Subsurface Habitats Research Articles

Earthquake-Related Changes in Species Spatial Niche Overlaps in Spring Communities

Species interactions between stygobites (obligate groundwater organisms) are poorly known, reflecting the difficulty in studying such organisms in their natural environments. Some insight can be gained from the study of the spatial variability in microcrustacean communities in groundwater-fed springs. Earthquakes can increase hydraulic conductivity in the recharge area of karstic aquifers and flow rates in discharge zones, thus dislodging stygobites from their original habitats to the spring outlets. Earthquakes are expected to alter species spatial niche overlap at the spring outlets, where stygobites coexist with non-stygobites living in benthic and subsurface habitats. We compared the abundance of stygobiotic and non-stygobiotic microcrustaceans in groundwater-fed springs before and after the 6.3-Mw earthquake that hit the karstic Gran Sasso Aquifer (Italy) in 2009. Pre-seismic (1997, 2005) overall niche overlaps were not different from null expectations, while post-seismic (2012) species mean niche overlaps were higher, following the redistribution of animals caused by the earthquake-triggered discharge. The reduced abundance of stygobites following their dislodgement from the aquifer and the concomitant displacement of non-stygobites led to a higher post-seismic co-occurrence of stygobites and non-stygobites. Changes in aquifer structure destroyed pre-seismic species segregation patterns by creating new or strengthening already existing interactions.

Pressurized brines in continental Antarctica as a possible analogue of Mars

Interest in brines in extreme and cold environments has recently increased after they have been found on Mars. Those brines can be potential new subsurface habitats for peculiar ecosystems. In the McMurdo Dry Valleys of the Antarctic, the best analogue for Mars conditions, only a few cases of brines have been identified in some perennially frozen lakes and in one case in an underground aquifer. Here, we present the occurrence of pressurized brines in a shallow perennially ice-covered lake south of 70°S in an ice-free area of Victoria Land, Antarctica. For the first time, we also imaged, by means of ground penetrating radar data, the existence of a pingo-like-feature (PLF) formed by the extrusion of brines, which has also been confirmed by borehole evidence. Those brines are fed by an underground talik external to the lake basin, enhancing the possibility of unexploited ecosystems that could find an analogue in Martian environments.

Aquarius, a reusable water-based interplanetary human spaceflight transport

Attributes of a reusable interplanetary human spaceflight transport are proposed and applied to example transits between the Earth/Moon system and Deimos, the outer moon of Mars. Because the transport is 54% water by mass at an interplanetary departure, it is christened Aquarius. In addition to supporting crew hydration/hygiene, water aboard Aquarius serves as propellant and as enhanced crew habitat radiation shielding during interplanetary transit. Key infrastructure and technology supporting Aquarius operations include pre-emplaced consumables and subsurface habitat at Deimos with crew radiation shielding equivalent to sea level on Earth, resupply in a selenocentric distant retrograde orbit, and nuclear thermal propulsion.

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy.

The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis, and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere.

Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities.

Fungi are one important group of eukaryotic microorganisms in a diverse range of ecosystems, but their diversity in groundwater ecosystems is largely unknown. We used DNA-based pyro-tag sequencing of the fungal internal transcribed spacer (ITS) rDNA gene to investigate the presence and community structure of fungi at different sampling sites of two superimposed limestone aquifers ranging from 8.5 to 84 m depth in the newly established Hainich Critical Zone Exploratory (Hainich CZE). We detected a diversity of fungal OTUs in groundwater samples of all sampling sites. The relative percentage abundance of Basidiomycota was higher in the upper aquifer assemblage, whilst Ascomycota dominated the lower one. In parallel to differences in the hydrochemistry we found distinct fungal communities at all sampling sites. Classification into functional groups revealed an overwhelming majority of saprotrophs. Finding taxa common to all analyzed groundwater sites, point to a groundwater specific fungal microbiome. The presence of different functional groups and, in particular plant and cattle pathogens that are not typical of subsurface habitats, suggests links between the surface and subsurface biogeosphere due to rapid transportation across the fracture networks typical of karstic regions during recharge episodes. However, further studies including sampling series extended in both time and space are necessary to confirm this hypothesis.

