Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

TLDR

The subterranean world hosts up to one-fifth of all biomass, with microbial communities driving key biogeochemical transformations, yet little is known about their structure and inter‑organism interactions. The study applies terabase‑scale cultivation‑independent metagenomics to aquifer sediments and groundwater to reconstruct 2,540 strain‑resolved genomes covering most known bacterial phyla and 47 novel phylum‑level lineages. Metabolic analyses across this diversity, covering up to 36 % of detected organisms, document pathway distributions among coexisting organisms. Few organisms perform multiple sequential redox transformations, and shifts in environmental conditions select different assemblages, thereby altering linkages among major biogeochemical cycles.

Abstract

Abstract The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth’s biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.