Person: Jan P. Amend

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Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation–decentralized innovation–hierarchical import model that accounts for the emergence of eukaryotic complexity.

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Chemolithotrophic microorganisms are key primary producers in hydrothermal environments. However, the complex thermal and compositional gradients that frequently describe these settings commonly obfuscate which reactions are fueling such complex ecosystems. Nonetheless, potential sources of microbial energy can be identified by combining analytical geochemical data from hydrothermal systems and thermodynamic calculations. This approach provides a quantitative assessment of how habitats are shaped by environmental conditions such as temperature, pressure, pH and the concentrations of electron donors and acceptors. In this study, we have calculated the Gibbs energy available from 730 redox reactions in 30 terrestrial, shallow-sea, and deep-sea hydrothermal systems around the world (326 geochemical datasets) to reveal trends in how energy availability can shape hydrothermal ecology. The most energy-yielding (exergonic) reactions were predominantly the reduction of O₂, NO₂⁻, NO₃⁻, and MnO₂ and the oxidation of Fe²⁺, pyrite, CO, and CH₄. In contrast, the reduction of N₂, CO, and CO₂ and oxidation of N₂, Mn²⁺, and NO₂⁻, though still often exergonic, yielded significantly less energy. Also, our results show that, in terms Gibbs energies of reactions, shallow-sea hydrothermal vent systems are more like terrestrial hot springs than deep-sea hydrothermal systems. Per kilogram of water in hydrothermal fluid, energy yields from inorganic redox reactions are much higher in deep-sea hydrothermal systems than in the other systems considered here. Our results provide a comprehensive view of the distribution of energy supplies from redox reactions in high-temperature ecosystems on a global scale.

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The subsurface is Earth’s largest reservoir of biomass. Micro‐organisms are the dominant lifeforms in this habitat, but the nature of their in situ activities remains largely unresolved. At the Deep Mine Microbial Observatory (DeMMO) located in the Sanford Underground Research Facility (SURF) in Lead, South Dakota (USA), we performed in situ electrochemical incubations designed to assess the potential for deep groundwater microbial communities to utilize extracellular electron transfer to support microbial respiration. DeMMO 4 was chosen for its stable geochemistry and microbial community. Graphite and indium tin oxide electrodes poised at −200 mV versus SHE were incubated along with open circuit controls and various minerals in a parallel flow reactor that split access to fluids across different treatments. From the patterns of net current over time (fluctuating between anodic and cathodic currents over the course of a few days to weeks) and the catalytic features measured using periodic cyclic voltammetry, evidence of both oxidative and reductive microbe‐electrode interactions was observed. The predominant catalytic activity ranged from −210 to −120 mV. The observed temporal variability in electrochemical activity was unexpected given the documented stability in major geochemical parameters. This suggests that the accessed fluids are more heterogeneous in electrochemically active microbial populations than previously predicted from the stable community composition. As previously reported, the fracture fluid and surface‐attached microbial communities at SURF differed significantly. However, only minimal differences in community composition were observed between poised potential electrodes, open circuit electrodes, and mineral incubations. These data support that in this environment the ability to attach to surfaces is a stronger driver of microbial community structure than the type or reactivity of the surface. We demonstrate that insight into specific activities can be gained from electrochemical methods, specifically chronoamperometry coupled with routine cyclic voltammetry, which provide a sensitive approach to evaluate microbial activities in situ.

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The availability of microbiological and geochemical data from island-based and high-arsenic hydrothermal systems is limited. Here, the microbial diversity in island-based hot springs on Ambitle Island (Papua New Guinea) was investigated using culture-dependent and -independent methods. Waramung and Kapkai are alkaline springs high in sulfide and arsenic, related hydrologically to previously described hydrothermal vents in nearby Tutum Bay. Enrichments were carried out at 24 conditions with varying temperature (45, 80 °C), pH (6.5, 8.5), terminal electron acceptors (O₂, SO₄ ²⁻, S⁰, NO₃ ⁻), and electron donors (organic carbon, H₂, As^III). Growth was observed in 20 of 72 tubes, with media targeting heterotrophic metabolisms the most successful. 16S ribosomal RNA gene surveys of environmental samples revealed representatives in 15 bacterial phyla and 8 archaeal orders. While the Kapkai 4 bacterial clone library is primarily made up of Thermodesulfobacteria (74 %), no bacterial taxon represents a majority in the Kapkai 3 and Waramung samples (40 % Proteobacteria and 39 % Aquificae, respectively). Deinococcus/Thermus and Thermotogae are observed in all samples. The Thermococcales dominate the archaeal clone libraries (65–85 %). Thermoproteales, Desulfurococcales, and uncultured Eury- and Crenarchaeota make up the remaining archaeal taxonomic diversity. The culturing and phylogenetic results are consistent with the geochemistry of the alkaline, saline, and sulfide-rich fluids. When compared to other alkaline, island-based, high-arsenic, or shallow-sea hydrothermal communities, the Ambitle Island archaeal communities are unique in geochemical conditions, and in taxonomic diversity, richness, and evenness.