Ensemble squid habitat model using three-dimensional ocean data

Abstract Neon flying squid (Ommastrephes bartramii) is a large pelagic squid internationally harvested in the North Pacific. Here, we examined its potential habitat in the central North Pacific using an ensemble modelling approach. Initially, ten statistical models were constructed by combining the squid fishing points, selected vertical layers of the sea temperature and salinity, sea surface height (SSH), and SSH gradient from the multi-variate ocean variational estimation system for the western North Pacific from June to July 1999–2011. The variable selection analyses have captured the importance of vertical temperature and salinity layers at the upper 300 and 440 m, respectively, coinciding with the reported vertical ranges of diel migration for the squid's primary prey species in the North Pacific. The evaluation of the habitat predictions using the independent sets of the presence data from 2012 to 2014 showed significant variability in the predictive accuracy, which is likely reflective of the interannual differences in environmental conditions across the validation periods. Our findings from ensemble habitat model approach using three-dimensional oceanographic data were able to characterize the near- and subsurface habitats of the neon flying squid. Moreover, our results underpinned the possible link between interannual environmental variability and spatio-temporal patterns of potential squid habitats. As such, these further suggest that an ensemble model approach could present a promising tool for operational fishery application and squid resource management.

New Bio-Indicators for Long Term Natural Attenuation of Monoaromatic Compounds in Deep Terrestrial Aquifers.

Deep subsurface aquifers despite difficult access, represent important water resources and, at the same time, are key locations for subsurface engineering activities for the oil and gas industries, geothermal energy, and CO2 or energy storage. Formation water originating from a 760 m-deep geological gas storage aquifer was sampled and microcosms were set up to test the biodegradation potential of BTEX by indigenous microorganisms. The microbial community diversity was studied using molecular approaches based on 16S rRNA genes. After a long incubation period, with several subcultures, a sulfate-reducing consortium composed of only two Desulfotomaculum populations was observed able to degrade benzene, toluene, and ethylbenzene, extending the number of hydrocarbonoclastic–related species among the Desulfotomaculum genus. Furthermore, we were able to couple specific carbon and hydrogen isotopic fractionation during benzene removal and the results obtained by dual compound specific isotope analysis (𝜀C = -2.4‰ ± 0.3‰; 𝜀H = -57‰ ± 0.98‰; AKIEC: 1.0146 ± 0.0009, and AKIEH: 1.5184 ± 0.0283) were close to those obtained previously in sulfate-reducing conditions: this finding could confirm the existence of a common enzymatic reaction involving sulfate-reducers to activate benzene anaerobically. Although we cannot assign the role of each population of Desulfotomaculum in the mono-aromatic hydrocarbon degradation, this study suggests an important role of the genus Desulfotomaculum as potential biodegrader among indigenous populations in subsurface habitats. This community represents the simplest model of benzene-degrading anaerobes originating from the deepest subterranean settings ever described. As Desulfotomaculum species are often encountered in subsurface environments, this study provides some interesting results for assessing the natural response of these specific hydrologic systems in response to BTEX contamination during remediation projects.

A sum greater than its parts: merging multi‐predator tracking studies to increase ecological understanding

