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Composition, Structure, and Function of Oxygenic and Anoxygenic Photosynthetic
Mat Communities in Yellowstone National Park
The Ward lab primarily studies cyanobacterial mat communities common
in alkaline siliceous hot springs in Yellowstone National Park. Earlier
studies revealed cyanobacterial (Synechococcus spp.) and green
nonsulfur bacteria-like (Roseiflexus spp.) 16S rRNA variants
different from and much more diverse than the cyanobacteria and filamentous
bacteria that can be readily cultivated from the mat. Many of these
genetic variants were closely related, yet exhibited different distributions
along temperature and light gradients, suggesting that each was a distinct
ecological population (ecotype). Temperature adaptation studies
of genetically relevant Synechococcus isolates demonstrated
that these closely related variants do have distinct temperature adaptations. Cases
in which ecologically distinct populations have identical 16S rRNA sequences
prompted higher-resolution approaches to detect ecotypes. We are
currently collaborating with colleagues from Wesleyan, The Carnegie Institution
(Stanford) and The Institute for Genome Research to conduct high resolution
population genetics analyses of mat Synechococcus genetic diversity
to determine whether diversity among individuals is organized into species-like
clusters with distinct ecological properties. We have determined
the genomic sequences of two Synechococcus isolates with distinct
temperature adaptations; comparison to mat metagenomic sequences reveals
that these genomes are highly representative of about 35-40% of the genes
in the mat community. We are using variation in protein-encoding
gene homologs of Synechococcus native to the mat and theory-based
population genetics analysis to identify putative Synechococcus ecotypes. We
have shown the in situ expression of individual Synechococcus genes
over a diel cycle and will be able to use single-gene and microarray
methods we are developing to test whether putative ecotypes have the
properties of true ecotypes.
The Ward lab is also focused on understanding the relationship between
mat cell component biomarkers and the community members that contribute
them to mats build by cyanobacteria and anoxygenic phototrophs. The
goal is to understand how biomarkers and isotopic signatures in
fossilized mats (stromatolites) should be interpreted. Through
collaboration with organic geochemists we have developed a lipid biomarker
database for relevant mat cyanobacteria and filamentous anoxygenic phototrophic
bacteria (e.g., Chloroflexus and Roseiflexus) . We
have used compound-specific isotope ratio monitoring to evaluate how
photosynthesis (and fermentation) by these kinds of community members
influences the stable carbon isotope signatures in the mat. In
collaboration with a colleague from Penn State, we have obtained the
genome sequence for a Roseiflexus isolate genetically relevant
to mat populations. We will test hypotheses resulting from lipid
biomarker observations using in situ gene expression studies. We
are also characterizing new anoxygenic phototrophs revealed by metagenome
analyses.
Current Laboratory Personnel
Natsuko Hamamura, Postdoctoral Associate
Eric Becraft, Ph.D. Student
Christian Klatt, Ph.D. Student
Melanie Melendrez, Ph.D. Student
Mary Bateson, Laboratory Manager
The Ward research group
Recent Publications:
Ward, D.M., F.M. Cohan, D. Bhaya, J.F. Heidelberg, M. Kühl and A. Grossman. 2008.
Genomics, environmental genomics and the issue of microbial species. Heredity 100:207-219.
Steunou, A.-S., S.I. Jensen, E. Brecht, E.D. Becraft, M. M. Bateson, O. Kilian, D. Bhaya, D. M. Ward, , J.W. Peters, A.R. Grossman and M. Kühl. 2008. Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat. ISME J. 2:364-378.
Koeppel, A, E.B. Perry, J. Sikorski, D. Krizanc, A. Warner, D.M. Ward, A.P. Rooney, E. Brambilla, N. Connor, E. Nevo, R.M. Ratcliff, and F.M. Cohan. 2008. Identifying the fundamental units of bacterial diversity:a paradigm shift to incorporate ecological diversification into bacterial systematics, Proc. Natl. Acad. Sciences, USA) 105:2504-2509.
Bhaya, D., A.R. Grossman, A.-S. Steunou, N. Khuri, F.M. Cohan, N.Hamamura, M.C. Melendrez, W. Nelson, M.M. Bateson, D.M. Ward and John F. Heidelberg. 2007. Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses. ISME J. 1:703-713.
Bryant, D.A.,A M. Garcia Costas, J. A. Maresca, A.Gomez Maqueo Chew, C.G. Klatt, M.M. Bateson, L.J. Tallon, J. Hostetler, W.C. Nelson, J.F. Heidelberg and D.M. Ward. 2007 Candidatus Chloracidobacterium thermophilum: An Aerobic Phototrophic Acidobacterium. Science 317:523-526.
Klatt, C.G., D.A. Bryant and D.M. Ward. 2007. Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats. Environ. Microbiol. 9:2067-2078.
van der Meer, M.T.J., S. Schouten, J.S. Sinninghe Damsté and D.M. Ward 2007. Impact of carbon metabolisms on 13C signatures of cyanobacteria and green nonsulfur-like bacteria inhabiting a microbial mat from an alkaline siliceous hot spring in Yellowstone National Park (USA) Environ. Microbiol. 9:482–491
Ward, D.M., M.M. Bateson, M.J. Ferris, M. Kühl, A. Wieland, A. Koeppel and F.M. Cohan. 2006. Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function. Phil. Trans. Royal Soc., London (Ser. B) 361:1997-2008.
Steunou, A.-S., D. Bhaya, M. M. Bateson, M.C. Melendrez, D. M. Ward, E. Brecht, J.W. Peters, M. Kühl and A.R. Grossman. 2006. In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats, Proc. Natl. Acad. Sci., U.S.A 103:2398-2403
Ward, D.M. 2006. A macrobiological perspective on microbial species. Microbe 1:269-278.
Collaborators:
Isaac Klapper, Montana State Univ.
Bill Inskeep, Montana State Univ.
Laurey Steinke, Univ. of Nebraska Med. Ctr., Omaha
Don Bryant, Pennsylvania State University
Fred Cohan, Wesleyan University
Doug Rusch, J. Craig Venter Institute
John Heidelberg, Univ. So. California
Michael Kühl, Univ. Copenhagen
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