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

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.

SUBMITTER: Muller EE

PROVIDER: S-EPMC4263124 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

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

Muller Emilie E L EE Pinel Nicolás N Laczny Cédric C CC Hoopmann Michael R MR Narayanasamy Shaman S Lebrun Laura A LA Roume Hugo H Lin Jake J May Patrick P Hicks Nathan D ND Heintz-Buschart Anna A Wampach Linda L Liu Cindy M CM Price Lance B LB Gillece John D JD Guignard Cédric C Schupp James M JM Vlassis Nikos N Baliga Nitin S NS Moritz Robert L RL Keim Paul S PS Wilmes Paul P

Nature communications 20141126

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 com ...[more]

PMID: 25424998

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

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

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