title: 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.
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Emilie E L
authors.initials: EE
authors.lastname: Muller
authors.affiliation: 1] Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg [2] Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA.
authors.forename: Nicolás
authors.initials: N
authors.lastname: Pinel
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Cédric C
authors.initials: CC
authors.lastname: Laczny
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Hoopmann
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Shaman
authors.initials: S
authors.lastname: Narayanasamy
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Laura A
authors.initials: LA
authors.lastname: Lebrun
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Hugo
authors.initials: H
authors.lastname: Roume
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Jake
authors.initials: J
authors.lastname: Lin
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Patrick
authors.initials: P
authors.lastname: May
authors.affiliation: TGen North, 3051 West Shamrell Boulevard, Flagstaff, Arizona 86001, USA.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Hicks
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Anna
authors.initials: A
authors.lastname: Heintz-Buschart
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Linda
authors.initials: L
authors.lastname: Wampach
authors.affiliation: TGen North, 3051 West Shamrell Boulevard, Flagstaff, Arizona 86001, USA.
authors.forename: Cindy M
authors.initials: CM
authors.lastname: Liu
authors.affiliation: TGen North, 3051 West Shamrell Boulevard, Flagstaff, Arizona 86001, USA.
authors.forename: Lance B
authors.initials: LB
authors.lastname: Price
authors.affiliation: TGen North, 3051 West Shamrell Boulevard, Flagstaff, Arizona 86001, USA.
authors.forename: John D
authors.initials: JD
authors.lastname: Gillece
authors.affiliation: Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, L-4422 Belvaux, Luxembourg.
authors.forename: Cédric
authors.initials: C
authors.lastname: Guignard
authors.affiliation: TGen North, 3051 West Shamrell Boulevard, Flagstaff, Arizona 86001, USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Schupp
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Nikos
authors.initials: N
authors.lastname: Vlassis
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA.
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.affiliation: TGen North, 3051 West Shamrell Boulevard, Flagstaff, Arizona 86001, USA.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Keim
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Paul
authors.initials: P
authors.lastname: Wilmes
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D017753:Ecosystem; D023281:Genomics; D040901:Proteomics; D062065:Wastewater / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins; D062065:Wastewater