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Microbial cells buried in subseafloor sediments comprise a substantial portion of Earth’s biosphere and control global biogeochemical cycles; however, the rate at which they use energy (i.e., power) is virtually unknown. Here, we quantify organic matter degradation and calculate the power utilization of microbial cells throughout Earth’s Quaternary-age subseafloor sediments. Aerobic respiration, sulfate reduction, and methanogenesis mediate 6.9, 64.5, and 28.6% of global subseafloor organic matter degradation, respectively. The total power utilization of the subseafloor sediment biosphere is 37.3 gigawatts, less than 0.1% of the power produced in the marine photic zone. Aerobic heterotrophs use the largest share of global power (54.5%) with a median power utilization of 2.23 × 10⁻¹⁸ watts per cell, while sulfate reducers and methanogens use 1.08 × 10⁻¹⁹ and 1.50 × 10⁻²⁰ watts per cell, respectively. Most subseafloor cells subsist at energy fluxes lower than have previously been shown to support life, calling into question the power limit to life.

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Microbial degradation of organic carbon in marine sediments is a key driver of global element cycles on multiple time scales. However, it is not known to what depth microorganisms alter organic carbon in marine sediments or how microbial rates of organic carbon processing change with depth, and thus time since burial, on a global scale. To better understand the connection between the dynamic carbon cycle and life’s limits in the deep subsurface, we have combined a number of global data sets with a reaction transport model (RTM) describing first, organic carbon degradation in marine sediments deposited throughout the Quaternary Period and second, a bioenergetic model for microbial activity. The RTM is applied globally, recognizing three distinct depositional environments – continental shelf, margin and abyssal zones. The results include the masses of particulate organic carbon, POC, stored in three sediment-depth layers: bioturbated Holocene (1.7 × 10¹⁷ g C), non-bioturbated Holocene (2.5 × 10¹⁸ g C) and Pleistocene (1.4 × 10²⁰ g C) sediments. The global depth-integrated rates of POC degradation have been determined to be 1.3 × 10¹⁵, 1.3 × 10¹⁴ and 3.0 × 10¹⁴ g C yr^-1 for the same three layers, respectively. A number of maps depicting the distribution of POC, as well as the fraction that has been degraded have also been generated. Using POC degradation as a proxy for microbial catabolic activity, total heterotrophic processing of POC throughout the Quaternary is estimated to be between 10^-11 – 10^-6 g C cm^-3 yr^-1, depending on the time since deposition and location. Bioenergetic modeling reveals that laboratory-determined microbial maintenance powers are poor predictors of sediment biomass concentration, but that cell concentrations in marine sediments can be accurately predicted by combining bioenergetic models with the rates of POC degradation determined in this study. Our model can be used to quantitatively describe both the carbon cycle and microbial activity on a global scale for marine sediments less than 2.59 million years old.

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Shallow-sea hydrothermal systems, like their deep-sea and terrestrial counterparts, can serve as relatively accessible portals into the microbial ecology of subsurface environments. In this study, we determined the chemical composition of 47 sediment porewater samples along a transect from a diffuse shallow-sea hydrothermal vent to a non-thermal background area in Paleochori Bay, Milos Island, Greece. These geochemical data were combined with thermodynamic calculations to quantify potential sources of energy that may support in situ chemolithotrophy. The Gibbs energies (ΔG_r) of 730 redox reactions involving 23 inorganic H-, O-, C-, N-, S-, Fe-, Mn-, and As-bearing compounds were calculated. Of these reactions, 379 were exergonic at one or more sampling locations. The greatest energy yields were from anaerobic CO oxidation with NO₂^– (-136 to -162 kJ/mol e^–), followed by reactions in which the electron acceptor/donor pairs were O₂/CO, NO₃^–/CO, and NO₂^–/H₂S. When expressed as energy densities (where the concentration of the limiting reactant is taken into account), a different set of redox reactions are the most exergonic: in sediments affected by hydrothermal input, sulfide oxidation with a range of electron acceptors or nitrite reduction with different electron donors provide 85~245 J per kg of sediment, whereas in sediments less affected or unaffected by hydrothermal input, various S⁰ oxidation reactions and aerobic respiration reactions with several different electron donors are most energy-yielding (80~95 J per kg of sediment). A model that considers seawater mixing with hydrothermal fluids revealed that there is up to ~50 times more energy available for microorganisms that can use S⁰ or H₂S as electron donors and NO₂^– or O₂ as electron acceptors compared to other reactions. In addition to revealing likely metabolic pathways in the near-surface and subsurface mixing zones, thermodynamic calculations like these can help guide novel microbial cultivation efforts to isolate new species.

