Inoculum 63(3) - Mycological Society of America

Zea mays is, arguably, the most economically important grass domesticated
by man. Yet, few studies have examined and fully characterized the fungal
root endophyte community inhabiting the belowground portion of the plant. Taxonomic
molecular identification of fungal species based upon the internal transcribed
spacer (ITS) region of rDNA obtained from roots reveal soil as a prominent
factor determining the composition of microfungal communities within the
roots of maize (Zea mays subsp. mays, previously fully sequenced variety B73)
and its progenitor, teosinte (Zea mays subsp. parviglumis), grown in Missouri clay
soil or Missouri clay soil mixed with desert soil from New Mexico. Fungal communities
in maize and teosinte grown in mixed soils were dominated by different
proportions of Hypocreales spp. and dark septate endophytes (Pleosporales spp.,
and Sordariales spp., primarily) while those grown only in Missouri clay soils
were dominated by Glomerales spp. Moreover, fungal communities colonizing
roots of Z. mays differed significantly from those colonizing roots of native (and
co-habiting) fescue grass (Festuca arundinacea). Interestingly, Pleosporean sequences
also include Paraphaeosphaeria spp., one of the dominant and common
fungal species described in various grass species across North America. The presence
of such cosmopolitan fungal root endophytes suggests that some fungal associations
are general in nature and could function as evolutionary hinges that
help plants develop adaptations to a variety of environmental challenges.
Hess, Jaqueline 1 , Inger Skrede 2 , and Anne Pringle 1 . 1 Department of Organismic
and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge,
MA 02130, 2 Microbial Evolution Research Group (MERG), Department of Biology,
University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway.
Transposable element dynamics in ectomycorrhizal genomes: a close-up
perspective
Ectomycorrhizal (ECM) symbiosis between plants and fungi has evolved
several times in the Fungal Kingdom. Ongoing genome sequencing of ectomycorrhizal
(ECM) fungi is increasing the understanding of the genetic mechanisms
central to the evolution of the symbiosis. Besides changes in gene content and
gene family sizes, differences in genome architecture are also apparent, likely
caused by changes in the ecology and population dynamics of ECM fungi. A
common feature of ECM genomes sequenced to date is greatly elevated transposable
element (TE) content: approximately 20% of the genome of Laccaria bicolor
and 60% of the genome of Tuber melamsporum is made up of TEs. The
genus Amanita encompasses an evolutionary transition from a free-living, saprotrophic
to ECM niche and provides a powerful model for interrogating genome
evolution across closely related, ecologically distinct species. To investigate
changes in TE dynamics after evolution of the ECM niche we used next generation
sequencing technologies to shotgun sequence the genomes of five species,
covering the major clades of the genus Amanita (three ECMs and two saprotrophs)
and the saprotrophic outgroup species Volvariella volvacea. We found the
ECM genome sizes to be expanded, ranging from one and a half to nearly double
the size compared to the saprotrophic genomes. Here, we will present our informatics
approach for TE detection from short read data and fragmented assemblies
and discuss the patterns of TE invasion in the different ECM clades of Amanita.
Hicks, Sarah L 1 , Emily Farrer 2 , Robert Sinsabaugh 1 , Andrea Porras-Alfaro 1,3 ,
and Katherine N Suding 2 . 1 Biology Dept, University of New Mexico, MSC03
2020 1 University of New Mexico Albuquerque, NM 87105, 2 Environmental
Science, Policy & Management University of California at Berkeley Berkeley,
CA 94720, 3 Department of Biological Sciences Western Illinois University 1
University Circle Waggoner Hall 372 Macomb, IL 61455. Effect of nitrogen
pollution on root fungal endophyte communities from two co-dominant
alpine tundra plants at Niwot, LTER
Due to pollution from Boulder and Denver, CO, Nitrogen (N) deposition
is increasing at Niwot Ridge, LTER. Over the last decade, one of the co-dominant
alpine tundra plants, Geum rossii, has experienced substantial dieback, while the
other co-dominant, Deschampsia caespitosa, gains dominance. G. rossii dieback
has been attributed to elevated soil N rather than inter-species competition. The
mechanism by which N kills G. rossii is still unknown. We hypothesize elevated
soil N causes shifts in endophytic fungal communities, and that these shifts are responsible
for G. rossii death. We expect G. rossii communities to become more
pathogenic and parasitic in response to N. G. rossii and D. caespitosa roots were
sampled from N-addition and control plots. Samples were surface sterilized prior
to DNA extraction and 454 titanium pyrosequencing of fungal ITS ribosomal
DNA. Sequences were clustered into OTUs by 97% similarity in Qiime. OTU
correlation with N was assessed with ANOVA and community composition correlation
with N was assessed with RDA, using the nlme and vegan packages in R
respectively. G. rossii endophyte communities only clustered by N treatment at
species level. Community shifts occurred among closely related species, and most
sensitive taxa responded to N positively, including taxa that belong to pathogenic
groups. Deschampsia caespitosa communities clustered by N at all taxonomic
levels, and community shifts occurred between distantly related species, so that
whole fungal Classes responded to N. Most affected taxa responded negatively.
