp of the 28S nuclear ribosomal DNA gene, 646 bp of the 

glyceraldehyde-3-phosphate dehydrogenase gene, 1438 bp 

of the heat shock protein 90 gene, and 993 bp of the enolase 

gene. The alignment, together with the tree from the Bayesian 

Analysis shown in Fig. 1, has been deposited in TreeBASE 

(www.treebase.org) under the accession number S11829. 

The general time reversible (GTR) model was selected for 

the concatenated alignment using Modeltest v. 3.7 (Posada 

& Crandall 1998) and PAUP v. 4.0b10 (Swofford 2002), with 

gamma-distributed substitution rates (shape parameter = 

0.69) and proportion of invariable sites (pinv = 0.54). The 

values of these parameters were included in the Bayesian 

and Minimum Evolution analyses. 

Minimum Evolution (ME) analysis was done using MEGA 

v. 4.0 (Tamura et al. 2007), with the gamma-distributed 

substitution rates as inferred by Modeltest and using 

the Maximum-Composite-Likelihood substitution model. 

For inferring tree robustness, 1000 bootstrap replicates 

(Felsenstein 1985) were computed. 

For Maximum Likelihood (ML) inference, the RAxML 

webserver at http://phylobench.vital-it.ch/raxml-bb/ 

(Stamatakis et al. 2008) was used with standard settings 

and maximum likelihood search, including an estimation of 

invariable sites. The analysis was repeated five times with 

100 bootstrap replicates each. The bootstrap support values 

obtained were averaged, because the rapid bootstrapping 

algorithm can lead to some deviation. 

For Bayesian analysis, MrBayes (Huelsenbeck & Ronquist 

2001) at the Phylemon2 webserver (http://phylemon.bioinfo. 

cipf.es/) and at a local server, for parallel runs, was used. 

Four incrementally heated simultaneous Markov Chain 

Monte Carlo chains were run for two million generations with 

every 1000 th tree sampled, under the general time reversible 

(GTR) model with the gamma-distributed substitution rates 

and proportion of invariable sites as inferred by Modeltest. 

Maintaining that the standard deviation of split frequencies 

was constantly below 0.01 and the stationary phase of the 

likelihood values was reached after 10 % of sampled trees 

when quitting the analysis. The first 1000 trees sampled this 

way were discarded, and the remaining 1000 trees were 

used to compute a 50 % majority rule consensus tree and 

to estimate the posterior probabilities. To ensure general 

reproducibility, the analysis was repeated twice using the 

webserver, and twice on a local server using MrBayes v. 

3.1.2. 

164 ima fUNGUS

High degree of paraphyly in Phytophthora 

-/-/0.53 

87 4 

* 

* 

9 

67/78/* 

* 

2 

5 

53/-/0.53 

91/97/* 

10 

*/99/* 

57/73/0.99 

10 

51/61/* 

14 

64 

* 

* 

84 

- 

0.66 

2 

94 

* 

* 

10 

97 

99 

* 

21 

9 

- 

86 

* 

3 

- 

80 

* 

2 

80/*/* 82 

84 

22 * 

 

* 

99/99/* 

98/*/* Ph. cactorum P0715 

77/*/* Ph. cactorum P0714 

* Ph. hedraiandra P11056 

51 Ph. idaei P6767 

Ph. pseudotsugae P10339 

93/*/* Ph. clandestina P3942 

* Ph. iranica P3882 

37 

Ph. tentaculata P8497 

* 

Ph. infestans P10650 

93/*/* 

Ph. infestans P10651 

Ph. andina P13365 

Ph. ipomoeae P10227 

Ph. ipomoeae P10225 

Phytophthora s.str. 

* Ph. ipomoeae P10226 

* 

118 Ph. mirabilis P3005 

* Ph. phaseoli P10145 

Ph. phaseoli P10150 

Ph. nicotianae P10802 




* Ph. nicotianae P10116 


Ph. arecae P10213 

Ph. palmivora P0255 

Ph. palmivora P0113 

Ph. quercetorum MD9-2 

Ph. megakarya P8516 

99/*/* 

Pseudoperonospora cubensis 

107 

Hyaloperonospora arabidopsidis 

Ph. quercina P10441 

Ph. quercina P10334 

Ph. inflata P10341 

Ph. citrophthora P6310 

* 

51 Ph. colocasiae P6317 

Ph. botryosa P6945 

Ph. meadii P6128 

Ph. capsici P1319 

90/99/* 



25 97 * 


* Ph. capsici P10386 

* Ph. mexicana P0646 

Ph. glovera P10619 

* Ph. tropicalis P10329 

* 


12 Ph. capsici P0630 

Ph. sp. P10417 

Ph. citricola P7902 

* Ph. multivesiculata P10327 

Ph. multivesiculata P10410 

Ph. bisheria P10117 

Ph. bisheria P1620 

* Ph. katsurae P3389 

Ph. katsurae P10187 

Ph. heveae P10167 

Ph. ilicis P3939 

Ph. psychrophila P10433 

Ph. nemorosa P10288 

Ph. pseudosyringae P10437 

Ph. inundata P8478 

* Ph. sp. P8619 

Ph. humicola P3826 

Ph. megasperma P3136 

Ph. gonapodyides P10337 

* Ph. asparagi P10690 

Ph. asparagi P10705 

Ph. alni P10568 

* Ph. cambivora P0592 

Ph. fragariae P3821 

* Ph. europaea P10324 

28 

Ph. uliginosa P10328 

* Ph. sinensis P1475 

* 94 

Ph. melonis P10994 

20 86 Ph. cajani P3105 

* * Ph. vignae P3019 

ê * 

Ph. sojae P3114 

7 Ph. niederhauserii P10617 

* 

* Ph. cinnamomi P2159 

Ph. cinnamomi P8495 

96/99/* 

Ph. erythroseptica P1699 



* Ph. richardiae P10355 

Ph. richardiae P10811 

Ph. richardiae P10359 

* Ph. richardiae P7788 

Ph. sp. P10672 

Ph. cryptogea P1088 

Ph. kelmania P10613 

99/*/* Ph. drechsleri P10331 

46 

* Ph. medicaginis P10683 

Ph. trifolii P7010 

Ph. sansomea P3163 

* 

- 

* 

* 

4 

98 

* 

-/56/0.93 70 

93 

* 92 

59 8 94 

0.91 * 

1 

7 

7 

* 

* 

* 

* 

35 

80 

-/*/* 

* 

88 

* 

Ph. primulae P10220 

* Ph. primulae P10224 

Ph. primulae P10333 

Ph. porri P6207 

* 

Ph. porri P10728 

Ph. brassicae P10153 

* 



Ph. syringae P10330 

Ph. ramorum P10301 

Ph. lateralis P3888 

Ph. hibernalis P3822 

Ph. foliorum P10969 

Ph. macrochlamydospora P10267 

* Ph. cuyabensis P8218 

Ph. cuyabensis P8224 

Ph. lagoariana P8223 

Ph. lagoariana P8618 

Ph. polonica P15004 

* Ph. polonica P15005 

Ph. polonica P15001 

* 

Ph. insolita P6703 

Ph. insolita P6195 

* Ph. fallax P10725 

Ph. captiosa P10719 

* 

Ph. kernoviae P10681 

49 

Ph. boehmeriae P6950 

Pythium vexans P3980 

Pythium undulatum P10342 

1a 

1b 

1c 

1.1 

4.2 

DM 

4.1 

2a 

2b 

7a 

7b 

8a 

8b 

8c 

9.1 

9.2 

1 

4 

2 

5 

3 

6 

7 

8 

9 

10 

ARTICLE 

0.02 

Fig. 1. Phylogenetic reconstruction for Phytophthora and the downy mildews (Bayesian Analysis), with support values in Minimum Evolution, 

Maximum Likelihood, and Bayesian Analysis, in the respective order, on the branches, and Bremer support below the branches. Small Asterisks 

denote maximum support in a single analysis, big asterisks denote maximum support in all three phylogenetic analyses. Clade designations are 

those of Blair et al. (2008), with some additional differentiation corresponding to the statistical testing of the tree topology as given in Table 1. 

Predominantly caducous and papillate clades are highlighted in blue, the clade containing downy mildews is highlighted in green and the clades 

with predominantly non-caducous, non-papillate or semi-papillate members are highlighted in brown. For Phytophthora, the highlighted areas 

are divided into blocks representing groups that lead to paraphyly of Phytophthora and could potentially serve as a basis for the description of 

new genera. 


165

Runge et al. 

ARTICLE 

Table 1. Results of the site-wise log-likelihoods generated under possible associations of species in base edges. The first column gives the 

possible associations for which the site-wise log-likelihoods were produced. Columns show the support values for the approximately unbiased 

(AU) test, the observed log-likelihood differences of the edges (OBS), Bootstrap probability tests (NP, BP; and PP), Kishino-Hasegawa (KH) 

test, Shimodaira-Hasegawa (SH) test, weighted Kishino-Hasegawa (WKH) test, and the weighted Shimodaira-Hasegawa (WSH) test. 

Possible associations AU OBS NP BP PP KH SH WKH WSH 

(4.2, DM) 0,983 -106,9 0,992 0,993 1,000 0,966 0,992 0,974 0,989 

(1, 4, DM) 0,983 -106,9 0,992 0,993 1,000 0,966 0,992 0,974 0,989 

(1, 2, 4, DM) 0,983 -106,9 0,992 0,993 1,000 0,966 0,992 0,974 0,989 

(4, DM) 0,979 -39,4 0,985 0,985 1,000 0,901 0,988 0,94 0,996 

(1c,1b) 0,882 -32,7 0,981 0,981 1,000 0,860 0,925 0,925 0,925 

(3, 6) 0,713 -28,2 0,918 0,919 1,000 0,753 0,753 0,753 0,753 

(1–8, 9.1, DM) 0,679 -14,1 0,648 0,646 1,000 0,721 0,909 0,666 0,916 

(1–4, 6, DM) 0,670 -5,6 0,47 0,467 0,997 0,592 0,967 0,592 0,967 

(2b, 2.2) 0,644 -5,1 0,407 0,399 0,973 0,593 0,911 0,593 0,927 

(5, 7) 0,617 -14,7 0,741 0,742 1,000 0,653 0,807 0,653 0,831 

(1, 2, 4, 5, 7, DM) 0,555 5,6 0,104 0,103 0,002 0,408 0,949 0,408 0,951 

(1, 2, 4, 5, DM) 0,440 14,7 0,251 0,252 0,000 0,347 0,815 0,347 0,806 

(1–6, DM) 0,383 14,7 0,259 0,258 0,000 0,347 0,678 0,347 0,676 

(2.1, 2b) 0,356 5,1 0,593 0,601 0,027 0,407 0,585 0,407 0,569 

(9.1,9.2) 0,321 14,1 0,352 0,354 0,000 0,279 0,678 0,334 0,668 

(3,5–7) 0,302 5,8 0,093 0,091 0,000 0,232 0,911 0,232 0,821 

(1–5, 7, DM) 0,287 28,2 0,082 0,081 0,000 0,247 0,636 0,247 0,645 

(1–4, DM) 0,287 28,2 0,082 0,081 0,000 0,247 0,636 0,247 0,645 

(1b,1.1) 0,118 32,7 0,019 0,019 0,000 0,140 0,596 0,075 0,330 

(3, 6, DM) 0,022 106,9 0,007 0,006 0,000 0,034 0,093 0,015 0,065 

(1, 4.1) 0,021 39,4 0,015 0,015 0,000 0,099 0,406 0,031 0,156 

(1, 4) 0,017 106,9 0,008 0,007 0,000 0,034 0,093 0,015 0,051 

(1, 2, 4, 5) 0,017 106,9 0,008 0,007 0,000 0,034 0,093 0,015 0,051 

(1, 2, 4) 0,017 106,9 0,008 0,007 0,000 0,034 0,093 0,015 0,051 

The following species were randomly chosen as representatives for the corresponding clades and subclades in the statistical analysis – 

1c, Phytophthora cactorum ; 1b, P. nicotianae; 1c, P. iranica; 1.1, P. infestans; 2ab, P. capsici; 2.1, P. bisheria; 2.2, P. multivesiculata; 

3, P. nemorosa; 4.1, P. quercina; 4.2, P. palmivora; 5, P. katsurae; 6, P. humicola; 7, P. europaea; 8, P. ramorum; 9.1, P. polonica; 

9.2, P. captiosa; 10, P. boehmeriae; DM, Pseudoperonospora cubensis. 

Inference of Bremer support was done using Maximum 

Parsimony with the Parsimony Ratchet implemented in 

PRAP2 (Müller 2003), using PAUP v. 4.0b10. The starting 

tree was obtained by stepwise addition and subsequently the 

tree-bisection-and-reconnection (TBR) algorithm was used. 

Two hundred replicates were run with 25 % randomly chosen 

characters weighted double and the shortest tree of each 

run was saved. Afterwards the decay index of each of the 

bisections was obtained in PRAP2. 

The Approximately Unbiased (AU) test (Shimodaira 2002) 

was applied to the 100 bootstrap replicate trees of the first 

Maximum Likelihood analysis and to the last 100 sampled 

trees of the first Bayesian Analysis using the CONSEL 

computer package (Shimodaira & Hasegawa 2001). The 

respectively most probable trees were compared to the 

topologies of the resulting trees of the ML, ME and Bayesian 

analyses and no conflicting support was found to be present. 

For conducting the AU testing of the position of the downy 

mildews within Phytophthora and additional statistical tests, 

representatives of each of the clades at a node important 

to infer the position of the downy mildews or the major 

monophyletic clades were chosen. For these 18 accessions, 

a Bayesian analysis was conducted as described above, but 

with estimation of the gamma-distribution and the proportion 

of invariable sites by MrBayes, for enabling the AU testing 

with CONSEL. The sampled accessions are given in Table 

1. The resulting tree was compared to the original tree 

and no conflicting support was present, and only minor 

changes in topology (placement of clade 5) were observed, 

ensuring the validity of the results. One hundred trees (i.e. 

every 20 000 th generation) of the Bayesian analysis were 

used to create a site-wise log-likelihood output in PAUP for 

bootstrap analysis and statistical testing in CONSEL. The 

TREEASS program of the CONSEL computer package 

assesses support for each possible association of species 

in base edges in the underlying trees and outputs p-values 

for the AU test, Bootstrap probability tests (NP, BP; and PP), 

Kishino-Hasegawa (KH) test, Shimodaira-Hasegawa (SH) 

166 ima fUNGUS


test, weighted Kishino-Hasegawa (WKH) test, and weighted 

Shimodaira-Hasegawa (WSH) test. Default settings of 10 

scaling factors of 0.5–1.4, with 10 000 pseudoreplicates 

for each, were used. Phytophthora boehmeria, of the most 

basal clade of Phytophthora, was used as an outgroup for 

the analyses. 