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Chemotrophic microorganisms gain energy for cellular functions by catalyzing oxidation‐reduction (redox) reactions that are out of equilibrium. Calculations of the Gibbs energy (∆G_r) can identify whether a reaction is thermodynamically favorable and quantify the accompanying energy yield at the temperature, pressure, and chemical composition in the system of interest. Based on carefully calculated values of ∆G_r, we predict a novel microbial metabolism—sulfur comproportionation (3H₂S + SO₄^2‐ + 2H⁺ ⇌ 4S⁰ + 4H₂O). We show that at elevated concentrations of sulfide and sulfate in acidic environments over a broad temperature range, this putative metabolism can be exergonic (∆G_r<0), yielding ~30‐50 kJ/mol. We suggest that this may be sufficient energy to support a chemolithotrophic metabolism currently missing from the literature. Other versions of this metabolism, comproportionation to thiosulfate (H₂S + SO₄^2‐ ⇌ S₂O₃^2‐ + H₂O) and to sulfite (H₂S + 3SO₄^2‐ ⇌ 4SO₃^2‐ + 2H⁺), are only moderately exergonic or endergonic even at ideal geochemical conditions. Natural and impacted environments, including sulfidic karst systems, shallow‐sea hydrothermal vents, sites of acid mine drainage, and acid‐sulfate crater lakes, may be ideal hunting grounds for finding microbial sulfur comproportionators.

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Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and Archaea.

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The Methanosarcinales, a lineage of cytochrome-containing methanogens, have recently been proposed to participate in direct extracellular electron transfer interactions within syntrophic communities. To shed light on this phenomenon, we applied electrochemical techniques to measure electron uptake from cathodes by Methanosarcina barkeri, which is an important model organism that is genetically tractable and utilizes a wide range of substrates for methanogenesis. Here, we confirm the ability of M. barkeri to perform electron uptake from cathodes and show that this cathodic current is linked to quantitative increases in methane production. The underlying mechanisms we identified include, but are not limited to, a recently proposed association between cathodes and methanogen-derived extracellular enzymes (e.g., hydrogenases) that can facilitate current generation through the formation of reduced and diffusible methanogenic substrates (e.g., hydrogen). However, after minimizing the contributions of such extracellular enzymes and using a mutant lacking hydrogenases, we observe a lower-potential hydrogen-independent pathway that facilitates cathodic activity coupled to methane production in M. barkeri. Our electrochemical measurements of wild-type and mutant strains point to a novel and hydrogenase-free mode of electron uptake with a potential near −484 mV versus standard hydrogen electrode (SHE) (over 100 mV more reduced than the observed hydrogenase midpoint potential under these conditions). These results suggest that M. barkeri can perform multiple modes (hydrogenase-mediated and free extracellular enzyme-independent modes) of electrode interactions on cathodes, including a mechanism pointing to a direct interaction, which has significant applied and ecological implications.

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Recent studies reveal that life in the terrestrial and marine subsurface exists on far less energy flux than is commonly understood from laboratory incubations with isolated organisms. This has profound implications for understanding the development of life on Earth, as well as for the search for life in the universe. Similarly, several recent research efforts have also addressed other limits to life, such as high temperature. This chapter presents an overview of the current understanding of the energetic limits of life on Earth.

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Mariprofundus sp. strain EBB-1 was isolated from a pyrrhotite biofilm incubated in seawater from East Boothbay (ME, USA). Strain EBB-1 is an autotrophic member of the class Zetaproteobacteria with the ability to form iron oxide biominerals. Here, we present the 2.88-Mb genome sequence of EBB-1, which contains 2,656 putative protein-coding sequences.

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The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of the standard Gibbs energy (ΔG_r⁰) define the direction and energy yield of a reaction; they do not. ΔG_r⁰ is one part of the actual Gibbs energy of a reaction (ΔG_r), with a second part accounting for deviations from the standard composition. It is also frequently assumed that ΔG_r⁰ applies only to 25 °C and 1 bar; it does not. ΔG_r⁰ is a function of temperature and pressure. Here, we review how to determine ΔG_r as a function of temperature, pressure and chemical composition for microbial catabolic reactions, including a discussion of the effects of ionic strength on ΔG_r and highlighting the large effects when multi‐valent ions are part of the reaction. We also calculate ΔG_r for five example catabolisms at specific environmental conditions: aerobic respiration of glucose in freshwater, anaerobic respiration of acetate in marine sediment, hydrogenotrophic methanogenesis in a laboratory batch reactor, anaerobic ammonia oxidation in a wastewater reactor and aerobic pyrite oxidation in acid mine drainage. These examples serve as templates to determine the energy yields of other catabolic reactions at environmentally relevant conditions.

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Bacterial populations in long-term stationary phase laboratory cultures can provide insights into physiological and genetic adaptations to low-energy conditions and population dynamics in natural environments. While overall population density remains stable, these communities are very dynamic and characterized by the rapid emergence and succession of distinct mutants expressing the Growth Advantage in Stationary Phase (GASP) phenotype, which can reflect an increased capacity to withstand energy limitations and environmental stress. Here we characterize the metabolic heat signatures and growth dynamics of GASP mutants within an evolving population using isothermal calorimetry. We aged Escherichia coli in anaerobic batch cultures over 20 days inside an isothermal nanocalorimeter and observed distinct heat events related to the emergence of three mutant populations expressing the GASP phenotype after 1.5, 3, and 7 days. Given the heat produced by each population, the maximum number of GASP mutant cells was calculated revealing abundances of ∼2.5 x 10⁷, ∼7.5 x 10⁶, and ∼9.9 x 10⁶ cells in the population, respectively. These data indicate that mutants capable of expressing the GASP phenotype can be acquired during the exponential growth phase and subsequently expressed in long-term stationary phase (LTSP) culture.

