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

Emilie E. L. Muller, Nicolás Pinel, Cédric C. Laczny, Michael R. Hoopmann, Shaman Narayanasamy, Laura A. Lebrun, Hugo Roume, Jake Lin, Patrick May, Nathan D. Hicks, Anna Heintz-Buschart, Linda Wampach, Cindy M. Liu, Lance B. Price, John D. Gillece, Cédric Guignard, James M. Schupp, Nikos Vlassis, Nitin S. Baliga, Robert L. Moritz, Paul S. Keim and Paul Wilmes ()
Additional contact information
Emilie E. L. Muller: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Nicolás Pinel: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Cédric C. Laczny: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Michael R. Hoopmann: Institute for Systems Biology
Shaman Narayanasamy: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Laura A. Lebrun: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Hugo Roume: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Jake Lin: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Patrick May: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Nathan D. Hicks: TGen North
Anna Heintz-Buschart: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Linda Wampach: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Cindy M. Liu: TGen North
Lance B. Price: TGen North
John D. Gillece: TGen North
Cédric Guignard: Centre de Recherche Public-Gabriel Lippmann
James M. Schupp: TGen North
Nikos Vlassis: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Nitin S. Baliga: Institute for Systems Biology
Robert L. Moritz: Institute for Systems Biology
Paul S. Keim: TGen North
Paul Wilmes: Luxembourg Centre for Systems Biomedicine, University of Luxembourg

Nature Communications, 2014, vol. 5, issue 1, 1-10

Abstract: Abstract 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.

Date: 2014
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DOI: 10.1038/ncomms6603

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