A global perspective on bacterial diversity in the terrestrial deep subsurface.

While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

86Kr excess and other noble gases identify a billion-year-old radiogenically-enriched groundwater system.

Deep within the Precambrian basement rocks of the Earth, groundwaters can sustain subsurface microbial communities, and are targets of investigation both for geologic storage of carbon and/or nuclear waste, and for new reservoirs of rapidly depleting resources of helium. Noble gas-derived residence times have revealed deep hydrological settings where groundwaters are preserved on millions to billion-year timescales. Here we report groundwaters enriched in the highest concentrations of radiogenic products yet discovered in fluids, with an associated 86Kr excess in the free fluid, and residence times >1 billion years. This brine, from a South African gold mine 3 km below surface, demonstrates that ancient groundwaters preserved in the deep continental crust on billion-year geologic timescales may be more widespread than previously understood. The findings have implications beyond Earth, where on rocky planets such as Mars, subsurface water may persist on long timescales despite surface conditions that no longer provide a habitable zone.

Earth-like Habitable Environments in the Subsurface of Mars.

In Earth's deep continental subsurface, where groundwaters are often isolated for >106 to 109 years, energy released by radionuclides within rock produces oxidants and reductants that drive metabolisms of non-photosynthetic microorganisms. Similar processes could support past and present life in the martian subsurface. Sulfate-reducing microorganisms are common in Earth's deep subsurface, often using hydrogen derived directly from radiolysis of pore water and sulfate derived from oxidation of rock-matrix-hosted sulfides by radiolytically derived oxidants. Radiolysis thus produces redox energy to support a deep biosphere in groundwaters isolated from surface substrate input for millions to billions of years on Earth. Here, we demonstrate that radiolysis by itself could produce sufficient redox energy to sustain a habitable environment in the subsurface of present-day Mars, one in which Earth-like microorganisms could survive wherever groundwater exists. We show that the source localities for many martian meteorites are capable of producing sufficient redox nutrients to sustain up to millions of sulfate-reducing microbial cells per kilogram rock via radiolysis alone, comparable to cell densities observed in many regions of Earth's deep subsurface. Additionally, we calculate variability in supportable sulfate-reducing cell densities between the martian meteorite source regions. Our results demonstrate that martian subsurface groundwaters, where present, would largely be habitable for sulfate-reducing bacteria from a redox energy perspective via radiolysis alone. We present evidence for crustal regions that could support especially high cell densities, including zones with high sulfide concentrations, which could be targeted by future subsurface exploration missions.

Hydrothermal 15N15N abundances constrain the origins of mantle nitrogen.

Nitrogen is the main constituent of the Earth's atmosphere, but its provenance in the Earth's mantle remains uncertain. The relative contribution of primordial nitrogen inherited during the Earth's accretion versus that subducted from the Earth's surface is unclear1-6. Here we show that the mantle may have retained remnants of such primordial nitrogen. We use the rare 15N15N isotopologue of N2 as a new tracer of air contamination in volcanic gas effusions. By constraining air contamination in gases from Iceland, Eifel (Germany) and Yellowstone (USA), we derive estimates of mantle δ15N (the fractional difference in 15N/14N from air), N2/36Ar and N2/3He. Our results show that negative δ15N values observed in gases, previously regarded as indicating a mantle origin for nitrogen7-10, in fact represent dominantly air-derived N2 that experienced 15N/14N fractionation in hydrothermal systems. Using two-component mixing models to correct for this effect, the 15N15N data allow extrapolations that characterize mantle endmember δ15N, N2/36Ar and N2/3He values. We show that the Eifel region has slightly increased δ15N and N2/36Ar values relative to estimates for the convective mantle provided by mid-ocean-ridge basalts11, consistent with subducted nitrogen being added to the mantle source. In contrast, we find that whereas the Yellowstone plume has δ15N values substantially greater than that of the convective mantle, resembling surface components12-15, its N2/36Ar and N2/3He ratios are indistinguishable from those of the convective mantle. This observation raises the possibility that the plume hosts a primordial component. We provide a test of the subduction hypothesis with a two-box model, describing the evolution of mantle and surface nitrogen through geological time. We show that the effect of subduction on the deep nitrogen cycle may be less important than has been suggested by previous investigations. We propose instead that high mid-ocean-ridge basalt and plume δ15N values may both be dominantly primordial features.

New ecosystems in the deep subsurface follow the flow of water driven by geological activity.

