A hydrogen-based subsurface microbial community dominated by methanogens

Methanogens and what they tell us about how life might survive on Mars

Space exploration and research are uncovering the potential for terrestrial life to survive in outer space, as well as the environmental factors that affect life during interplanetary transfer. The presence of methane in the Martian atmosphere suggests the possibility of methanogens, either extant or extinct, on Mars. Understanding how methanogens survive and adapt under space-exposed conditions is crucial for understanding the implications of extraterrestrial life. In this article, we discuss methanogens as model organisms for obtaining energy transducers and producing methane in a simulated Martian environment. We also explore the chemical evolution of cellular composition and growth maintenance to support survival in extraterrestrial environments. Neutral selective pressure is imposed on the chemical composition of cellular components to increase cell survival and reduce growth under physiological conditions. Energy limitation is an evolutionary driver of macromolecular polymerization, growth maintenance, and survival fitness of methanogens. Methanogens grown in a Martian environment may exhibit global alterations in their metabolic function and gene expression at the system scale. A space systems biology approach would further elucidate molecular survival mechanisms and adaptation to a drastic outer space environment. Therefore, identifying a genetically stable methanogenic community is essential for biomethane production from waste recycling to achieve sustainable space-life support functions.

Artificial SLiMEs and gas storage in deep subsurface

Over the next few years, it is planned to convert all or part of the underground gas storage (UGS) facilities used for natural gas (salt caverns, depleted hydrocarbon reservoirs and deep aquifers) into underground hydrogen (H2) storage (UHS) reservoirs. These deep environments host microbial communities, some of which are hydrogenotrophic (sulfate reducers, acetogens and methanogens). The current state of microbiological knowledge is thus presented for the three types of UGS facilities. In the mid-1990s, the concept of anaerobic subsurface lithoautotrophic microbial ecosystems, or SLiMEs, emerged. It is expected that the large-scale injection of hydrogen into subsurface environments will generate new microbial ecosystems called artificial SLiMEs, which could persist over time. These artificial SLiMEs could lead to hydrogen loss, an intense methanogenic activity, a degradation of gas quality and a risk to installations through sulfide production. However, recent studies on salt caverns and deep aquifers suggest that hydrogenotrophic microbial activity also leads to alkalinisation (up to pH 10), which can constrain hydrogenotrophy. Therefore, studying and understanding these artificial SLiMEs is both a necessity for the development of the hydrogen industry and presents an opportunity for ecologists to monitor the evolution of deep environments in real time.

Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden

The continental bedrock contains groundwater-bearing fractures that are home to microbial populations that are vital in mediating the Earth's biogeochemical cycles. However, their diversity is poorly understood due to the difficulty of obtaining samples from this environment. Here, a groundwater-bearing fracture at 975 m depth was isolated by employing packers in order to characterize the microbial community via metagenomes combined with prokaryotic and eukaryotic marker genes (16S and 18S ribosomal RNA gene). Genome-resolved analyses revealed a community dominated by sulfate-reducing Bacillota, predominantly represented by Candidatus Desulforudis audaxviator and with Wood-Ljungdahl as the most prevalent pathway for inorganic carbon fixation. Moreover, the eukaryotic community had a considerable diversity and was comprised of mainly flatworms, chlorophytes, crustaceans, ochrophytes, and fungi. These findings support the important role of the Bacillota, with the sulfate reducer Candidatus Desulforudis audaxviator as its main representative, as primary producers in the often energy-limited groundwaters of the continental subsurface.

The Saint-Leonard Urban Glaciotectonic Cave Harbors Rich and Diverse Planktonic and Sedimentary Microbial Communities

The terrestrial subsurface harbors unique microbial communities that play important biogeochemical roles and allow for studying a yet unknown fraction of the Earth's biodiversity. The Saint-Leonard cave in Montreal City (Canada) is of glaciotectonic origin. Its speleogenesis traces back to the withdrawal of the Laurentide Ice Sheet 13,000 years ago, during which the moving glacier dislocated the sedimentary rock layers. Our study is the first to investigate the microbial communities of the Saint-Leonard cave. By using amplicon sequencing, we analyzed the taxonomic diversity and composition of bacterial, archaeal and eukaryote communities living in the groundwater (0.1 µm- and 0.2 µm-filtered water), in the sediments and in surface soils. We identified a microbial biodiversity typical of cave ecosystems. Communities were mainly shaped by habitat type and harbored taxa associated with a wide variety of lifestyles and metabolic capacities. Although we found evidence of a geochemical connection between the above soils and the cave's galleries, our results suggest that the community assembly dynamics are driven by habitat selection rather than dispersal. Furthermore, we found that the cave's groundwater, in addition to being generally richer in microbial taxa than sediments, contained a considerable diversity of ultra-small bacteria and archaea.

Assessment of the in situ biomethanation potential of a deep aquifer used for natural gas storage

The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of underground geological storage sites, such as deep aquifers, used for natural gas storage into future underground hydrogen storage sites is the favored scenario. However, these sites contain microorganisms capable of consuming H2, mainly sulfate reducers and methanogens. Methanogenesis is, therefore expected but its intensity must be evaluated. Here, in a deep aquifer used for underground geological storage, 17 sites were sampled, with low sulfate concentrations ranging from 21.9 to 197.8 µM and a slow renewal of formation water. H2-selected communities mainly were composed of the families Methanobacteriaceae and Methanothermobacteriaceae and the genera Desulfovibrio, Thermodesulfovibrio, and Desulforamulus. Experiments were done under different conditions, and sulfate reduction, as well as methanogenesis, were demonstrated in the presence of a H2 or H2/CO2 (80/20) gas phase, with or without calcite/site rock. These metabolisms led to an increase in pH up to 10.2 under certain conditions (without CO2). The results suggest competition for CO2 between lithoautotrophs and carbonate mineral precipitation, which could limit microbial H2 consumption.