Understanding how animals find prey in heterogeneous environments is a central goal of ecology. Placing this process in an environmental context requires a lot of information regarding the characteristics of both the habitat selected by the animal and its surroundings. In high‐latitude marine systems, information about subsurface habitats of marine predators is often very limited. Animal‐borne oceanographic instruments have added a new modality to improve our understanding of marine predators and their habitats. While these instruments do not collect environmental information beyond that experienced by the animals carrying them, our study makes use of an oceanographic dataset collected by southern elephant seals (Mirounga leonina; N = 15), to provide environmental context for two sympatrically foraging penguin species in the waters close to the subantarctic island of Bouvetøya. The seals collected 154 CTD profiles during the study period, averaging 4.9 (±3.67) profiles per day, documenting the stratification of the upper water layer in terms of both seawater density and temperature. Using these data, we quantitatively describe the relationship between the diving behavior of the penguins (N = 3,745 dives) and the hydrographic properties of the three‐dimensional area in which they were foraging. Both penguin species appeared to favor water characterized by a shallow mixed layer. The chinstrap penguins (Pygoscelis antarctica) dove within a shallow, unstable body of water close to the colony, whereas macaroni penguins (Eudyptes chrysolophus) exploited the bottom of the surface mixed layer further offshore. The hydrographic properties preferred by the penguins match closely those that describe the highest densities of their preferred prey, krill (Euphausia superba), identified during a temporally and spatially concurrent study. We demonstrate how merging multiple telemetric data streams from animals can shed new light on aspects of foraging behavior beyond simply relating movements to two‐dimensional, remotely sensed measurements of the environment.

Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific.

Thermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, making biogeographic patterns and evolutionary relationships apparent. Isolates were differentiated into regionally endemic populations however there was also evidence in some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus. In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus. The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.

Exploring copepod distribution patterns at three nested spatial scales in a spring system: habitat partitioning and potential for hydrological bioindication

<p>In groundwater-fed springs, habitat characteristics are primarily determined by a complex combination of geomorphic features and physico-chemical parameters, while species assemblages are even more intricate. Springs host species either inhabiting the spring mouth, or colonizing spring habitats from the surface or from the aquifers which feed the springs. Groundwater species living in springs have been claimed as good candidates for identifying dual aquifer flowpaths or changes in groundwater pathways before reaching the spring outlets. However, the reliability of spring species as hydrological biotracers has not been widely investigated so far. Our study was aimed at analysing a large karstic spring system at three nested spatial scales in order: i) to assess, at whole spring system scale, the presence of a groundwater divide separating two aquifers feeding two spring units within a single spring system, by combining isotope analyses, physico-chemistry, and copepod distribution patterns; ii) to test, at vertical spring system scale, the effectiveness of copepods in discriminating surface and subsurface habitat patches within the complex mosaic spring environment; iii) to explore, at local spring unit level, the relative role of hydrochemistry and sediment texture as describers of copepod distribution among microhabitats. The results obtained demonstrated the presence of a hierarchical spatial structure, interestingly reflected in significant differences in assemblage compositions. Copepod assemblages differed between the two contiguous spring units, which were clearly characterized by their hydrochemistry and by significant differences in the groundwater flowpaths and recharge areas, as derived by the isotope analyses. The biological results suggested that stygobiotic species seem to be related to the origin of groundwater, suggesting their potential role as hydrological biotracers. At vertical scale, assemblage composition in surface and subsurface habitats was significantly different, both between spring units and among microhabitats, supporting strong habitat preferences of copepod species. At the smaller local scale, the response to habitat patchiness of subsurface copepod assemblages resulted in distribution patterns primarily defined by sediment texture, while the sensitivity to differences in hydrochemistry was negligible.</p>

Evidence for methane in Martian meteorites.

The putative occurrence of methane in the Martian atmosphere has had a major influence on the exploration of Mars, especially by the implication of active biology. The occurrence has not been borne out by measurements of atmosphere by the MSL rover Curiosity but, as on Earth, methane on Mars is most likely in the subsurface of the crust. Serpentinization of olivine-bearing rocks, to yield hydrogen that may further react with carbon-bearing species, has been widely invoked as a source of methane on Mars, but this possibility has not hitherto been tested. Here we show that some Martian meteorites, representing basic igneous rocks, liberate a methane-rich volatile component on crushing. The occurrence of methane in Martian rock samples adds strong weight to models whereby any life on Mars is/was likely to be resident in a subsurface habitat, where methane could be a source of energy and carbon for microbial activity.

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships.

Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes.

