Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer

Abstract

Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable. IMPORTANCE This study describes the potential metabolic pathways by which microbial communities in a serpentinite-influenced aquifer may produce biomass from the products of serpentinization. Serpentinization is a widespread geochemical process, taking place over large regions of the seafloor and at continental margins, where ancient seafloor has accreted onto the continents. Because of the difficulty in delineating abiotic and biotic processes in these environments, major questions remain related to microbial contributions to the carbon cycle and physiological adaptation to serpentinite habitats. This research explores multiple mechanisms of carbon fixation and assimilation in serpentinite-hosted microbial communities.

A dynamic microbial sulfur cycle in a serpentinizing continental ophiolite

“…MAG data for thiosulfate oxidation pathways discussed here show that MAGs for Hydrogenophaga in CSWold host the complete pathway for thiosulfate oxidation via SOX, whereas two MAGs related to the Rhodobacteraceae host partial SOX pathways (Seyler et al ., ). Populations within the genera Dethiobacter (Clostridia) identified by PhyloPythiaS+ are likely to mediate thiosulfate disproportionation, as these capabilities have been recorded in recent genome sequencing and physiological studies of these taxa (Sorokin et al ., ; Poser et al ., ; Melton et al ., ).…”

“…Metagenome-assembled genomes (MAGs) created from these data (described and reported extensively in Seyler et al, 2020) show that the capability to mediate different sulfur metabolisms was segregated into different taxonomic groups. Of the most abundant organisms in CSWold (Supporting Information Table S9), three MAGs within the Clostridiales, related to the Candidate genus Desulforudis, contained genes associated with the key components of the dissimilatory sulfate reduction pathways, dsrAB and aprAB.…”

“…The arguments – metagenome and – proteins were used with Prokka v.1.12 (Seemann, ) to indicate that genes should be predicted with the implementation of Prodigal v.2.6.2 (Hyatt et al ., ) optimized for metagenomes as described by Twing et al ., . All details for MAG assembly and datasets are reported in the methods of Seyler and colleagues ().…”

Biogeochemical Gradients in a Serpentinization‐Influenced Aquifer: Implications for Gas Exchange Between the Subsurface and Atmosphere

“…These bins were compared to MAG bins from Seyler et al (2020) (bins 105, 148, 151, 243, 244) and complete genomes of Dethiobacter alkaliphilus, Desulfotomaculum hydrothermale, Natranaerobius thermophilus, and Carboxydothermus hydrogenoformans (Figure 5). Dethiobacter bins 105-244 ranged in completion from 54%-94%, and 1.5%-4.3% contamination (Seyler et al, 2020 With this information, a conceptual diagram was created to visualize the relationships between these dominant genera and model the biogeochemical interactions occurring (Figure 6).…”

“…Similarly, work by Twing et al (2017) showed pH, CO, and CH 4 best explained the variability in bacterial community composition across the site, with positive correlations between both Dethiobacter and members of the Comamonadaceae family to CH 4 (p ≤ 0.05). Metagenomic data and metagenome assembled genomes (MAGs) from the CROMO fluids provided evidence for carbon fixation pathways such as CH 4 oxidation to formaldehyde, the Calvin-Benson-Bassham cycle (CBB), and the reductive acetyl coenzyme A (acetyl-CoA; Wood-Ljungdahl) pathway (Seyler et al, 2020).…”