Eukarya have been discovered in the deep subsurface at several locations in South Africa, but how organisms reach the subsurface remains unknown. We studied river-subsurface fissure water systems and identified Eukarya from a river that are genetically identical for 18S rDNA. To further confirm that these are identical species one metazoan species recovered from the overlying river interbred successfully with specimen recovered from an underlying mine at -1.4 km. In situ seismic simulation experiments were carried out and show seismic activity to be a major force increasing the hydraulic conductivity in faults allowing organisms to create ecosystems in the deep subsurface. As seismic activity is a non-selective force we recovered specimen of algae and Insecta that defy any obvious other explanation at a depth of -3.4 km. Our results show there is a steady flow of surface organisms to the deep subsurface where some survive and adapt and others perish. As seismic activity is also present on other planets and moons in our solar system the mechanism elucidated here may be relevant for future search and selection of landing sites in planetary exploration.

Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability.

The concentrations of electron donors and acceptors in the terrestrial subsurface biosphere fluctuate due to migration and mixing of subsurface fluids, but the mechanisms and rates at which microbial communities respond to these changes are largely unknown. Subsurface microbial communities exhibit long cellular turnover times and are often considered relatively static-generating just enough ATP for cellular maintenance. Here, we investigated how subsurface populations of CH4 oxidizers respond to changes in electron acceptor availability by monitoring the biological and geochemical composition in a 1339 m-below-land-surface (mbls) fluid-filled fracture over the course of both longer (2.5 year) and shorter (2-week) time scales. Using a combination of metagenomic, metatranscriptomic, and metaproteomic analyses, we observe that the CH4 oxidizers within the subsurface microbial community change in coordination with electron acceptor availability over time. We then validate these findings through a series of 13C-CH4 laboratory incubation experiments, highlighting a connection between composition of subsurface CH4 oxidizing communities and electron acceptor availability.

Hydrogen Isotopic Composition of Arctic and Atmospheric CH4 Determined by a Portable Near-Infrared Cavity Ring-Down Spectrometer with a Cryogenic Pre-Concentrator.

In this study, near-infrared continuous wave cavity ring-down spectroscopy was applied to the measurement of the δ2H of methane (CH4). The cavity ring-down spectrometer (CRDS) system consisted of multiple DFB laser diodes to optimize selection of spectral line pairs. By rapidly switching measurements between spectral line peaks and the baseline regions, the long-term instrumental drift was minimized, substantially increasing measurement precision. The CRDS system coupled with a cryogenic pre-concentrator measured the δ2H of terrestrial atmospheric CH4 from 3 standard liters of air with a precision of ±1.7‰. The rapidity with which both C and H isotopic measurements of CH4 can be made with the CRDS will enable hourly monitoring of diurnal variations in terrestrial atmospheric CH4 signatures that can be used to increase the resolution of global climate models for the CH4 cycle. Although the current instrument is not capable of measuring the δ2H of 10 ppbv of martian CH4, current technology does exist that could make this feasible for future spaceflight missions. As biological and abiotic CH4 sources have overlapping carbon isotope signatures, dual-element (C and H) analysis is key to reliable differentiation of these sources. Such an instrument package would therefore offer improved ability to determine whether or not the CH4 recently detected in the martian atmosphere is biogenic in origin. Key Words: Arctic-Hydrogen isotopes-Atmospheric CH4-CRDS-Laser. Astrobiology 16, 787-797.

Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa.

Following the discovery of the first Eukarya in the deep subsurface, intense interest has developed to understand the diversity of eukaryotes living in these extreme environments. We identified that Platyhelminthes, Rotifera, Annelida and Arthropoda are thriving at 1.4 km depths in palaeometeoric fissure water up to 12,300 yr old in South African mines. Protozoa and Fungi have also been identified; however, they are present in low numbers. Characterization of the different species reveals that many are opportunistic organisms with an origin due to recharge from surface waters rather than soil leaching. This is the first known study to demonstrate the in situ distribution of biofilms on fissure rock faces using video documentation. Calculations suggest that food, not dissolved oxygen is the limiting factor for eukaryal population growth. The discovery of a group of Eukarya underground has important implications for the search for life on other planets in our solar system.

Measurement of the 13C/12C of atmospheric CH4 using near-infrared (NIR) cavity ring-down spectroscopy.

A near-infrared (NIR) continuous-wave-cavity ring-down spectrometry (CW-CRDS) device was developed with the goal of measuring seasonal changes in the isotopic composition of atmospheric CH4 on Earth and eventually on Mars. The system consisted of three distributed feedback laser diodes (DFB-LDs), two of which were tuned to the absorption line peaks of (12)CH4 and (13)CH4 at 6046.954 cm(-1) and 6049.121 cm(-1), respectively, and a third that measured the baseline at 6050.766 cm(-1). The multiple laser design improved the long-term stability of the system and increased the data acquisition rate. The acquisition frequency was further increased by utilizing a semiconductor optical amplifier (SOA) to initiate cavity ring-down events. The high repetition rate combined with the superhigh reflectivity mirrors yielded precise isotopic measurements in this NIR region, even though the line strengths of CH4 in this region are 200 times weaker than those of the strongest mid-IR absorption bands. The current system has a detection limit of 1.9 × 10(-12) cm(-1), corresponding to 10 pptv of CH4 at 100 Torr. For ambient air samples that contained 1.9 ppmv CH4, the δ(13)C of the CH4 was determined to be -48.7 ± 1.7‰ (1σ).

