@article{f6b7c0cb8e1d43c48dd2683b6e0243cf,
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.",
author = "Muller, {Emilie E.L.} and Nicol{\'a}s Pinel and Laczny, {C{\'e}dric C.} and Hoopmann, {Michael R.} and Shaman Narayanasamy and Lebrun, {Laura A.} and Hugo Roume and Jake Lin and Patrick May and Hicks, {Nathan D.} and Anna Heintz-Buschart and Linda Wampach and Liu, {Cindy M.} and Price, {Lance B.} and Gillece, {John D.} and C{\'e}dric Guignard and Schupp, {James M.} and Nikos Vlassis and Baliga, {Nitin S.} and Moritz, {Robert L.} and Keim, {Paul S.} and Paul Wilmes",
note = "Funding Information: We thank the scientists and technical staff of the Luxembourg Centre for Systems Biomedicine and TGen North, particularly Dr Ren{\'e} Hussong and Dr Owain Moss for their assistance and support; Mr Bissen and Mr Di Pentima from the Syndicat Intercommunal {\`a} Vocation Ecologique (SIVEC), for their permission to collect samples and access to the monitoring platform of the Schifflange wastewater treatment plant; Jo{\"e}lle Fritz, Sheri Simmons and Rudi Balling for their comments on the manuscript. Bioinformatic analyses presented in this paper were carried out using the high-performance computing facilities of the University of the Luxembourg. This work was supported by an ATTRACT programme grant (ATTRACT/A09/03) and a European Union Joint Programming in Neurodegenerative Diseases grant (INTER/JPND/12/01) both to P.W., and Aide {\`a} la Formation Recherche (AFR) grants to H.R. (PHD/MARP-04), C.C.L. (PHD/4964712), S.N. (PHD-2014-1/7934898), L.W. (PHD-2013-1/BM) and E.E.L.M. (PRD-2011-1/SR), all funded by the Luxembourg National Research Fund (FNR). The project received financial support from the Integrated Biobank of Luxembourg with funds from the Luxembourg Ministry of Higher Education and Research. The work of N.P., J.L. and P.M. was funded by the {\textquoteleft}Plan Technologies de la Sant{\'e} du Gouvernement du Grand-Duch{\'e} de Luxembourg{\textquoteright} through the Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg. The work was also, in part, supported by US federal funds from the National Science Foundation (MRI grant No. 0923536), by funds from the National Institutes of Health and by funds from the US National Institute of General Medical Sciences (grant No. 2P50 GM076547/Center for Systems Biology and S10RR027584) to R.L.M. and M.R.H. Publisher Copyright: {\textcopyright} 2014 Macmillan Publishers Limited. All rights reserved.",
year = "2014",
month = nov,
day = "26",
doi = "10.1038/ncomms6603",
language = "English (US)",
volume = "5",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
}