Microbial hydrogen sinks in the sand-bentonite backfill material for the deep geological disposal of radioactive waste

The activity of subsurface microorganisms can be harnessed for engineering projects. For instance, the Swiss radioactive waste repository design can take advantage of indigenous microorganisms to tackle the issue of a hydrogen gas (H2) phase pressure build-up. After repository closure, it is expected that anoxic steel corrosion of waste canisters will lead to an H2 accumulation. This occurrence should be avoided to preclude damage to the structural integrity of the host rock. In the Swiss design, the repository access galleries will be back-filled, and the choice of this material provides an opportunity to select conditions for the microbially-mediated removal of excess gas. Here, we investigate the microbial sinks for H2. Four reactors containing an 80/20 (w/w) mixture of quartz sand and Wyoming bentonite were supplied with natural sulfate-rich Opalinus Clay rock porewater and with pure H2 gas for up to 108 days. Within 14 days, a decrease in the sulfate concentration was observed, indicating the activity of the sulfate-reducing bacteria detected in the reactor, e.g., from Desulfocurvibacter genus. Additionally, starting at day 28, methane was detected in the gas phase, suggesting the activity of methanogens present in the solid phase, such as the Methanosarcina genus. This work evidences the development, under in-situ relevant conditions, of a backfill microbiome capable of consuming H2 and demonstrates its potential to contribute positively to the long-term safety of a radioactive waste repository.

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

BACKGROUND

Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling.

RESULTS

Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems.

CONCLUSIONS

Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.

Microbial interactions with phosphorus containing glasses representative of vitrified radioactive waste

The presence of phosphorus in borosilicate glass (at 0.1 - 1.3 mol% P2O5) and in iron-phosphate glass (at 53 mol% P2O5) stimulated the growth and metabolic activity of anaerobic bacteria in model systems. Dissolution of these phosphorus containing glasses was either inhibited or accelerated by microbial metabolic activity, depending on the solution chemistry and the glass composition. The breakdown of organic carbon to volatile fatty acids increased glass dissolution. The interaction of microbially reduced Fe(II) with phosphorus-containing glass under anoxic conditions decreased dissolution rates, whereas the interaction of Fe(III) with phosphorus-containing glass under oxic conditions increased glass dissolution. Phosphorus addition to borosilicate glasses did not significantly affect the microbial species present, however, the diversity of the microbial community was enhanced on the surface of the iron phosphate glass. Results demonstrate the potential for microbes to influence the geochemistry of radioactive waste disposal environments with implication for wasteform durability.

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.

Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters

The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood-Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community's capacity, with up to 9.9% of fermentation, 6.4% of the Wood-Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.

Monolithic Three-Dimensional Integration of Carbon Nanotube Circuits and Sensors for Smart Sensing Chips

Semiconducting carbon nanotube (CNT) film is a promising material for constructing high-performance complementary metal-oxide-semiconductor (CMOS) integrated circuits (ICs) and highly sensitive field-effect transistor (FET) bio/chemical sensors. Moreover, CNT logic transistors and sensors can be integrated through a compatible low-temperature fabrication process, providing enough thermal budget to construct monolithic three-dimensional (M3D) systems for smart sensors. However, an M3D sensing chip based on CNT film has not yet been demonstrated. In this work, we develop M3D technology to fabricate CNT CMOS ICs and CNT sensor arrays in two different layers; then, we demonstrate a preliminary M3D sensing system comprising CNT CMOS interfacing ICs in the bottom layer and CNT sensors in the upper layer through interlayer vias as links. As a typical example, a highly sensitive hydrogen sensing IC has been demonstrated to perform in situ sensing and processing functions through upper-layer FET-based hydrogen sensors exposed to the environment and bottom-layer CNT CMOS voltage-controlled oscillator (VCO) interfacing circuits. The M3D CNT sensing ICs convert hydrogen concentration information (8-128 ppm) to digital frequency information (0.78-1.11 GHz) with a sensitivity of 2.75 MHz/ppm. M3D sensing technology is expected to provide a universal sensing system for future smart sensing chips, including multitarget detection and ultralow power sensors.

A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters

Oxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and climate active trace gas production and consumption. Global warming is causing oxygen-deficient waters to expand and intensify. Therefore, studies focused on microbial communities inhabiting oxygen-deficient regions are necessary to both monitor and model the impacts of climate change on marine ecosystem functions and services. Here we present a compendium of 5,129 single-cell amplified genomes (SAGs) from marine environments encompassing representative OMZ and AMZ geochemical profiles. Of these, 3,570 SAGs have been sequenced to different levels of completion, providing a strain-resolved perspective on the genomic content and potential metabolic interactions within OMZ and AMZ microbiomes. Hierarchical clustering confirmed that samples from similar oxygen concentrations and geographic regions also had analogous taxonomic compositions, providing a coherent framework for comparative community analysis.

Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt

Microbial activity is a major contributor to the biogeochemical cycles that make up the life support system of planet Earth. A 613 m deep geomicrobiological perforation and a systematic multi-analytical characterization revealed an unexpected diversity associated with the rock matrix microbiome that operates in the subsurface of the Iberian Pyrite Belt (IPB). Members of 1 class and 16 genera were deemed the most representative microorganisms of the IPB deep subsurface and selected for a deeper analysis. The use of fluorescence in situ hybridization allowed not only the identification of microorganisms but also the detection of novel activities in the subsurface such as anaerobic ammonium oxidation (ANAMMOX) and anaerobic methane oxidation, the co-occurrence of microorganisms able to maintain complementary metabolic activities and the existence of biofilms. The use of enrichment cultures sensed the presence of five different complementary metabolic activities along the length of the borehole and isolated 29 bacterial species. Genomic analysis of nine isolates identified the genes involved in the complete operation of the light-independent coupled C, H, N, S and Fe biogeochemical cycles. This study revealed the importance of nitrate reduction microorganisms in the oxidation of iron in the anoxic conditions existing in the subsurface of the IPB.

