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.
Highlights
Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches
To obtain a detailed view of oleaginous mixed microbial communities (OMMCs) (Supplementary Fig. 1a) lipid accumulation and bacterial composition, we first applied coupled metabolomics and 16S rRNA gene sequencing to samples taken over space and time
Using gas chromatography coupled to tandem mass spectrometry (GC-MS/MS), absolute quantifications of the 14 major long-chain fatty acids were obtained for OMMC biomass and wastewater, respectively (Methods)
Summary
Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. We have recently developed the required laboratory methods that enable us to isolate representative biomolecular fractions (DNA, RNA, proteins and small molecules) from single microbial community samples[12,13] We expand this concept by performing integrated omic analyses of purified biomolecular fractions from oleaginous mixed microbial communities (OMMCs) located on the surface of an anoxic biological wastewater treatment tank to study how microbial lifestyle strategies relate to ecological success and the associated community-level phenotypes in this fluctuating but wellcharacterized environment. Building on the recently developed methodologies for the systematic molecular characterization of microbial consortia[12,13], and for resolving and reconstructing populationlevel genomic complements from community-wide sequence data[16], here, we integrate multi-omic data sets to resolve microbial lifestyle strategies in situ, identify finely tuned gene expression governing resource usage by a dominant bacterial generalist population and reveal that genetic variation within this population is constrained likely due to fitness trade-offs
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