Dissolved hydrogen and methane in the oceanic basaltic biosphere

The oceanic basaltic crust is the largest aquifer on Earth and has the potential to harbor substantial subsurface microbial ecosystems, which hitherto remains largely uncharacterized and is analogous to extraterrestrial subsurface habitats. Within the sediment-buried 3.5 Myr old basaltic crust of the eastern Juan de Fuca Ridge flank, the circulating basement fluids have moderate temperature (∼65 °C) and low to undetectable dissolved oxygen and nitrate concentrations. Sulfate, present in high concentrations, is therefore expected to serve as the major electron acceptor in this subsurface environment. This study focused on the availability and potential sources of two important electron donors, methane (CH4) and hydrogen (H2), for the subseafloor biosphere. High integrity basement fluids were collected via fluid delivery lines associated with Integrated Ocean Drilling Program (IODP) Circulation Obviation Retrofit Kits (CORKs) that extend from basement depths to outlet ports at the seafloor. Two new CORKs installed during IODP 327 in 2010, 1362A and 1362B, were sampled in 2011 and 2013. The two CORKs are superior than earlier style CORKs in that they are equipped with coated casing and polytetrafluoroethylene fluid delivery lines, reducing the interaction between casing materials with the environment. Additional samples were collected from an earlier style CORK at Borehole 1301A.The basement fluids are enriched in H2 (0.05–1.8 μmol/kg), suggesting that the ocean basaltic aquifer can support H2-driven metabolism. The basement fluids also contain significant amount of CH4 (5–32 μmol/kg), revealing CH4 as an available substrate for subseafloor basaltic habitats. The δ13C values of CH4 from the three boreholes ranged from −22.5 to −58‰, while the δ2H values ranged from −316 to 57‰. The isotopic compositions of CH4 and the molecular compositions of hydrocarbons suggest that CH4 in the basement fluids is of both biogenic and abiotic origins, varying among sites and sampling times. The δ2H values of CH4 in CORK 1301A fluid samples are much more positive than found in all other marine environments investigated to date and are best explained by the partial microbial oxidation of biogenic CH4. In conclusion, our study shows that CH4 and H2 are persistently available to fuel the deep biosphere and that CH4 is both produced and potentially consumed by microorganisms in the oceanic basement.

Formation of H2, CH4 and N-species during low-temperature experimental alteration of ultramafic rocks

Hydrogen, methane and ammonium are important chemical species for chemolithotrophic microorganisms that sustain subsurface endolithic communities. It is well known that production of H2 through serpentinization of the primary Fe(II)-containing minerals, olivine and pyroxene, in ultramafic rocks and reduction of CO2 to CH4 are processes that occur at higher temperatures. Knowledge is, however, limited about these reactions under low-temperature conditions, and how they are affected by Fe(II)-containing secondary minerals, such as brucite and serpentine, which are commonly found in these environments. In this experimental study, we explored the formation of H2, CH4 and NH4 during low-temperature (25°C) reactions between deionised water and 1) unaltered, 2) medium altered and 3) highly altered dunites, over a period of 99days.Hydrogen was detected in all three experiments and the concentration increased over time. The O2 concentration decreased over time, but O2 was still present at significant levels when H2 started to form. This suggests that the H2 was formed locally at the surface of mineral grains rather than in the hypoxic solution. The highly altered dunite gave the highest and the unaltered dunite the lowest H2 concentrations, and while the O2 concentration decreased fast with the medium altered dunite, significant amounts of O2 still remained with the unaltered dunite at the end of the experiments. Both the medium and highly altered dunite gave O2 concentrations close to or below the detection limit during the last part of the experiment. Factors that likely affected the H2 production are Fe-content, mineralogy, dissolution rates and surface areas of the minerals as well as the presence of catalytic minerals such as chromite and magnetite.Methane was also detected and increased with time in all experiments. The results indicate that CH4 formation also occurred locally on the surface of minerals. Detection of both NH4 and NO3 in the aqueous solutions indicates that previously absorbed N-species were leached out during the experiment. Increasing NH4 and decreasing NO3 concentrations over time suggest NO3 reduction, likely catalysed by mineral surfaces.The results imply that low-temperature water–rock reactions in moderately to highly altered ultramafic rocks provide reduced chemical species that can be utilized as electron donors in energy-yielding metabolic processes by subsurface microorganisms. Such reactions could play an important role in sustaining subsurface microbial communities, particularly in ophiolites and near seafloor parts of the ultramafic oceanic lithosphere at slow-spreading mid-ocean ridges and possibly also in other rocks and sediments. The results suggest that brucite and possibly also serpentine may be more important sources of Fe(II) and thus H2 formation than olivine in low-temperature ultramafic systems. Formation of H2 in reducing microenvironments on mineral surfaces surrounded by oxic conditions increases the extent of H2 formation and the subsurface habitat for aerobic H2-oxidizing microorganisms.