Microbiological analysis, antimicrobial activity, heavy-metals content and physico-chemical properties of Fijian mud pool samples

The hot springs are home to a rich bacterial diversity which could be the source of enzymes, antibiotics and many other commercially important products. Most of the hot springs present in Fiji are unexplored and their analysis of microbial diversity could be of great interest in facilitating various industrial, agricultural and medicinal applications. This study is an attempt to evaluate the heavy metal concentration and to analyze the comprehensive bacterial diversity of two Fijian thermal mud pools, namely Sabeto and Tifajek. The two hot springs have a pH of 7.28 to 7.19 and a temperature of 32.2 to 38.8 °C, respectively. Mean metal concentrations of the studied mud samples ranged from 4.758 to 6.870 mg/kg and followed a decreasing sequence as Fe > Mn > Zn > Na > Ni > Cd > Ca > Cr > Cu. Levels of Fe, Na, Mn, Zn, Ni, Cd, Ca, Cr, Cu in the mud pool samples were within World Health Organisation (WHO) limits, while Cd was above regulatory limits. The heavy metals analysis results showed that both mud pools had high values for Cd, above the WHO limit of 3 mg/kg. In addition, 8 strains of actinomycetes were successfully identified for the first time in the Sabeto mud pool, where most of them showed antibacterial activity. The genetic identification of most isolates was determined in BLASTn analyses of their 16S rRNA sequences. Isolates were identified as that of Streptomyces, Nocardia and Rhodococcus genus. Further, AntiSMASH results of the closest relatives of cultured actinobacteria have shown to produce antibiotics, natural pesticides and other compounds of various usage. This study also found no fecal coliforms and supports existing knowledge and practice of using Fijian thermal mud pools for their therapeutic properties. Overall, the presented work indicated that the studied mud pools have therapeutic properties, harboring wealth of bacteria with antibiotic profiles and were risk free from health-related issues of heavy metals and disease-causing pathogens. It provides great insight into the studied mud pools which serves as a baseline from which further heavy metal monitoring or mitigation programs and microbial researches can be conducted.

Science Objectives for Flagship-Class Mission Concepts for the Search for Evidence of Life at Enceladus

Cassini revealed that Saturn's Moon Enceladus hosts a subsurface ocean that meets the accepted criteria for habitability with bio-essential elements and compounds, liquid water, and energy sources available in the environment. Whether these conditions are sufficiently abundant and collocated to support life remains unknown and cannot be determined from Cassini data. However, thanks to the plume of oceanic material emanating from Enceladus' south pole, a new mission to Enceladus could search for evidence of life without having to descend through kilometers of ice. In this article, we outline the science motivations for such a successor to Cassini, choosing the primary science goal to be determining whether Enceladus is inhabited and assuming a resource level equivalent to NASA's Flagship-class missions. We selected a set of potential biosignature measurements that are complementary and orthogonal to build a robust case for any life detection result. This result would be further informed by quantifications of the habitability of the environment through geochemical and geophysical investigations into the ocean and ice shell crust. This study demonstrates that Enceladus' plume offers an unparalleled opportunity for in situ exploration of an Ocean World and that the planetary science and astrobiology community is well equipped to take full advantage of it in the coming decades.

Transformation of low molecular weight organic acids by microbial endoliths in subsurface mafic and ultramafic igneous rock

A growing body of work indicates that continental subsurface rocks host a substantial portion of the Earth's biosphere. However, the activities of microbial cells inhabiting pore spaces and microfractures in subsurface rocks remain underexplored. Here, we develop and optimize microcosm assays to detect organic acid transformation activities of cells residing in mafic to ultramafic igneous rocks. Application of this assay to gabbro core from the Stillwater Mine, Montana, USA, revealed maximal methane production from acetate at temperatures approximating that of the mine. Controls show that these activities are not due to contamination introduced during drilling, exhumation, or laboratory processing of the core. The assay was then applied to rocks cored from the Samail Ophiolite, Oman, which is undergoing low temperature serpentinization. Production of i) carbon dioxide from acetate and formate and ii) methane from formate were detected in a dunite/harzburgite rock core interfacing pH 9.6 waters, and estimates of microbial activities were up to three orders of magnitude higher in the rock core pore space than in corresponding waters. The detection of endolithic microbial activities in igneous rocks has implications for life detection on other planetary bodies where similar rock types prevail, such as Mars, Europa, and Enceladus. This article is protected by copyright. All rights reserved.

Particulate Matter in Swine Barns: A Comprehensive Review

Particulate matter (PM) represents an air quality management challenge for confined swine production systems. Due to the limited space and ventilation rate, PM can reach relatively high concentrations in swine barns. PM in swine barns possesses different physical, chemical, and biological characteristics than that in the atmosphere and other indoor environments. As a result, it exerts different environmental and health effects and creates some unique challenges regarding PM measurement and mitigation. Numerous research efforts have been made, generating massive data and information. However, relevant review reports are sporadic. This study aims to provide an updated comprehensive review of swine barn PM, focusing on publications since 1990. It covers various topics including PM characteristics, sources, measurement methods, and in-barn mitigation technologies. As PM in swine barns is primarily of biological origins, bioaerosols are reviewed in great detail. Relevant topics include bacterial/fungal counts, viruses, microbial community composition, antibiotic-resistant bacteria, antibiotic resistance genes, endotoxins, and (1→3)-β-D-glucans. For each topic, existing knowledge is summarized and discussed and knowledge gaps are identified. Overall, PM in swine barns is complicated in chemical and biological composition and highly variable in mass concentrations, size, and microbial abundance. Feed, feces, and skins constitute the major PM sources. Regarding in-barn PM mitigation, four technologies (oil/water sprinkling, ionization, alternation of feed and feeders, and recirculating air filtration) are dominant. However, none of them have been widely used in commercial barns. A collective discussion of major knowledge gaps and future research needs is offered at the end of the report.

