Comment on "Abiotic controls on H2 production from basalt-water reactions and implications for aquifer biogeochemistry"

Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing

Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO₂ along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere.

Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.

Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution-derived hydrogen

The basal zone of glaciers is characterized by physicochemical properties that are distinct from firnified ice due to strong interactions with underlying substrate and bedrock. Basal ice (BI) ecology and the roles that the microbiota play in biogeochemical cycling, weathering, and proglacial soil formation remain poorly described. We report on basal ice geochemistry, bacterial diversity (16S rRNA gene phylogeny), and inferred ecological roles at three temperate Icelandic glaciers. We sampled three physically distinct basal ice facies (stratified, dispersed, and debris bands) and found facies dependent on biological similarities and differences; basal ice character is therefore an important sampling consideration in future studies. Based on a high abundance of silicates and Fe-containing minerals and, compared to earlier BI literature, total C was detected that could sustain the basal ice ecosystem. It was hypothesized that C-fixing chemolithotrophic bacteria, especially Fe-oxidisers and hydrogenotrophs, mutualistically support associated heterotrophic communities. Basal ice-derived rRNA gene sequences corresponding to genera known to harbor hydrogenotrophic methanogens suggest that silicate comminution-derived hydrogen can also be utilized for methanogenesis. PICRUSt-predicted metabolism suggests that methane metabolism and C-fixation pathways could be highly relevant in BI, indicating the importance of these metabolic routes. The nutrients and microbial communities release from melting basal ice may play an important role in promoting pioneering communities establishment and soil development in deglaciating forelands.

Lithogenic hydrogen supports microbial primary production in subglacial and proglacial environments

Life in environments devoid of photosynthesis, such as on early Earth or in contemporary dark subsurface ecosystems, is supported by chemical energy. How, when, and where chemical nutrients released from the geosphere fuel chemosynthetic biospheres is fundamental to understanding the distribution and diversity of life, both today and in the geologic past. Hydrogen (H₂) is a potent reductant that can be generated when water interacts with reactive components of mineral surfaces such as silicate radicals and ferrous iron. Such reactive mineral surfaces are continually generated by physical comminution of bedrock by glaciers. Here, we show that dissolved H₂ concentrations in meltwaters from an iron and silicate mineral-rich basaltic glacial catchment were an order of magnitude higher than those from a carbonate-dominated catchment. Consistent with higher H₂ abundance, sediment microbial communities from the basaltic catchment exhibited significantly shorter lag times and faster rates of net H₂ oxidation and dark carbon dioxide (CO₂) fixation than those from the carbonate catchment, indicating adaptation to use H₂ as a reductant in basaltic catchments. An enrichment culture of basaltic sediments provided with H₂, CO₂, and ferric iron produced a chemolithoautotrophic population related to Rhodoferax ferrireducens with a metabolism previously thought to be restricted to (hyper)thermophiles and acidophiles. These findings point to the importance of physical and chemical weathering processes in generating nutrients that support chemosynthetic primary production. Furthermore, they show that differences in bedrock mineral composition can influence the supplies of nutrients like H₂ and, in turn, the diversity, abundance, and activity of microbial inhabitants.

Visualizing Microorganism-Mineral Interaction in the Iberian Pyrite Belt Subsurface: The Acidovorax Case

Despite being considered an extreme environment, several studies have shown that life in the deep subsurface is abundant and diverse. Microorganisms inhabiting these systems live within the rock pores and, therefore, the geochemical and geohydrological characteristics of this matrix may influence the distribution of underground biodiversity. In this study, correlative fluorescence and Raman microscopy (Raman-FISH) was used to analyze the mineralogy associated with the presence of members of the genus Acidovorax, an iron oxidizing microorganisms, in native rock samples of the Iberian Pyrite Belt subsurface. Our results suggest a strong correlation between the presence of Acidovorax genus and pyrite, suggesting that the mineral might greatly influence its subsurface distribution.

Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India

Archaeal community structure and potential functions within the deep, aphotic, oligotrophic, hot, igneous provinces of ∼65 Myr old basalt and its Archean granitic basement was explored through archaeal 16S rRNA gene amplicon sequencing from extracted environmental DNA of rocks. Rock core samples from three distinct horizons, basaltic (BS), transition (weathered granites) (TZ) and granitic (GR) showed limited organic carbon (4–48 mg/kg) and varied concentrations (<1.0–5000 mg/kg) of sulfate, nitrate, nitrite, iron and metal oxides. Quantitative PCR estimated the presence of nearly 10³–10⁴ archaeal cells per gram of rock. Archaeal communities within BS and GR horizons were distinct. The absence of any common OTU across the samples indicated restricted dispersal of archaeal cells. Younger, relatively organic carbon- and Fe₂O₃-rich BS rocks harbor Euryarchaeota, along with varied proportions of Thaumarchaeota and Crenarchaeota. Extreme acid loving, thermotolerant sulfur respiring Thermoplasmataceae, heterotrophic, ferrous-/H-sulfide oxidizing Ferroplasmaceae and Halobacteriaceae were more abundant and closely interrelated within BS rocks. Samples from the GR horizon represent a unique composition with higher proportions of Thaumarchaeota and uneven distribution of Euryarchaeota and Bathyarchaeota affiliated to Methanomicrobia, SAGMCG-1, FHMa11 terrestrial group, AK59 and unclassified taxa. Acetoclastic methanogenic Methanomicrobia, autotrophic SAGMCG-1 and MCG of Thaumarcheaota could be identified as the signature groups within the organic carbon lean GR horizon. Sulfur-oxidizing Sulfolobaceae was relatively more abundant in sulfate-rich amygdaloidal basalt and migmatitic gneiss samples. Methane-oxidizing ANME-3 populations were found to be ubiquitous, but their abundance varied greatly between the analyzed samples. Changes in diversity pattern among the BS and GR horizons highlighted the significance of local rock geochemistry, particularly the availability of organic carbon, Fe₂O₃ and other nutrients as well as physical constraints (temperature and pressure) in a niche-specific colonization of extremophilic archaeal communities. The study provided the first deep sequencing-based illustration of an intricate association between diverse extremophilic groups (acidophile-halophile-methanogenic), capable of sulfur/iron/methane metabolism and thus shed new light on their potential role in biogeochemical cycles and energy flow in deep biosphere hosted by hot, oligotrophic igneous crust.

Subsurface Microbial Hydrogen Cycling: Natural Occurrence and Implications for Industry

Hydrogen is a key energy source for subsurface microbial processes, particularly in subsurface environments with limited alternative electron donors, and environments that are not well connected to the surface. In addition to consumption of hydrogen, microbial processes such as fermentation and nitrogen fixation produce hydrogen. Hydrogen is also produced by a number of abiotic processes including radiolysis, serpentinization, graphitization, and cataclasis of silicate minerals. Both biotic and abiotically generated hydrogen may become available for consumption by microorganisms, but biotic production and consumption are usually tightly coupled. Understanding the microbiology of hydrogen cycling is relevant to subsurface engineered environments where hydrogen-cycling microorganisms are implicated in gas consumption and production and corrosion in a number of industries including carbon capture and storage, energy gas storage, and radioactive waste disposal. The same hydrogen-cycling microorganisms and processes are important in natural sites with elevated hydrogen and can provide insights into early life on Earth and life on other planets. This review draws together what is known about microbiology in natural environments with elevated hydrogen, and highlights where similar microbial populations could be of relevance to subsurface industry.

Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India

Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.

