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 - 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 -