Results 

When used independently, the loci of the concatenated 

alignment always yielded topologies with no significantly 

supported inconsistencies (data not shown). The Maximum 

Likelihood (ML) analysis of the concatenated alignment 

resulted in a best tree with a log-likelihood of -62481.32, a 

Minimum Evolution (ME) tree with a sum of branch lengths of 

1.04068070, and the best tree from Bayesian Analysis (BA) 

had a log-likelihood score of -62678.74. The best tree from 

the BA, with posterior probabilities and bootstrap support 

values from the other analyses, is given in Fig. 1. In addition, 

Bremer support values are given for all clades and subclades. 

Under the given tree, Bremer decay indices > 5 can be 

considered as significant support and values of 10 or higher 

as strong support. It should be noted that the Bremer support 

is not linearly correlated with bootstrap support. Species 

of Phytophthora were grouped into nine highly supported 

clades, with clade 9 also including clade 10 of Blair et al. 

(2008). Tree topology was similar to the one found in Blair et 

al. (2008) and no supported conflicts were observed, with the 

exception of the before-mentioned inclusion of clade 10 into 

clade 9. Downy mildews, represented by the two divergent 

genera, Hyaloperonospora and Pseudoperonospora, were 

grouped together with maximum support in ML and BA 

and strong support in ME inference, and were consistently 

found among the members of clade 4 of Blair et al. (2008) 

with varying support in the full dataset (Fig. 1). The sistergroup 

relationship of downy mildews with a part of clade 4, 

comprised of Phytophthora megakarya, P. quercetorum, P. 

palmivora, and P. areceae received 70 % bootstrap support 

in ME, 59 % in ML and a posterior probability of 0.91, at a 

confidence interval at 95 % for the trees sampled. This 

group was found sister to P. quercina, although this grouping 

received significant support only in the BA. Clade 1 and the 

monophyletic group containing the downy mildews and the 

clade 4 species of Phytophthora were consistently grouped 

together in all analyses, with varying support of 57 % bootstrap 

support in ME, 73 % in ML, and a posterior probability of 0.99. 

The Bremer decay index was 7 for the grouping of DM with 

P. megakarya, P. quercetorum, P. palmivora, and P. areceae 

and also 7 for the sister-group placement of the above 

assemblage with P. quercina. The sister-group relationship 

of clade 1 with clade 4 (including downy mildews) was 

supported by a Bremer decay index of 10, thus providing 

an independent support for the monophyly of this grouping. 

The monophyly of clade 1 was well supported with moderate 

to maximum support in the phylogenetic analyses and a 

Bremer decay index of 24. The monophyly of clades 2 and 

5 was also strongly supported; however, their sister-group 

relationship did not receive significant support in any of the 

analyses. Clades 1, 4 (plus downy mildews), 2, and 5 were 

grouped together with weak support in ME and ML analyses, 

but maximum support in the BA. This group was grouped 

together with clades 3, 6, and 7 with weak support in ME (67 

%), moderate support in ML (78 %) and maximum support in 

the BA. Clades 3, 6, and 7 were all found to be monophyletic 

with strong to maximum support in all analyses. However, 

their grouping as a monophyletic assemblage received only 

weak support in ME and BA. Clade 8 was placed basal to 

the before-mentioned clades 1–7 and its monophyly received 

strong to maximum support in all analyses. A deep divergence 

was found between clades 1–8 on the one side and clades 

9 and 10 on the other side, resulting in a strong to maximum 

support for the monophyly of the assemblage comprised of 

clades 1–8 in all phylogenetic analyses, and a Bremer decay 

index of 10. Clade 10 was found to be nested within clade 

9 in ML and BA, and the monophyly of the group containing 

these clades was weakly supported in ME, but strongly 

supported in ML and BA, and also received a Bremer decay 

index of 9. In the reduced dataset (Fig. S1, Supplementary 

Information, online only) the downy mildews, represented 

by Pseudoperonospora cubensis, grouped together with 

Phytophthora palmivora of clade 4 with maximum support, 

and P. quercina was found to be the sister taxon of this 

group with strong statistical support. The group comprising 

the downy mildew and clade 4 representatives was found 

to be sister to clade 1 with maximum support. An alternative 

topology was observed for some weakly supported nodes, 

as the grouping of clades 3 and 6 as well as the grouping of 

clades 5 and 7 received significant support. 

To test the robustness of the observed grouping of the 

clades, especially with respect to the placement of the downy 

mildews within Phytophthora, and to infer the probability of 

alternative groupings, several tests were performed, which 

are summarised in Table 1. The analyses were carried out 

without constraints, seeking for all possible groupings of 

the clades and subclades of Phytophthora and the downy 

mildews. The clustering of downy mildews with clade 4.2 had 

the highest AU values and also received the highest scores in 

all other analyses, and also the larger clusters of clades 1, 4, 

and DM, and 1, 2, 4, and DM scored equally high. The latter 

of these groupings is, in contrast to the tree presented in 

Fig. 1, as it excludes clade 5, which was grouped together in 

the full phylogenetic analysis with clade 2 without significant 

support. But in the phylogeny of the clade representatives, 

the grouping that scored high in the AU analysis could also be 

observed (Fig. S1). The nesting of the downy mildews within 

clade 4 received almost equally high support, with 0.979 in 

the AU analysis. Thus the topology of the tree presented 

in Fig. 1 with respect to the immediate relationships of the 

downy mildews received the highest support in the AU 

analysis and all other tests employed. Only four contradicting 

clusters were found to be possible. These include an 

alternative placement of the downy mildews with clades 3 

and 6; the clustering of clades 1 and 4 with the exclusion of 

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Runge et al. 

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downy mildews; the clustering of clades 1, 2, 4 and 5 with 

the exclusion of downy mildews; and the clustering of clades 

1, 2, and 4 with the exclusion of downy mildews. But the 

high improbability of these groupings is reflected by very low 

AU scores, which were 0.022 for the first and 0.017 for the 

other groupings. Groupings of Phytophthora which received 

significant support are the clustering of clades 1b and 1c (AU 

0.882); although these scored less than for the position of 

downy mildews as a sister group of clade 4.2 and their nested 

placement in clade 4. The grouping of clades 3 and 6, which 

were affiliated to other clades without significant support in 

the phylogenetic analyses, received moderate support (AU 

0.713). Another grouping which was not observed in the 

phylogenetic analysis is the clustering of clades 5 and 7, 

which was also moderately supported (AU 0.617). Moderate 

support was also obtained for the grouping of clades 1–8, 

including downy mildews, together with 9.1 (AU 0.679), and 

clades 1–4, including downy mildews, together with clade 6 

(AU 0.670). 

Discussion 

The genus Phytophthora is one of the largest genera of 

the oomycetes and contains about 100 currently accepted 

species, of which about 60 species were included in the 

monograph of Erwin & Ribeiro (1996), and to which about 

40 species have been added subsequently (Érsek & Ribeiro 

2010). As many of the species are of ecological and economic 

interest, Phytophthora has received much attention in the past 

decades, and as a consequence, the genome sequencing 

of several of its members has been undertaken (Tyler et al. 

2006, Haas et al. 2009). New species are being discovered in 

the previously species-poor basal clades (Brasier et al. 2005, 

Belbahri et al. 2006, Dick et al. 2006), and it seems likely 

that only a small fraction of the evolutionary diversity of this 

genus has been discovered. The genus Phytophthora has 

often been considered a member of Pythiaceae (Waterhouse 

1973, Dick et al. 1984, Dick 2001), while the obligate 

biotrophic downy mildews were viewed as constituting the 

family Peronosporaceae. Dick et al. (1984) even placed the 

Peronosporaceae together with the Albuginaceae into the 

order Peronosporales and opposed this to the cultivable 

Pythiales, which also included Phytophthora. However, 

Gäumann (1952) already realised that Phytophthora and 

the downy mildews were likely to be closely related, and this 

hypothesis was later corroborated with the first molecular 

phylogenies including members of both Phytophthora and the 

downy mildews (Cooke et al. 2000, Riethmüller et al. 2002). 

The strict split between downy mildews and Phytophthora 

is rather synthetic, as there are species with intermediate 

character states that bridge the apparent gulf between the 

necrotrophic and hemibiotrophic members of Phytophthora 

and the obligate biotrophic downy mildews (Thines 2009). 

For example, the downy mildew genus Viennotia (Göker et 

al. 2003) possesses sporangiophores capable of additional 

growth after sporulation, Poakatesthia (Thines et al. 2007) 

forms intracellular mycelium apart from haustoria, and 

Sclerophthora has hyphal sporangiophores which do not 

form sporangia simultaneously (Payak & Renfro 1967). All of 

these features are usually attributed to Phytophthora species, 

although other characteristics place these genera among the 

downy mildews (Thines 2009). The chimeric appearance of 

Sclerophthora is so pronounced that it was even included in 

the monograph of Phytophthora by Erwin & Ribeiro (1996). It 

is also noteworthy that evolution of the downy mildews may 

have been initiated as parasites of grass relatives (Thines 

et al. 2007, Thines 2009). Support for this hypothesis is 

provided by Phytophthora species from Cyperaceae which 

have also been considered members of an independent 

genus, Kawakamia, and are not readily cultivable (Erwin & 

Ribeiro 1996). On the other hand, there are reports of axenic 

cultivation for Sclerospora graminicola (Tiwari & Arya 1969) 

and Sclerophthora macrospora (Tokura 1975), although these 

results have not been confirmed by independent experiments 

of other groups. Unfortunately, none of the above-mentioned 

parasites of grasses could be included in the present study 

because of difficulties of amplification using the primers 

available. Also, for downy mildews in general, the primers 

used by Blair et al. (2008) do not readily amplify the targeted 

genes, therefore we obtained these sequences directly from 

the genomes of Hyaloperonospora arabidopsidis (Baxter 

et al. 2010) and Pseudoperonospora cubensis (Tian et al. 

2011). However, as the downy mildews most likely represent 

a monophyletic group (Göker et al. 2007), the inclusion of only 

these two exemplars from largely divergent downy mildew 

genera can be considered valid for inferring the placement 

of this group amongst the phylogenetic lineages currently 

placed in Phytophthora. 

The topology of the tree shown here is mostly congruent 

with the topology presented by Blair et al. (2008). However, 

the inclusion of the downy mildews has in some cases resulted 

in lower support values, especially on the backbone and to 

a grouping of clades 2 and 5 without significant support. In 

Blair et al. (2008), clade 5 was inferred as being basal to 

clade 2 with weak to moderate support. In our investigations, 

however, the downy mildews were consistently grouped 

together with some members of clade 4, which is in line with 

the sister-group relationship for Peronospora sparsa with a 

group made up of Phytophthora arecae, P. palmivora, and 

P. megakarya as observed by Cooke et al. (2000) on the 

basis of ITS sequence data, although it cannot be ruled out 

that the finding in that study was influenced by alignment 

artefacts (Thines et al. 2009) and a bias of the Neighbourjoining 

analysis. In our study, which is based on the multilocus 

dataset of Blair et al. (2008) to which sequences from 

downy mildew representatives have been added, the close 

relationship of the downy mildews with members of clade 

4 is also supported by several phylogenetic methods and 

statistical tests, in which the sister-group relationship of 

clade 4.2 with the downy mildews and the grouping of downy 

mildews within clade 4 as a whole received strong support. As 

discussed in previous publications on the global phylogeny of 

Phytophthora (e.g. Blair et al. 2008, Cooke et al. 2000, Kroon 

168 ima fUNGUS


et al. 2004), there are no clear-cut synapomorphies identified 

for the different clades so far. However, four of the five groups 

with predominantly papillate or caducous sporangia (1, 2, 4, 

and 5), together with the downy mildews, form the crown 

group of Phytophthora, and it is thus likely that caducous 

and papillate sporangia represent a derived character state. 

This is in contrast to the conclusion of Kroon et al. (2004), 

who, based on a smaller set of loci, deduced that papillate 

sporangia could also be a plesiomorphic trait. Clade 3, which 

was considered papillate by Kroon et al. (2003), was found 

to sister to clade 6 in this study, although the support for this 

grouping, and also the further clustering of clades 3 and 6 

with clade 7, was low. An alternative placement closer to the 

other predominantly papillate clades can therefore not be 

ruled out at present, although moderate support for a sistergroup 

relationship of clades 3 and 6 was also observed in 

the AU analysis. In line with Blair et al. (2008), P. quercina, 

which was considered a member of clade 3 in Cooke et al. 

(2000), was placed in clade 4, and is referred to as clade 

4.1 in this study, as this species was found to be basal to 

the group of the other members of clade 4 and the downy 

mildews. This placement received varying support in analysis 

of the full dataset and strong support in the reduced dataset. 

The predominantly non-papillate clades 6–10 were found 

predominantly in a basal position with respect to the crown 

group, providing evidence that the non-papillate stage 

might be ancestral, and the development of semi-papillate 

sporangia in clade 8b and clade 9 (sensu Blair et al. 2008) 

represents a homoplasy. Clade 9 (including clade 10) was 

found to be separated from the other Phytophthora clades 

with strong support and represented the most basal clade 

of Phytophthora. As was previously attested by Cooke et 

al. (2000), no obvious phylogenetic pattern with respect to 

temperature or climate adaptation can be observed from the 

phylogenetic analyses. 

Cooke et al. (2000) doubted if the species in these 

clades could be retained in Phytophthora and stated that it 

is likely that further investigation would lead to their exclusion 

from Phytophthora. As revealed in this study, paraphyly 

of Phytophthora is pronounced, rendering Phytophthora 

a typical example of a paraphyletic genus, with the most 

derived linages sharing some synapomorphies with downy 

mildews, while the more basal clades are more similar to 

Halophytophthora, Phytopythium and Pythium. This is similar 

to the situation in Peronosporales as a whole, for which Hulvey 

et al. (2010) recently proposed a broad circumscription of 

Peronosporaceae, encompassing all downy mildew genera, 

Halophytophthora, and Phytopythium, to avoid the description 

of several new, poorly differentiated families. If a similar option 

were chosen for the genus Phytophthora, this would mean an 

inclusion of all downy mildew genera and Phytophthora into a 

single genus. The oldest available name for this assemblage 

on genus level would be Peronospora (Corda 1837), which 

was described much earlier than Phytophthora (de Bary 

1876), thus, if Phytophthora were not conserved that would 

necessitate the inclusion of about 300 species of downy 

mildews, currently placed in other well-defined and widely 

accepted genera, e.g. Basidiophora, Bremia, Plasmopara, 

Peronosclerospora, Pseudoperonospora, and Scleropsora 

(Thines 2006, Voglmayr 2008), and about 100 species of 

Phytophthora (Waterhouse 1963, Erwin & Ribeiro 1996, 

Érsek & Ribeiro 2010) into this genus. This would not only be 

a nomenclatural nightmare but would also result in a highly 

heterogeneous group, encompassing species with divergent 

physiological, ecological, and morphological properties. 

For these reasons, but also because even more namechanges 

would be necessary, conservation of Phytophthora 

and an inclusion of all downy mildew genera (necessitating 

about 400–500 name changes for Peronospora alone), is 

not preferable. If this option were chosen, 700–800 names 

would have to be changed, including many well-known 

pathogens in the genera Bremia (e.g. Bremia lactucae), 

Plasmopara (e.g. Plasmopara viticola and Pl. halstedii), 

Hyaloperonospora (Hyaloperonospora brassicae, H. 

arabidopsidis, H. parasitica), and Peronospora (e.g. Pe. 

tabacina, Pe. destructor, Pe. effusa, Pe. farinosa, Pe. lamii). 

