Deep Subsurface Environments Research Articles

Microbial ecology of the deep terrestrial subsurface.

The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.

Biohydrogen production by a novel strain Petroclostridium sp. X23 isolated from the production water of oil reservoirs

Biohydrogen production from H2-producing has been considered a promising alternative for the replacement of fossil fuels. However, the mechanisms that affect the H2-producing capacities of wild-type strains remain largely elusive. To explore the capabilities of biohydrogen production from microorganisms in the deep subsurface oil-reservoir environment, we isolated an H2-producing bacteria identified as the genus Petroclostridium from a long-term methanogenic crude oil-degrading enrichment culture of the production water from oil reservoir. The impact of various temperature, pH, and glucose concentrations on hydrogen production by Petroclostridium sp. X23 was investigated. Under the conditions of 37 °C, initial pH 8.0, and glucose concentration of 4 g/L, the strain X23 achieved its maximum hydrogen yield at 1.82 ± 0.12 mol H2/mol glucose. When compared to the previously reported strain SK-Y3, X23 exhibited enhanced H2-producing ability, with lesser energy biomass production. Comparative genomic analysis revealed that the genome of X23 contains more genes associated with hydrogen generation than SK-Y3. These findings proposed Petroclostridium sp. X23 is a potential candidate for dark fermentative hydrogen production under alkaline and mesophilic conditions. It also increased our knowledge of genotypes related to high H2-producing capability, which may provide instructions for future selection of high-yielding strains and reasonable metabolic engineering of wild-type H2-producing strains.

Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community.

Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.

A unique prokaryotic vertical distribution in the groundwaters of deep sedimentary geological settings in Hokkaido, Japan

The purpose of this study is to clarify the vertical prokaryotic distribution in groundwater in a terrestrial subsurface sedimentary environment with a geological complex. Six groundwater samples were collected from a coastal 1200-m-deep borehole in which digging strata deposited between 2.3 and 1.5 Ma in Horonobe, Hokkaido, Japan. The studied succession was divided into three vertical zones that were geochemically differentiated according to their chloride contents and water-stable isotopes. The upper zone (UZ; shallower than 500 m) primarily contained fresh water supplied by penetrating meteoric water, the connate water zone (CWZ; deeper than 790 m) contained paleo-seawater, and the diffusion zone (DZ; 500–790 m depth) located between UZ and CWZ. Fluctuations in the prokaryotic density and constituents were observed across these three zones. The prokaryotic density decreased from UZ toward DZ, and the density of DZ was two orders of magnitude lower than that of UZ and CWZ. High prokaryotic activity was observed in CWZ below DZ. The upward expansion of prokaryotic distribution from CWZ, where high prokaryotic potential expressed by biomass can be maintained almost equivalent to that in the marine environment, probably occurred on a geological timescale from 80 ka to 1.3 Ma, as shown by the groundwater age of DZ. The DZ is a zone where the geochemistry has changed drastically owing to the mixing of penetrating meteoric water and the diffusion of deep paleo-seawater, preserving a unique subsurface environment. This chemically mixed zone might be considered as a buffering zone for prokaryotes to prevent the expansion of prokaryotic density and activity provided by diffusion and their in situ growth from both above and below the zones, which is expected to be maintained over a geological timescale. This zone is considered important for using subsurface space in the deep subsurface environment of the island arc.

Global distribution and diversity of antimicrobial genes across subsurface bacterial and archaeal metagenome assembled genomes

Microorganisms have the capability to produce antimicrobial compounds through secondary metabolism, which are not essential within their natural environments, but have been found to have many effects on the ecosystem. Antimicrobial production genes have been identified in a wide range of microorganisms; however, research into natural ecosystems has historically been limited to continental soil environments. Antimicrobial production research has been limited in the deep continental subsurface and marine environments, especially deeply buried marine sediments. We analyzed 466 high-quality metagenome assembled genomes (MAGs) collected from continental and marine subsurface environments through the Deep Carbon Observatory’s Census of Deep Life. A total of 383 MAGs contained biosynthetic gene clusters, namely Type I and Type III polyketide synthase genes, non-ribosomal peptide synthetase genes, and other unspecified ribosomally synthesized and post-translationally modified peptide products. All of these genes were found across continental mines, subglacial lakes, hotsprings, and serpentinizing environments. These environments have previously not been investigated via metagenomics for antimicrobial gene diversity, which may be produced for competition or communication purposes. All other biosynthetic genes identified in this study were less than 50% similar to reference biosynthesis genes indicating the novelty of secondary metabolism in subsurface microorganisms. The majority of predicted antimicrobial products were found to be produced exergonically, which could indicate microbial populations use energy-conserving mechanisms to produce compounds that could offer a competitive advantage.

Viruses, Vesicles, and other Biological Nanoparticles: The Sub-cellular Biosphere of a Deeply Buried 2km-Deep, 20-Million-Year-Old Coalbed Community

Horizontal gene transfer is an important driver of adaptation and evolution in microorganisms. Transducing biological nanoparticles such as viral particles are believed to be key facilitators of horizontal gene transfer. In deep subseafloor sediments, energy can be highly limiting, supporting only extremely slow metabolisms. In such low-energy, isolated environments where communities may subsist for millions of years, the mechanisms of subsurface microbial adaptation and evolution remain a mystery. Virus particles have been found everywhere that life has been found, including deep subsurface environments. Although microorganisms are abundant and active in the Earth's subsurface, the role of viruses in shaping and influencing these slow-growing communities is only recently starting to be explored. Here, we analyzed the deeply buried microbial community from a lignite coalbed layer 2km below the seafloor offshore Shimokita, Japan (IODP Expedition 337) that had been buried for 20 million years. We harvested cells (>0.2µm) and biological nanoparticles (<0.2µm) from a bioreactor enrichment seeded by lignite core samples. We sequenced DNA from the cells and nanoparticles and subsequently analyzed the metagenomes. Within the nanoparticle metagenome, numerous complete novel virus genomes were reconstructed. Comparison of the virus genomes to the prokaryotic MAGs (metagenome assembled genomes) revealed that many of the virus genomes had been integrated prophage within bacterial genomes, suggesting the potential for virus-host interactions to occur in the deep subseafloor. Additionally, lysogeny may be an important survival mechanism for viruses in deeply buried, low-energy environments. Host genes were found to be packaged by viral particles, demonstrating the potential for specialized and general transduction by viruses. Not only viral particles, but there was also evidence that membrane vesicles and gene transfer agents may participate in transduction in this deep subsurface community. Horizontal gene transfer mediated by biological nanoparticles may be an important mechanism of adaptation for deep subsurface microbial communities and may provide insight into possible evolutionary processes shaping microbial communities in the deep subsurface. These results may also shed some light onto the nature of viral infection in the subsurface, potentially revealing insights about the long-term persistence of life under extreme energy limitation and how viruses may survive this over geological timescales.

Integrative Genomics Sheds Light on Global Deep Terrestrial Biosphere Communities

Active microbial lineages inhabit the deep terrestrial subsurface (Fry et al. 1997, Lopez-Fernandez et al. 2018) with estimates suggesting deep subsurface ecosystems to host ca. 90% of the total bacterial and archaeal biomass on Earth and about 10-20% of all terrestrial biomass (McMahon and Parnell 2014, Bar-On et al. 2018, Magnabosco et al. 2018, Drake and Reiners 2021). This highlights deep subsurface ecosystems as a vast reservoir of genetic innovation that remains poorly characterized. The biological diversity of deep subsurface ecosystems seem to be influenced by parameters such as temperature, pressure, water residence times, and geochemistry (Drake and Reiners 2021). The deep subsurface environment remains underrepresented in metagenomic databases, and yet the publicly available datasets are not synoptically analyzed in an integrated way. In this project, we collected a large set of publicly available and published metagenomes, published metagenome assembled genomes (MAGs) as well as single cell amplified genomes (SAGs) originating from global deep oligotrophic terrestrial subsurface samples (>70 m). Reconstructed MAGs/SAGs from this survey were integrated in to our own existing Fennoscandian Shield Genomic Database (FSGD) (Holmfeldt et al. 2021, Mehrshad et al. 2021). This expanded global database of the deep oligotrophic terrestrial subsurface contains >4000 MAGs/SAGs. In this dataset, representatives of phyla Firmicutes, Desulfobacterota, Patescibacteria, and Chlroflexota were the most prevalent taxa. The presence of Candidatus Desulforudis audaxviator across different continents and samples highlighted its adaptation to different deep biosphere environments. In addition, novel bacterial lineages at the class level were identified in several locations, pointing to the importance and necessity of further studies to characterize deep biosphere microbial diversity. This extensive study of the global deep oligotrophic terrestrial subsurface will reveal whether deep terrestrial populations are ubiquitous and how their distribution patterns are affected by different physicochemical variables such as water types and geology. By Identifying key populations present across multiple global groundwaters, our study will advance our understanding of the global diversity hosted in deep oligotrophic terrestrial subsurface ecosystems.

The Mystery of Piezophiles: Understudied Microorganisms from the Deep, Dark Subsurface.

Microorganisms that can withstand high pressure within an environment are termed piezophiles. These organisms are considered extremophiles and inhabit the deep marine or terrestrial subsurface. Because these microorganisms are not easily accessed and require expensive sampling methods and laboratory instruments, advancements in this field have been limited compared to other extremophiles. This review summarizes the current knowledge on piezophiles, notably the cellular and physiological adaptations that such microorganisms possess to withstand and grow in high-pressure environments. Based on existing studies, organisms from both the deep marine and terrestrial subsurface show similar adaptations to high pressure, including increased motility, an increase of unsaturated bonds within the cell membrane lipids, upregulation of heat shock proteins, and differential gene-regulation systems. Notably, more adaptations have been identified within the deep marine subsurface organisms due to the relative paucity of studies performed on deep terrestrial subsurface environments. Nevertheless, similar adaptations have been found within piezophiles from both systems, and therefore the microbial biogeography concepts used to assess microbial dispersal and explore if similar organisms can be found throughout deep terrestrial environments are also briefly discussed.

Microbial survival mechanisms within serpentinizing Mariana forearc sediments.

Marine deep subsurface sediment is often a microbial environment under energy-limited conditions. However, microbial life has been found to persist and even thrive in deep subsurface environments. The Mariana forearc represents an ideal location for determining how microbial life can withstand extreme conditions including pH 10-12.5 and depleted nutrients. The International Ocean Discovery Program Expedition 366 to the Mariana Convergent Margin sampled three serpentinizing seamounts located along the Mariana forearc chain with elevated concentrations of methane, hydrogen, and sulfide. Across all three seamount summits, the most abundant transcripts were for cellular maintenance such as cell wall and membrane repair, and the most abundant metabolic pathways were the Entner-Doudoroff pathway and tricarboxylic acid cycle. At flank samples, sulfur cycling involving taurine assimilation dominated the metatranscriptomes. The in situ activity of these pathways was supported by the detection of their metabolic intermediates. All samples had transcripts from all three domains of Bacteria, Archaea, and Eukarya, dominated by Burkholderiales, Deinococcales, and Pseudomonales, as well as the fungal group Opisthokonta. All samples contained transcripts for aerobic methane oxidation (pmoABC) and denitrification (nirKS). The Mariana forearc microbial communities show activity not only consistent with basic survival mechanisms, but also coupled metabolic reactions.

Inline small-angle X-ray scattering-coupled chromatography under extreme hydrostatic pressure.

As continuing discoveries highlight the surprising abundance and resilience of deep ocean and subsurface microbial life, the effects of extreme hydrostatic pressure on biological structure and function have attracted renewed interest. Biological small-angle X-ray scattering (BioSAXS) is a widely used method of obtaining structural information from biomolecules in solution under a wide range of solution conditions. Due to its ability to reduce radiation damage, remove aggregates, and separate monodisperse components from complex mixtures, size-exclusion chromatography-coupled SAXS (SEC-SAXS) is now the dominant form of BioSAXS at many synchrotron beamlines. While BioSAXS can currently be performed with some difficulty under pressure with non-flowing samples, it has not been clear how, or even if, continuously flowing SEC-SAXS, with its fragile media-packed columns, might work in an extreme high-pressure environment. Here we show, for the first time, that reproducible chromatographic separations coupled directly to high-pressure BioSAXS can be achieved at pressures up to at least 100 MPa and that pressure-induced changes in folding and oligomeric state and other properties can be observed. The apparatus described here functions at a range of temperatures (0°C-50°C), expanding opportunities for understanding biomolecular rules of life in deep ocean and subsurface environments.

