Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

Muller, Emilie L.; Pinel, Nicolás; Laczny, Cédric C.; Hoopmann, Michael R.; Narayanasamy, Shaman; Lebrun, Laura A.; Roume, Hugo; Lin, Jake; May, Patrick; Hicks, Nathan D.; Heintz-Buschart, Anna; Wampach, Linda; Liu, Cindy M.; Price, Lance B.; Gillece, John D.; Guignard, Cédric; Schupp, James M.; Vlassis, Nikos; Baliga, Nitin S.; Moritz, Robert L.; Keim, Paul S.; Wilmes, Paul

doi:10.1038/ncomms6603

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

Journal Article · Wed Nov 26 00:00:00 EST 2014 · Nature Communications

DOI:https://doi.org/10.1038/ncomms6603· OSTI ID:1797290

Muller, Emilie L. ^[1]; Pinel, Nicolás ^[2]; Laczny, Cédric C. ^[1]; Hoopmann, Michael R. ^[3]; Narayanasamy, Shaman ^[1]; Lebrun, Laura A. ^[1]; Roume, Hugo ^[1]; Lin, Jake ^[1]; May, Patrick ^[1]; Hicks, Nathan D. ^[4]; Heintz-Buschart, Anna ^[1]; Wampach, Linda ^[1]; Liu, Cindy M. ^[4]; Price, Lance B. ^[4]; Gillece, John D. ^[4]; Guignard, Cédric ^[5]; Schupp, James M. ^[4]; Vlassis, Nikos ^[1]; Baliga, Nitin S. ^[3]; Moritz, Robert L. ^[3] more »

Univ. of Luxembourg, Esch-sur-Alzette, (Luxembourg). Luxembourg Center for Systems Biomedicine
Univ. of Luxembourg, Esch-sur-Alzette, (Luxembourg). Luxembourg Center for Systems Biomedicine; Institute for Systems Biology, Seattle, WA (United States)
Institute for Systems Biology, Seattle, WA (United States)
TGen North, Falstaff, AZ (United States)
Centre de Recherche Public-Gabriel Lippmann, Belvaux (Luxembourg)

Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: Luxembourg National Research Fund; National Institutes of Health (NIH); National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1797290

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 5; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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