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

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.