An alternative solution would be to resolve the paraphyly 

of this group by introducing new generic names where none 

existed for the lineages not belonging to the monophyletic 

subtree that includes Phytophthora infestans (the type 

species of Phytophthora). Judging from the results of this 

study, Phytophthora is at least six times paraphyletic as 

revealed by the phylogenetic investigations, but possibly 

seven times paraphyletic with respect to the downy mildews 

judging from the results obtained from the statistical tests. 

This would necessitate the introduction of new generic 

names (or the adoption of currently unused generic names) 

for clades 4.1, 4.2, 8, and the group (9, 10). In addition to 

these clusters, additional generic names would have to be 

introduced for groups formed by members of clades 2, 3, 

5, 6, and 7. In the phylogenetic analysis, while the groups 

(2, 5) and (3, 6, 7) were observed, their monophyly could 

not be ascertained; indeed, some support for alternative 

clusters (3, 6) and (5, 7), with clade 2 as an independent 

linage, was received in statistical tests. Several loci will 

need to be added in future phylogenetic studies to clarify 

the evolutionary relationships of these groups. Based on 

the current data, it can be assumed that Phytophthora is 

at least six, but possibly seven times paraphyletic with 

respect to downy mildews. Species of clade 1, which 

include the economically most important pathogen of the 

genus, Phytophthora infestans, as well as the well-known 

pathogens, P. nicotianae and P. cactorum, would retain their 

original names. This solution would need only a quarter 

of the name changes (less than 100) needed for the first 

option (inclusion of all downy mildew and Phytophthora 

species into Peronospora), and only about 15 % of the 

name changes that would be needed if Phytophthora were 

conserved and all downy mildews were transferred into 

this genus. In addition, it would leave the names of most 

of the most important pathogens of the Peronosporaceae 

unchanged, like Bremia lactucae, Hyaloperonospora 

brassicae, Phytophthora infestans, Plasmopara halstedii, 

Plasmopara viticola, Pseudoperonospora cubensis and 

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Pseudoperonospora humuli. Therefore, we feel that this 

solution is to be preferred. But to introduce the new names 

for the clades outlined above will necessitate a search for 

characters defining synapomorphies for these groups, which 

might not be easy, judging from the apparent discrepancies 

between the morphological classification of Waterhouse 

(1963), and recent phylogenetic studies (Cooke et al. 2000, 

Kroon et al. 2004, Blair et al. 2008). Probably, these genera 

might have to be defined with the aid on DNA sequence 

synapomorphies, rather than only morphology. But retaining 

the usage of the generic name Phytophthora for all the at 

least six monophyletic groups between Halophytophthora 

and at the same time retaining the 19 downy mildew genera, 

would not only be contrary to the widely accepted idea of 

ideally having monophyletic taxa only, but also hamper the 

awareness of the unique evolution of these organisms, 

stepwise towards obligate biotrophy (Thines & Kamoun 

2010). For example, in terms of evolution, Phytophthora 

infestans is much closer to downy mildews than to P. sojae or 

even P. ramorum. But for the understanding of the evolution 

of obligate biotrophy, which is one of the most fascinating 

and fundamental evolutionary tipping points for any group of 

pathogens, it will be even more important to obtain genome 

sequences for members of the clades 4.1 and 4.2, which 

are apparently the closest relatives of the downy mildews, 

and of the neglected species of Phytophthora affecting 

Cyperaceae. 


Fabian Runge is supported by a fellowship of the Ministry of Science 

and Education of Baden-Württemberg. This study was supported 

by the research funding programme “LOEWE – Landes-Offensive 

zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz” of the 

Ministry of Higher Education, Research, and the Arts of Hesse. Work 

in the laboratory of BD was supported by a Michigan State University 

GREEEN grant (GR10-021) 

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Validation and justification of the phylum name Cryptomycota phyl. nov. 

Meredith D.M. Jones 1,2 , Thomas A. Richards 1,2 , David L. Hawksworth 3 , and David Bass 2 

1 

School of Biosciences, University of Exeter, Exeter EX4 4QD, UK; corresponding author e-mail: d.bass@nhm.ac.uk 

2 

Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK 

3 

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal, 28040 Madrid, 

Spain; and Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, UK 

ARTICLE 

Abstract: The recently proposed new phylum name Cryptomycota phyl. nov. is validly published in order to facilitate its 

use in future discussions of the ecology, biology, and phylogenetic relationships of the constituent organisms. This name 

is preferred over the previously tentatively proposed “Rozellida” as new data suggest that the life-style and morphology 

of Rozella is not representative of the large radiation to which it and other Cryptomycota belong. Furthermore, taxa at 

higher ranks such as phylum are considered better not based on individual names of included genera, but rather on some 

special characteristics – in this case the cryptic nature of this group and that they were initially revealed by molecular 

methods rather than morphological discovery. If the group were later viewed as a member of a different kingdom, the 

name should be retained to indicate its fungal affinities, as is the practice for other fungal-like protist groups. 

Key words: 

chitin 

chytrid 

Fungi 

phylogeny 

Rozella 

Rozellida 

Article info: Submitted 26 September 2011; Accepted 2 November 2011; Published 11 November 2011. 

Introduction 

The designation “cryptomycota” was introduced by Jones 

et al. (2011) to accommodate a well-supported clade (using 

ribosomal DNA (rDNA) phylogenies) of organisms putatively 

branching deep within the fungal radiation. The rank of phylum 

is the most appropriate for this group as current results show 

that it has fungal characteristics but is distinct from other fungi 

in not having a chitin-rich cell wall in the major stages of its lifecycle 

so far identified, including putative trophic interactions. 

However, Cryptomycota was not validly published as a 

scientific name in that work as no Latin diagnosis was provided 

(McNeill et al. 2006: Art. 36). A Latin diagnosis is provided here 

in order to formally establish the name. In addition, comments 

are made on our decision to introduce this name rather than 

take up the earlier informal name “Rozellida”, and on the 

distinctive features of the phylum and its position. 

TAXONOMY 

Cryptomycota M. D. M. Jones & T. A. Richards, phyl. 

nov. 


Etymology: crypto- – hidden; and -mycota, a phylum of fungi. 

Fungi unicellulares, zoosporis unicellularis, uniflagellatibus, flagellis 

microtubularis, cystes sine tunica chitinosa vel cellulosa. Consortia 

epibiontica formata. 

Fungi unicellular, zoospores single-celled with a single 

microtubular flagellum, and cysts without a chitin/cellulose 

cell wall. Forming epibiontic associations. 

Representatives: GenBank accession nos AJ130857, 

AJ130849.1, AJ130850, FJ687265, FJ687267 and FJ687268, 

and Rozella. 

Illustrations: Jones et al. (2011: figs 1d, 2a–e). 

DISCUSSION 

It has been demonstrated that Rozella occupies a deep 

branching position in phylogenetic analyses of kingdom 

Fungi (James et al. 2006a, b), although bootstrap support for 

this relationship is inconsistent and often weak in the most 

comprehensively sampled phylogenies (James et al. 2006a, 

b, Jones et al. 2011). The name “Rozellida” was coined by 

Lara et al. (2010) to accommodate Rozella and a number of 

environmental sequences that form a distinct clade, but we 

refer to this group henceforth as Cryptomycota for reasons 

indicated below. Jones et al. (2011) showed that Cryptomycota 

are more diverse than previously recognised and that the 

molecular diversity of this group may be as diverse as the rest 

of the known Fungi according to rDNA gene markers. 

Members of Cryptomycota are found in freshwater, soil, 

sediment, and some marine habitats. Jones et al. (2011) used 



Attribution: 







Jones et al. 

ARTICLE 

lineage-specific fluorescence in situ hybridization (FISH), cell 

wall stains, and immuno-fluorescence staining to show two 

distinct lineages within Cryptomycota, which comprised ovoid 

cells of ca. 5 µm diam, existing in at least three morphologies 

in freshwater environments: uniflagellate zoospores, more 

variably-shaped cells without flagella attached to other eukaryotic 

microscopic organisms (e.g. diatom hosts), and non-flagellate 

cysts. None of these stages were shown to possess a chitin or 

cellulose wall, although other life-cycle phases with a chitin and/ 

or cellulose cell wall may remain undetected. A chitin cell wall is 

sometimes cited as defining feature of kingdom Fungi, although 

we note that this is not a reliable diagnostic feature as distantly 

related protist groups also possess chitin on their cell surface 

(e.g. Kneipp et al. 1998). 

The name “Rozellida” was applied to this phylum by Lara 

et al. (2010) but in an informal way between inverted commas 

and with no formal diagnosis. The ICZN (International Code 

of Zoological Nomenclature; International Commission on 

Zoological Nomenclature 1999) does not apply to names 

above the rank of family-group, but if it were in those ranks 

it would be viewed as unavailable as a conditional name 

(Art. 15.1). For names introduced under the ICZN which 

later are found to belong to Fungi, the ICN (International 

Code of Nomenclature for algae, fungi, and plants) now 

accepts them as available under Art. 45.4 (as revised at the 

Melbourne Congress in July 2011; McNeill et al. 2011). Thus, 

no Latin diagnosis was required, as it was for fungal names 

introduced between 1935 and 1 January 2012). However, we 

are inclined not to accept “Rozellida” because of the use of 

the inverted commas suggesting the usage was a tentative 

suggestion and in any case note that it is not mandatory to 

follow the principle of priority of publication for names above 

the rank of family (ICN) or family group (ICZN). Indeed, the 

ICZN does not cover ranks higher than family group. 

We decided that it would be better not to definitely 

establish a name based on Rozella for several reasons: 

(1) The fungal termination to be used for names in the 

rank of phylum is “-mycota” under the ICN (McNeill et al. 2006; 

Art 16.4), and that termination has also been used for phyla 

traditionally studied by mycologists but which are no longer 

considered Fungi but placed in other kingdoms. Examples 

include Hyphochytriomycota R.H. Whittaker (Whittaker 1969: 

154) now placed in Straminipila M.W. Dick 2001, Myxomycota 

Bold (Bold 1957: 152) for slime moulds in the Protozoa, and 

Oomycota Arx (Arx 1967: 16) for fungal analogues in the 

Straminipila. This practice has been employed in standard 

reference works (e.g. Kirk et al. 2001) and also the most 

recent textbooks (e.g. Moore et al. 2011). 

(2) Cryptomycota represent a very diverse radiation, 

potentially equivalent to or larger than the rest of the known 

fungi. Of the three lineages within the radiation for which 

morphological data exist, Rozella appears to be exceptional 

in that it is primarily an intracellular parasite; indeed the 

possession of intracellular sporangia is included in the 

generic description of Rozella species (Held 1981). To extend 

the implication of this life-cycle characteristic across the rest 

of the radiation – where there is no evidence of this lifecycle 

characteristic – would be misleading. Lara et al. (2010) 

were also hesitant commending the use of the proposed 

name “between quotation marks until morphological and/or 

ultrastructural synapomorphies are defined to diagnose and 

validate this entire group”. Jones et al. (2011) demonstrate 

that this key characteristic of Rozella does not seem to extend 

across the whole group and therefore the name “Rozellida” is 

not representative of the group as a whole. 

(3) It is important to recognize that our current knowledge 

of the life stages of the newly discovered Cryptomycota 

and of Rozella is very incomplete. As Jones et al. (2011) 

suggest, chitin may be present in the walls of some currently 

unknown Cryptomycota life-cycle stage(s) and/or present in 

uncharacterized lineages within Cryptomycota, and even in 

currently unknown stages in Rozella. It would be premature, 

therefore, to separate Cryptomycota from the kingdom Fungi 

on the single character that they do not possess chitin walls 

(which, as mentioned above is not diagnostic for Fungi). 

(4) Cryptomycota have some strong resemblances to 

Chytridiomycota (‘chytrids’) in both structure (e.g. flagellar 

apparatus) and ecology, if not in cell wall chemistry. There is 

no agreed defining non-molecular characteristic for identifying 

the boundaries of kingdom Fungi. Therefore, as several other 

key characteristics are shared by Cryptomycota and some 

Fungi, the former are most sensibly and parsimoniously 

considered as belonging to the latter as they form the closest 

branches on phylogenetic trees (James et al. 2006a, b, 

Lara et al. 2010, Jones et al. 2011). This stance is entirely 

consistent with the historical position regarding Rozella: for 

the last 40 years leading mycologists have classified this 

genus within Fungi (e.g. Held, 1981; Kirk et al. 2008). 

(5) Cryptomycota (including Rozella) consistently branch 

with Fungi in all phylogenies so far constructed. However, their 

position as the primary branch within fungi is much weaker 

(e.g. James et al. 2006; Jones et al. 2011). Indeed, they could 

actually occupy a higher branching position within Fungi. If 

this is the case, their lack of some traditionally diagnostic 

fungal features such as a chitin cell wall may be the result of 

secondary losses, which would not preclude them from being 

considered Fungi. In this case, excluding Cryptomycota from 

the Fungi could potentially make the rest of fungi paraphyletic 

– a highly undesirable and not logically sustainable situation. 

In the absence of a strong morphological argument to exclude 

this group from the fungal kingdom – we must therefore look 

to the only available data, which is phylogenetic, and argues 

that Cryptomycota are most reasonably considered to be 

within Fungi. 

(6) Consequently, we agree with Lara et al. (2010) that 

there are sound reasons for considering Rozella (and now 

we suggest other Cryptomycota) as Fungi. Whether or not 

Cryptomycota other than Rozella prove to be phagocytotic 

(which in itself would not be a sufficiently strongly deterministic 

trait for inclusion in – or exclusion from – Fungi, as some 

plant lineages and oomycetes have also lost phagotrophy), 

their chytrid-like uniflagellate zoospore stage and particularly 

their phylogenetic position argue most parsimoniously for a 

fungal affiliation. 

174 ima fUNGUS

Validation of the phylum name Cryptomycota 

(7) The names used for taxa at the highest ranks, such as 

phylum, are better not based on names of included genera, 

but rather on some special characteristic, as is the case with, 

for example, the phyla Ascomycota and Basidiomycota. In 

this way the names immediately convey some feature of 

the taxon. In this case, we highlight the cryptic nature of 

Cryptomycota in that they were hidden from science until 

revealed by molecular methods rather than morphological 

discovery. 

In conclusion, we consider the formal validation of the 

name Cryptomycota to be justified, and commend it for use 

for this group of organisms as it emphasises the fungal affinity 

and attributes of the organisms so far known within this 

group. Even if in some future classification these organisms 

were placed outside the Fungi, we consider the name should 

be retained to reflect their nature as fungal analogues. 


We thank Ramon Massana, Irene Forn, Caterina Gadelha, and Martin 

Egan for useful discussions, and Joost A Stalpers for checking the 

Latin diagnosis. D. L. H. acknowledges support from the Ministerio 

de Ciencia e Innovación in Spain (project CGL 2008-01600). 

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[and 64 others], (2006a) Reconstructing the early evolution of 

Fungi using a six-gene phylogeny. Nature 443: 818–822. 

