Deep Subsurface Aquifer Research Articles

Uncultured bacteria and methanogenic archaea predominate in the microbial community of Western Siberian deep subsurface aquifer

Uncultured bacteria and methanogenic archaea predominate in the microbial community of Western Siberian deep subsurface aquifer

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study.

The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles.

Impact of leaky wells on nitrate cross-contamination in a layered aquifer system: Methodology for and demonstration of quantitative assessment and prediction

Poorly constructed wells can cause deterioration of groundwater quality by carrying surface contaminants into a deep subsurface aquifer system. In this study, the impact of leaky wells on groundwater contamination was quantitatively evaluated in a layered aquifer system of the Gosan agricultural fields, Jeju Island, Korea, where degradation in groundwater quality by nitrate has been reported. We introduce a leaky-well module and a double-domain integration method to compute nitrate cross-contamination through a layered aquifer system. The simulation results clearly revealed that the leaky wells rapidly degraded the water quality of the underlying aquifer by acting as a direct pathway for nitrate-rich shallow groundwater. The model results predicted that in order to decrease the NO3-N concentration at the regional groundwater wells below the maximum contamination level (MCL), the maximum allowable fertilizer amount of Gosan would be 45–65% of the currently applied fertilizer level, whereas sealing of the regional groundwater wells would rapidly decrease the NO3-N concentration below the MCL without reducing fertilizer usage. Our study demonstrated that the well conditions and hydrogeological system play major roles in the occurrence of nitrate in the underlying aquifer in Gosan; therefore, a proper groundwater management plan against nitrate contamination should be established on the basis of a comprehensive understanding of the hydrogeologic system of the area.

Hypotheses for Near-Surface Exchange of Methane on Mars.

The Curiosity rover recently detected a background of 0.7 ppb and spikes of 7 ppb of methane on Mars. This in situ measurement reorients our understanding of the martian environment and its potential for life, as the current theories do not entail any geological source or sink of methane that varies sub-annually. In particular, the 10-fold elevation during the southern winter indicates episodic sources of methane that are yet to be discovered. Here we suggest a near-surface reservoir could explain this variability. Using the temperature and humidity measurements from the rover, we find that perchlorate salts in the regolith deliquesce to form liquid solutions, and deliquescence progresses to deeper subsurface in the season of the methane spikes. We therefore formulate the following three testable hypotheses. The first scenario is that the regolith in Gale Crater adsorbs methane when dry and releases this methane to the atmosphere upon deliquescence. The adsorption energy needs to be 36 kJ mol(-1) to explain the magnitude of the methane spikes, higher than existing laboratory measurements. The second scenario is that microorganisms convert organic matter in the soil to methane when they are in liquid solutions. This scenario does not require regolith adsorption but entails extant life on Mars. The third scenario is that deep subsurface aquifers produce the bursts of methane. Continued in situ measurements of methane and water, as well as laboratory studies of adsorption and deliquescence, will test these hypotheses and inform the existence of the near-surface reservoir and its exchange with the atmosphere. Mars-Methane-Astrobiology-Regolith. Astrobiology 16, 539-550.

Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.

Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.

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.

Dissecting the deep biosphere: retrieving authentic microbial communities from packer-isolated deep crystalline bedrock fracture zones

Deep fracture zones in Finnish crystalline bedrock have been isolated for long, the oldest fluids being tens of millions of years old. To accurately measure the native microbial diversity in fracture-zone fluids, water samples were obtained by isolating the borehole fraction spanning a deep subsurface aquifer fracture zone with inflatable packers (500 and 967 m) or by pumping fluids directly from the fracture zone. Sampling frequency was examined to establish the time required for the space between packers to be flushed and replaced by indigenous fracture fluids. Chemical parameters of the fluid were monitored continuously, and samples were taken at three points during the flushing process. Microbial communities were characterized by comparison of 16S ribosomal genes and transcripts and quantification of dsrB (dissimilatory sulfate reduction) gene. Results suggest that fracture-zones host microbial communities with fewer cells and lower diversity than those in the drill hole prior to flushing. In addition, each fracture zone showed a community composition distinct from that inhabiting the drill hole at corresponding depth. The highest diversity was detected from the 967-m fracture zone. We conclude that the applied packer method can successfully isolate and sample authentic microbial fracture-zone communities of deep bedrock environments.

Monitoring of the microbial community composition in deep subsurface saline aquifers during CO2 storage in Ketzin, Germany

Abstract This study characterized the composition and activity of the autochthonous microbial community in formation fluids of a saline CO 2 storage aquifer during CO 2 injection and during an N 2 lift. The clean-up of the wells prior CO 2 injection by N 2 lift decreased the total microbial cell numbers, and the number of sulphate reducing bacteria (SRB) was reduced by at least two orders of magnitude. Fluorescence in situ Hybridisation (FISH) and molecular fingerprinting demonstrated that the microbial community was strongly influenced by the CO 2 injection. Before CO 2 arrival, up to 106 cells ml-1 were detected by DAPI-staining at a depth of 647 m below the surface. The microbial community was dominated by fermentative halophilic bacteria and sulphate reducing bacteria. Both the FISH and fingerprinting analyses revealed quantitative and qualitative changes after CO 2 arrival. An enhanced activity and quantity of the microbial population after five months of CO 2 storage indicated that the community was able to adapt to the extreme conditions of the deep biosphere and to the extreme changes of these anthropogenically modified conditions.

