Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy

Abstract

The production of hydrogen and methane by geochemical reactions associated with the serpentinization of ultramafic rocks can potentially support subsurface microbial ecosystems independent of the photosynthetic biosphere. Methanogenic and methanotrophic microorganisms are abundant in marine hydrothermal systems heavily influenced by serpentinization, but evidence for methane-cycling archaea and bacteria in continental serpentinite springs has been limited. This report provides metagenomic and experimental evidence for active methanogenesis and methanotrophy by microbial communities in serpentinite springs of the Voltri Massif, Italy. Methanogens belonging to family Methanobacteriaceae and methanotrophic bacteria belonging to family Methylococcaceae were heavily enriched in three ultrabasic springs (pH 12). Metagenomic data also suggest the potential for hydrogen oxidation, hydrogen production, carbon fixation, fermentation, and organic acid metabolism in the ultrabasic springs. The predicted metabolic capabilities are consistent with an active subsurface ecosystem supported by energy and carbon liberated by geochemical reactions within the serpentinite rocks of the Voltri Massif.

Geochemical, biological and clumped isotopologue evidence for substantial microbial methane production under carbon limitation in serpentinites of the Samail Ophiolite, Oman

“…Literature values for c CO2 in ophiolitic Ca 2+ −OH − waters are often higher than those predicted by reaction path modeling, but the lower range of reported values approaches 1 µmol • L −1 (Barnes et al, 1967;Barnes & O'Neil, 1969;Barnes et al, 1978;Neal & Stanger, 1985;Bruni et al, 2002;Cipolli et al, 2004;A. N. Paukert et al, 2012;Falk et al, 2016;Brazelton et al, 2017;Canovas III et al, 2017;Crespo-Medina et al, 2017;Rempfert et al, 2017;Fones et al, 2019;Paukert Vankeuren et al, 2019). This spread in the data could reflect groundwater mixing, atmospheric contamination during sampling, differences in reaction temperature and progress, and/or kinetic inhibitions to carbonate mineral precipitation.…”

“…This notion is generally supported by our calculations in that formatotrophic methanogenesis had more negative ∆G r than hydrogenotrophic methanogenesis in all Ca 2+ −OH − conditions tested, whereas the reverse was true for the Mg 2+ − HCO − 3 case at 1 µmol • kg −1 H 2 .Remarkably, although acetoclastic methanogenesis had the most negative ∆G r of the investigated CH 4 -forming reactions (Table5), it has the least microbiological evidence of being a major methanogenic pathway in the Samail Ophiolite. Conversion of isotopically labeled acetate ( 13 CH 3 OO − ) to13 CH 4 , has, however, been documented in cultures from serpentinite springs in the Voltri Massif, Italy(Brazelton et al, 2017), indicating that acetoclastic methanogenesis can operate in some serpentinizing settings.In the aquifers sampled via wells in the Samail Ophiolite, methanogens may be out-competed for acquisition of acetate by other groups of microbes, such as sulfate reducers. Indeed, geochemical evidence of microbial acetate oxidation coupled to sulfate reduction has been reported in alkaline, H 2 -rich, crystalline rock aquifers inhabited by microbial communities dominated by sulfate reducing bacteria and methanogens(Moser et al, 2005).…”

Sulfide Dissolution and Awaruite Formation in Continental Serpentinization Environments and Its Implications to Supporting Life

“…Microbial communities are found within chimney structures of hydrothermal vent fields and as microbial mats and biofilms around vent sites (Brazelton et al., 2011; Lang & Brazelton, 2020). They have been inferred to thrive within the serpentinite basement rock (Alt & Shanks, 1998; Schwarzenbach, Gill, & Johnston, 2018) and have been identified in emanating vent fluids (Brazelton et al., 2006, 2017; Morrill et al., 2013; Zwicker et al., 2018). Notably, in continental systems, the availability of vitally important elements such as sodium and sulfate is very limited, and concentrations are significantly lower than in marine environments where these species are abundant in seawater, which may limit the habitability of continental serpentinization systems (Suzuki et al., 2013).…”

Spatial and temporal constraints on the composition of microbial communities in subsurface boreholes of the Edgar Experimental Mine

“…Terrestrial sites have increased our knowledge of where microbial ecosystems flourish, expanding to subsurface ultra-basic and high temperature serpentinized systems [9,10,11]. The terrestrial subsurface can offer more geologic and hydrologic variability compared to marine environments due to the presence of unconstrained fluid sourcing and lithology in surface soils and bedrock [7,[12][13][14].…”