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Fermentation plays a fundamental role in organic carbon degradation on a global scale. However, little is known about how environmental variables influence this process. In a step towards quantifying how temperature and composition influence fermentation, we have calculated the Gibbs energies of 47 fermentation reaction, ΔG_r, from 0–150 °C for a broad range of compositions representing microbial habitats as variable as sediments, estuaries, soils, and crustal rocks. The organic compounds in these reactions include amino acids, nucleic acid bases, monosaccharides, carboxylates, methanogenic compounds and more. The amount of energy available varies considerably, from +54 kJ (mol C)⁻¹ for palmitate fermentation, to −184 kJ (mol C)⁻¹ for methylamine disproportionation. For some reactions, there is little difference in ΔG_r between low and high energy systems (e.g., the monosaccharide reactions) while others span a much broader range (e.g., the nucleic acid bases). There is no clear-cut trend between exergonicity and temperature, and the values of standard state Gibbs energies of reactions, ΔG⁰_r, for nearly half of the reactions lie outside the range of ΔG_r values. To carry out some of these calculations, the thermodynamic properties for six organic compounds were estimated: dimethylamine, trimethylamine, resorcinol, phloroglucinol and cyclohexane carboxylate and its conjugate acid.

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The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane, and potentially propane. The number of archaeal clades encoding the MCR continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.

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Globally, marine sediments are a vast repository of organic matter which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e. labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 to 67 meters below seafloor, and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated to carbon content and depositional conditions. Fermentation-related genes were found in all samples, and encoded for multiple fermentation strategies. Notably, genes conferring alcohol metabolism were amongst the most abundant of these genes, indicating this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities.

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Microorganisms buried in marine sediments are known to endure starvation over geologic timescales. However, the mechanisms of how these microorganisms cope with prolonged energy limitation is unknown and therefore yet to be captured in a quantitative framework. Here, we present a novel mathematical model that considers (a) the physiological transitions between the active and dormant states of microorganisms, (b) the varying requirement for maintenance power between these phases, and (c) flexibility in the provenance (i.e., source) of energy from exogenous and endogenous catabolism. The model is applied to sediments underlying the oligotrophic South Pacific Gyre where microorganisms endure ultra‐low fluxes of energy for tens of millions of years. Good fits between model simulations and measurements of cellular carbon and organic carbon concentrations are obtained and are interpreted as follows: (a) the unfavourable microbial habitat in South Pacific Gyre sediments triggers rapid mortality and a transition to dormancy; (b) there is minimal biomass growth, and organic carbon consumption is dominated by catabolism to support maintenance activities rather than new biomass synthesis; (c) the amount of organic carbon that microorganisms consume for maintenance activities is equivalent to approximately 2% of their carbon biomass per year; and (d) microorganisms must rely solely on exogenous rather than endogenous catabolism to persist in South Pacific Gyre sediments over long timescales. This leads us to the conclusion that under oligotrophic conditions, the fitness of an organism is determined by its ability to simply stay alive, rather than to grow. This modelling framework is designed to be flexible for application to other sites and habitats, and thus serves as a new quantitative tool for determining the habitability of and an ultimate limit for life in any environment.

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With the generous support from the C-DEBI research exchange grant, I had the opportunity to participate in the International Geobiology Course, which was directed by Drs. Alex Session, Victoria Orphan, and Woody Fischer from the California Institute of Technology (in conjuction with the Agouron Institute, Simons Foundation and USC Wrigley Institute). In this course, I traveled with 15 other geobiology graduate students to Mono Lake, Naples Beach, and Santa Paula Creek where we learned how to collect biological and geochemical samples for analysis at Caltech. At Caltech, I learned cutting-edge laboratory techniques including SEM, stable isotope analysis, SIMS, and NanoSIMS. Finally, on Catalina Island, I worked with three other students on a project that investigated the sulfur cycle at Santa Paula Creek, which we will be presenting at the AGU annual meeting. Participating in this course provided not only comprehensive training in geobiology, but also a unique opportunity to network with established scientists and peers that I hope to collaborate with in the future. Since returning from this course, I have a stronger understanding of current interdisciplinary topics and questions in geobiology and the ways in which these ideas are addressed. I look forward to continuing to pursue research in geobiology and collaborating with the scientists I have connected with on this course.

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Cool hydrothermal systems (CHSs) are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15^∘C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations. 16S rRNA gene sequencing revealed that Thaumarchaea, Proteobacteria, and Planctomycetes were the most abundant phyla in all sediments across the system regardless of influence from seepage. Members of the Thaumarchaeota (Marine Group I), Alphaproteobacteria (Rhodospirillales), Nitrospirae, Nitrospina, Acidobacteria, and Gemmatimonadetes were enriched in the sediments influenced by CHS advection. Of the various geochemical parameters investigated, nitrate concentrations correlated best with microbial community structure, indicating structuring based on seepage of nitrate-rich fluids. A comparison of microbial communities from hydrothermal sediments, seafloor basalts, and local seawater at Dorado Outcrop showed differences that highlight the distinct niche space in CHS. Sediment microbial communities from Dorado Outcrop differ from those at previously characterized, warmer CHS sediment, but are similar to deep-sea sediment habitats with surficial ferromanganese nodules, such as the Clarion Clipperton Zone. We conclude that cool hydrothermal venting at seafloor outcrops can alter the local sedimentary oxidation–reduction pathways, which in turn influences the microbial communities within the fluid discharge affected sediment.