22 Inoculum 63(3), June 2012
These data indicate that endophyte communities of D. caespitosa and G. rossii respond
substantially differently to N addition. Deschampsia caespitosa endophyte
communities appear to change more fundamentally. These changes may be important
to D. caespitosa’s ability to adapt to changing nutrients. If so, these data
may provide insight into the mechanisms by which abiotic soil factors alter above
ground vegetation dynamics.
Hobbie, Erik A. Earth Systems Research Center, University of New Hampshire,
Durham, New Hampshire, USA. Assessing fungivory in rodents, marsupials,
and kiwi from stable isotope evidence
Fungivory is both a common dispersal mechanism for many fungi and an
important source of nutrients and energy for many small animals, particularly rodents
and marsupials. Studies of fungivory generally rely on scat or gut content
analyses. An alternate technique, stable isotope measurements on animal protein,
relies on sporocarps of ectomycorrhizal fungi having distinctive carbon and nitrogen
isotope ratios ( 13 C/ 12 C and 15 N/ 14 N, expressed as d 13 C and d 15 N) compared
to other ecosystem components. This approach allows retrospective studies
by using archived museum specimens; here, I present three case studies of this approach.
In studies of western Oregon rodents, mean isotopic values for the five
sampled taxa separate into three main groups, with creeping vole and red tree vole
quite similar (low in d 13 C and d 15 N, herbivorous), red-backed vole and flying
squirrel similar (high in d13C and d15N, indicating high levels of fungivory), and
Douglas squirrel different from the other two groupings (high in d 13 C, low in
d 15 N, probably primarily a seed-eater). In ten genera of Australian marsupials,
potoroos and bettongs appeared highly fungivorous, as expected from prior dietary
studies. Kiwi in New Zealand may perform the same dispersal function for
truffles as small mammals do elsewhere. Kiwis were isotopically distinct from
frugivorous and insectivorous birds, but truffle consumption probably cannot be
distringuished isotopically from consumption of soil invertebrates. Isotopic analysis
appears to be a potentially useful tool to determine levels of fungivory in historic
and current animal populations.
Hodgins-Davis, Andrea 1 , Aleksandra Adomas 2 , Daniel Rice 3 , and Jeffrey
Townsend 1 . 1 Department of Ecology and Evolutionary Biology, Yale University,
New Haven, CT 06520, 2 National Institute of Environmental Health Sciences,
Research Triangle Park, NC 27709, 3 Department of Organismic and Evolutionary
Biology, Harvard University, Cambridge, MA 02138. Modelling transcriptional
reaction norm evolution in the model yeast Saccharomyces cerevisiae
Genetic variation for plastic phenotypes has the potential to contribute a
large proportion of the phenotypic variation available to selection for novel adaptation.
Models for linking population variation with plasticity make predictions
about how selection may constrain the evolution of gene expression variation
across transcriptional reaction norms. To empirically test these models, we have
characterized population variation for transcriptional reaction norms in Saccharomyces
cerevisiae for an ecologically relevant gradient of copper concentrations
from starvation to toxicity. We find that although the vast majority of transcriptional
variation is small in magnitude, not just some, but most genes demonstrate
variable expression across environments or genetic backgrounds. Functionally,
the most highly expressed genes defined three distinct cellular states across the
copper reaction norm consistent with previous results characterizing eukaryotic
responses to copper starvation, copper-replete fermentation, and copper overdose.
These cellular states included direct transcriptional responses to intracellular levels
of copper ions and diverse indirect metabolic adjustments to the consequences
of changed copper levels. Indirect homeostatic changes of expression were more
variable among genotypes in their direction of response than were the reaction
norms of genes directly regulated by copper-binding transcription factors. To interpret
this variability in transcriptional reaction norms in the context of the
processes of natural selection and neutral drift, we account for variation in mutation
and regulatory degree across the genome by parameterizing classic models of
phenotypic evolution. Empirically estimating population genetic variance, mutational
variance, and regulatory degree, we infer the strength of stabilizing selection
operating on gene expression levels. We present evidence consistent with either
weak or infrequent stabilizing selection on most gene expression phenotypes,
and discuss the implications of the lack of constraint for the evolvability of transcriptional
reaction norms.
Hodkinson, Brendan P 1 and James C Lendemer 2 . 1 International Plant Science
Center, The New York Botanical Garden, 2900 Southern Blvd., Bronx, NY
10458-5126, 2 Institute of Systematic Botany, The New York Botanical Garden,
2900 Southern Blvd., Bronx, NY 10458-5126. A modern, high-throughput
workflow for biodiversity research integrating floristics, taxonomy, phylogeny,
ecology and conservation
Continued on following page