Hydrogeologic controls on episodic H2 release from precambrian fractured rocks--energy for deep subsurface life on earth and mars.

Dissolved H(2) concentrations up to the mM range and H(2) levels up to 9-58% by volume in the free gas phase are reported for groundwaters at sites in the Precambrian shields of Canada and Finland. Along with previously reported dissolved H(2) concentrations up to 7.4 mM for groundwaters from the Witwatersrand Basin, South Africa, these findings indicate that deep Precambrian Shield fracture waters contain some of the highest levels of dissolved H(2) ever reported and represent a potentially important energy-rich environment for subsurface microbial life. The delta (2)H isotope signatures of H(2) gas from Canada, Finland, and South Africa are consistent with a range of H(2)-producing water-rock reactions, depending on the geologic setting, which include both serpentinization and radiolysis. In Canada and Finland, several of the sites are in Archean greenstone belts characterized by ultramafic rocks that have under-gone serpentinization and may be ancient analogues for serpentinite-hosted gases recently reported at the Lost City Hydrothermal Field and other hydrothermal seafloor deposits. The hydrogeologically isolated nature of these fracture-controlled groundwater systems provides a mechanism whereby the products of water-rock interaction accumulate over geologic timescales, which produces correlations between high H(2) levels, abiogenic hydrocarbon signatures, and the high salinities and highly altered delta (18)O and delta (2)H values of these groundwaters. A conceptual model is presented that demonstrates how periodic opening of fractures and resultant mixing control the distribution and supply of H(2) and support a microbial community of H(2)-utilizing sulfate reducers and methanogens.

Abiogenic formation of alkanes in the Earth's crust as a minor source for global hydrocarbon reservoirs.

Natural hydrocarbons are largely formed by the thermal decomposition of organic matter (thermogenesis) or by microbial processes (bacteriogenesis). But the discovery of methane at an East Pacific Rise hydrothermal vent and in other crustal fluids supports the occurrence of an abiogenic source of hydrocarbons. These abiogenic hydrocarbons are generally formed by the reduction of carbon dioxide, a process which is thought to occur during magma cooling and-more commonly-in hydrothermal systems during water-rock interactions, for example involving Fischer-Tropsch reactions and the serpentinization of ultramafic rocks. Suggestions that abiogenic hydrocarbons make a significant contribution to economic hydrocarbon reservoirs have been difficult to resolve, in part owing to uncertainty in the carbon isotopic signatures for abiogenic versus thermogenic hydrocarbons. Here, using carbon and hydrogen isotope analyses of abiogenic methane and higher hydrocarbons in crystalline rocks of the Canadian shield, we show a clear distinction between abiogenic and thermogenic hydrocarbons. The progressive isotopic trends for the series of C1-C4 alkanes indicate that hydrocarbon formation occurs by way of polymerization of methane precursors. Given that these trends are not observed in the isotopic signatures of economic gas reservoirs, we can now rule out the presence of a globally significant abiogenic source of hydrocarbons.

Stable carbon isotope evidence for intrinsic bioremediation of tetrachloroethene and trichloroethene at area 6, Dover Air Force Base.

Area 6 at Dover Air Force Base (Dover, DE) has been the location of an in-depth study by the RTDF (Remediation Technologies Development Forum Bioremediation of Chlorinated Solvents Action Team) to evaluate the effectiveness of natural attenuation of chlorinated ethene contamination in groundwater. Compound-specific stable carbon isotope measurements for dissolved PCE and TCE in wells distributed throughout the anaerobic portion of the plume confirm that stable carbon isotope values are isotopically enriched in 13C consistent with the effects of intrinsic biodegradation. During anaerobic microbial reductive dechlorination of chlorinated hydrocarbons, the light (12C) versus heavy isotope (13C) bonds are preferentially degraded, resulting in isotopic enrichment of the residual contaminant in 13C. To our knowledge, this study is the first to provide definitive evidence for reductive dechlorination of chlorinated hydrocarbons at a field site based on the delta13C values of the primary contaminants spilled at the site, PCE and TCE. For TCE, downgradient wells show delta13C values as enriched as -18.0/1000 as compared to delta13C values for TCE in the source zone of -25.0 to -26.0/1000. The most enriched delta13C value on the site was observed at well 236, which also contains the highest concentrations of cis-DCE, VC, and ethene, the daughter products of reductive dechlorination. Stable carbon isotope signatures are used to quantify the relative extent of biodegradation between zones of the contaminant plume. On the basis of this approach, it is estimated that TCE in downgradient well 236 is more than 40% biodegraded relative to TCE in the proposed source area.