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Geothermobacter sp. strain HR-1 was isolated from the Lō‘ihi Seamount vent system in the Pacific Ocean at a depth of 1,000 m. Reported here is its 3.84-Mb genome sequence.

This research was funded as part of the 2017 NSF Community College Cultivation Cohort (C4) Research Experience for Undergraduates.

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As we train the next generation of Science, Technology, Engineering, and Math (STEM) researchers, it is imperative that we expand our recruitment to community college students. Many of these students are highly motivated and extremely talented, but they often lack exposure to cutting edge technology found at R1 institutions, much less have the opportunities to participate in original research. The Center for Dark Energy Biosphere Investigations (C-DEBI) at the University of Southern California (USC) started a community college research internship summer program in 2013. The non-residential and residential programs combined so far have trained 60 students in the biogeosciences, with 46 of them having transferred to four-year institutions and 95% remaining in STEM fields. Their introduction to and acquired competence in several advanced technologies have further prepared these students to pursue graduate degrees and rewarding careers in research-based STEM fields.

The Marine Technology Society is a not-for-profit, international, professional association. Founded in 1963, the Society believes that the advancement of marine technology and the productive, sustainable use of the oceans depend upon the active exchange of ideas between government, industry and academia. See www.mtsociety.org. Ⓒ 2018 Marine Technology Society. This article is for personal use only, and is not to be distributed in any format.

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Microbial ecology within oligotrophic marine sediment is poorly understood, yet is critical for understanding geochemical cycles. Here, 16S rRNA sequences from RNA and DNA inform the structure of active and total microbial communities in oligotrophic sediment on the western flank of the Mid-Atlantic Ridge. Sequences identified as Bacillariophyta chloroplast were detected within DNA, but undetectable within RNA, suggesting preservation in 5.6-million-year-old sediment. Statistical analysis revealed that RNA-based microbial populations correlated significantly with nitrogen concentrations, whereas DNA-based populations did not correspond to measured geochemical analytes. Bioenergetic calculations determined which metabolisms could yield energy in situ, and found that denitrification, nitrification, and nitrogen fixation were all favorable. A metagenome was produced from one sample, and included genes mediating nitrogen redox processes. Nitrogen respiration by active bacteria is an important metabolic strategy in North Pond sediments, and could be widespread in the oligotrophic sedimentary biosphere.

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Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions. In particular, our results demonstrate that catabolic rates are not necessarily coupled to rates of cell division, but rather, to physiological rearrangements of S. oneidensis MR-1 upon growth phase transitions. In addition, we conclude that the heat released by growing microorganisms can be measured in order to understand the physiochemical nature of the energy transformation and dissipation associated with microbial metabolic activity in conditions approaching those found in natural systems.

Abstract

Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated autotrophic growth through the oxidation of thiosulfate and iron. Here, we present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding genes.

Abstract

The in situ production of necromass and its role as a power source in sustaining heterotrophic microorganisms in natural settings has never been quantified. Here, we quantify the power availability from necromass oxidation to living microorganisms buried in marine sediments over millions of years, first in the oligotrophic South Pacific Gyre (SPG), and second on a global scale. We calculate that power from autochthonously produced necromass in the upper meter of sediment at SPG provides only a small fraction (~0.02%) of the maintenance power demand of the living community (1.9×10^-19 W cell^-1). Power from necromass oxidation diminishes considerably with increasing sediment depth (and thus sediment age). Alternatively, the oxidation of allochthonous organic matter, and of radiolytic H₂, provides power equivalent to or in excess of the maintenance demands of living microorganisms at SPG. On a global scale, necromass may support the maintenance power demand of 2 to 13% of the microbial community in relatively young sediments (<10,000 years) when it is oxidized with SO₄^2- and O₂ respectively. However, in older sediments, the power supplied by necromass is negligible (<0.01%). Nevertheless, the oxidation of a single dead cell per year provides sufficient power to support the maintenance demands of dozens to thousands of cells in low-energy marine sediments. This raises the possibility that the production and oxidation of necromass may provide a mechanism for non-growing microorganisms to endure unfavorable, low-energy settings over geological timescales.

