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. MoritzPaul S. Keim, Paul Wilmes

Research output: Contribution to journalArticlepeer-review

64 Scopus citations


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.

Original languageEnglish (US)
Article number5603
JournalNature Communications
StatePublished - Nov 26 2014

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy


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