Genomic Description of ‘Candidatus Abyssubacteria,’ a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes

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.

A Comparative Analysis of Aquatic and Polyethylene-Associated Antibiotic-Resistant Microbiota in the Mediterranean Sea

“…Chlamydiae, known as human obligate intracellular pathogens, were found only in one freshwater sample [ 51 ], while some phyla, i.e., Dadabacteria and Hydrogenedentes, only in seawater PE wastes. Our results confirm those obtained by recent studies on Dadabacteria, considered as cosmopolitan bacteria of the marine environment [ 52 ] and Hydrogenedentes, assumed as putative organic carbon degraders, potentially hydrolyzing carbon compounds such as phthalates, of which plastics are made of [ 53 ].…”

“…The exceeding presence of ca. 250,000 tons [ 53 ] of plastic constitute another possible carrier of ARGs. This represents an alarming aspect concerning the marine pollution caused by this debris since the actual amount of plastic is strongly underestimated due to the absence of microplastics in the above-reported quantification [ 54 ].…”

Contrasting Variable and Stable Subsurface Microbial Populations: an ecological time series analysis from the Deep Mine Microbial Observatory, South Dakota, USA

“…Early efforts in this sphere revealed strong gradients in microbial taxa with depth (Pedersen, 2001;Haveman and Pedersen, 2002), unusual monophyletic communities (Chivian et al, 2008), and stark differences between attached and planktonic biomass (Pedersen, 1996;Lehman et al, 2001). More recent applications of second and third generation sequencing technologies have expanded on these results, revealing vast diversity of subsurface taxa particularly in uncultivated groups and spatial separation of populations with depth and between aquifers (Anantharaman et al, 2016;Jungbluth et al, 2016;Probst et al, 2017;Momper, Jungbluth, Lee, and Amend, 2017a;Probst et al, 2018), as well as key as genomic adaptations in deep intraterrestrials (Lau et al, 2016;Momper et al, 2018).…”

Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer

“…Instead, these environments are home to their own endemic, uncultivated, and previously unknown organisms such as the aptly named Deep Sea Archaeal Group, novel branches of Chloroflexi, or Candidate Phyla (Takai et al, 2001;Inagaki et al, 2006;Jørgensen and Boetius, 2007;Osburn et al, 2014). The terrestrial deep biosphere, accessed via boreholes or mines, has proven especially fruitful for the discovery of novel microbial diversity, including from the site in this study (Figure 1; Chivian et al, 2008;Sahl et al, 2008;Teske and Sørensen, 2008;Breuker et al, 2011;Osburn et al, 2014;Momper et al, 2017Momper et al, , 2018Sackett, 2018;Sackett et al, 2019). Little is known, however, about the changes in deep subsurface systems of yearly or longer timescales.…”