The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects

Rocks that react with liquid water are widespread but spatiotemporally limited throughout the solar system, except for Earth. Rock-forming minerals with high iron content and accessory minerals with high amounts of radioactive elements are essential to support rock-hosted microbial life by supplying organics, molecular hydrogen, and/or oxidants. Recent technological advances have broadened our understanding of the rocky biosphere, where microbial inhabitation appears to be difficult without nutrient and energy inputs from minerals. In particular, microbial proliferation in igneous rock basements has been revealed using innovative geomicrobiological techniques. These recent findings have dramatically changed our perspective on the nature and the extent of microbial life in the rocky biosphere, microbial interactions with minerals, and the influence of external factors on habitability. This study aimed to gather information from scientific and/or technological innovations, such as omics-based and single-cell level characterizations, targeting deep rocky habitats of organisms with minimal dependence on photosynthesis. By synthesizing pieces of rock-hosted life, we can explore the evo-phylogeny and ecophysiology of microbial life on Earth and the life’s potential on other planetary bodies.

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

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

Biological production of H2 , CH4 and CO2 in the deep subsurface of the Iberian Pyrite Belt

Most of the terrestrial deep subsurfaces are oligotrophic environments in which some gases, mainly H₂ , CH₄ and CO₂ , play an important role as energy and/or carbon sources. In this work, we assessed their biotic and abiotic origin in samples from subsurface hard-rock cores of the Iberian Pyrite Belt (IPB) at three different depths (414, 497 and 520 m). One set of samples was sterilized (abiotic control) and all samples were incubated under anaerobic conditions. Our results showed that H₂ , CH₄ and CO₂ remained low and constant in the sterilized controls while their levels were 4, 4.1 and 2.5 times higher respectively, in the unsterilized samples compared to the abiotic controls. The δ¹³ C_CH4 -values measured in the samples (range -31.2 to -43.0 ‰) reveals carbon isotopic signatures that are within the range for biological methane production. Possible microorganisms responsible for the biotic production of the gases were assessed by CARD-FISH. The analysis of sequenced genomes of detected microorganisms within the subsurface of the IPB allowed to identify possible metabolic activities involved in H₂ (Rhodoplanes, Shewanella and Desulfosporosinus), CH₄ (Methanobacteriales) and CO₂ production. The obtained results suggest that part of the H₂ , CH₄ and CO₂ detected in the deep subsurface has a biological origin.

A novel relationship for the maximum specific growth rate of a microbial guild

One of the major parameters that characterizes the kinetics of microbial processes is the maximum specific growth rate. The maximum specific growth rate for a single microorganism (${\mu _{max}}$) is fairly constant. However, a certain microbial process is typically catalyzed by a group of microorganisms (guild) that have various ${\mu _{max}}$ values. In many occasions, it is not feasible to breakdown a guild into its constituent microorganisms. Therefore, it is a common practice to assume a constant maximum specific growth rate for the guild ($\acute{\mu}_{max}$) and determine its value by fitting experimental data. This assumption is valid for natural environments, where microbial guilds are stabilized and dominated by microorganisms that grow optimally in those environments' conditions. However, a change in an environment's conditions will trigger a community shift by favoring some of the microorganisms. This shift leads to a variable ${\acute{\mu}_{max}}$ as long as substrate availability is significantly higher than substrate affinity constant. In this work, it is illustrated that the assumption of constant ${\acute{\mu}_{max}}$ may underestimate or overestimate microbial growth. To circumvent this, a novel relationship that characterizes changes in ${\acute{\mu}_{max}}$ under abundant nutrient availability is proposed. The proposed relationship is evaluated for various random microbial guilds in batch experiments.

Characterization of Microbial Diversity and Community Structure in Fermentation Pit Mud of Different Ages for Production of Strong-Aroma Baijiu

In the traditional fermentation process of strong-aroma Baijiu, a fermentation pit mud (FPM) provides many genera of microorganisms for fermentation. However, the functional microorganisms that have an important effect on the quality of Baijiu and their changes with the age of fermentation pit (FP) are poorly understood. Herein, the Roche 454 pyrosequencing technique and a phospholipid fatty-acid analysis were employed to reveal the structure and diversity of prokaryotic communities in FPM samples that have been aged for 5, 30, and 100 years. The results revealed an increase in total prokaryotic biomass with an FP age; however, Shannon’s diversity index decreased significantly (p < 0.01). These results suggested that a unique microbial community structure evolved with uninterrupted use of the FP. The number of functional microorganisms, which could produce the flavor compounds of strong-aroma Baijiu, increased with the FP age. Among them, Clostridium and Ruminococcaceae are microorganisms that directly produce caproic acid. The increase of their relative abundance in the FPM might have improved the quality of strong-aroma Baijiu. Syntrophomonas, Methanobacterium, and Methanocorpusculum might also be beneficial to caproic acid production. They are not directly involved but provide possible environmental factors for caproic acid production. Overall, our study results indicated that an uninterrupted use of the FP shapes the particular microbial community structure in the FPM. This research provides scientific support for the concept that the aged FP yields a high-quality Baijiu.