Anaerobic Biodegradation of BTEX by Original Bacterial Communities from an Underground Gas Storage Aquifer

BTEX biodegradation by an indigenous deep subsurface microbial community was evaluated in a water sample collected in the area of an underground gas storage. Five different sulfate-reducing microbial communities able to use at least either benzene, toluene, ethylbenzene, or xylene (BTEX) compounds were studied. A total of 21 different bacterial phylotypes were identified, each community containing three to nine bacterial phylotypes. Archaeal phylotypes were retrieved from only three communities. The analysis of 16S rRNA gene sequences showed that i) these consortia were mainly composed of novel species, some of which belonging to bacterial groups not previously suspected to be involved in BTEX anaerobic degradation, ii) three consortia were dominated by an uncultured Pelobacter sp. previously detected in biodegraded oil reservoirs, iii) a deeply branching species distantly affiliated to Thermotogales was abundant in two consortia, and that iv) Firmicutes related to the Desulfotomaculum and Carboxydocella genera represented the only three detectable phylotypes in a toluene-degrading consortium. This work shows that subdominant microbial populations present in a deep subsurface aquifer used for seasonal underground gas storage could be involved in the natural attenuation of the traces of BTEX coinjected with methane in the deep subsurface.

Desulfovibrio putealis sp. nov., a novel sulfate-reducing bacterium isolated from a deep subsurface aquifer

A novel sulfate-reducing bacterium was isolated from a well that collected water from a deep aquifer at a depth of 430 m in the Paris Basin, France. The strain, designated B7-43T, was made up of vibrioid cells that were motile by means of a single polar flagellum. Cells contained desulfoviridin. In the presence of sulfate, the following substrates were used as energy and carbon sources: lactate, pyruvate, malate, fumarate, ethanol, butanol, acetate/H2 and glycine. Sulfite and thiosulfate were also used as electron acceptors in the presence of lactate. In the absence of electron acceptors, pyruvate, malate and fumarate were fermented. Optimal growth was obtained in 1 g NaCl l(-1) and at pH 7. On the basis of 16S rRNA gene sequence analysis, the isolate was most closely related to members of the genus Desulfovibrio (90 % similarity). It is thus proposed that strain B7-43T (=DSM 16056T=ATCC BAA-905T) represents a novel species within this genus, Desulfovibrio putealis sp. nov.

Abiotic Controls on H2 Production from Basalt−Water Reactions and Implications for Aquifer Biogeochemistry

Abiotic production of H{sub 2} from basalt reactions in aqueous solutions is hypothesized to support microbial ecosystems in deep subsurface aquifers, such as those found in the Columbia River Basalt group (CRB). The authors investigated factors controlling this phenomenon, including rock composition, pH, temperature, sterilization method, reducing agents, and product removal. Ferrous silicate minerals were found to be the basalt components responsible for H{sub 2} production from anaerobic water-rock interactions. H{sub 2} evolution was faster at pH < 7 but occurred from pH 5 to pH 11, which covers the pH range (7--10) measured in CRB groundwaters. The onset of H{sub 2} evolution coincided with the appearance of dissolved Fe{sup 2+}, and an apparent alkaline inhibition could be alleviated by the addition of excess FeCl{sub 2}. This may reflect, in part, the low redox conditions needed for H{sub 2} evolution and suggests that H{sub 2} may be controlled by reaction rates of ferrous silicate minerals. Rates were higher at 60 C than at 30 C, suggesting that the geothermal gradient may lead to increased H{sub 2} production at depth. The results were consistent with the hypothesis at depth. The results were consistent with the hypothesis that basalt-redox reactions support primarymore » production by microorganisms in some terrestrial subsurface environments.« less

On the possibility of chemosynthetic ecosystems in subsurface habitats on Mars

We have reexamined the question of extant microbial life on Mars in light of the most recent information about the planet and recently discovered nonphotosynthetic microbial ecosystems on Earth—deep sea hydrothermal vent communities and deep subsurface aquifer communities. On Mars, protected subsurface niches associated with hydrothermal activity could have continued to support life even after surface conditions became inhospitable. Geochemical evidence from the SNC meteorites and geomorphological evidence for recent volcanism suggest that such habitats could persist to the present time. There are also extensive geological features that attest to the ubiquitous nature of volcano-ground ice interactions on Mars. We suggest a possible deep subsurface microbial ecology similar to those discovered to depths of several kilometers below the surface of the Earth. We focus on anaerobic systems utilizing CO 2 as the primary source of carbon. Liquid water could be provided by the heat of geothermal or volcanic activity melting permafrost or other subsurface water sources. Gases from volcanic activity deep in the planet could provide reducing power (as CH 4, H 2, or H 2S) percolating up from below and enabling the development of a microbial community based upon chemolithoautotrophy. We suggest a methanogen (or acetogen) and sulfur-based microbial ecology as one possible basis for microbial primary production. Our hypothetical ecosystem is neither supported, nor excluded, by current observations of Mars. Tests for such a subsurface system involve locating active geothermal areas associated with ground ice or detecting trace quantities of reduced atmospheric gases that would leak from such a system.