Abstract
The subsurface biosphere is a massive repository of fixed carbon, harboring approximately 90% of Earth’s microbial biomass. These microbial communities drive transformations central to Earth’s biogeochemical cycles. However, there is still much we do not understand about how complex subterranean microbial communities survive and how they interact with these cycles. Recent metagenomic investigation of deeply circulating terrestrial subsurface fluids revealed the presence of several novel lineages of bacteria. In one particular example, phylogenomic analyses do not converge on any one previously identified taxon; here we describe the first full genomic sequences of a new bacterial lineage within the candidate phylum Hydrogenedentes, ‘Candidatus Abyssubacteria.’ A global survey revealed that members of this proposed lineage are widely distributed in both marine and terrestrial subsurface environments, but their physiological and ecological roles have remained unexplored. Two high quality metagenome assembled genomes (SURF_5: 97%, 4%; SURF_17: 91% and 4% completeness and contamination, respectively) were reconstructed from fluids collected 1.5 kilometers below surface in the former Homestake gold mine—now the Sanford Underground Research Facility (SURF)—in Lead, South Dakota, United States. Metabolic reconstruction suggests versatile metabolic capability, including possible nitrogen reduction, sulfite oxidation, sulfate reduction and homoacetogenesis. This first glimpse into the metabolic capabilities of these cosmopolitan bacteria suggests that they are involved in key geochemical processes, including sulfur, nitrogen, and carbon cycling, and that they are adapted to survival in the dark, often anoxic, subsurface biosphere.
Highlights
The subsurface biosphere is devoid of light and is often extremely carbon and energylimited, it is home to the vast majority of Earth’s microbes, as much as 90% by the most recent estimates (Whitman et al, 1998; Kallmeyer et al, 2012; Mcmahon and Parnell, 2014; Parkes et al, 2014; Bar-On et al, 2018)
We present the phylogenetic and metabolic analysis of the first two genomes of a novel bacterial lineage that was recently identified in the deep terrestrial subsurface (Momper et al, 2017a)
Of the metagenomic data combined with differentialcoverage based binning methods yielded near-complete recovery of two novel, distinct genomes: SURF_5 and SURF_17 (97 and 91% completeness, respectively, both with 4% contamination)
Summary
The subsurface biosphere is devoid of light and is often extremely carbon and energylimited, it is home to the vast majority of Earth’s microbes, as much as 90% by the most recent estimates (Whitman et al, 1998; Kallmeyer et al, 2012; Mcmahon and Parnell, 2014; Parkes et al, 2014; Bar-On et al, 2018). Turnover of carbon, nitrogen, and sulfur reservoirs in the subsurface biosphere. Newly identified microbial lineages are commonly implicated in major geochemical cycles (Rasigraf et al, 2014; Baker et al, 2016). It follows that there is substantial metabolic diversity yet to be discovered within the marine and terrestrial subsurface ecosystems. To better describe and model the microbial networks that catalyze carbon, nitrogen, and sulfur cycling in the subsurface, we need to incorporate newly identified microbial lineages along with their metabolic capabilities
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