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

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.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

“…1). They are more complete than those typically derived using single-cell genomics 4 and are of similar quality to those reported in other studies considering MAGs 10,11,44 . We have focused on these genomes, which represent only ~12% of the 64,295 recovered bins, as they are of sufficient quality to inform analyses such as resolving phylogenetic relationships 4,30 and comparing inter-and intralineage genomic features [45][46][47] .…”

“…Although these approaches continue to provide valuable reference genomes, the former is restricted to microorganisms amenable to cultivation and the latter is hampered by technical challenges and the need for specialised equipment 9 . Obtaining genomes from metagenomes is an emerging approach with the potential for large-scale recovery of near-complete genomes [10][11][12] .…”

“…Nearly 8,000 draft-quality genomes were recovered from over 1,500 metagenomes, more than a threefold increase over large initiatives to genomically populate the tree of life such as the Genomic Encyclopedia of Bacteria and Archaea 35 (~2,000 genomes), the Human Microbiome Project 3 (~2,000) and the largest previous MAG study 11 (~2,500). We refer to our set of MAGs as the Uncultivated Bacteria and Archaea (UBA) data set.…”

New CRISPR–Cas systems from uncultivated microbes

“…We hypothesized that other distinct types of effector proteins might exist within uncultivated microbes whose genomes were reconstructed from our metagenomic datasets. Indeed, a new type of class 2 CRISPR-Cas system was found in the genomes of two bacteria recovered from groundwater and sediment samples 26 . This system includes Cas1, Cas2, Cas4 and an uncharacterized ~980 aa protein that we refer to as CasX.…”

“…For the AMD data, DNA extraction methods and short read sequencing were reported by Denef and Banfield (2012) 36 and Miller et al (2011) 37 . For the Rifle data, DNA extraction, sequencing, assembly, and genome reconstruction were described by Anantharaman et al (2016) 26 and Brown et al (2015) 6 . For samples from Crystal Geyser, methods follow those described by Probst et al (2016) 38 and Emerson et al (2016) 39 .…”