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D, Powell MJ, Griffith GW, Vilgalys R (2006b) A molecular 

phylogeny of the flagellated fungi (Chytridiomycota) and 

description of a new phylum (Blastocladiomycota). Mycologia 

98: 860–871. 

Jones MDM, Forn I, Gadelha C, Egan MJ, Bass D, Massana R, 

Richards TA (2011) Discovery of novel intermediate forms 

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& Bisby’s Dictionary of the Fungi. 9 th edn. Wallingford: CABI 

Publishing. 

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& Bisby’s Dictionary of the Fungi. 10 th edn. Wallingford: CABI 

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Travassos LR (1998) Trichomonas vaginalis and Trichomonas 

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Parasitology 89: 195–204. 

Lara E, Moreira D, López-Garcia P (2010) The environmental clade 

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Botanical Congress: preliminary mail vote and report of congress 

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Fungi. Cambridge: Cambridge University Press. 

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Molecular techniques for pathogen identification and fungus detection in the 

environment 

Clement K.M. Tsui 1 , James Woodhall 2 , Wen Chen 3 , C. André Lévesque 3 , Anna Lau 4 *, Cor D. Schoen 5 , Christiane Baschien 6** , 

Mohammad J. Najafzadeh 7,8 , and G. Sybren de Hoog 7 

ARTICLE 

1 

Department of Forest Sciences, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; corresponding author e-mail: 

clementsui@gmail.com 

2 

The Food and Environment Research Agency, Sand Hutton, York YO41 1LZ, UK 

3 

Central Experimental Farm, Agriculture and Agri-Food Canada, Ottawa, Canada, K1A OC6 

4 

Centre for Infectious Diseases and Microbiology and the University of Sydney, Westmead Hospital, Westmead, NSW 2145, Australia 

5 

Plant Research International, Business Unit Bio-Interactions and Plant Health, PO Box 16, 6700 AA, Wageningen, The Netherlands 

6 

Technische Universität Berlin, Environmental Microbiology, Sekr. FR1-2, Franklinstrasse 29, 10587 Berlin, Germany 

7 

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands 

8 

Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran 

*Current mailing address: Department of Laboratory Medicine, 10 Center Drive, National Institutes of Health, Bethesda, MD 20892, USA 

**Current mailing address: Federal Environment Agency Germany, Corrensplatz 1, 14195 Berlin, Germany 

Abstract: Many species of fungi can cause disease in plants, animals and humans. Accurate and robust 

detection and quantification of fungi is essential for diagnosis, modeling and surveillance. Also direct 

detection of fungi enables a deeper understanding of natural microbial communities, particularly as a great 

many fungi are difficult or impossible to cultivate. In the last decade, effective amplification platforms, probe 

development and various quantitative PCR technologies have revolutionized research on fungal detection 

and identification. Examples of the latest technology in fungal detection and differentiation are discussed 

here. 

Key words: 

FISH 

LAMP 

macroarray 

medical mycology 

molecular diagnostics 

molecular ecology 

padlock probe 

pathogenic fungi 

plant pathology 

rolling circle amplification 

Article info: Submitted 17 October 2011; Accepted 3 November 2011; Published 18 November 2011. 

Introduction 

Fungi represent the greatest eukaryotic diversity on earth and 

they are among the primary decomposers in ecosystems. It is 

conservatively estimated that 1.5 million species of fungi exist 

(Hawksworth 1991). Many fungal species are important plant 

and human pathogens (Agrios 2005). Rapid and accurate 

detection of fungal pathogens to species or strain level is 

often essential for disease surveillance and implementing a 

disease management strategy. Developing direct detection 

assays is challenging because fungal pathogens can exist 

as multiple species complexes or at very low concentration 

in clinical and natural environments. Different molecular 

genotypes/varieties can also exist within species, and may 

have different pathogenic profiles and virulence levels to 

the host. In addition, unculturable and non-sporulating 

fungi remain a major challenge when studying biotrophic, 

endophytic, and mycorrhizal groups. Therefore, novel 

techniques are required when attempting to detect fungi in 

the environment. 

Increasingly molecular techniques are employed in 

studies requiring the detection of fungi in the environment. 

In this paper, based on presentations at a Special 

Interest Group meeting convened during the International 

Mycological Congress (IMC9) in Edinburgh, UK, August 

2010, some of the latest diagnostic techniques employed 

in the detection of fungi, including fluorescence in situ 

hybridisation (FISH), DNA array technology, Multiplex 

tandem PCR, and Padlock probe technology with 

rolling circle amplification and loop-mediated isothermal 

amplification (LAMP) were discussed. The importance of 

DNA extraction and sampling methodologies were also 

briefly discussed. 



Attribution: 







Tsui et al. 

ARTICLE 

GENERAL CONSIDERATIONS 

Suitable methodologies to isolate nucleic acids from the 

enormous range of habitats that fungi can occupy are crucial 

to all molecular detection methods. Critical to the successful 

isolation of nucleic acids are the methods used for extraction 

and sample preparation, as well as the sampling strategy 

employed. 

DNA extraction methods 

An enormous variety of nucleic acid extraction methods 

is available. For many applications, commercial kits are 

available, but these are not always suitable. For example, in 

the case of soil, none of the kits presently available are able 

to extract efficiently using sample sizes typically required 

(see below). Therefore, with unusual and difficult sample 

types, customized methods are typically employed. Key to 

this is the cell disruption/homogenisation step in the presence 

of an appropriate buffer (typically a CTAB or guanidinium 

thiocyanate based buffer). A wide variety of methods can be 

used, including specialist equipments such as a planetary 

ball mill (Brierley et al. 2009), appropriate bead beaters, 

pressure cycling technology (Okubara et al. 2007), and novel 

approaches using equipment such as a paint shaker for soil 

samples (Reeleder et al. 2003), or even a conventional food 

blender for plant and food samples. All cell disruption steps are 

potentially damaging to the nucleic acid quantity and quality, 

either through direct shearing of the nucleic acid, or through 

the co-extraction of humic acids (an inhibitor of PCR) present 

in plant and soil samples. Therefore, methods which provide an 

adequate level of cell disruption to enable satisfactory nucleic 

acid extraction, but without too much nucleic acid damage or 

release of potential PCR inhibitors, are required. 

Following cell disruption and subsequent extraction steps, 

the nucleic acid can be purified using standard methods, 

including pelleting, silica membrane spin filter, and silicamagnetic 

particle separation. When selecting a purification 

step, consideration needs to be given to the nucleic acid 

quality/quantity required, cost, speed of extraction and ability 

to automate any process. The method of analysing the nucleic 

acid will determine what purification method is used. For 

example, DNA profiling and metagenomic studies using next 

generation sequencing approaches will require pure, high 

quality nucleic acid extracts. Conversely, cruder, less pure 

extracts may be used where real-time PCR is used for routine 

diagnostic purposes where the emphasis is on nucleic acid 

quantity, speed and cost of extraction because the downstream 

application is more tolerant of impurities in the DNA extract. 

Sample preparation 

Innovative sample preparation can enhance chances of 

detection. For example, organic matter can be removed 

from soil and processed separately for fungal targets which 

survive solely in that component of the soil. Sclerotiumforming 

pathogens may be separated from the rest of the soil 

by sieving or floating prior to nucleic acid extraction. These 

approaches effectively concentrate the fungal target, thereby 

increasing the chance of successful detection. Where 

appropriate, a baiting approach could be used in conjunction 

with nucleic acid extraction and PCR. This has the added 

benefit of confirming the target is viable. 

Sampling strategy 

In addition, an appropriate and statistically robust sampling 

strategy should be utilised. This will vary between fungal 

targets, depending upon the biology (and possibly 

epidemiology) of the organism to be detected. For example, a 

‘W’ sampling strategy across an area may not be appropriate 

for a target with a highly clustered distribution, and a grid 

sampling approach should be used instead. The individual 

sample size processed for DNA extraction should also be 

large enough to be biologically relevant (Ophel-Keller et al. 

2008). A wide variety of methods exist, and no one approach 

is likely to be suitable for all targets. Knowledge of the biology 

of the target species is essential for designing and determining 

the optimum sampling and extraction methodology in any 

particular case. 

Sequencing independent methods 

DNA sequencing of the internal transcribed spacer (ITS) and 

large subunit (LSU) regions of rRNA, followed by comparative 

sequence analysis, has been the ‘gold standard’ for molecular 

identification of most fungi, particularly of culturable fungi. This 

strategy is fast and accurate, but is dependent on sequence 

quality in existing reference databases. In many recently 

evolved fungal groups, however, the ribosomal genes are 

insufficiently variable, and sequencing of additional genes 

is necessary. Costs could also be a challenge for routine 

diagnostic laboratories, and therefore various sequencing 

independent methods that are available can be used. 

Fluorescent in situ hybridisation 

Since fungi are ubiquitous, it is important to understand their 

biodiversity and abundance, as well as their ecological roles 

in different habitats, such as soil, decaying leaves and wood, 

and also indoor environments or humans. Indeed, it is critical 

to identify the metabolically active species (‘real players’) 

in communities or ecosystems in order to understand 

the ecosystem processes that involve fungi. PCR based 

methods, such as fingerprinting or molecular cloning, do not 

discriminate between ‘real players’ and fungi that are dormant. 

Also, DNA and RNA extraction protocols may be biased due 

to rigid cell walls of fungal hyphae. Immuno-staining provides 

a means to identify species in situ but is extremely laborious 

in the experimental preparation. All these kinds of technical 

difficulties, can, however, be overcome by fluorescence in 

situ hybridisation (FISH). 

FISH is a powerful method for the in situ detection of 

active growing organisms in environmental samples (Amann 

et al. 1995). The technique can visualize the precise location 

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Fig. 1. Examples of fluorescence in situ hybridisation. A. Clavariopsis aquatica growing on aquatic leaf litter, probed with 18 rRNA-targeted 

MY1574 domain specific probe (from Baschien et al. 2008). B. Accessibility of Tetracladium marchalianum conidia for FISH 28SrRNA-targeted 

species specific probe TmarchB10 (modified from Baschien et al. 2008). 

of particular DNA or RNA sequences in the cytoplasm, 

organelles, or nuclei of biological materials. As a result, the 

technique can detect metabolically active fungi directly in the 

environment without cultivation when RNA is present. The 

spatial distribution of growing mycelia on or within colonized 

substrata can also be investigated (Li et al. 1996, Baschien et 

al. 2001, McArthur et al. 2001, Robin et al. 1986). 

The major step of FISH involves the preparation of 

biological materials or environmental samples, and the 

labelling (incorporation of a fluorescent label/marker) of a 

nucleic acid sequence to form a probe. Then, under controlled 

experimental conditions, the probe is hybridized to the DNA 

or RNA in biological materials to form a double-stranded 

molecule. Finally, the sites of hybridization are detected 

and visualized. FISH is commonly used in the ‘top-bottom 

approach’ research followed with feedback to the top level 

(Amann et al. 1995). The molecular biology and genetics 

of targeted organism is well-understood, and the probe is 

designed based on the nucleotide sequence which has been 

well characterized. 

FISH probes often target sequences of ribosomal RNA 

or mitochondrial genes because they are abundant in 

sequence databases and in multiple copies in each cell. The 

probes can be designed by computer-assisted search from 

target organisms for “signatures”. These signature regions 

can be specific at different phylogenetic levels depending 

on the variability of the target molecule sequences. The 

probe comprises a short sequence, ranging from 15 to 

20 nucleotides, that is specific for one or several taxa at 

species, genus, or higher taxonomic ranks. The probe or 

oligonucleotide is then labelled with a fluorochrome, for 

example a carboindocyanine dye (CY3). 

A particular attraction is that FISH probes can be applied 

to formaldehyde or ethanol fixed environmental samples, or 

to cultures. At the ribosomes, the probe will specifically anneal 

to its complementary sequence resulting in a heteroduplex. 

After incubation, a washing step is crucial to discriminate the 

target from non-target organisms. Probes that do not bind 

to an rRNA sequence will be washed away, resulting in a 

fluorescent signal of exclusively target organisms. The probe 

conferred signal is correlated with the ribosome content, and 

therefore increases in cells with higher metabolic activity. 

The first FISH probe targeting a living fungus was 

designed by Li et al. (1996) for Aureobasidium pullulans 

on the phylloplane of apple seedlings; this was the first 

time that a living fungus had been visualized by FISH. 

Examples of situations in which the method has been used 

are very varied. Fungi belonging to Eurotiomycetes were 

demonstrated to be more abundant than Dothideomycetes in 

an extremely acidic mine drainage using 18S rRNA-targeted 

probes (Baker et al. 2004). Baschien et al. (2008) designed 

nine taxon-specific probes targeting the 18S or 28S rRNA 

for the detection of aquatic hyphomycetes in leaf litter (Fig. 

1A, B). Domain specific probes were also used to detect 

active fungi in mice (Scupham et al. 2006) and in waste water 

sewage granule biofilms (Weber et al. 2007). Most probes 

have been designed to target the 18S or 28S rRNA gene, and 

their specificity needs to be kept under review as sequence 

databases expand. 

Several factors can influence the efficiency of FISH, for 

example the sterical and electrostatical properties of rRNA, 

the features of the probe, and hybridisation conditions such 

as the fixation method, buffers, the stringency of probe 

binding, and incubation time. Inacio et al. (2003) investigated 


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the different accessibility of the rRNA molecule for FISH 

probes. They designed 32 different probes that targeted the 

26S (large subunit) of rRNA for yeasts, and investigated the 

conferred signal intensity generated from the probes. They 

concluded that the prerequisite for successful FISH is the 

specificity of probes (Inácio et al. 2003). 

Limitations of the FISH method can include fungal and 

substrate inherent autofluorescence, insufficient permeability 

of cell walls, non-specific binding of probes, and low ribosome 

contents. Autofluorescence of fungi can also lead to false 

positive fluorescence signals. A fluorescence scan conducted 

by confocal laser scanning microscopy revealed that many 

freshwater fungi emit a green autofluorescence (Baschien et 

al. 2001), and, consequently, a green-labelled FISH probe 

could not be used. It is, therefore, important to check for 

autofluorescence of both target and non-target organisms 

before selecting the fluorochrome for probe labelling. 

Environmental samples and substrates such as leaves, wood, 

and animal tissues, also emit strong autofluorescence in 

several wavelengths at the same time, interfering with probe 

signals. However, the pin-hole technique of a laser scanning 

microscope is helpful in reducing background emissions 

compared to conventional epifluorescence (Baschien et al. 

2001). 

Low or no permeability of fungal cell walls can lead to 

weak or no signals because of the failure of FISH probes to 

penetrate rigid cell walls (Brul et al. 1997). One possible way 

to overcome this problem is to use cell wall lysing enzymes, 

such as chitinases and glucanases. A more elegant method 

is the use of peptide nucleic acid (PNA) probes. PNA probes 

are mimics in which the negatively charged sugar-backbone 

of DNA is replaced with a non-charged polyamide backbone. 

