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

By Karthik Anantharaman, C. Brown, L. Hug, Itai Sharon, C. Castelle, Alexander J. Probst, Brian C. Thomas, Andrea Singh, M. Wilkins, U. Karaoz and 4 more. Nature Communications, 2016

997 citations recorded by the source corpus.

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. Microorganisms from the terrestrial subsurface are understudied. Here, Anantharamanet al. analyse aquifer sediments and groundwater by genome-resolved metagenomics and reconstruct 2,540 genomes representing the majority of known bacterial phyla as well as 47 new phylum-level lineages.

Subfields: Ecology, Environmental Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d3925ae37c07c905543dd5f957c41ca22b3f2777

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Citations in the corpus

Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT (2019, neutral): “Because assembly and binning can be done de novo, these questions can be applied to organisms that have never been seen before, and the discovery of entirely novel phyla is common still [8].”
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