Abiotic formation of condensed carbonaceous matter in the hydrating oceanic crust

Thermodynamic modeling has recently suggested that condensed carbonaceous matter should be the dominant product of abiotic organic synthesis during serpentinization, although it has not yet been described in natural serpentinites. Here we report evidence for three distinct types of abiotic condensed carbonaceous matter in paragenetic equilibrium with low-temperature mineralogical assemblages hosted by magma-impregnated, mantle-derived, serpentinites of the Ligurian Tethyan ophiolite. The first type coats hydroandraditic garnets in bastitized pyroxenes and bears mainly aliphatic chains. The second type forms small aggregates (~2 µm) associated with the alteration rims of spinel and plagioclase. The third type appears as large aggregates (~100–200 µm), bearing aromatic carbon and short aliphatic chains associated with saponite and hematite assemblage after plagioclase. These assemblages result from successive alteration at decreasing temperature and increasing oxygen fugacity. They affect a hybrid mafic-ultramafic paragenesis commonly occurring in the lower oceanic crust, pointing to ubiquity of the highlighted process during serpentinization.

Thermodynamic calculations suggest that condensed carbonaceous matter should be the dominant product of abiotic organic synthesis during serpentinization of the oceanic crust at Mid-Ocean Ridges. Here the authors report natural occurrences of such carbonaceous matter formed during low temperature alteration.

Influence of CO2 Degassing on the Microbial Community in a Dry Mofette Field in Hartoušov, Czech Republic (Western Eger Rift)

The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO₂ in mofette fields. The Hartoušov mofette field shows a daily CO₂ flux of 23-97 tons of CO₂ released over an area of 0.35 km² and a soil gas concentration of up to 100% CO₂. The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO₂ concentrations on the geochemistry and microbial community of soils and sediments. To sample the strata, two 3-m cores were recovered. One core stems from the center of the degassing structure, whereas the other core was taken 8 m from the ENE and served as an undisturbed reference site. The sites were compared regarding their geochemical features, microbial abundances, and microbial community structures. The mofette site is characterized by a low pH and high TOC/sulfate contents. Striking differences in the microbial community highlight the substantial impact of elevated CO₂ concentrations and their associated side effects on microbial processes. The abundance of microbes did not show a typical decrease with depth, indicating that the uprising CO₂-rich fluid provides sufficient substrate for chemolithoautotrophic anaerobic microorganisms. Illumina MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences microbial composition and explains around 38.7% of the variance at the mofette site and 22.4% of the variance between the mofette site and the undisturbed reference site. Accordingly, acidophilic microorganisms (e.g., OTUs assigned to Acidobacteriaceae and Acidithiobacillus) displayed a much higher relative abundance at the mofette site than at the reference site. The microbial community at the mofette site is characterized by a high relative abundance of methanogens and taxa involved in sulfur cycling. The present study provides intriguing insights into microbial life and geo-bio interactions in an active seismic region dominated by emanating mantle-derived CO₂-rich fluids, and thereby builds the basis for further studies, e.g., focusing on the functional repertoire of the communities. However, it remains open if the observed patterns can be generalized for different time-points or sites.

Hydrogen Utilization Potential in Subsurface Sediments

Subsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material. We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i) increasing importance of fermentation in successively deeper biogeochemical zones and (ii) adaptation of H₂ases to successively higher concentrations of H₂ in successively deeper zones.

Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem

The geochemical energy budgets for high-temperature microbial ecosystems such as occur at Yellowstone National Park have been unclear. To address the relative contributions of different geochemistries to the energy demands of these ecosystems, we draw together three lines of inference. We studied the phylogenetic compositions of high-temperature (>70 degrees C) communities in Yellowstone hot springs with distinct chemistries, conducted parallel chemical analyses, and carried out thermodynamic modeling. Results of extensive molecular analyses, taken with previous results, show that most microbial biomass in these systems, as reflected by rRNA gene abundance, is comprised of organisms of the kinds that derive energy for primary productivity from the oxidation of molecular hydrogen, H2. The apparent dominance by H2-metabolizing organisms indicates that H2 is the main source of energy for primary production in the Yellowstone high-temperature ecosystem. Hydrogen concentrations in the hot springs were measured and found to range up to >300 nM, consistent with this hypothesis. Thermodynamic modeling with environmental concentrations of potential energy sources also is consistent with the proposed microaerophilic, hydrogen-based energy economy for this geothermal ecosystem, even in the presence of high concentrations of sulfide.