PNA probes share the same nucleotide bases as the 

conventional DNA probes. However, PNA probes penetrate 

cell walls more effectively due to their neutrality and they do 

not have to overcome the destabilizing electrostatic repulsion 

during hybridisation (Wilson et al. 2005, Shepard et al. 2008). 

Low ribosome contents can arise from either a scarcity of 

potential substrate in oligotrophic habitats, or the presence of 

components inhibiting fungal growth. However, the Catalysed 

Reporter Deposition FISH (CARD-FISH) is a variant of the 

FISH method designed to enhance probe conferred signals. 

The major difference is that the probes are labelled with horseradish-oxidase 

instead of a fluorochrome. Fluorescencelabelled 

tyramide is then added to the cells after hybridisation. 

The horse-radish-oxidase catalyses the deposition of the 

reporter, and this reaction leads to 20 to 30 fold stronger FISH 

signals than conventional FISH. Consequently, the number of 

active rRNA molecules necessary to detect a probe conferred 

signal decreases by using CARD FISH (Pernthaler et al. 

2002). 

DNA array hybridization 

DNA array hybridization, also known as Reverse Dot Blot 

Hybridization (RDBH) or macroarray, is a technique based 

on hybridization of amplified and labelled genome regions 

of interest to immobilized oligonucleotides spotted on a 

solid support platform. It was originally developed to detect 

mutations of human genes, and is still an important diagnostic 

tool in clinical research (Chehab & Wall 1992, Yang et al. 

2001, Zhang et al. 1991). It is now considered a powerful 

and practical technique for the detection and identification 

of fungi and other microbes, such as bacteria, from complex 

environmental samples without the need for isolation in 

culture (Chen et al., 2009, Ehrmann et al. 1994, Lévesque et 

al. 1998, Tambong et al. 2006, Uehara et al. 1999, Wu et al. 

2007, Zhang et al. 2007, 2008). For this type of application, 

oligonucleotides, or microcodes (Summerbell et al. 2005), are 

designed from a taxonomically complete dataset of suitable 

genome region(s) (Chen et al. 2009, Tambong et al. 2006). 

The oligonucleotides can be selected manually, by analysing 

multi-sequence alignments, or through computer programs, 

such as SigOli (Zahariev et al. 2009) and Array Designer 

(Premier Biosoft International, Palo Alto, CA). Synthesized 

oligonucleotides with 5’-amine modifications are then spotted 

onto a supporting platform, such as a nylon membrane or 

glass slide, either manually or robotically. Robotic spotting 

can significantly increase the maximum density of the array 

which can favour the detection of broader taxonomic groups 

(Chen et al. 2009). Amplicons of the target gene region(s) 

are amplified by PCR, labelled with digoxygenin (DIG) and 

subjected to the DNA hybridization procedure previously 

described (Fessehaie et al. 2003). A positive reaction between 

an amplicon and a perfectly matched (PM) oligonucleotide 

generates a chemiluminescent signal which can be detected 

by X-ray film or a digital camera in dark rooms. Captured 

images are then analysed on a computer program such as 

GenePix Pro (Molecular Devices, Sunnyvale, CA). 

The design of species or group-specific oligonucleotides 

is a crucial step in this process since it defines the specificity 

and sensitivity of the assay (Lievens et al. 2006, Pozhitkov 

et al. 2006, Urakawa et al. 2003). It is generally agreed 

that the length of the oligonucleotide, the number, type and 

position of SNPs contained in an oligonucleotide, determine 

its discriminatory potential for DNA hybridization. A desirable 

oligonucleotide should: (1) have suitable thermodynamic 

characters such as melting temperature; (2) contain as 

many polymorphic sites as possible located close to the 

centre or on the 3’-half of the sequence; and (3) have the 

least probability of hairpin or dimer formation (Kawasaki et al. 

1993, Lievens et al. 2006). Oligonucleotide lengths ranging 

from 25 to 35 mer have displayed the best balance between 

specificity and sensitivity (Chen et al. 2009). Longer lengths 

(> 35 mer) of oligonucleotides reduce the ratio of mismatched 

to matched base pairs, yet increase the number of bases 

available for hybridization, providing lower specificity but 

higher sensitivity to an array (Dorris et al. 2003, Lievens et al. 

2006). Oligonucleotides up to 70 mer, however, have been 

used in macroarrays for the detection of plant viruses using 

gene sequences that are widely different between the closely 

related pathogens (Agindotan & Perry 2007, 2008). It has 

also been demonstrated that more complicated parameters, 

such as actual sequence arrangement and the mismatched 

duplex type, and their interactions, can play important roles 

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Fig. 2. DNA macroarray hybridization results from frozen cranberry fruit sample collected from Massachusetts, USA (adapted from Robideau 

et al. 2008). The x-ray film is overlaid with the oligonucleotide spotting pattern on DNA array membrane for cranberry fruit rot fungi. The top 

left pair of spots and bottom right pair of spots are oligonucleotides which served as positive controls. This array is showing positive signal for 

Phyllosticta, Coleophoma, Epicoccum, Godronia, Alternaria, Pestalotia, and Pilidium. 

in affecting the discriminatory power of an oligonucleotide 

(Urakawa et al. 2003, Lievens et al. 2006, Pozhitkov et al. 

2006). Despite numerous attempts to predict the behaviour 

of oligonucleotides in DNA hybridization, the thermodynamic 

interaction between the probes and oligonucleotides remains 

poorly understood (Pozhitkov et al. 2007). 

Most DNA macroarrays that have been developed are 

based on a single region for the detection of a specific 

taxonomic group. Among these regions, 16S ribosomal DNA 

has been used for the detection of bacteria (Fessehaie et 

al. 2003, Xiong et al. 2006). Various genome regions, such 

as ribosomal DNA spacers (ITS), mitochondrial genes (e.g. 

cytochrome oxydase c subunit 1, cox1) and some protein 

coding regions (β-tubulin, EF-1α, etc), were chosen to target 

fungi and fungus-like organisms (Chen et al. 2009, Gilbert et 

al. 2008, Harper et al. 2011, Ning et al. 2007, 2008, Seifert 

& Lévesque 2004). Oligonucleotides with higher specificity 

are often designed from polymorphic sites located at indels 

present in multi-sequence alignments (Robideau et al. 2008, 

Tambong et al. 2006). Oligonucleotides extracted from a 

locus that can be well aligned with low sequence divergence 

tends to cross-react with non-target amplicons and display 

strong false positive signals even when tested with pure 

cultures because of the low frequency of polymorphisms 

in the specific oligonucleotides. This has been observed in 

arrays using cox1 in Penicillium subgen. Penicillium (Chen 

et al. 2009, Seifert et al. 2007). In a recent study, DNA 

arrays were constructed from multiple loci of Phytophthora 

species, including ITS, cox1 and the intergenic region (cox2- 

1 spacer, CS) between cytochrome c oxidase 2 (cox2) and 

cox1 (W. Chen et al. pers. comm.). In comparison to the 

cox1 region, the length variation and the presence of indels 

in the sequence alignments of ITS and CS provided better 

opportunities to select highly specific oligonucleotides. The 

combination of all three arrays increased the discrimination 

potential, detection accuracy, and redundancy of the assay. 

DNA arrays have been developed for the detection of 

plant pathogens in a wide range of environmental samples, 

such as greenhouse crops (Le Floch et al. 2007, Lievens et 

al. 2003), potatoes (Fessehaie et al. 2003), ginseng (Punja 

et al. 2007), and fruits (Robideau et al. 2008, Sholberg et al. 

2005, 2006). Macroarrays are also effective diagnostic tools 

for the detection of phytopathogenic bacteria (Fessehaie et 

al. 2003), fungi and fungus-like organisms (Chen et al. 2009, 

Lévesque et al. 1998, Tambong et al. 2006), nematodes 

(Uehara et al. 1999), and viruses (Agindotan & Perry 2007, 

2008). 

DNA array hybridization is highly sensitive as are most 

PCR-based approaches. With the unlimited capacity for 

the accommodation of oligonucleotides on one membrane 

and the reusability of the membranes, it shows superior 

multiplexing detection capability at a lower cost over other 

PCR-based methods. In a biodiversity study, the species 

profile could be revealed by hybridizing the oligonucleotide 

array with a mixed pool of DIG-labelled PCR products 

amplified from the total DNA of a query sample. This assay 

would be especially valuable for the simultaneous detection 

of multiple plant pathogens which cover a broad taxonomic 

range but are specific to a certain host. As an example, 

Robideau et al. (2008) developed a DNA array for cranberry 

fruit rot (CFR) fungal pathogens with over 2000 field samples 

being tested. This array had the ability to detect species from 

24 genera of fungi known on cranberry with a single test. 

Fig. 2 shows that this DNA macroarray was able to detect 

species of Phyllosticta, Cladosporium, Epicoccum, Godronia, 

Alternaria, Pestalotia, and Pilidium from a single frozen 

cranberry fruit sample (Robideau et al. 2008). 

The macroarray technology is now available commercially 

in four European countries under the name DNA Multiscan 

(http://www.dnamultiscan.com) and at the Guelph Pest 

Diagnostic Clinic (http://www.guelphlabservices.com/) for 

the test of plant pathogens in greenhouse nutrient solutions 

and roots of crops. There are very significant advances in next 

generation sequencing technology that have reduced the need 

of DNA array technology in functional genomics. However, 

there are developments in lab-on-a-chip array technology for 

very quick and for large-scale testing. A recent example is 

a low density array for Phytophthora detection, where amino- 


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Fig. 3. Schematic representation of the multiplex tandem–PCR 

procedure illustrating specific detection and identification from a blood 

sample containing Candida albicans and C. glabrata. Reproduced 

from Lau et al. (2009) with the permission of Future Medicine. 

labelled oligonucleotides are spotted over a gap between two 

electrodes inside a microchip (Julich et al. 2011). Hybridization 

is detected by a current passing through a silver deposit over 

the gap. Because of such developments, array-based assays 

are likely to remain a popular option for diagnostics. 

Multiplex tandem PCR 

Multiplexed-tandem PCR (MT-PCR) is a technology platform 

developed for highly multiplexed gene expression profiling 

and the rapid identification of clinically important pathogens 

(Stanley et al. 2005). The platform consists of two rounds 

of amplification (Fig. 3). In the first step, a multiplex PCR is 

performed at 10 to 15 cycles to allow enrichment of target 

DNA without creating competition between amplicons (Lau 

et al. 2009). This product is diluted and used as template for 

the second amplification that consists of multiple individual 

quantitative PCR reactions with primers nested within 

those used in the multiplex PCR. Up to 72 different PCR 

reactions can be multiplexed and performed simultaneously. 

Fluorescence is measured by SYBR green technology at 

the end of each extension cycle, and melt-curve analysis 

provides species-specific or gene-specific identification. 

The incorporation of two sets of species-specific primers for 

each target ensures correct amplification and detection, thus 

avoiding the expense of DNA probes. SYBR green detection 

also increases the multiplexing and quantitative capacity 

of real-time PCR systems, which are usually limited by the 

availability of fluorescent channels and the need to optimize 

each individual multiplex PCR. 

In the clinical setting, invasive fungal infections (IFIs) 

remain a leading cause of morbidity and mortality in 

immune-compromised hosts. MT-PCR was considered a 

suitable alternative for the rapid detection and identification 

of fungal pathogens directly from clinical specimens, thus 

circumventing the need for gold standard culture and 

histology, which is slow, insensitive and non-specific. Faster 

and accurate molecular identification would also enable 

better guidance and earlier administration of targeted 

antifungal therapies. As such, the laboratory at Westmead 

hospital, in conjunction with AusDiagnostics (Alexandria, 

NSW, Australia), developed several MT-PCR assays to 

detect the16 major causes of fungal bloodstream infections. 

The targets included 11 species of Candida, Cryptococcus 

neoformans complex, Saccharomyces cerevisiae, pan- 

Fusarium, F. solani, and Scedosporium prolificans. Primers 

were designed using sequence variations within the ITS 

regions, elongation factor 1-a (EF1-a), and b-tubulin genes. 

Fungal targets were selected according to their frequency 

of causing infections, their potential resistance to frontline 

antifungal agents (especially fluconazole), and their high 

attributable mortality. 

The MT-PCR platform was initially evaluated on 70 blood 

cultures in which a yeast or mould was seen in Gram’s stain 

preparations, as well as 200 bacterial blood cultures and 30 

samples which did not flag positive (Lau et al. 2008a). The 

sensitivity and specificity of the assay was 100 %. This included 

the correct identification of fungi in five cases with bacterial 

co-infection. In addition, no interference was observed in 

simulated cases of polyfungal infection. Unfortunately, three 

rare disease-causing yeasts (Candida lambica, C. nivariensis 

and Kodamaea ohmeri) were not detected by MT-PCR as 

targets were not available on the fungal panel. Nevertheless, 

this study demonstrated the diagnostic usefulness of the 

platform to rapidly identify common fungal pathogens within 

four hours of blood culture flagging (including automated 

nucleic acid extraction), which is considerably faster than the 

48-96 h required by gold standard methods. 

An expanded version of the MT-PCR fungal platform was 

then evaluated on 255 EDTA whole blood, 29 serum, and 24 

plasma specimens obtained from 109 patients with proven 

candidemia (Lau et al. 2010) with the aim of circumventing 

the technical and sensitivity issues inherent in routine blood 

culture diagnosis. Although the MT-PCR assay was less 

sensitive than blood culture (75% sensitivity), the diagnosis 

of candidemia and pathogen identification was expedited by 

up to four days. The results also supported the contention 

that serum and plasma samples were better than whole 

blood samples for the molecular detection of candidemia. 

Using a technique known as colony MT-PCR (Lau et 

al. 2008b), the fungal assay was also able to provide rapid 

(1.5 h) and unambiguous identification of yeasts direct from 

primary isolation plates without the need for DNA extraction or 

separation from mixed fungal/bacterial cultures. As such, colony 

MT-PCR offered a faster and better alternative to biochemical 

assays which are often subjective, prone to misidentification, 

and dependent on a pure culture being obtained. Current work 

is aimed at integrating identification panels with targets to 

detect molecular mechanisms of antifungal resistance. 

Overall, the fungal MT-PCR assay compares favourably 

to other commercial platforms and integrates well into the 

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Fig. 4. Schematic overview of the padlock principle combined with OpenArray ® , Technology for multiplex detection of three different targets 

(adapted from van Doorn et al. 2007). 

routine workflow of diagnostic laboratories. Automated 

operations and use of commercial reagents further enables 

standardized procedures to be established. Nevertheless, the 

major limitation of all molecular diagnostic assays is target 

availability, which is often dictated by an effort to balance out 

costs and turn-around time with maximum throughput. The 

increased sensitivity of molecular assays and its ability to 

detect viable and non-viable cells should also place heavy 

emphasis on interpreting results with other microbiological 

data and clinical information. 

ISOTHERMAL SYSTEMS 

Isothermal systems do not require a thermal cycler to produce 

rapid temperature changes, but require only a simple platform 

such as heating blocks or water bath. Isothermal systems 

include rolling circle amplification (RCA) and loop-mediated 

isothermal amplification (LAMP). 