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

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

A Model of Aerobic and Anaerobic Metabolism of Hydrogen in the Extremophile Acidithiobacillus ferrooxidans

Hydrogen can serve as an electron donor for chemolithotrophic acidophiles, especially in the deep terrestrial subsurface and geothermal ecosystems. Nevertheless, the current knowledge of hydrogen utilization by mesophilic acidophiles is minimal. A multi-omics analysis was applied on Acidithiobacillus ferrooxidans growing on hydrogen, and a respiratory model was proposed. In the model, [NiFe] hydrogenases oxidize hydrogen to two protons and two electrons. The electrons are used to reduce membrane-soluble ubiquinone to ubiquinol. Genetically associated iron-sulfur proteins mediate electron relay from the hydrogenases to the ubiquinone pool. Under aerobic conditions, reduced ubiquinol transfers electrons to either cytochrome aa ₃ oxidase via cytochrome bc ₁ complex and cytochrome c ₄ or the alternate directly to cytochrome bd oxidase, resulting in proton efflux and reduction of oxygen. Under anaerobic conditions, reduced ubiquinol transfers electrons to outer membrane cytochrome c (ferrireductase) via cytochrome bc ₁ complex and a cascade of electron transporters (cytochrome c ₄, cytochrome c ₅₅₂, rusticyanin, and high potential iron-sulfur protein), resulting in proton efflux and reduction of ferric iron. The proton gradient generated by hydrogen oxidation maintains the membrane potential and allows the generation of ATP and NADH. These results further clarify the role of extremophiles in biogeochemical processes and their impact on the composition of the deep terrestrial subsurface.

Metagenomics revealing molecular profiling of community structure and metabolic pathways in natural hot springs of the Sikkim Himalaya

BACKGROUND

Himalaya is an ecologically pristine environment. The geo-tectonic activities have shaped various environmental niches with diverse microbial populations throughout the Himalayan biosphere region. Albeit, limited information is available in terms of molecular insights into the microbiome, including the uncultured microbes, of the Himalayan habitat. Hence, a vast majority of genomic resources are still under-explored from this region. Metagenome analysis has simplified the extensive in-depth exploration of diverse habitats. In the present study, the culture-independent whole metagenome sequencing methodology was employed for microbial diversity exploration and identification of genes involved in various metabolic pathways in two geothermal springs located at different altitudes in the Sikkim Himalaya.

RESULTS

The two hot springs, Polok and Reshi, have distinct abiotic conditions. The average temperature of Polok and Reshi was recorded to be 62 °C and 43 °C, respectively. Both the aquatic habitats have alkaline geochemistry with pH in the range of 7-8. Community profile analysis revealed genomic evidence of plentiful bacteria, with a minute fraction of the archaeal population in hot water reservoirs of Polok and Reshi hot spring. Mesophilic microbes belonging to Proteobacteria and Firmicutes phyla were predominant at both the sites. Polok exhibited an extravagant representation of Chloroflexi, Deinococcus-Thermus, Aquificae, and Thermotogae. Metabolic potential analysis depicted orthologous genes associated with sulfur, nitrogen, and methane metabolism, contributed by the microflora in the hydrothermal system. The genomic information of many novel carbohydrate-transforming enzymes was deciphered in the metagenomic description. Further, the genomic capacity of antimicrobial biomolecules and antibiotic resistance were discerned.

CONCLUSION

The study provided comprehensive molecular information about the microbial treasury as well as the metabolic features of the two geothermal sites. The thermal aquatic niches were found a potential bioresource of biocatalyst systems for biomass-processing. Overall, this study provides the whole metagenome based insights into the taxonomic and functional profiles of Polok and Reshi hot springs of the Sikkim Himalaya. The study generated a wealth of genomic data that can be explored for the discovery and characterization of novel genes encoding proteins of industrial importance.

Design of a bioaugmented multistage biofilter for accelerated municipal wastewater treatment and deactivation of pathogenic microorganisms

Biological treatment of municipal wastewater for reuse in irrigation is highly required, especially with the current global financial and water shortage crises. Bioaugmentation is a simple and cost-effective technology which could be a useful tool in alleviating this challenge. Thus, this study aimed to enhance the biological treatment of municipal wastewater using a bioaugmented substance supplemented in a three-stages bio-filter consisting of a sedimentation step followed by gravel biofiltration and then sand biofiltration at a laboratory scale. Also, a toxicity assay, the antimicrobial effect of the bioaugmented substance against pathogenic microorganisms, and identification of the synergistic effect of the bacterial consortium involved in the bioaugmented substance were studied. The bioaugmented substance was nontoxic and had an antimicrobial effect against the tested potentially pathogenic microorganisms (Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Staphylococcus aureus, and Candida albicans). The minimum effective concentration of the bioaugmented substance for organic, inorganic and microbial pollutants removal from high strength wastewater was 2.5 ppm with a contact time of 6-8 h. The removal efficiencies of H₂S, COD, BOD₅, total solids (TS), total dissolved solids, total suspended solids, ammonia, nitrate, phosphorus, and oil and grease reached 85, 93.4, 83.5, 37, 49.2, 93.4, 100, 55.7, 76.6 and 76.6%, respectively in the treated effluent after sand biofiltration. The physicochemical parameters of the treated wastewater effluent were below the Egyptian recommended limits (Law 84/1984) for use in irrigation. However, COD and BOD values were 90.33 and 38.46 mgO₂/L, respectively, and were still above the regulations (COD ≤60 and BOD ≤20). The high fecal coliforms count in the wastewater influent (8.4 × 10⁸ MPN-index/100 mL) were 95.1% removed after the sedimentation stage, and 99.99% removal was achieved after gravel and sand biofiltration. Thus, this study successfully designed a bioaugmented multistage biofiltration system for the effective removal of pollutants from wastewater, especially in resource-limited areas.