Abstract

Marine sediments constitute one of the most energy-limited habitats on Earth, in which microorganisms persist over extraordinarily long timescales with very slow metabolisms. This habitat provides an ideal environment in which to study the energetic limits of life. However, the bioenergetic factors that can determine whether microorganisms will grow, lie dormant, or die, as well as the selective environmental pressures that determine energetic trade-offs between growth and maintenance activities, are not well understood. Numerical models will be pivotal in addressing these knowledge gaps. However, models rarely account for the variable physiological states of microorganisms and their demand for energy. Here, we review established modeling constructs for microbial growth rate, yield, maintenance, and physiological state, and then provide a new model that incorporates all of these factors. We discuss this new model in context with its future application to the marine subsurface. Understanding the factors that regulate cell death, physiological state changes, and the provenance of maintenance energy (i.e., endogenous versus exogenous metabolism), is crucial to the design of this model. Further, measurements of growth rate, growth yield, and basal metabolic activity will enable bioenergetic parameters to be better constrained. Last, biomass and biogeochemical rate measurements will enable model simulations to be validated. The insight provided from the development and application of new microbial modeling tools for marine sediments will undoubtedly advance the understanding of the minimum power required to support life, and the ecophysiological strategies that organisms utilize to cope under extreme energy limitation for extended periods of time.

Abstract

Geothermobacter sp. strain EPR-M was isolated from a hydrothermal vent on the East Pacific Rise and has been shown to participate in the reduction of Fe(III) oxides. Here, we report its 3.73-Mb draft genome sequence.

Abstract

Life may have emerged on early Earth in serpentinizing systems, where ultramafic rocks react with aqueous solutions to generate high levels of dissolved H₂ and CH₄ and, on meeting seawater, steep redox, ionic, and pH gradients. Most extant life harnesses energy as ion (e.g., H⁺, Na⁺) gradients across membranes, and it seems reasonable to suggest that environments with steep ion gradients would have also been important for early life forms. The Strytan Hydrothermal Field (SHF) is a mid-ocean ridge–flank submarine hydrothermal (~70 °C) vent in Iceland that produces steep Na⁺ (<3–468 mM) and pH (8.1–10.2) gradients, concomitant with enrichments in methane (0.5–1.4 μM) and hydrogen (0.1–5.2 μM), relative to seawater. Large (up to 55 m) saponite towers create ideal “incubators” similar to other proposed origin-of-life analogs (e.g., Lost City hydrothermal field in the mid-Atlantic). However, the SHF is basalt hosted. We suggest that the observed conditions are generated by (1) plagioclase hydrolysis, coupled with calcite precipitation, and (2) hydration of Mg in pyroxene and olivine in basalt. Along with microbial activity, aqueous reactions of Fe in olivine and pyroxene are possible sources of the observed H₂. Although the δ¹³C-CH₄ values were highly variable (–53‰ to –8‰), isotopically heavy CH₄ suggests possible abiotic formation or the imprint of methane oxidation. If environments similar to SHF occurred on the early Earth, they should be considered as potential origin-of-life environments.

Abstract

Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity, and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete, and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes. Targeted sequencing of 16S rRNA transcripts showed Atribacteria (an uncultured phylum) and Chloroflexi to be among the dominant and the active members of the community. Metatranscriptomic analysis identified methane cycling, sulfur cycling, and halogenated compound utilization as active in situ respiratory metabolisms. Genes for cellular maintenance, cellular division, motility, and antimicrobial production were also transcribed. This indicates that microbial life in deep subsurface Baltic Sea Basin sediments was not only alive, but thriving.

Abstract

We have analyzed the dissolved organic carbon, OC, in ocean basement fluids using Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry (FT-ICR-MS). The compounds identified at the two sites, near the Juan de Fuca and Mid-Atlantic Ridges (North Pond), differ substantially from each other and from seawater. Compared to Juan de Fuca, North Pond organics had a lower average molecular weight (349 vs. 372 g/mol), 50% more identifiable compounds (2181 vs. 1482), and demonstrably lower average nominal oxidation state of carbon (-0.70 vs. -0.57). The North Pond fluids were also found to have many more N- and S-bearing compounds. Based on our data, the marine subsurface can alter the types of dissolved OC, DOC, compounds in seawater.

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Abstract

Serpentinization is a geologic process that produces highly reduced, hydrogen-rich fluids that support microbial communities under high pH conditions. We investigated the activity of microbes capable of extracellular electron transfer in a terrestrial serpentinizing system known as “The Cedars”. Measuring current generation with an on-site two-electrode system, we observed daily oscillations in current with the current maxima and minima occurring during daylight hours. Distinct members of the microbial community were enriched. Current generation in lab-scale electrochemical reactors did not oscillate, but was correlated with carbohydrate amendment in Cedars-specific minimal media. Gammaproteobacteria and Firmicutes were consistently enriched from lab electrochemical systems on δ-MnO₂ and amorphous Fe(OH)₃ at pH 11. However, isolation of an electrogenic strain proved difficult as transfer cultures failed to grow after multiple rounds of media transfer. Lowering the bulk pH in the media allowed us to isolate a Firmicutes strain (Paenibacillus sp.). This strain was capable of electrode and mineral reduction (including magnetite) at pH 9. This report provides evidence of the in situ activity of microbes using extracellular substrates as sinks for electrons at The Cedars, but also highlights the potential importance of community dynamics for supporting microbial life through either carbon fixation and/or moderating pH stress.