Padlock probe technology and rolling circle 

amplification 

Detection and characterization of single nucleotide 

polymorphisms (SNPs) is becoming increasing popular 

for pathogen identification, but was considered a major 

challenge for conventional real-time PCR using regular 

oligonucleotides detected by fluorescent dyes (e.g. SYBR 

green or TaqMan probes). In order to recognize SNPs among 

different genotypes, padlock probe techniques are required. 

Padlock probes (PLPs) are long oligonucleotides (about 100 

bp) carrying a non-target-complementary segment flanked 

by the target complementary regions at their 5’ and 3’ ends, 

which recognize adjacent sequences on the target DNA 

(Nilsson et al. 1994). Thus, on hybridization, the ends of 

the probes occupy adjacent positions, and can be joined by 

enzymatic ligation (Figs 4–5). Ligation occurs and the probes 

are circularized only when both end segments correctly 

recognize the target sequences (Landegren et al. 1988). The 

helical nature of double-stranded DNA (dsDNA) enables the 


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Fig. 5. Schematic representation of the steps in padlock probe 

technology coupled with hyperbranched rolling circle amplification 

(H-RCA) for SNPs detection. 1. The hybridization of padlock probes 

(containing the complementary sequences at the 5’ and 3’ ends) to 

the target templates. 2. During a perfect match, the probe forms a 

circular molecular with the aid of DNA ligase; while in the case of 

mismatch, no circular molecules formed. 3. Non-hybridized template 

will be removed during the exonucleolysis reactions (digestion 

by exonucleases I and III). 4. H-RCA is performed using two predesigned 

primers and Bst polymerase, but no amplification will take 

place in the absence of a circular molecular. 5. The accumulation of 

dsDNA products during isothermal rolling circle amplification of DNA 

minicircles is monitored in a real time PCR thermocycler with the 

addition of SYBR green. 

probe to topologically bind to the target strand and the probe 

can’t be displaced (Nilsson et al. 1994). 

Padlock probes were initially introduced for in situ 

DNA localization and detection (Nilsson et al. 1994). They 

were developed originally for discrimination of centromeric 

sequence variation in human chromosomes (Nilsson et 

al. 1997). However, the method has now been applied to 

detection of genetically modified organisms (Prins et al. 

2008). This concept also provides extensive multiplex 

potential for pathogen detection as the interaction between 

padlock probes does not give rise to circular molecules, 

which can be easily removed from the detection system 

(Nilsson et al. 1994, 1996). Recently, padlock probe-based 

applications for multiplex quantitative targets detection and 

for genotyping fungal and microbial community analysis 

using high throughput real-time PCR on OpenArrays ® have 

been developed (van Doorn et al. 2007). Advantages of 

PLP-based diagnostic applications developed are a flexible 

and easily adaptable design, specificity, and multiplexing, 

universal downstream processing after ligation, and highthroughput 

format with real-time analysis (Tsui et al. 2012) 

(Fig. 4). 

Briefly, various padlock probes are designed to target 

organisms and ligated to DNA extracted from environmental 

samples or cultures (van Doorn et al. 2007). Targets for 

ligation present in complex DNA samples such as soil or recirculated 

water can be generated by PCR pre-amplification, 

through Phi29 polymerase and whole genome amplification to 

ensure efficient detection. Real-time quantification for multiple 

targets is performed in OpenArrays ® , which can accommodate 

up to 3072 x 33 nl PCR amplification with preloaded probespecific 

primers (Fig. 4). Multiplex padlock ligation is followed 

by single-plex amplification using unique probe-specific primer 

pairs and SYBR green based detection in nano-litre PCR 

array (van Doorn et al. 2007). The performance of the padlock 

probe detection system has been demonstrated using 13 

probes targeting several plant pathogens at various taxonomic 

levels (Szemes et al. 2005, van Doorn et al. 2007). All 

probes specifically detected their corresponding targets, and 

provided perfect discrimination against non-target organisms 

with very similar target sites. Pathogen quantification was 

robust in single target versus mixed target assays. This novel 

assay enables very specific, high-throughput, quantitative 

detection of multiple pathogens over a wide range of target 

concentrations, and should be easily adaptable for versatile 

diagnostic purposes (van Doorn et al. 2007). 

Also, padlock probes containing zip-code sequence or a 

biotin-labelled moiety and internal endonuclease cleavage 

site, in conjunction with quantitative PCR and Luminex TM 

technology or microarray technology, can be used for 

multiplex pathogen detection and quantification (Szemes et 

al. 2005, Eriksson et al. 2009, van Doorn et al. 2009). 

Alternatively, the signal by which the target hybridizes 

perfectly to the padlock probes can be amplified by 

hyperbranched rolling circle amplification (H-RCA) (Banér 

et al. 1998). Rolling circle amplification (RCA) is based on 

the rolling replication of short single stranded DNA (ssDNA) 

circular molecules (Lizardi et al. 1998, Fire & Xu 1995). RCA 

involves a single forward primer complementary to the linker 

region of the padlock probe and a DNA polymerase with strand 

displacement activity in an isothermal condition (Pickering 

et al. 2002). As a result, the padlock probe signal can be 

amplified several thousand-fold because the polymerase 

extends the bound primer along the padlock probes for many 

cycles and displaces upstream sequences, producing a long 

ssDNA molecule comprising multiple repeats of the probe 

sequence. Two primers are employed: a first forward primer 

that binds to the padlock probe and initializes RCA, and a 

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Fig. 6. Schematic representation of the mechanism of LAMP. A. 

General location of the LAMP primer set in relation to defined regions 

of the target DNA. Forward (F3) and backward (B3) outer primers 

and forward (FIP) and backward (BIP) inner primers are indicated. 

B, C. Basic principle and amplification steps in LAMP. In general 

new DNA strands are synthesizes from the F3 and B3 primers, and 

these strands are recognized by FIP and BIP to start loop-mediated 

autocycling amplifications. The final products are stem-loop DNAs 

with several inverted repeats of the target DNA, and cauliflower-like 

structures bearing multiple loops (modified from diagrams at © Eiken Chemical. 

second primer that targets the repeated ssDNA sequence of 

the primary RCA product, finally generating large numbers of 

copies of the DNA fragments. This is called hyperbranching 

RCA (H-RCA) (Lizardi et al. 1998) (Fig. 5). 

Padlock probe coupled with H-RCA offers a significant 

advantage for the detection of SNPs (Tsui et al. 2012). The 

formation of circular probes via ligation occurs when both 

ends of the padlock probes perfectly hybridize to the target at 

juxtaposition (Fig. 5). The subsequent H-RCA amplification of 

a target probe could be carried out when circularized probes 

become available. These two strict conditions create an ideal 

detection platform for highly sensitive and specific SNPs 

detection. By increasing the hybridization temperature and 

shortening the 3’ arm (below the reaction temperature), the 

discrimination of SNP can be further improved (Pickering et 

al. 2002, Faruqi et al. 2001). This method for SNPs detection 

based on DNA ligase-mediated single nucleotide discrimination 

with consecutive signal amplification by H-RCA has been 

developed for various groups of pathogenic organisms, 

including fungi, bacteria, and viruses (Kong et al. 2008, Zhou 

et al. 2008, Kaocharoen et al. 2008, Wang et al. 2009, 2010). 

Recently, the technology has been used to differentiate and to 

detect two closely related conifer pathogens vectored by the 

mountain pine beetles (Tsui et al. 2010). 

Loop mediated isothermal amplification 

Loop-mediated isothermal amplification (LAMP) is a powerful 

and novel nucleic acid amplification method that amplifies 

a few copies of target DNA with high specificity, efficiency, 

and rapidity under isothermal conditions, using a set of four 

specially designed primers and a DNA polymerase with strand 

displacement activity (Notomi et al. 2000, Parida et al. 2008, 

Tomita et al. 2008). The cycling reactions can result in the 

accumulation of 10 9 to 10 10 -fold copies of target in less than 

an hour. Considering the advantages of rapid amplification, 

simple operation and easy detection, LAMP has potential 

applications for clinical diagnosis as well as surveillance of 

infectious diseases in developing countries without requiring 

sophisticated equipment or skilled personnel (Mori & Notomi 

2009, Parida et al. 2008). 

The technique was first described and initially evaluated 

for detection of hepatitis B virus DNA by Notami et al. 

(Notomi et al. 2000). LAMP assays have been mostly used 

for the diagnostics of bacteria (Chen et al. 2011, Han et 

al. 2011), virus (Wang et al. 2011, Zhao et al. 2011), and 

parasites (Ikadai et al. 2004, Iseki et al. 2007), but it has 

also been developed for the rapid detection of pathogenic 

or allergenic fungi. Ohori et al. (2006) used the technique for 

rapid identification of Ochroconis gallopava, an emerging 

fungal pathogen and causative agent of zoonotic infections, 

while Sun and co-workers, used it for the rapid diagnosis of 

Penicillium marneffei in archived tissue samples (Sun et al. 

2010a) and of Fonsecaea agents of chromoblastomycosis 

(Sun et al. 2010b). Similarly Endo et al. (2004) and Tatibana 

et al. (2009) detected the presence of the gp43 gene in 

Paracoccidioides brasiliensis by LAMP, and Lucas et al. 

(2010) used LAMP for differentiation of Cryptococcus 

neoformans varieties from C. gattii based on CAP59 

sequences. Recently, Lu et al. (2011) utilized the technology 

for the identification of Pseudallescheria and Scedosporium 

species. 

Two inner and two outer primers are required for LAMP 

(Fig. 6A). In the initial steps of the LAMP reaction, all four 

primers are employed, but in the later cycling steps only 

the inner primers are used for strand displacement DNA 

synthesis. The outer primers are referred to as F3 and B3, 

while the inner primers are forward inner primer (FIB) and 

backward inner primer (BIP). Both FIP and BIP contains two 

distinct sequences corresponding to the sense and antisense 

sequences of the target DNA, one for priming in the first 

stage and the other for self-priming in later stages (Notomi et 

al. 2000). The size and sequence of the primers was chosen 

so that their melting temperature (Tm) is between 60-65 °C, 

the optimal temperature for Bst polymerase. The F1c and 

B1c Tm values should be a little higher than those of F2 and 

B2 to form the looped-out structure. The Tm values of the 

outer primers F3 and B3 have to be lower than those of F2 

and B2 to assure that the inner primers start synthesis earlier 

than the outer primers. Additionally, the concentrations of the 

inner primers are higher than the concentrations of the outer 

primers (Notomi et al. 2000, Tomita et al. 2008). Furthermore, 

it is critical for LAMP to form a stem-loop DNA from a dumb- 

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ARTICLE 

bell structure. Various sizes of the loop between F2c and 

F1c and between B2c and B1c were examined, and the best 

results are obtained when loops of 40 nucleotides (40nt) 

or longer are used (Notomi et al. 2000). The size of target 

DNA is an important factor that LAMP efficiency depends 

on, because the rate limiting step for amplification is strand 

displacement DNA synthesis. 

LAMP relies on auto-cycling strand displacement DNA 

synthesis in the presence of Bst DNA polymerase, specific 

primers and the target DNA template. The mechanism of 

the LAMP amplification reaction includes three steps: 

production of starting material, cycling amplification, and 

recycling (Notomi et al. 2000, Tomita et al. 2008) (Fig. 6B, C). 

To produce the starting material, inner primer FIB hybridizes 

to F2c in the target DNA and initiates complementary strand 

synthesis. Outer primer F3 hybridizes to F3c in the target 

and initiates strand displacement DNA synthesis, releasing 

a FIP-linked complementary strand, which forms a loopedout 

structure at one end (DNA amplification proceeds with 

BIP in a similar manner). This single stranded DNA serves 

as template for BIP-initiated DNA synthesis and subsequent 

B3-primed strand displacement DNA synthesis leading to 

the production of a dumb-bell form DNA which is quickly 

converted to a stem loop DNA. This then serves as the 

starting material for LAMP cycling, the second stage of the 

LAMP reaction. During cycling amplification, FIP hybridizes 

to the loop in the stem-loop DNA and primes strand 

displacement DNA synthesis, generating as an intermediate 

one gapped stem loop DNA with an additional inverted copy 

of the target sequence in the stem, and a loop formed at 

the opposite end via the BIP sequence. Subsequent selfprimed 

strand displacement DNA synthesis yields one 

complementary structure of the original stem-loop DNA, and 

one gap repaired stem-loop DNA with a stem elongated to 

twice as long and a loop at the opposite end. Both of these 

products then serve as templates for BIP-primed strand 

displacement in the subsequent cycles, the elongation and 

recycling step. The final product is a mixture of stem loop 

DNA with various stem length and cauliflower-like structures 

with multiple loops formed by annealing between alternately 

inverted repeats of the target sequence in the same strand 

(Notomi et al. 2000, Tomita et al. 2008). 

LAMP products can be directly observed by the naked eye 

or using a UV transilluminator in the reaction tube by adding 

2.0 µl of 10 fold diluted SYBR Green I stain to the reaction 

tube separately. Under UV illumination, the gel shows a 

ladder-like structure from the minimum length of target DNA 

up to the loading well, which are the various length stem-loop 

products of the LAMP reaction. 

Conclusion 

Numerous detection methodologies are now available, but 

regardless of the approach, important questions need to be 

answered prior to their inclusion into experiments. These 

include sensitivity, accuracy, robustness, frequency of testing, 

and cost. Despite many novel technologies being available, 

challenges remain to identify as yet unculturable fungi, to 

detect cryptic species, and to characterize the assemblage 

and diversity of fungal communities in different environments 

without bias. There is always a need to characterize fungi 

quickly and accurately. No one knows how many fungal 

species exist, but sequencing of environmental DNA may 

improve the accuracy of current estimates (Hawksworth 

2001). Next-generation sequencing and pyrosequencing 

approaches will also provide promising ways of enlarging the 

scope of molecular-detection studies. 


We would like to thank the IMC9 organizers for supporting this SIG 

symposium. We are thankful to Satoko Yamamoto (Eiken Chemical, 

Japan) for permission to use diagrams of LAMP from . 

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Advances in Glomeromycota taxonomy and classification 

Fritz Oehl 1 , Ewald Sieverding 2 , Javier Palenzuela 3 , Kurt Ineichen 4 , and Gladstone Alves da Silva 5 

1 

Agroscope Reckenholz-Tänikon Research Station (ART), Ecological Farming Systems, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland; 

corresponding author e-mail: fritz.oehl@art.admin.ch 

2 

Institute of Plant Production and Agroecology in the Tropics and Subtropics, University of Hohenheim, Garbenstrasse 13, D-70593 Stuttgart, 

Germany 

3 

Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 

Granada, Spain 

4 

Basel-Zürich Plant Science Center, Institute of Botany, University of Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland 

5 

Departamento de Micologia, CCB, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves s/n, Cidade Universitaria, 50670-420, 

Recife, PE, Brazil 

ARTICLE 

Abstract: Concomitant morphological and molecular analyses have led to major breakthroughs in the taxonomic 

organization of the phylum Glomeromycota. Fungi in this phylum are known to form arbuscular mycorrhiza, and so 

far three classes, five orders, 14 families and 29 genera have been described. Sensu lato, spore formation in 10 of 

the arbuscular mycorrhiza-forming genera is exclusively glomoid, one is gigasporoid, seven are scutellosporoid, 

four are entrophosporoid, two are acaulosporoid, and one is pacisporoid. Spore bimorphism is found in three 

genera, and one genus is associated with cyanobacteria. Here we present the current classification developed in 

several recent publications and provide a summary to facilitate the identification of taxa from genus to class level. 

