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 journalArticle

40 Citations (Scopus)

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.

Original languageEnglish (US)
Article number5603
JournalNature Communications
Volume5
DOIs
StatePublished - Nov 26 2014
Externally publishedYes

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Gene expression
Wastewater treatment
Large scale systems
resources
Bacteria
Dynamical systems
Lipids
Metagenomics
Biota
Metabolomics
Workflow
Waste Water
Population Density
Proteomics
Life Style
phenotype
fitness
gene expression
complex systems
Phenotype

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemistry(all)
  • Physics and Astronomy(all)

Cite this

Muller, E. E. L., Pinel, N., Laczny, C. C., Hoopmann, M. R., Narayanasamy, S., Lebrun, L. A., ... Wilmes, P. (2014). Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nature Communications, 5, [5603]. https://doi.org/10.1038/ncomms6603

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. / Muller, Emilie E 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.

In: Nature Communications, Vol. 5, 5603, 26.11.2014.

Research output: Contribution to journalArticle

Muller, EEL, Pinel, N, Laczny, CC, Hoopmann, MR, Narayanasamy, S, Lebrun, LA, Roume, H, Lin, J, May, P, Hicks, ND, Heintz-Buschart, A, Wampach, L, Liu, CM, Price, LB, Gillece, JD, Guignard, C, Schupp, JM, Vlassis, N, Baliga, NS, Moritz, RL, Keim, PS & Wilmes, P 2014, 'Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage', Nature Communications, vol. 5, 5603. https://doi.org/10.1038/ncomms6603
Muller EEL, Pinel N, Laczny CC, Hoopmann MR, Narayanasamy S, Lebrun LA et al. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nature Communications. 2014 Nov 26;5. 5603. https://doi.org/10.1038/ncomms6603
Muller, Emilie E 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. / Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. In: Nature Communications. 2014 ; Vol. 5.
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