Microscale Mapping of Alteration Conditions and Potential Biosignatures in Basaltic-Ultramafic Rocks on Early Earth and Beyond

Subseafloor environments preserved in Archean greenstone belts provide an analogue for investigating potential subsurface habitats on Mars. The c. 3.5-3.4 Ga pillow lava metabasalts of the mid-Archean Barberton greenstone belt, South Africa, have been argued to contain the earliest evidence for microbial subseafloor life. This includes candidate trace fossils in the form of titanite microtextures, and sulfur isotopic signatures of pyrite preserved in metabasaltic glass of the c. 3.472 Ga Hooggenoeg Formation. It has been contended that similar microtextures in altered martian basalts may represent potential extraterrestrial biosignatures of microbe-fluid-rock interaction. But despite numerous studies describing these putative early traces of life, a detailed metamorphic characterization of the microtextures and their host alteration conditions in the ancient pillow lava metabasites is lacking. Here, we present a new nondestructive technique with which to study the in situ metamorphic alteration conditions associated with potential biosignatures in mafic-ultramafic rocks of the Hooggenoeg Formation. Our approach combines quantitative microscale compositional mapping by electron microprobe with inverse thermodynamic modeling to derive low-temperature chlorite crystallization conditions. We found that the titanite microtextures formed under subgreenschist to greenschist facies conditions. Two chlorite temperature groups were identified in the maps surrounding the titanite microtextures and record peak metamorphic conditions at 315 ± 40°C (XFe3+(chlorite) = 25-34%) and lower-temperature chlorite veins/microdomains at T = 210 ± 40°C (lower XFe3+(chlorite) = 40-45%). These results provide the first metamorphic constraints in textural context on the Barberton titanite microtextures and thereby improve our understanding of the local preservation conditions of these potential biosignatures. We suggest that this approach may prove to be an important tool in future studies to assess the biogenicity of these earliest candidate traces of life on Earth. Furthermore, we propose that this mapping approach could also be used to investigate altered mafic-ultramafic extraterrestrial samples containing candidate biosignatures.

The dark side of springs: what drives small-scale spatial patterns of subsurface meiofaunal assemblages?

Springs are amongst the most relevant Groundwater Dependent Ecosystems (GDEs) and are key research environments in freshwater ecology and biology. The strict dependency on ground water of surface spring biodiversity is widely recognized, whereas the biodiversity occurring below the spring is very poorly known. This study analyzes copepod assemblages in the subsurface habitat of a karstic rheolimnocrenic spring in relation to seventeen environmental parameters. Subsurface copepod assemblages were sensitive to microspatial variation in habitat structure, and species distributions were mostly driven by groundwater flowpath and substratum type, resulting in biologically distinct limnocrenic and rheocrenic sectors at the spring system scale. Habitat patchiness was reflected in differences in the microdistribution of subsurface copepods, stygobiotic assemblages being more sensitive to the measured environmental gradients than non-stygobiotic ones. In spite of the apparent stability of spring environments, copepods, as a target group, performed well as descriptors of sediment texture and hydrodynamics, and may offer relevant information for a better understanding of the potential changes generated by anthropogenic disturbance on these ecosystems.