Advanced redox zonation of the San Pedro Sula alluvial aquifer (Honduras) using data fusion and multivariate geostatistics

The incorrect wastewater management and the land use distribution lead to severe environmental problems, creating heavy eutrophication condition in surface-water; when surface-water/groundwater relationships exist, the organic matter transferred to the aquifer oxidizes and triggers redox processes (i.e. Terminal Electron Accepting Processes, TEAPs), that provoke severe groundwater quality modifications and complicate its exploitation and management. For this reason, the definition of the redox zonation within an aquifer is an effective tool for the identification of the contamination sources and for the conceptual model refinement, when remediation strategies need to be planned. Although the redox processes are dynamic reactions, the aquifer redox zonation is generally aimed to identify homogenous zones, characterized by a predominant TEAP. To overcome this methodological approach, the Multi-Collocated Factorial Kriging (MCFK) was applied to redox-related physico-chemical parameters, which allowed identifying their spatial relationships at different scales, transferring this method from precision agriculture and soil science to hydrogeochemistry. The selected study area is the San Pedro Sula aquifer (Honduras), a multi-layer alluvial aquifer characterized by well-known surface-water/groundwater interactions and heavy eutrophicated streams. Here, high concentrations of Mn and Fe were found in the aquifer. The MCFK results identified a short-range (2300 m) factor, highlighting a strong relation between Mn concentrations and anoxic conditions, due to the organic matter transfer from eutrophicated surface-water into the aquifer. Simultaneously, the relationship between Fe and turbidity is related to a fine Fe(III) oxi-hydroxide colloidal phase, developed when different redox conditions of groundwater mix up in the wells. The long-range (6000 m) factor points out that Fe is related to redox processes at a wider scale, especially in the northern San Pedro Sula alluvial plain. These results are supported by both the Principal Component Analysis and the hydrogeochemical numerical modeling. As a result, different TEAPs occur simultaneously in contaminated areas, acting at multiple scales.

Microbially Mediated Ore-Forming Processes and Cell Mineralization

Sedimentary black shale-hosted manganese carbonate and oxide ores were studied by high-resolution in situ detailed optical and cathodoluminescence microscopy, Raman spectroscopy, and FTIR spectroscopy to determine microbial contribution in metallogenesis. This study of the Urucum Mn deposit in Brazil is included as a case study for microbially mediated ore-forming processes. The results were compared and interpreted in a comparative way, and the data were elaborated by a complex, structural hierarchical method. The first syngenetic products of microbial enzymatic oxidation were ferrihydrite and lepidocrocite on the Fe side, and vernadite, todorokite, birnessite, and manganite on the Mn side, formed under obligatory oxic (Mn) and suboxic (Fe) conditions and close to neutral pH. Fe- and Mn-oxidizing bacteria played a basic role in metallogenesis based on microtextural features, bioindicator minerals, and embedded variable organic matter. Trace element content is determined by source of elements and microbial activity. The present Urucum (Brazil), Datangpo (China), and Úrkút (Hungary) deposits are the result of complex diagenetic processes, which include the decomposition and mineralization of cell and extracellular polymeric substance (EPS) of Fe and Mn bacteria and cyanobacteria. Heterotrophic cell colonies activated randomly in the microbialite sediment after burial in suboxic neutral/alkaline conditions, forming Mn carbonates and variable cation-bearing oxides side by side with lithification and stabilization of minerals. Deposits of variable geological ages and geographical occurrences show strong similarities and indicate two-step microbial metallogenesis: a primary chemolithoautotrophic, and a diagenetic heterotrophic microbial cycle, influenced strongly by mineralization of cells and EPSs. These processes perform a basic role in controlling major and trace element distribution in sedimentary environments on a global level and place biogeochemical constraints on the element content of natural waters, precipitation of minerals, and water contaminants.

Paleo-Rock-Hosted Life on Earth and the Search on Mars: A Review and Strategy for Exploration

Here we review published studies on the abundance and diversity of terrestrial rock-hosted life, the environments it inhabits, the evolution of its metabolisms, and its fossil biomarkers to provide guidance in the search for life on Mars. Key findings are (1) much terrestrial deep subsurface metabolic activity relies on abiotic energy-yielding fluxes and in situ abiotic and biotic recycling of metabolic waste products rather than on buried organic products of photosynthesis; (2) subsurface microbial cell concentrations are highest at interfaces with pronounced chemical redox gradients or permeability variations and do not correlate with bulk host rock organic carbon; (3) metabolic pathways for chemolithoautotrophic microorganisms evolved earlier in Earth's history than those of surface-dwelling phototrophic microorganisms; (4) the emergence of the former occurred at a time when Mars was habitable, whereas the emergence of the latter occurred at a time when the martian surface was not continually habitable; (5) the terrestrial rock record has biomarkers of subsurface life at least back hundreds of millions of years and likely to 3.45 Ga with several examples of excellent preservation in rock types that are quite different from those preserving the photosphere-supported biosphere. These findings suggest that rock-hosted life would have been more likely to emerge and be preserved in a martian context. Consequently, we outline a Mars exploration strategy that targets subsurface life and scales spatially, focusing initially on identifying rocks with evidence for groundwater flow and low-temperature mineralization, then identifying redox and permeability interfaces preserved within rock outcrops, and finally focusing on finding minerals associated with redox reactions and associated traces of carbon and diagnostic chemical and isotopic biosignatures. Using this strategy on Earth yields ancient rock-hosted life, preserved in the fossil record and confirmable via a suite of morphologic, organic, mineralogical, and isotopic fingerprints at micrometer scale. We expect an emphasis on rock-hosted life and this scale-dependent strategy to be crucial in the search for life on Mars.

Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin

Deep fractured rock ecosystems across most of North America have not been studied extensively. However, the US Great Basin, in particular the Nevada National Security Site (NNSS, formerly the Nevada Test Site), has hosted a number of influential subsurface investigations over the years. This investigation focuses on resident microbiota recovered from a hydrogeologically confined aquifer in fractured Paleozoic carbonate rocks at 863 - 923 meters below land surface. Analysis of the microorganisms living in this oligotrophic environment provides a perspective into microbial metabolic strategies required to endure prolonged hydrogeological isolation deep underground. Here we present a microbiological and physicochemical characterization of a deep continental carbonate ecosystem and describe a bacterial genus isolated from the ecosystem. Strain DRI-13T is a strictly anaerobic, moderately thermophilic, fumarate-respiring member of the phylum Firmicutes. This bacterium grows optimally at 55°C and pH 8.0, can tolerate a concentration of 100 mM NaCl, and appears to obligately metabolize fumarate to acetate and succinate. Culture-independent 16S rRNA gene sequencing indicates a global subsurface distribution, while the closest cultured relatives of DRI-13T are Pelotomaculum thermopropionicum (90.0% similarity) and Desulfotomaculum gibsoniae (88.0% similarity). The predominant fatty acid profile is iso-C15 : 0, C15 : 0, C16 : 0 and C14 : 0. The percentage of the straight-chain fatty acid C15 : 0 is a defining characteristic not present in the other closely related species. The genome is estimated to be 3,649,665 bp, composed of 87.3% coding regions with an overall average of 45.1% G + C content. Strain DRI-13T represents a novel genus of subsurface bacterium isolated from a previously uncharacterized rock-hosted geothermal habitat. The characterization of the bacterium combined with the sequenced genome provides insights into metabolism strategies of the deep subsurface biosphere. Based on our characterization analysis we propose the name Thermoanaerosceptrum fracticalcis (DRI-13T = DSM 100382T = ATCC TSD-12T).

Geological gas-storage shapes deep life

Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H₂ ) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time.

Rock-crushing derived hydrogen directly supports a methanogenic community: significance for the deep biosphere

Microbial populations exist to great depths on Earth, but with apparently insufficient energy supply. Earthquake rock fracturing produces H₂ from mechanochemical water splitting, however, microbial utilization of this widespread potential energy source has not been directly demonstrated. Here, we show experimentally that mechanochemically generated H₂ from granite can be directly, long-term, utilized by a CH₄ producing microbial community. This is consistent with CH₄ formation in subsurface rock fracturing in the environment. Our results not only support water splitting H₂ generation as a potential deep biosphere energy source, but as an oxidant must also be produced, they suggest that there is also a respiratory oxidant supply in the subsurface which is independent of photosynthesis. This may explain the widespread distribution of facultative aerobes in subsurface environments. A range of common rocks were shown to produce mechanochemical H₂ , and hence, this process should be widespread in the subsurface, with the potential for considerable mineral fuelled CH₄ production.

Seawater recirculation through subducting sediments sustains a deeply buried population of sulfate-reducing bacteria

Subseafloor sulfate concentrations typically decrease with depth as this electron acceptor is consumed by respiring microorganisms. However, studies show that seawater can flow through hydraulically conductive basalt to deliver sulfate upwards into deeply buried overlying sediments. Our previous work on IODP Site C0012A (Nankai Trough, Japan) revealed that recirculation of sulfate through the subducting Philippine Sea Plate stimulated microbial activity near the sediment-basement interface (SBI). Here, we describe the microbial ecology, phylogeny, and energetic requirements of population of aero-tolerant sulfate-reducing bacteria in the deep subseafloor. We identified dissimilatory sulfite reductase gene (dsr) sequences 93% related to oxygen-tolerant Desulfovibrionales species across all reaction zones while no SRB were detected in drilling fluid control samples. Pore fluid chemistry revealed low concentrations of methane (<0.25 mM), while hydrogen levels were consistent with active bacterial sulfate reduction (0.51-1.52 nM). Solid phase total organic carbon (TOC) was also considerably low in these subseafloor sediments. Our results reveal the phylogenetic diversity, potential function, and physiological tolerance of a community of sulfate-reducing bacteria living at ~480 m below subducting seafloor.

Subsurface Microbial Hydrogen Cycling: Natural Occurrence and Implications for Industry

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

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

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

Why Springs Bubble: A Framework for Gas Discharge in Groundwater

The mechanisms leading to the formation of bubbles in springs and wells have received minimal attention beyond causation. Free-phase gas quantification provides insight into a range of topics, from hazards that need to be managed to the economic value of soda waters. The presence of free-phase gas or vapor bubbles in groundwater may provide valuable information about the subsurface flow system. Additionally, free-phase gas or vapor bubbles may strip dissolved gasses from solution and introduce error into the assessment of gasses in springs, affecting analyses such as groundwater dating techniques. Similar to Meinzer's (1927) classification of springs by discharge rate, this paper proposes a framework for discussing free-phase gas and bubble phenomenon in groundwater to organize literature and foster future research. The naming, description, and categorization of free-phase gas or bubbles in groundwater provided in this review use seven common bubble manifestations or facies. These facies are based upon the processes in which the groundwater is charged with a gaseous species and the processes that bring the gas out of solution. Gas bubbles found in groundwater rarely occur as a single gas; therefore, these facies may overlap, but the proposed structure provides a useful framework. A glossary of bubble terms is provided to assist in clarity of describing free-phase gas phenomena.

Serpentinization: Connecting Geochemistry, Ancient Metabolism and Industrial Hydrogenation

Rock⁻water⁻carbon interactions germane to serpentinization in hydrothermal vents have occurred for over 4 billion years, ever since there was liquid water on Earth. Serpentinization converts iron(II) containing minerals and water to magnetite (Fe₃O₄) plus H₂. The hydrogen can generate native metals such as awaruite (Ni₃Fe), a common serpentinization product. Awaruite catalyzes the synthesis of methane from H₂ and CO₂ under hydrothermal conditions. Native iron and nickel catalyze the synthesis of formate, methanol, acetate, and pyruvate-intermediates of the acetyl-CoA pathway, the most ancient pathway of CO₂ fixation. Carbon monoxide dehydrogenase (CODH) is central to the pathway and employs Ni⁰ in its catalytic mechanism. CODH has been conserved during 4 billion years of evolution as a relic of the natural CO₂-reducing catalyst at the onset of biochemistry. The carbide-containing active site of nitrogenase-the only enzyme on Earth that reduces N₂-is probably also a relic, a biological reconstruction of the naturally occurring inorganic catalyst that generated primordial organic nitrogen. Serpentinization generates Fe₃O₄ and H₂, the catalyst and reductant for industrial CO₂ hydrogenation and for N₂ reduction via the Haber⁻Bosch process. In both industrial processes, an Fe₃O₄ catalyst is matured via H₂-dependent reduction to generate Fe₅C₂ and Fe₂N respectively. Whether serpentinization entails similar catalyst maturation is not known. We suggest that at the onset of life, essential reactions leading to reduced carbon and reduced nitrogen occurred with catalysts that were synthesized during the serpentinization process, connecting the chemistry of life and Earth to industrial chemistry in unexpected ways.

