Reference : Integration of time-series meta-omics data reveals how microbial ecosystems respond t...

	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Microbiology
	To cite this reference:	http://hdl.handle.net/10993/45372

Title :	Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance
Language :	English
Author, co-author :	Herold, Malte [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; Epidemiology and Microbial Genomics, Laboratoire National de Santé, Luxembourg]
	Martinez Arbas, Susana [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
	Narayanasamy, Shaman [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > > > > ; Megeno S.A., Luxembourg]
	Sheik, Abdul R. [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)]
	Kleine-Borgmann, Luise A. K. [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)]
	Lebrun, Laura [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
	Kunath, Benoît [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
	Roume, Hugo [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > > > > ; MetaGenoPolis, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Université Paris-Saclay, Domaine de Vilvert, Bâtiment 325, 78350 Jouy-en-Josas, France]
	Bessarab, Irina [Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Dr, Singapore 637551, Singapore.]
	Williams, Rohan B. H. [Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Dr, Singapore 637551, Singapore.]
	Gillece, John D. [The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ 86001, USA]
	Schupp, James M. [The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ 86001, USA]
	Keim, Paul S. [The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ 86001, USA]
	Jäger, Christian [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Scientific Central Services >]
	Hoopman, Michael R. [Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA]
	Moritz, Robert L. [Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA]
	Ye, Yuhzen [School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA]
	Li, Sujun [School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA]
	Tang, Haixu [School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA]
	Heintz-Buschart, Anna [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > > > > ; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany > > > ; Helmholtz Centre for Environmental Research GmbH – UFZ, Theodor-Lieser-Str. 4, 06120 Halle, Germany]
	May, Patrick [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core >]
	Muller, Emilie E. L. [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > > > > ; Equipe Adaptations et Interactions Microbiennes, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France]
	Laczny, Cedric Christian [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
	Wilmes, Paul [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
Publication date :	19-Oct-2020
Journal title :	Nature Communications
Publisher :	Nature Publishing Group
Peer reviewed :	Yes (verified by ORBilu)
e-ISSN :	2041-1723
City :	London
Country :	United Kingdom
Keywords :	[en] activated sludge ; wastewater ; lipid accumulating organisms ; metagenomics ; metatranscriptomics ; metaproteomics ; meta-metabolomics ; time series ; ecological niche
Abstract :	[en] The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.
Permalink :	http://hdl.handle.net/10993/45372
DOI :	10.1038/s41467-020-19006-2

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