25th International Meeting on Organic Geochemistry IMOG 2011

P-444
Isolating and cultivating environmentally relevant microorganisms
as reference point for linking phylogeny to activity in
situ based on biomarker lipids
Marcel van der Meer 1 , Christian Klatt 2 , Jason Wood 2 , Donald Bryant 4 , Mary Bateson 2 ,
Laurens Lammerts 1 , Stefan Schouten 1 , Jaap Sinninghe Damste 1 , Michael Madigan 3 ,
David Ward 2
1 NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands, 2 Montana State University,
Bozeman, United States of America, 3 Southern Illinois University, Carbondale, United States of America,
4 The Pennsylvania State University, University Park, United States of America (corresponding
author:Marcel.van.der.Meer@nioz.nl)
Biomarker lipids and their stable carbon
isotope ratios, both natural abundance and from
labelling studies, have been a useful tool in linking
activity to phylogeny in situ. However, the
interpretation of the sources of biomarker lipids in
natural environments is strongly relying on culturebased
information and cultivated isolates are often not
representative of the micro-organisms actual present
in the environment, according to molecular
microbiology studies.
For example, in the past we have made
inferences about the activity of green nonsulfur
bacteria present in hot spring microbial mats based
on the stable carbon isotope ratios of C30-C35 wax
esters found in hot spring microbial mats (1). Similar,
but not identical, wax ester distributions had been
reported for cultivated Chloroflexus spp. (2). However,
phylogenetic analysis of especially the microbial mats
in low sulfide systems indicated that Chloroflexus spp.
only form a very small fraction of the green nonsulfur
bacteria in situ (3). The closest cultivated relative of
the majority of the green nonsulfur bacteria in these
mats is Roseiflexus castenholzii (4), an organism that
produces completely different wax esters than those
found the Yellowstone hot spring microbial mats (5).
This raises the question how valid the inferences are
based on biomarker distributions of green nonsulfur
bacteria that are only a minor component of the
microbial mat.
In this study we were able to isolate and
cultivate Roseiflexus spp. strains from a microbial mat
of an alkaline siliceous hot spring in Yellowstone
National Park. These strains are genetically closely
related to predominant green nonsulfur bacteria found
in the mat, as judged by the high similarity of smallsubunit
rRNA, and genomic and metagenomic
sequences. Like R. castenholzii, the Yellowstone
isolates contain bacteriochlorophyll a, but not
bacteriochlorophyll c or chlorosomes, and grow
photoheterotrophically or chemoheterotrophically
under dark aerobic conditions. The genome of one
isolate, Roseiflexus sp. strain RS1 contains genes
necessary to support these metabolisms. This
genome also contains genes encoding the 3hydroxypropionate
pathway for CO2 fixation and a
hydrogenase, which might enable photoautotrophic
metabolism, even though neither isolate could be
grown photoautotrophically with H2 or H2S as a
possible electron donor. The isolates exhibit
temperature, pH, and sulfide preferences typical of
their habitat. Importantly, the wax esters produced by
these isolates, C30-C35 straight and iso-branched,
match much better with those found in the
Yellowstone mats than wax esters produced by R.
castenholzii or Chloroflexus isolates (see Fig.1).
Our study thus shows that there is a need for
environmentally relevant microbial isolates as
reference organisms for molecular and lipid
biomarkers studies in linking phylogeny to activity.
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Leeuw, D. M. Ward, Env. Microbiol. 2, 428 (2000).
2. J. Shiea, S. C. Brassell, D. M. Ward, Org.
Geochem. 17, 309 (1991).
3. U. Nübel, M. M. Bateson, V. Vandieken, M. Kühl,
D. M. Ward, Appl. Environ. Microbiol. 68, 4593
(2002).
4. S. Hanada, S. Takaichi, K. Matsuura, K. Nakamura,
Int. J. Syst. Evol. Microbiol. 52, 187 (2002).
5. M. T. J. van der Meer et al., Arch. Microbiol. 178,
229 (2002)
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