Organoclastic sulfate reduction in deep-buried sediments: Evidence from authigenic carbonates of the Gulf of Mexico

The fate of organic matter in deep-buried marine sediments determines the formation of hydrocarbon reservoirs, shapes the deep biosphere, and affects the global carbon cycle. Several geochemical processes such as silicate weathering, iron and manganese (hydr)oxide reduction, and sulfate reduction influence the remineralization of organic matter in buried sediments. However, little information on deep-seated organoclastic sulfate reduction is available and the involved geochemical processes are largely unknown. Here, authigenic carbonates recovered from Ship Shoal Block 296 (SS296) of the Gulf of Mexico, all dominated by low-magnesium calcite, were investigated to constrain organoclastic sulfate reduction in deep-buried sediments. The SS296 carbonates had been previously suggested to be of a deep origin and transported upward by salt diapirism. The presence of cone-in-cone textures in samples 3110R1 and 3110R2 as well as vitrinite reflectance values of 0.48% to 0.58% indicate carbonate formation at a relatively deep burial. Likewise, clumped isotope thermometry yielded formation temperatures from 45 °C to 53 °C for sample 3110R1, 60 °C for sample 3110R2, and 11 °C to 37 °C for sample 3110R3. In spite of formation at greater depth, the temperatures of samples 3110R1 and 3110R2 are still within the temperature range of microbial sulfate reduction, reflecting formation depths between 1 km and 2.7 km. The presence of framboidal pyrite and its relatively low δ34S values (−27.8‰ to +11.5‰) agree with the occurrence of microbial sulfate reduction during carbonate precipitation. The carbon isotopic composition of the carbonates (δ13C: −16.6‰ to −8.9‰) and enclosed organic matter (δ13Corg: −26.8‰ to −20.5‰) suggests that organic matter is the dominant carbon source of carbonate minerals. This study confirms that microbial sulfate reduction occurs in deep-buried sediments, driving the degradation of organic matter. Our findings suggest that organoclastic sulfate reduction might be common in deep-seated sedimentary environments, controlling the fate of organic matter in deep subsurface environments and affecting the global carbon cycle.

Structural Responses of Nucleic Acids to Mars-Relevant Salts at Deep Subsurface Conditions.

High pressure deep subsurface environments of Mars may harbor high concentrations of dissolved salts, such as perchlorates, yet we know little about how these salts influence the conditions for life, particularly in combination with high hydrostatic pressure. We investigated the effects of high magnesium perchlorate concentrations compared to sodium and magnesium chloride salts and high pressure on the conformational dynamics and stability of double-stranded B-DNA and, as a representative of a non-canonical DNA structure, a DNA-hairpin (HP), whose structure is known to be rather pressure-sensitive. To this end, fluorescence spectroscopies including single-molecule FRET methodology were applied. Our results show that the stability both of the B-DNA as well as the DNA-HP is largely preserved at high pressures and high salt concentrations, including the presence of chaotropic perchlorates. The perchlorate anion has a small destabilizing effect compared to chloride, however. These results show that high pressures at the kbar level and perchlorate anions can modify the stability of nucleic acids, but that they do not represent a barrier to the gross stability of such molecules in conditions associated with the deep subsurface of Mars.

Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion.

Sulfate-reducing bacteria (SRB) have a unique ability to respire under anaerobic conditions using sulfate as a terminal electron acceptor, reducing it to hydrogen sulfide. SRB thrives in many natural environments (freshwater sediments and salty marshes), deep subsurface environments (oil wells and hydrothermal vents), and processing facilities in an industrial setting. Owing to their ability to alter the physicochemical properties of underlying metals, SRB can induce fouling, corrosion, and pipeline clogging challenges. Indigenous SRB causes oil souring and associated product loss and, subsequently, the abandonment of impacted oil wells. The sessile cells in biofilms are 1,000 times more resistant to biocides and induce 100-fold greater corrosion than their planktonic counterparts. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation and corrosion. Here, we examine the critical genes involved in biofilm formation and microbiologically influenced corrosion and categorize them into various functional categories. The current effort also discusses chemical and biological methods for controlling the SRB biofilms. Finally, we highlight the importance of surface engineering approaches for controlling biofilm formation on underlying metal surfaces.

Novel Microbial Groups Drive Productivity in an Archean Iron Formation.

Deep subsurface environments are decoupled from Earth’s surface processes yet diverse, active, and abundant microbial communities thrive in these isolated environments. Microbes inhabiting the deep biosphere face unique challenges such as electron donor/acceptor limitations, pore space/fracture network limitations, and isolation from other microbes within the formation. Of the few systems that have been characterized, it is apparent that nutrient limitations likely facilitate diverse microbe-microbe interactions (i.e., syntrophic, symbiotic, or parasitic) and that these interactions drive biogeochemical cycling of major elements. Here we describe microbial communities living in low temperature, chemically reduced brines at the Soudan Underground Mine State Park, United States. The Soudan Iron mine intersects a massive hematite formation at the southern extent of the Canadian Shield. Fractured rock aquifer brines continuously flow from exploratory boreholes drilled circa 1960 and are enriched in deuterium compared to the global meteoric values, indicating brines have had little contact with surface derived waters, and continually degas low molecular weight hydrocarbons C1-C4. Microbial enrichments suggest that once brines exit the boreholes, oxidation of the hydrocarbons occur. Amplicon sequencing show these borehole communities are low in diversity and dominated by Firmicute and Proteobacteria phyla. From the metagenome assemblies, we recovered approximately thirty genomes with estimated completion over 50%. Analysis of genome taxonomy generally followed the amplicon data, and highlights that several of the genomes represent novel families and genera. Metabolic reconstruction shows two carbon-fixation pathways were dominant, the Wood-Ljungdahl (acetogenesis) and Calvin-Benson-Bassham (via RuBisCo), indicating that inorganic carbon likely enters into the microbial foodweb with differing carbon fractionation potentials. Interestingly, methanogenesis is likely driven by Methanolobus and suggests cycling of methylated compounds and not H2/CO2 or acetate. Furthermore, the abundance of sulfate in brines suggests cryptic sulfur cycling may occur, as we detect possible sulfate reducing and thiosulfate oxidizing microorganisms. Finally, a majority of the microorganisms identified contain genes that would allow them to participate in several element cycles, highlighting that in these deep isolated systems metabolic flexibility may be an important life history trait.

High-resolution, long-term isotopic and isotopologue variation identifies the sources and sinks of methane in a deep subsurface carbon cycle

This study applies a combined isotope and doubly-substituted isotopologue (‘clumped’) methane approach to samples collected over a 9-year long-term experiment at the Kidd Creek scientific observatory located 2.4 and 2.9 km depth below surface, combined with previously published data from 2.1 km below surface. The observatory is located in a fractured rock system within Kidd Creek Mine in Timmins, Ontario, Canada, situated within a 2.7 Ga Volcanogenic Massive Sulphide (VMS) deposit on the Canadian Shield. Isotope and isotopologue methane data suggest a temporal variation in the various sources of methane within the fracture fluids system between 2.1 and 2.9 km below surface. Predominantly abiogenic methane is identified in samples collected from the deepest level of the mine (2.9 km). Comparing new data from the 2.4 km level with previous data from 2.1 km suggests addition of a small component of microbially-generated methane to the fracture water systems at 2.4 km. The temporal evolution of the methane isotopologue signatures suggest an additional process is occurring within these waters. Specifically, methane in samples from 2.4 km (and some from 2.9 km) approach low-temperature thermodynamic equilibrium in clumped isotopologue space, which is not consistent with kinetically-controlled methane production (either microbial or abiogenic). Anaerobic Oxidation of Methane (AOM) during microbial methanotrophy is shown to be the most likely process to drive such re-equilibration via isotopic bond re-ordering. This study provides an unprecedented high-resolution temporal record over more than a decade for methane in a deep subsurface crystalline environment and demonstrates the advantages of clumped isotopologue studies to identify multiple processes controlling the methane cycle in these systems including both abiotic and biotic methane production and methanotrophy.

High pressures increase \u03b1-chymotrypsin enzyme activity under perchlorate stress

Deep subsurface environments can harbour high concentrations of dissolved ions, yet we know little about how this shapes the conditions for life. We know even less about how the combined effects of high pressure influence the way in which ions constrain the possibilities for life. One such ion is perchlorate, which is found in extreme environments on Earth and pervasively on Mars. We investigated the interactions of high pressure and high perchlorate concentrations on enzymatic activity. We demonstrate that high pressures increase α-chymotrypsin enzyme activity even in the presence of high perchlorate concentrations. Perchlorate salts were shown to shift the folded α-chymotrypsin phase space to lower temperatures and pressures. The results presented here may suggest that high pressures increase the habitability of environments under perchlorate stress. Therefore, deep subsurface environments that combine these stressors, potentially including the subsurface of Mars, may be more habitable than previously thought.

Repetitive Sampling and Control Threshold Improve 16S rRNA Gene Sequencing Results From Produced Waters Associated With Hydraulically Fractured Shale

Sequencing microbial DNA from deep subsurface environments is complicated by a number of issues ranging from contamination to non-reproducible results. Many samples obtained from these environments – which are of great interest due to the potential to stimulate microbial methane generation – contain low biomass. Therefore, samples from these environments are difficult to study as sequencing results can be easily impacted by contamination. In this case, the low amount of sample biomass may be effectively swamped by the contaminating DNA and generate misleading results. Additionally, performing field work in these environments can be difficult, as researchers generally have limited access to and time on site. Therefore, optimizing a sampling plan to produce the best results while collecting the greatest number of samples over a short period of time is ideal. This study aimed to recommend an adequate sampling plan for field researchers obtaining microbial biomass for 16S rRNA gene sequencing, applicable specifically to low biomass oil and gas-producing environments. Forty-nine different samples were collected by filtering specific volumes of produced water from a hydraulically fractured well producing from the Niobrara Shale. Water was collected in two different sampling events 24 h apart. Four to five samples were collected from 11 specific volumes. These samples along with eight different blanks were submitted for analysis. DNA was extracted from each sample, and quantitative polymerase chain reaction (qPCR) and 16S rRNA Illumina MiSeq gene sequencing were performed to determine relative concentrations of biomass and microbial community composition, respectively. The qPCR results varied across sampled volumes, while no discernible trend correlated contamination to volume of water filtered. This suggests that collecting a larger volume of sample may not result in larger biomass concentrations or better representation of a sampled environment. Researchers could prioritize collecting many low volume samples over few high-volume samples. Our results suggest that there also may be variability in the concentration of microbial communities present in produced waters over short (i.e., hours) time scales, which warrants further investigation. Submission of multiple blanks is also vital to determining how contamination or low biomass effects may influence a sample set collected from an unknown environment.

Potential for Liquid Water Biochemistry Deep under the Surfaces of the Moon, Mars, and beyond

Abstract We investigate the prospects for the past or current existence of habitable conditions deep underneath the surfaces of the Moon and Mars, as well as generic bound and free-floating extrasolar rocky objects. We construct a simple model that takes into account the thermal limits of life as well as the size, surface temperature, and relative radionuclide abundance of a given object and yields the spatial extent of the subsurface habitable region. We also investigate the constraint imposed by pressure on habitability, and show that it is unlikely to rule out the prospects for life altogether. We estimate the maximum biomass that might be sustainable in deep subsurface environments as a function of the aforementioned parameters from an energetic perspective. We find that it might be a few percent that of Earth’s subsurface biosphere, and three orders of magnitude smaller than Earth’s global biomass, under ideal circumstances. We conclude with a brief exposition of the prevalence of rocky objects with deep biospheres and methods for detecting signatures of biological activity through forthcoming missions to visit the Moon and Mars.

Influence of chromate adsorption and reduction on transport and retention of biochar colloids in saturated porous media

Biochar (BC) has been proposed as an effective and promising adsorbent for the remediation of contaminated soils. While growing numbers of studies have reported the adsorption and immobilization of Cr(VI) on BC materials, very little is known about the mobility and retention of Cr-sorbed BC (Cr-BC) colloids, which may act as a carrier of the adsorbed Cr species, migrate along the soil profile and pose risk to deep subsurface environments. In this study, wheat straw BC samples prepared through pyrolysis at 450 °C and 600 °C (BC450 and BC600) were applied in Cr(VI) adsorption, and the resultant Cr-BC450 and Cr-BC600 colloids were further used to examine the effects of Cr(VI) adsorption amount, ionic strength and pyrolysis temperature on Cr-BC transport and retention in saturated porous media. Our results indicated that the reductive adsorption of Cr(VI) resulted in less negative zeta potential and enlarged hydrodynamic diameter of the BC colloids. For BC produced at a specific temperature, the mobility of Cr-BC colloids decreased with increasing Cr(VI) adsorption amount. For BC450 incubated with Cr(VI) (pH 2.0, 20 h), increasing ionic strength (1-5 mM NaCl) decreased the colloid mobility, and a transition from blocking to ripening occurred. In comparison to BC600, BC450 not only possessed higher Cr(VI) adsorption capacity, but also demonstrated higher mobility after Cr(VI) adsorption and reduction. The Derjaguin-Landau-Verwey-Overbeek theory and the two-site kinetic retention model were utilized to interpret the transport behaviors. Our findings suggested that the mobility of BC colloid was retarded after Cr(VI) adsorption and reduction, which could provide lasting benefits for Cr(VI) stabilization. However, the transport of Cr-BC cannot be neglected and should be considered during the application of BC in remediation of contaminated soil. This study for the first time revealed the importance of reductive adsorption in affecting the mobility of BC colloids. The transport of Cr species that associated with BC carriers should be considered during remediation of Cr(VI)-contaminated sites.

Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context.

The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.