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-BuschartPatrick May, Emilie E.L. Muller, Cedric C. Laczny, Paul Wilmes

Research output: Contribution to journalArticlepeer-review

46 Scopus citations


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.

Original languageEnglish (US)
Article number5281
JournalNature Communications
Issue number1
StatePublished - Dec 1 2020

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy


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