Abstract

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Abstract

Summary

• The oceans that cover 70% of the Earth’s surface lie above 3×10⁸ km³ of sediment containing an estimated 3×10²⁹ microbial cells.
• The role played by spores in low-energy sedimentary ecosystems remains an enigma.
• Despite conflicting results from earlier analyses, archaea and bacteria apparently exist in similar abundances within deep-sea sediments.
• Within these sediments, anaerobic metabolisms dominate, especially those in which sulfate reduction and oxidation of organic matter are coupled.
• Modeling proves crucial when trying to connect sedimentary microorganisms to their appropriate geochemical environments.

Abstract

Marine sediments contribute significantly to global element cycles on multiple time scales. This is due in large part to microbial activity in the shallower layers and abiotic reactions resulting from increasing temperatures and pressures at greater depths. Quantifying the rates of these diagenetic changes requires a three-dimensional description of the physiochemical properties of marine sediments. In a step toward reaching this goal, we have combined global data sets describing bathymetry, heat conduction, bottom-water temperatures, and sediment thickness to quantify the three-dimensional distribution of temperature in marine sediments. This model has revealed that ∼35% of sediments are above 60 °C, conditions that are suitable for petroleum generation. Furthermore, significant microbial activity could be inhibited in ∼25% of marine sediments, if 80 °C is taken as a major thermal barrier for subsurface life. In addition to a temperature model, we have calculated new values for the total volume (3.01 × 10⁸ km³) and average thickness (721 m) of marine sediments, and provide the only known determination of the volume of marine-sediment pore water (8.46 × 10⁷ km³), equivalent to ∼6.3% of the volume of the ocean. The results presented here can be used to help quantify the rates of mineral transformations, lithification, catagenesis, and the extent of life in the subsurface on a global scale.

Abstract

One of the most important classic and contemporary interests in biology is the connection between cellular composition and physiological function. Decades of research have allowed us to understand the detailed relationship between various cellular components and processes for individual species, and have uncovered common functionality across diverse species. However, there still remains the need for frameworks that can mechanistically predict the tradeoffs between cellular functions and elucidate and interpret average trends across species. Here we provide a comprehensive analysis of how cellular composition changes across the diversity of bacteria as connected with physiological function and metabolism, spanning five orders of magnitude in body size. We present an analysis of the trends with cell volume that covers shifts in genomic, protein, cellular envelope, RNA and ribosomal content. We show that trends in protein content are more complex than a simple proportionality with the overall genome size, and that the number of ribosomes is simply explained by cross-species shifts in biosynthesis requirements. Furthermore, we show that the largest and smallest bacteria are limited by physical space requirements. At the lower end of size, cell volume is dominated by DNA and protein content—the requirement for which predicts a lower limit on cell size that is in good agreement with the smallest observed bacteria. At the upper end of bacterial size, we have identified a point at which the number of ribosomes required for biosynthesis exceeds available cell volume. Between these limits we are able to discuss systematic and dramatic shifts in cellular composition. Much of our analysis is connected with the basic energetics of cells where we show that the scaling of metabolic rate is surprisingly superlinear with all cellular components.

Abstract

Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-AprilT. Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-AprilT grew at temperatures between 4 °C and 40 °C (optimum 30–37 °C), at pH 3.5 to 8.3 (optimum pH 5–6) and in the presence of up to 2.7 % NaCl (optimum 0–1.0 %). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-AprilT was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-AprilT belongs to the genus Burkholderiaand shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum(99.8 %), Burkholderia phytofirmans(98.8 %), Burkholderia caledonica(98.4 %) and Burkholderia sediminicola(98.4 %). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA–DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia, for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-AprilT ( = DSM 28142T = LMG 28183T).

Abstract

Amorphous orpiment-like As-sulfides (As₂S₃) are the most common As phases precipitating in hydrothermal systems, yet there is a lack of information regarding their solid-state characterization. Using a combination of optical, SEM–EDS, micro-Raman and XANES/EXAFS applications, we investigated yellow-orange As- and S-rich sediments occurring in the shallow-water hydrothermal system off the coast of Milos Island, Greece. The precipitates have several morphologies, but are dominantly colloidal. Intriguing “biological” morphologies also exist (e.g., cell-like (~ 10 μm), spirals (~ 20 μm), and rounded “cinnamon bun” shapes (~ 20 μm)). SEM–EDS data indicated that the precipitates have an As:S ratio similar to orpiment (average = 0.58, range 0.51–0.63; n = 8). Micro-Raman spectra indicated that orange colored precipitates appear to be dominated by poorly crystalline and/or amorphous arsenic sulfides with micro-amounts of more crystalline orpiment and impure sulfur. The yellow sediments also contained crystalline elemental sulfur in the form S₈. Bulk As K-edge XANES spectra of the As-sulfide precipitates proved a valence of As corresponding to orpiment-type (As₂S₃) compounds (− 1 to + 3). EXAFS fitting results indicated that the studied material exhibits an amorphous orpiment-like structure with As ions coordinated by 3 sulfur atoms (CN = 3.0). The As–S interatomic distance of the first shell is calculated at 2.279 Å and the Debye–Waller factor (σ²) is 0.00427. These data suggest that the modeled structure of the studied precipitates is slightly S-deficient and ordered only in the first shell around As, resembling an orpiment-type structure, whereas higher shells are not present and must be disordered. The disorder phenomenon may be strictly produced either by the existence of occasional As–S–As bridges with As–As bonds or by the occurrence of As–O–As bridges, causing twisting of the AsS₃ pyramids in the initial orpiment structure. This distortion in the higher coordination shells of the structural sheets creates the amorphous orpiment.