Laser spectroscopic real time measurements of methanogenic activity under simulated Martian subsurface analog conditions

On Earth, chemolithoautothrophic and anaerobic microorganisms such as methanogenic archaea are regarded as model organisms for possible subsurface life on Mars. For this reason, the methanogenic strain Methanosarcina soligelidi (formerly called Methanosarcina spec. SMA-21), isolated from permafrost-affected soil in northeast Siberia, has been tested under Martian thermo-physical conditions. In previous studies under simulated Martian conditions, high survival rates of these microorganisms were observed. In our study we present a method to measure methane production as a first attempt to study metabolic activity of methanogenic archaea during simulated conditions approaching conditions of Mars-like environments. To determine methanogenic activity, a measurement technique which is capable to measure the produced methane concentration with high precision and with high temporal resolution is needed. Although there are several methods to detect methane, only a few fulfill all the needed requirements to work within simulated extraterrestrial environments. We have chosen laser spectroscopy, which is a non-destructive technique that measures the methane concentration without sample taking and also can be run continuously. In our simulation, we detected methane production at temperatures down to −5°C, which would be found on Mars either temporarily in the shallow subsurface or continually in the deep subsurface. The pressure of 50kPa which we used in our experiments, corresponds to the expected pressure in the Martian near subsurface. Our new device proved to be fully functional and the results indicate that the possible existence of methanogenic archaea in Martian subsurface habitats cannot be ruled out.

Bacterial Communities Associated with Subsurface Geochemical Processes in Continental Serpentinite Springs

Reactions associated with the geochemical process of serpentinization can generate copious quantities of hydrogen and low-molecular-weight organic carbon compounds, which may provide energy and nutrients to sustain subsurface microbial communities independently of the photosynthetically supported surface biosphere. Previous microbial ecology studies have tested this hypothesis in deep sea hydrothermal vents, such as the Lost City hydrothermal field. This study applied similar methods, including molecular fingerprinting and tag sequencing of the 16S rRNA gene, to ultrabasic continental springs emanating from serpentinizing ultramafic rocks. These molecular surveys were linked with geochemical measurements of the fluids in an interdisciplinary approach designed to distinguish potential subsurface organisms from those derived from surface habitats. The betaproteobacterial genus Hydrogenophaga was identified as a likely inhabitant of transition zones where hydrogen-enriched subsurface fluids mix with oxygenated surface water. The Firmicutes genus Erysipelothrix was most strongly correlated with geochemical factors indicative of subsurface fluids and was identified as the most likely inhabitant of a serpentinization-powered subsurface biosphere. Both of these taxa have been identified in multiple hydrogen-enriched subsurface habitats worldwide, and the results of this study contribute to an emerging biogeographic pattern in which Betaproteobacteria occur in near-surface mixing zones and Firmicutes are present in deeper, anoxic subsurface habitats.

Microbial life associated with low‐temperature alteration of ultramafic rocks in the Leka ophiolite complex

Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions.

Deep subsurface microbiology: a guide to the research topic papers

Deep subsurface microbiology is a rising field in geomicrobiology, environmental microbiology and microbial ecology that focuses on the molecular detection and quantification, cultivation, biogeographic examination, and distribution of bacteria, archaea, and eukarya that permeate the subsurface biosphere. The deep biosphere includes a variety of subsurface habitats, such as terrestrial deep aquifer systems or mines, deeply buried hydrocarbon reservoirs, marine sediments and the basaltic ocean crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and—at best—incompletely understood microbial populations. So far, microbial cells and DNA remain detectable at sediment depths of more than 1 km and life appears limited mostly by heat in the deep subsurface. Severe energy limitation, either as electron acceptor or donor shortage, and scarcity of microbially degradable organic carbon sources are among the evolutionary pressures that may shape the genomic and physiological repertoire of the deep subsurface biosphere. Its biogeochemical importance in long-term carbon sequestration, subsurface elemental cycling and crustal aging, is a major focus of current research at the interface of microbiology, geochemistry, and biosphere/geosphere evolution. The papers of this Frontiers e-volume bear evidence of the rapid advances in deep subsurface microbiology.