The last universal common ancestor between ancient Earth chemistry and the onset of genetics

All known life forms trace back to a last universal common ancestor (LUCA) that witnessed the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the most common way being to look for traits that are common to all cells, like ribosomes or the genetic code. With the availability of genomes, we can, however, also ask what genes are ancient by virtue of their phylogeny rather than by virtue of being universal. That approach, undertaken recently, leads to a different view of LUCA than we have had in the past, one that fits well with the harsh geochemical setting of early Earth and resembles the biology of prokaryotes that today inhabit the Earth's crust.

Low Energy Subsurface Environments as Extraterrestrial Analogs

Earth's subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth's low energy subsurface habitats.

The deep, hot biosphere: Twenty-five years of retrospection

Twenty-five years ago this month, Thomas Gold published a seminal manuscript suggesting the presence of a "deep, hot biosphere" in the Earth's crust. Since this publication, a considerable amount of attention has been given to the study of deep biospheres, their role in geochemical cycles, and their potential to inform on the origin of life and its potential outside of Earth. Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings. Furthermore, it has become apparent that much of this life is dependent on lithogenically sourced high-energy compounds to sustain productivity. A vast diversity of uncultivated microorganisms has been detected in subsurface environments, and we show that H₂, CH₄, and CO feature prominently in many of their predicted metabolisms. Despite 25 years of intense study, key questions remain on life in the deep subsurface, including whether it is endemic and the extent of its involvement in the anaerobic formation and degradation of hydrocarbons. Emergent data from cultivation and next-generation sequencing approaches continue to provide promising new hints to answer these questions. As Gold suggested, and as has become increasingly evident, to better understand the subsurface is critical to further understanding the Earth, life, the evolution of life, and the potential for life elsewhere. To this end, we suggest the need to develop a robust network of interdisciplinary scientists and accessible field sites for long-term monitoring of the Earth's subsurface in the form of a deep subsurface microbiome initiative.

A physiological perspective on the origin and evolution of photosynthesis

The origin and early evolution of photosynthesis are reviewed from an ecophysiological perspective. Earth's first ecosystems were chemotrophic, fueled by geological H2 at hydrothermal vents and, required flavin-based electron bifurcation to reduce ferredoxin for CO2 fixation. Chlorophyll-based phototrophy (chlorophototrophy) allowed autotrophs to generate reduced ferredoxin without electron bifurcation, providing them access to reductants other than H2. Because high-intensity, short-wavelength electromagnetic radiation at Earth's surface would have been damaging for the first chlorophyll (Chl)-containing cells, photosynthesis probably arose at hydrothermal vents under low-intensity, long-wavelength geothermal light. The first photochemically active pigments were possibly Zn-tetrapyrroles. We suggest that (i) after the evolution of red-absorbing Chl-like pigments, the first light-driven electron transport chains reduced ferredoxin via a type-1 reaction center (RC) progenitor with electrons from H2S; (ii) photothioautotrophy, first with one RC and then with two, was the bridge between H2-dependent chemolithoautotrophy and water-splitting photosynthesis; (iii) photothiotrophy sustained primary production in the photic zone of Archean oceans; (iv) photosynthesis arose in an anoxygenic cyanobacterial progenitor; (v) Chl a is the ancestral Chl; and (vi), anoxygenic chlorophototrophic lineages characterized so far acquired, by horizontal gene transfer, RCs and Chl biosynthesis with or without autotrophy, from the architects of chlorophototrophy-the cyanobacterial lineage.

Microbial Composition and Diversity Patterns in Deep Hyperthermal Aquifers from the Western Plain of Romania

A limited number of studies have investigated the biodiversity in deep continental hyperthermal aquifers and its influencing factors. Here, we present the first description of microbial communities inhabiting the Pannonian and Triassic hyperthermal aquifers from the Western Plain of Romania, the first one being considered a deposit of "fossilized waters," while the latter is embedded in the hydrological cycle due to natural refilling. The 11 investigated drillings have an open interval between 952 and 3432 m below the surface, with collected water temperatures ranging between 47 and 104 °C, these being the first microbial communities characterized in deep continental water deposits with outflow temperatures exceeding 80 °C. The abundances of bacterial 16S rRNA genes varied from approximately 10⁵-10⁶ mL^-1 in the Pannonian to about 10²-10⁴ mL^-1 in the Triassic aquifer. A 16S rRNA gene metabarcoding analysis revealed distinct microbial communities in the two water deposits, especially in the rare taxa composition. The Pannonian aquifer was dominated by the bacterial genera Hydrogenophilus and Thermodesulfobacterium, together with archaeal methanogens from the Methanosaeta and Methanothermobacter groups. Firmicutes was prevalent in the Triassic deposit with a large number of OTUs affiliated to Thermoanaerobacteriaceae, Thermacetogenium, and Desulfotomaculum. Species richness, evenness, and phylogenetic diversity increased alongside with the abundance of mesophiles, their presence in the Triassic aquifer being most probably caused by the refilling with large quantities of meteoric water in the Carpathian Mountains. Altogether, our results show that the particular physico-cheminal characteristics of each aquifer, together with the water refilling possibilities, seem to determine the microbial community structure.

The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures

Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology-Biosignatures-Coevolution of Earth and life-Mars. Astrobiology 18, 1-27.

Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny

This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70–90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities.