TY - JOUR
T1 - Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance
AU - Herold, Malte
AU - Martínez Arbas, Susana
AU - Narayanasamy, Shaman
AU - Sheik, Abdul R.
AU - Kleine-Borgmann, Luise A.K.
AU - Lebrun, Laura A.
AU - Kunath, Benoît J.
AU - Roume, Hugo
AU - Bessarab, Irina
AU - Williams, Rohan B.H.
AU - Gillece, John D.
AU - Schupp, James M.
AU - Keim, Paul S.
AU - Jäger, Christian
AU - Hoopmann, Michael R.
AU - Moritz, Robert L.
AU - Ye, Yuzhen
AU - Li, Sujun
AU - Tang, Haixu
AU - Heintz-Buschart, Anna
AU - May, Patrick
AU - Muller, Emilie E.L.
AU - Laczny, Cedric C.
AU - Wilmes, Paul
N1 - Funding Information:
We thank 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. We also thank Dr. Olivia Judson for her feedback on the title and abstract. 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 INTER programme grant (INTER/SYSAPP/14/05), two CORE programme grants (C15/SR/10404839, C17/SR/11689322), and a PRIDE doctoral training unit grant (PRIDE15/10907093) to P.W., and a grant to A.R.S (PDR-2013-1/5748561) all funded by the Luxembourg National Research Fund (FNR). As one of the authors (A.R.S.) holds a position at the European Commission the following applies: “The views expressed are purely those of the writer and may not in any circumstances be regarded as stating an official position of the European Commission.”
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-020-19006-2
DO - 10.1038/s41467-020-19006-2
M3 - Article
C2 - 33077707
AN - SCOPUS:85092768177
SN - 2041-1723
VL - 11
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 5281
ER -