Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance

Malte Herold, Susana Martínez Arbas, Shaman Narayanasamy, Abdul R. Sheik, Luise A. K. Kleine-Borgmann, Laura A. Lebrun, Benoît J. Kunath, Hugo Roume, Irina Bessarab, Rohan B. H. Williams, John D. Gillece, James M. Schupp, Paul S. Keim, Christian Jäger, Michael R. Hoopmann, Robert L. Moritz, Yuzhen Ye, Sujun Li, Haixu Tang, Anna Heintz-Buschart, Patrick May, Emilie E. L. Muller, Cedric C. Laczny and Paul Wilmes ()
Additional contact information
Malte Herold: University of Luxembourg
Susana Martínez Arbas: University of Luxembourg
Shaman Narayanasamy: University of Luxembourg
Abdul R. Sheik: University of Luxembourg
Luise A. K. Kleine-Borgmann: University of Luxembourg
Laura A. Lebrun: University of Luxembourg
Benoît J. Kunath: University of Luxembourg
Hugo Roume: University of Luxembourg
Irina Bessarab: Singapore Centre for Environmental Life Sciences Engineering
Rohan B. H. Williams: Singapore Centre for Environmental Life Sciences Engineering
John D. Gillece: The Translational Genomics Research Institute
James M. Schupp: The Translational Genomics Research Institute
Paul S. Keim: The Translational Genomics Research Institute
Christian Jäger: University of Luxembourg
Michael R. Hoopmann: Institute for Systems Biology
Robert L. Moritz: Institute for Systems Biology
Yuzhen Ye: Indiana University
Sujun Li: Indiana University
Haixu Tang: Indiana University
Anna Heintz-Buschart: University of Luxembourg
Patrick May: University of Luxembourg
Emilie E. L. Muller: University of Luxembourg
Cedric C. Laczny: University of Luxembourg
Paul Wilmes: University of Luxembourg

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: Abstract 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.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19006-2

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DOI: 10.1038/s41467-020-19006-2

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