Key words: 

Archaeosporomycetes 

endomycorrhizas 

evolution 

Gigasporales 

Glomerales 

Glomeromycetes 

Paraglomeromycetes 

phylogeny 

VA mycorrhiza 

Article info: Submitted 10 November 2011; Accepted: 16 November 2011; Published: 18 November 2011. 

Introduction 

Glomeromycota taxonomy was largely morphologically driven 

up to the end of the last millennium. All glomeromycotean 

fungi, except one genus, are known to form arbuscular 

mycorrhiza. Their identification was based on spore 

morphology, spore formation, and spore wall structure 

(e.g. Gerdemann & Trappe 1974, Walker & Sanders 1986, 

Morton & Benny 1990, Schenck & Pérez 1990). However, 

as soon as molecular phylogenetic tools became available, 

they were included in taxonomic analyses (e.g. Simon et al. 

1992) and soon became the drivers of the establishment 

of a new taxonomy (Morton & Redecker 2001, Schüßler et 

al. 2001). In 1990, without the benefit of molecular aspects, 

the arbuscular mycorrhiza-forming fungi were organized 

in three families (Acaulosporaceae, Gigasporaceae, and 

Glomeraceae) and six genera (Acaulospora, Entrophospora, 

Gigaspora, Glomus, Sclerocystis, and Scutellospora) 

within one order, Glomerales (Morton & Benny 1990) of the 

fungal phylum Zygomycota. That classification was based 

on spore morphology and spore formation characteristics 

(acaulosporoid, entrophosporoid, gigasporoid, glomoid, 

radial-glomoid, and scutellosporoid). Differences in spore 

wall structure were used at the species level. 

Today, we accept three classes (Archaeosporomycetes, 

Glomeromycetes, and Paraglomeromycetes), five orders 

(Archaeosporales, Diversisporales, Gigasporales, Glomerales 

and Paraglomerales), 14 families, 29 genera and approximately 

230 species (e.g. Morton & Redecker 2001, Schüßler et al. 

2001, Oehl & Sieverding 2004, Walker & Schüßler 2004, 

Sieverding & Oehl 2006, Spain et al. 2006, Oehl et al. 2008, 

2011a–d, Palenzuela et al. 2008). 

Until recently, it was unclear whether glomoid and 

gigasporoid species could be further divided into different 

morphological groups congruent with the major phylogenetic 

clades obtained by molecular analyses. A first revision of the 

sporogenous cell forming (gigasporoid and scutellosporoid) 

Glomeromycetes according to concomitant morphological 

and phylogenetic features (Oehl et al. 2008) was not accepted 

by all mycologists (Morton & Msiska 2010). However, later 

studies with a broader database (e.g. Goto et al. 2010, 2011, 

Oehl et al. 2010, 2011b) confirmed that the revised genus 

Scutellospora, as well as the new Racocetra, Cetraspora, 

Dentiscutata, and Orbispora, are monophyletic. 



Attribution: 







Oehl et al. 

ARTICLE 

A large group of species forms glomoid spores, and it 

had been believed that there were too few morphological 

characters of significance to differentiate them. Taxonomists 

have consequently started basing groupings of the glomoid 

species almost exclusively on molecular phylogenetic 

characters. A recent revision of these glomoid species 

has, however, shown that molecular phylogeny is actually 

congruent with the morphological characteristics of these 

fungi (Oehl et al. 2011c). Fungal species with entrophosporoid 

spore formation were also revised (Oehl et al. 2011d). 

The objective of this paper is to present the current overall 

classification system of Glomeromycota that has emerged 

from these recent studies, and to summarize the major 

morphological features in the phylum down to genus level. 


The morphological, molecular, and phylogenetic analyses 

performed are presented in a series of recent publications 

dealing with different species groups of Glomeromycota (e.g. 

Oehl et al. 2006, 2010, 2011a, b, d, f, Sieverding & Oehl 

2006, Silva et al. 2006, Spain et al. 2006, Palenzuela et al. 

2008, 2010, 2011). 

Results and Discussion 

Figure 1 is a schematic tree for Glomeromycota based on 

molecular phylogenetic analyses of the SSU, ITS region, partial 

LSU of the rRNA gene, and partial β-tubulin gene (e.g. Oehl et 

al. 2008, 2010, 2011a–d). In Table 1, the major morphological 

features of all higher level taxa are presented, with the taxa 

arranged according to their taxonomic rank down to genus. 

Three glomeromycotean classes, five orders, 14 families, and 

29 genera have been recognized to date (Table 1). Sensu lato, 

spore formation in 10 of the arbuscular mycorrhiza-forming 

genera have exclusively glomoid, one has gigasporoid, seven 

have scutellosporoid, four have entrophosporoid, two genera 

have acaulosporoid, and one has pacisporoid spore formation, 

while three genera show spore bimorphism, and one genus 

is associated with cyanobacteria (the only one not forming 

arbuscular mycorrhizas). 

Hitherto, Paraglomeromycetes are monogeneric (Table 

1), are characterized by mono-walled spores formed 

terminally on hyphae (i.e. glomoid spores sensu lato), and 

germinate directly through the spore wall. Their arbuscular 

mycorrhizal structures do not or only faintly stain in trypan 

blue. Archaeosporomycetes includes organisms that are 

exclusively bimorphic since they form either acaulosporoid or 

entrophosporoid spores simultaneously with glomoid spores, 

or are associated with cyanobacteria. The mycorrhizal 

structures of Archaeosporaceae are similar to those of 

Paraglomeraceae, while Ambisporaceae form vesiculararbuscular 

mycorrhizal structures staining pale blue in trypan 

blue. In contrast, mycorrhizal structures in Glomeromycetes 

stain blue to dark blue in trypan blue. In Glomeromycetes, 

Gigasporales species do not form intraradical vesicles but 

auxiliary cells in soils, which clearly distinguish them from 

Glomerales and Diversisporales. 

Gigasporales exhibit gigasporoid or scutellosporoid spore 

formation (Oehl et al. 2011b), i.e. spores formed terminally 

on sporogenous cells and with either germ warts on the 

inner surface of the mono-walled spore wall (gigasporoid; 

Gigasporaceae), or a discrete germination shield on the 

innermost (= ‘germinal wall’) of 2–4 walls (scutellosporoid). 

There are three families with scutellosporoid spore formation 

(sensu lato): Dentiscutataceae, Racocetraceae and 

Scutellosporaceae (Oehl et al. 2008). Scutellosporaceae form 

mono-lobed (Orbispora) or bi-lobed (Scutellospora), hyaline 

germination shields (Figs 2–4). Racocetraceae species form 

wavy-like, multiply lobed, hyaline germination shields and 

have either two (Racocetra) or three (Cetraspora) spore walls 

(Figs 5–8). Dentiscutataceae species form yellow-brown to 

brown germ shields that are bi-lobed (Fuscutata; Fig. 9) or 

with multiple compartments (Dentiscutata, triple-walled; 

Quatunica four-walled; Figs 10–11). 

In Archaeosporales and Diversisporales, four genera 

have spore formation laterally on the neck of terminal or 

intercalary sporiferous saccules (= acaulosporoid sensu 

lato; Table 1): Acaulospora, Otospora, and the bi-morphic 

Ambispora and Archaeospora. These genera can easily be 

separated on spore wall number and spore wall structure 

(Palenzuela et al. 2008). Triple-walled Acaulospora 

species have a characteristic granular, ‘beaded’ inner wall 

surface (Morton & Benny 1990), which is absent in acauloambisporoid 

spores of triple-walled Ambispora species 

(Spain et al. 2006, Palenzuela et al. 2011). The wall structure 

of the bi-walled Otospora is more complex than that of biwalled 

Archaeospora species (Palenzuela et al. 2008). 

In Archaeosporales, Diversisporales, and Glomerales, 

there are five genera with spore formation within the 

neck of terminal or intercalary sporiferous saccules (i.e. 

entrophosporoid sensu lato; Table 1): Entrophospora, 

Kuklospora, Sacculospora, Tricispora, and bimorphic 

Intraspora (Oehl et al. 2011d). Triple-walled Kuklospora has 

the characteristic granular, ‘beaded’ inner wall surface of 

Acaulosporaceae (Sieverding & Oehl 2006), which is absent 

in spores of triple-walled Sacculospora (Oehl et al. 2011d). 

The wall structure of bi-walled Entrophospora and Tricispora 

is more complex than that of bi-walled, bimorphic Intraspora 

species (Sieverding & Oehl 2006, Oehl et al. 2011d). 

Entrophospora and Tricispora can be distinguished through 

the two cicatrices (scars) and pore structures proximal and 

distal to the sporiferous saccule: the proximal pore is wide 

in Tricispora and closed by a septum, while it is narrow and 

closed by a plug in Entrophospora. The distal pore and scar 

is absent in Entrophospora from the structural layer, and 

formed only on the overlying, hyaline, evanescent layer, 

while, in light microscopy, the distal pore with a distal scar is 

obvious in Tricispora (Sieverding & Oehl 2006, Palenzuela et 

al. 2010, Oehl et al. 2011d). 

192 ima fUNGUS

Advances in Glomeromycota classification 

ARTICLE 

Fig. 1. Representative tree of the phylum Glomeromycota based on molecular (SSU, ITS region, partial LSU of the rRNA gene, and partial 

β-tubuline gene) and morphological analyses (spore wall structures, structures of the spore bases and subtending hyphae, germination, and 

germination shield structures). Adapted from (Oehl et al. 2008, 2011a–d). The drawings in the central columns show the spore formation types 

of the genera, and the typical germination shields for those genera which form persistent shields already during spore formation. 


193

Oehl et al. 

ARTICLE 

Table 1. Major morphological characters for higher level taxa of Glomeromycota from class to genus level. 

Class 

Order 

Family Genus Spore formation Number of 

spore walls 

Germination; specific 

germination structure 

Mycorrhizal structures; 

staining in Trypan blue 

Glomeromycetes Germ tube (gt) Vesicles, Arbuscles, 

Hyphae 

Glomerales Glomeraceae Glomus Glomoid (terminally on hyphae) 

Funneliformis Glomoid 

Funneliformoid sensu stricto 

Septoglomus Glomoid 

Septoglomoid sensu stricto 

1 

1 

1 

gt through hypha 


gt through hyphae 

V, A, H 

V, A, H 

V, A, H 

Simiglomus Glomoid 

Simiglomoid sensu stricto 

1 

gt through hypha? 

V, A, H 

Entrophosporaceae Claroideoglomus Glomoid sensu lato 

Claroideoglomoid sensu stricto 

1 


V, A, H 

Albahypha Glomoid 

Claroideoglomoid sensu lato 

1 


V, A, H 

Viscospora Glomoid 

Claroideoglomoid sensu lato 

1 


V, A, H 

Entrophospora Entrophosporoid (in the neck of a saccule) 

gt through wall? 

2 

V, A, H 

Diversisporales Diversisporaceae Diversispora Glomoid 

Diversisporoid sensu stricto 

1 


V, A, H 

Redeckera Glomoid 

(Diversisporo-)Redeckeroid sensu stricto 

1 


V, A, H 

Otospora Acaulosporoid (on the neck of sporiferous 

saccule): otosporoid sensu stricto 2 

Unknown? 

V, A, H 

Tricispora Entrophosporoid 

Tricisporoid sensu stricto 2 

Unknown? 

V, A, H 

Sacculosporaceae Sacculospora Entrophosporoid 

Sacculosporoid sensu stricto 3 

Unknown? 

V, A, H 

Pacisporaceae Pacispora Pacisporoid 

2 

gt through wall; multiply 

lobed germ structure V, A, H 

Acaulosporaceae Kuklospora Entrophosporoid 

Kuklosporoid sensu stricto 3 

Acaulospora Acaulosporoid 

3 

gt through wall; monolobed, 

hyaline germ shield 

(=orb) 

gt through wall; mono-(to 

multiply) lobed, hyaline 

germ shield (=orb) 

V, A, H 

V, A, H 

194 ima fUNGUS


ARTICLE 

Gigasporales Scutellosporaceae Orbispora Scutellosporoid (on sporogenous cells, and 

forming germ shields); Orbisporoid sensu 

stricto 

Scutellospora Scutellosporoid 

Dentiscutataceae Fuscutata Scutellosporoid 

Fuscutatoid sensu stricto 

Dentiscutata Scutellosporoid 

Dentiscutatoid sensu stricto 

Quatunica Scutellosporoid 

Dentiscutatoid sensu stricto 

Racocetraceae Cetraspora Scutellosporoid 

Racocetroid sensu stricto 

Racocetra Scutellosporoid 

Racocetroid sensu stricto 

Gigasporaceae Gigaspora Gigasporoid (on sporogenous cells, and 

forming germ warts) 1 

Archaeosporomycetes 

Archaeosporales Ambisporaceae Ambispora Bimorph: Acaulo- & Glomo-ambisporoid 

Archaeosporaceae Archaeospora Bimorph: Acaulo- & Glomo-archaeosporoid 

Intraspora Bimorph: Entropho-& Glomo-intrasporoid 

Geosiphonaceae Geosiphon Glomoid sensu lato 

Paraglomeromycetes 

Paraglomerales Paraglomeraceae Paraglomus Glomoid sensu lato 

3 

3 

3 

3 

4 

3 

2 

3 (Ac) 

1 (Gl) 

2 (Ac) 

1 (Gl) 

2 (Ac) 

1 (Gl) 

1 

1 

gt through wall; monolobed, 

hyaline germ shield 

(=orb) 

gt through wall; bi-lobed, 

hyaline, violin-shaped germ 

shield 

A, H 

A, H 

gt through wall; bi-lobed, 

brown, oval shield A, H 

gt through wall; brown germ 

shield with multiple small 

compartments 

gt through wall; brown 

germ shield with multiple 

compartments 

A, H 

A, H 


lobed, hyaline germ shield A, H 


lobed, hyaline germ shield A, H 

gt through wall; germ warts 

on inner spore wall layer A, H 

Multiply-lobed germ 

structure (Ac) & gt through 

hypha (Gl) 

V, A, H 

gt through wall; germ trunk 

(Ac), & gt through hypha 

(Gl)? 

A, H 

Unknown? 

