Thermochronologic perspectives on the deep-time evolution of the deep biosphere

Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden

The continental bedrock contains groundwater-bearing fractures that are home to microbial populations that are vital in mediating the Earth's biogeochemical cycles. However, their diversity is poorly understood due to the difficulty of obtaining samples from this environment. Here, a groundwater-bearing fracture at 975 m depth was isolated by employing packers in order to characterize the microbial community via metagenomes combined with prokaryotic and eukaryotic marker genes (16S and 18S ribosomal RNA gene). Genome-resolved analyses revealed a community dominated by sulfate-reducing Bacillota, predominantly represented by Candidatus Desulforudis audaxviator and with Wood-Ljungdahl as the most prevalent pathway for inorganic carbon fixation. Moreover, the eukaryotic community had a considerable diversity and was comprised of mainly flatworms, chlorophytes, crustaceans, ochrophytes, and fungi. These findings support the important role of the Bacillota, with the sulfate reducer Candidatus Desulforudis audaxviator as its main representative, as primary producers in the often energy-limited groundwaters of the continental subsurface.

Radiolytic support for oxidative metabolism in an ancient subsurface brine system

Long-isolated subsurface brine environments (Ma-Ga residence times) may be habitable if they sustainably provide substrates, e.g. through water-rock reactions, that support microbial catabolic energy yields exceeding maintenance costs. The relative inaccessibility and low biomass of such systems has led to limited understanding of microbial taxonomic distribution, metabolism, and survival under abiotic stress exposure in these extreme environments. In this study, taxonomic and metabolic annotations of 95 single-cell amplified genomes were obtained for one low biomass (103-104 cells/ml), hypersaline (246 g/L), and radiolytically enriched brine obtained from 3.1 km depth in South Africa's Moab Khotsong mine. The majority of single-cell amplified genomes belonged to three halophilic families (Halomondaceae (58%), Microbacteriaceae (24%), and Idiomarinaceae (8%)) and did not overlap with any family-level identifications from service water or a less saline dolomite aquifer sampled in the same mine. Functional annotation revealed complete metabolic modules for aerobic heterotrophy (organic acids and xenobiotic oxidation), fermentation, denitrification, and thiosulfate oxidation, suggesting metabolic support in a microoxic environment. Single-cell amplified genomes also contained complete modules for degradation of complex organics, amino acid and nucleotide synthesis, and motility. This work highlights a long-isolated subsurface fluid system with microbial metabolism fueled by radiolytically generated substrates, including O2, and suggests subsurface brines with high radionuclide concentrations as putatively habitable and redox-sustainable environments over long (ka-Ga) timescales.