A, H 

gt through hypha? Associated with 

cyanobacteria 

gt through wall 

A, H 


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ARTICLE 

Figs 2–11. Characteristic germination shields in Gigasporales with germ pore (gp) as connection between spore cell contents and shields that 

are positioned on the surface of the germinal wall; germ tubes emerge from germ tube initiations (gti). Fig. 2. Orbispora pernambucana (isotype, 

ZT Myc 641) with mono-lobed, hyaline germ shield (orb). Figs 3–4. Scutellospora calospora (photo taken at INVAM) and S. dipurpurescens 

(holotype OSC #83343) have bi-lobed, violin-shaped, hyaline shields. Figs 5–8. Racocetra coralloidea (type, OSC #31026), R. castanea (ex 

type, ZT Myc 4377), Cetraspora nodosa (isotype, DPP, Szczecin, Poland) and C. helvetica (isotype, ZT Myc 3038) have wavy-like, multiply 

lobed, hyaline shields. Figs 9–11. Dentiscutataceae shields are yellow brown to brown. Fig. 9. Dentiscutata reticulata (photo taken at INVAM) 

shields with multiple small compartments. Fig. 10. Quatunica erythropa (photo taken at INVAM) is assumed to be the only known species in 

Glomeromycota with four spore walls. Fig. 11. Fuscutata heterogama (ex type, ZT Myc 642) has a bi-lobed, oval to ovoid shield. 

196 ima fUNGUS


ARTICLE 

Figs 12–21. Characteristic spore bases and subtending hyphae (sh) in Glomeromycetes genera with glomoid spore formation. Figs 12–13. 

Glomus ambisporum (Oehl collection, from Bolivia) and G. aureum (type, ZT Myc 822) with two wall layers (SWL1 and SWL2), marked introverted 

wall thickening at sb and in sh, and a small, bridging septum (sp). Fig. 14. Funneliformis coronatus (ex type, Oehl collection) with funnelshaped 

sh and conspicuous sp; introverted wall thickening is lacking. Fig. 15. Septoglomus constrictum (Oehl collection, from Switzerland) with 

conspicuous septum that sometimes resembles a plug. Fig. 16. Simiglomus hoi (Oehl collection, specimen mounted at York university) with 

cylindrical sh; sh wall thickened over long distances; several septae are regularly observed within the hyphae; no introverted wall thickening 

at sb, pore at sb generally opened. Fig. 17. Claroideoglomus etunicatum (Oehl collection, from Bolivia) with funnel/bill-shaped, white sh; all 

Entrophosporaceae (syn. Claroideoglomeraceae) with characteristic color change of structural wall layer at sb, if spores are pigmented. Fig. 

18. Albahypha drummondii (type, DPP) with slightly funnel-shaped, white sh. Fig. 19. Viscospora viscosa (ex type, photo taken at INVAM) with 

cylindrical, white hypha; sp within sh in some distance of sb; introverted wall thickening of sh at sp position, here not that obvious as usually found 

for this species; viscose spore surface. Fig. 20. Diversispora versiformis with short, fragile sh that is principally continuous with semi-persistent 

outermost spore wall layer (SWL1) but not with structural layer SWL2 (Oehl collection, from Tibet). Fig. 21. Redeckera fulva (Oehl ex Trappe 

collection) with inflating sh and conspicuous broad sp exactly at spore base. 

In Diversisporales and Glomerales, 10 genera exclusively 

differentiate mono-walled, glomoid (9) or bi-walled pacisporoid 

(1) spores, all formed on subtending hyphae (Oehl & Sieverding 

2004, Oehl et al. 2011a). The morphological differentiation of 

the glomoid species is mainly based on the morphology of the 

subtending hyphae of the spores, and spore wall structure. 

Spores of Funneliformis, Glomus, Septoglomus, and Simiglomus 

species have subtending hyphae that are concolorous or slightly 

lighter in colour than the spore wall (Table 1, Figs 12–16). 

Albahypha, Claroideoglomus, and Viscospora form spores in 

which the structural wall layer is continuous with the subtending 

hyphal wall layer, but the subtending hyphae are hyaline (Figs 

17–19). In contrast, Diversispora and Redeckera form spores 

whose structural wall layer is not obviously continuous with 

the hyphal wall layer (Figs 20–21); consequently, such spores 

appear to have included ‘endospores’. 


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ARTICLE 

Funneliformis, Glomus, Septoglomus, and Simiglomus 

can be separated by the structure of the spore base and 

subtending hyphae (sh). Glomus species often have an 

introverted wall thickening (Oehl et al. 2011a; Figs 12–13) 

which is only otherwise seen in Viscospora. Funneliformis 

species generally have an easily visible septum in the area 

of the spore base, and their sh are regularly funnel-shaped to 

cylindrical (Fig. 14). Septoglomus species have constricted 

to cylindrical sh, and usually there is a septum at the spore 

base (Fig. 15). In Simiglomus, sh are cylindrical and thickwalled, 

and they have several septa some distance from the 

spore base (Fig. 16). Claroideoglomus has funnel- to birdbill-shaped 

sh, with sh and sh walls that are > 2.5 times wider 

at the spore base than some distance from the base (Fig. 

17). Albahypha has slightly funnel to bill-shaped sh and sh 

walls that are < 2.0 times wider at the spore base than at 

some distance from the base (Fig. 18), and Viscospora has 

cylindrical sh (Fig. 19) with an sh wall that may be thickened 

over large distances and may bear septa in the hyphae 

with introverted wall thickenings in the area of the septum. 

In Diversispora, the sh are usually quite fragile and hyaline, 

distal to the pore closure at the spore base or in the sh (Fig. 

20). Redeckera species have a broad septum at the spore 

base (Fig. 21), and the structural wall layer does not continue 

more than 5–15 µm into the subtending hypha, and thus, the 

sh may inflate at this distance from the spore base. 

There are three bi-morphic genera with glomoid spore 

formation. Glomo-ambisporoid spores have a subhyaline 

to ochraceous, evanescent outer wall layer continuous with 

the outer acaulo-ambisporoid spore wall, while the second, 

structural layer is hyaline and continuous with the middle wall 

of acaulo-ambisporoid spores (Spain et al. 2006, Palenzuela 

et al. 2011). Glomo-archaeosporoid and Glomo-intrasporoid 

spores are among the smallest within Glomeromycota (ca. 30 

µm), and thus difficult to observe. 

FURB, Santa Catarina State, Brazil), GINCO-BEL in Louvain- 

La-Neuve (Glomeromycota In Vitro Collection at the Catholic 

University of Louvain, Belgium), or SAF in Zurich (Swiss 

Collection of Arbsucular Mycorrhizal Fungi at Agroscope 

ART, Switzerland) will facilitate further progresses in the 

taxonomy of glomeromycotean fungi that were thought to 

have not enough criteria to morphologically separate them 

unequivocally into the higher level taxa they phylogenetically 

belong to. Currently, several arbuscular mycorrhizal fungi 

are being described as new to science each year by an 

increasing numbers of research groups. A simple, but well 

justified conclusion is that, as a result of future concomitant 

morphological and molecular analyses, yet more higher level 

taxa will be proposed in this ancient fungal phylum, at all 

levels from class down to genus. 

AcknowledgEments 

We acknowledge the help of many current and former students and 

technicians in Switzerland, Spain, and Brazil for outstanding support 

(especially David Schneider, Robert Bösch, Giacomo Busco, Louis 

Lawouin, Domingo Alvarez, Danielle Silva, Natália Sousa, and 

Daniele Magna). This study has been supported within the Swiss 

National Science Foundation (SNSF) Project 315230_130764/1, 

by the SNSF Programme NFP48 ‘Landscapes and habitats of the 

Alps’, by the Spanish Ministry of Environment (MMA-OAPN, project 

70/2005) and FAECA (Junta de Andalucía, Spain, Project 92162/11), 

and by the Fundação de Amparo à Ciência e Tecnologia do Estado 

de Pernambuco (FACEPE) and the UFPE which provided grants 

to F. Oehl as ‘visiting professor’, and FACEPE which also provided 

financial support for G.A. Silva. 

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ARTICLE 


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All submitted materials must be digitized and submitted electronically to d.hawksworth@nhm.ac.uk and p.crous@cbs.knaw.nl, with the 

manuscript ideally in Microsoft Word. Illustrations (Line drawings (600 dpi or higher) and half tone pictures (300 dpi or higher) should be 

submitted separately, never embedded in Word files. Phylogenetic trees will only be accepted when submitted as Powerpoint files, or in Adobe 

(never as pictures). 

The corresponding author should confirm that: (a) all named authors have agreed to publication of the work; and (b) the manuscript does not 

infringe any personal or other copyright or property rights. 

Papers cited as “in press” should be provided for the benefit of the referees. 

The content should be structured as follows: ABSTRACT, INTRODUCTION, MATERIALS AND METHODS, RESULTS, TAXON- 

OMY, DISCUSSION, ACKNOWLEDGEMENTS and REFERENCES. Key words and a Running Head should also be provided. 

English-English is preferred, and used for all non-article material. Authors of articles can use American-English, provided that it is consistent 

within their contributions. Words of non-English origin, like bona fide, prima facie, in vitro, in situ, should be placed in italic, together with 

scientific names of any rank (e.g. Ascomycota, Dothideales, Mycosphaerellaceae, Mycosphaerella nubilosa). 

Common abbreviations are as follows: h, min, s, mL, µL, mg/L, °C, Fig., d, wk, but also ITS, RPD, RFLP, rDNA, 18S etc. 

Authorities of fungal taxa should be omitted from the general text, unless novelties and synonymies are listed, or nomenclatural issues 

discussed. In these cases, authorities for taxa should follow the list of authors’ names, see http://www.speciesfungorum.org/AuthorsOf- 

FungalNames.htm, followed by the year of publication of the name. Journal abbreviations in the text (species synonymies, descriptions, 

etc.) should follow the International Plant Name Index (see http://www.ipni.org/index.html). 

Experimental procedures must be reproducible and must follow Good Cultural Practice (Mycological Research 106: 1378–1379), with 

sequences lodged at GenBank, alignments in TreeBASE, voucher specimens in a public reference collection recognized in Index, or another 

recognized in Index Herbariorum (online) or the World Directory of Collections and Cultures of Microorganisms (online), with acronym and accession 

numbers (where allocated), and ex-type and other representative cultures in long-term genetic resource depositaries or collections. For 

new scientific names a MycoBank number is required (see www.MycoBank.org), and should be obtained on acceptance for publication. 

Collections must be cited as: 

Specimens examined. Country: State/Province/County: location, substratum, date (e.g. 10 Dec. 1993), collector (e.g. S. Uper & F. Ungus) 

(COLLECTION ACRONYM and ACCESSION NUMBER -- holotypus; cultures ex-holotype COLLECTION ACRONYM(S) and 

ACCESSION NUMBER(S)). 

Reference citation in text: References in the text should be chronological, and given in the following form: “Smith & Jones (1965) have 

shown ...”, or, “some authors (Zabetta 1928, Taylor & Palmer 1970, Zabetta 1970) consider that ...”. The names of collaborating authors are 

joined by an ampersand (&). Where there are three or more authors, names should be cited by the first name only, adding “et al.”, e.g. “Bowie, 

Black & White (1964)” are given as “Bowie et al. (1964)” or “(Bowie et al. 1964)”. Where authors have published more than one work in a 

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citations in text should be in ascending order of year first, followed by authors’ names. Each reference should include the full title of the 

paper and journal, volume number, and the final as well as the first page number. In the case of chapters in books, the names of editors, first 

and last page numbers of the articles, publisher and place of publication are needed. 

Examples: 

Black JA, Taylor JE (1999a) Article title. Studies in Mycology 13: 1–10. 

Black JA, Taylor JE (In press) Article title. Fungal Biology. 

Black JA, Taylor JE, White DA (1981) Article title. In: Book Title (KA Seifert, W Jones & P. Jones, eds): 11–30. Town (and country if not 

well-known): Press. 

Simpson H, Seifert KA (2000) Book Title. 2nd edn. Town (and country if not well-known): Press. 

White DA (2001) Dissertation Title. PhD thesis, Department, University, Country. 

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INSTRUCTIONS TO AUTHORS 

EDITORIAL BOARD

Editorial 

One Fungus One Name: a plant pathologists’s view (39) 

News 

1000 fungal genomes to be sequenced – The Ug99 stem rust (Puccinia graminis) of wheat threatens global supplies 

– A DNA barcode for Fungi proposed for adoption – New world record for the largest fungal basidiome – International 

meetings planned to discuss fungal nomenclature – MycoKeys 

Reports 

Genomics in China – International Association for Lichenology (IAL) – XVI Congress of European Mycologists 

(CEM XVI) – 30 th ECCO Annual Meeting in Utrecht – Mycological Society of America – 20 th Nordic Mycological 

Congress (NMC 20) 

(41) 

(46) 

Awards and Personalia 

IMA Young Mycologist Awards 2011 (Ethel Mary Doidge Medal; Keisuke Tubaki Medal; Daniel McAlpine Medal; 

Arthur Henry Reginald Buller Medal) 

(52) 

Distinguished Asian Mycologist Award: Kevin Hyde (53) 

Birthday Greeting: Jiang-Chun Wei’s 80 th (54) 

In Memoriam: Aino Marjatta Henssen (1925–2011); Zang Mu (1930–2011) (55) 

Research News 

Horizontal Gene Transfer (HGT) from Fungi is the basis for plant pathogenicity in oomycetes (57) 

Fungal pathogens as a driver of tree species diversity in tropical forests (58) 

A new system for the arbuscular mycorrhizal fungi (Glomeromycota) (59) 

New insights into global fungal species numbers? (59) 

Powdery mildews under scrutiny (60) 

Book News (62) 

Forthcoming Meetings (67) 

Articles 

“One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR” by John W. Taylor 113 

“Penicillium menonorum, a new species related to P. pimiteouiense” by Stephen W. Peterson, Samantha S. Orchard, 121 

and Suresh Menon 

“What is Scirrhia?” by Pedro W. Crous, Andrew M. Minnis, Olinto L. Pereira, Acelino C. Alfenas, Rafael F. Alfenas, 127 

Amy Y. Rossman, and Johannes Z. Groenewald 

“A new species of Antherospora supports the systematic placement of its host plant” by Marcin Piątek, Matthias Lutz, 135 

Paul A. Smith, and Arthur O. Chater 

“Ascospore discharge, germination and culture of fungal partners of tropical lichens, including the use of a novel culture 

technique” by Ek Sangvichien, David L. Hawksworth, and Anthony J.S. Whalley 

143 

“A new dawn for the naming of fungi: impacts of decisions made in Melbourne in July 2011 on the future publication 155 

and regulation of fungal names” by David L. Hawksworth 

“The inclusion of downy mildews in a multi-locus-dataset and its reanalysis reveals a high degree of paraphyly in 

163 

Phytophthora” by Fabian Runge, Sabine Telle, Sebastian Ploch, Elizabeth Savory, Brad Day, Rahul Sharma, and 

Marco Thines 

“Validation and justification of the phylum name Cryptomycota phyl. nov.” by Meredith D.M. Jones, Thomas A. Richards, 

David L. Hawksworth, and David Bass 

173 

“Molecular techniques for pathogen identification and fungus detection in the environment” by Clement K.M. Tsui, 177 

James Woodhall, Wen Chen, C. André Lévesque, Anna Lau, Cor D. Schoen, Christiane Baschien, Mohammad 

Najafzadeh, and G. Sybren de Hoog 

“Advances in Glomeromycota taxonomy and classification” by Fritz Oehl, Ewald Sieverding, Javier Palenzuela, Kurt 191 

Ineichen, and Gladstone Alves da Silva

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