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Abstract

Although fluids within the upper oceanic basaltic crust harbor a substantial fraction of the total prokaryotic cells on Earth, the energy needs of this microbial population are unknown. In this study, a nanocalorimeter (sensitivity down to 1.2 nW ml^-1) was used to measure the enthalpy of microbially catalyzed reactions as a function of temperature in samples from two distinct crustal fluid aquifers. Microorganisms in unamended, warm (63°C) and geochemically altered anoxic fluids taken from 292 meters sub-basement (msb) near the Juan de Fuca Ridge produced 267.3 mJ of heat over the course of 97 h during a step-wise isothermal scan from 35.5 to 85.0°C. Most of this heat signal likely stems from the germination of thermophilic endospores (6.66 × 10⁴ cells ml^-1_FLUID) and their subsequent metabolic activity at temperatures greater than 50°C. The average cellular energy consumption (5.68 pW cell^-1) reveals the high metabolic potential of a dormant community transported by fluids circulating through the ocean crust. By contrast, samples taken from 293 msb from cooler (3.8°C), relatively unaltered oxic fluids, produced 12.8 mJ of heat over the course of 14 h as temperature ramped from 34.8 to 43.0°C. Corresponding cell-specific energy turnover rates (0.18 pW cell^-1) were converted to oxygen uptake rates of 24.5 nmol O₂ ml^-1_FLUID d^-1, validating previous model predictions of microbial activity in this environment. Given that the investigated fluids are characteristic of expansive areas of the upper oceanic crust, the measured metabolic heat rates can be used to constrain boundaries of habitability and microbial activity in the oceanic crust.

Abstract

Extreme thermal gradients and compressed metabolic zones limit the depth range of microbial colonization in hydrothermally active sediments at Guaymas Basin. We investigated the physicochemical characteristics of this ecosystem and their influence on microbial community structure. Temperature‐related trends of δ¹³C values of methane and dissolved inorganic carbon from 36 sediment cores suggest in situ thermal limits for microbial anaerobic methane oxidation and organic carbon re‐mineralization near 80°C and 100°C respectively. Temperature logging probes deposited in hydrothermal sediments for 8 days demonstrate substantial thermal fluctuations of up to 25°C. Putative anaerobic methanotroph (ANME) populations dominate the archaeal community, transitioning from ANME‐1 archaea in warm surficial sediments towards ANME‐1 Guaymas archaea as temperatures increase downcore. Since ANME archaea performing anaerobic oxidation of methane double on longer time scales (months) compared with relatively rapid in situ temperature fluctuations (hours to days), we conclude that ANME archaea possess a high tolerance for short‐term shifts in the thermal regime.

Abstract

The environmental conditions that describe an ecosystem define the amount of energy available to the resident organisms and the amount of energy required to build biomass. Here, we quantify the amount of energy required to make biomass as a function of temperature, pressure, redox state, the sources of C, N and S, cell mass and the time that an organism requires to double or replace its biomass. Specifically, these energetics are calculated from 0 to 125°C, 0.1 to 500 MPa and −0.38 to +0.86 V using CO₂, acetate or CH₄ for C, NO₃⁻ or NH₄⁺ for N and SO₄²⁻ or HS⁻ for S. The amounts of energy associated with synthesizing the biomolecules that make up a cell, which varies over 39 kJ (g cell)⁻¹, are then used to compute energy-based yield coefficients for a vast range of environmental conditions. Taken together, environmental variables and the range of cell sizes leads to a ~4 orders of magnitude difference between the number of microbial cells that can be made from a Joule of Gibbs energy under the most (5.06 × 10¹¹ cells J⁻¹) and least (5.21 × 10⁷ cells J⁻¹) ideal conditions. When doubling/replacement time is taken into account, the range of anabolism energies can expand even further.

Abstract

To better understand the origin, evolution, and extent of life, we seek to determine the minimum flux of energy needed for organisms to remain viable. Despite the difficulties associated with direct measurement of the power limits for life, it is possible to use existing data and models to constrain the minimum flux of energy required to sustain microorganisms. Here, a we apply a bioenergetic model to a well characterized marine sedimentary environment in order to quantify the amount of power organisms use in an ultralow-energy setting. In particular, we show a direct link between power consumption in this environment and the amount of biomass (cells cm^-3) found in it. The power supply resulting from the aerobic degradation of particular organic carbon (POC) at IODP Site U1370 in the South Pacific Gyre is between ∼10^-12 and 10^-16 W cm^-3. The rates of POC degradation are calculated using a continuum model while Gibbs energies have been computed using geochemical data describing the sediment as a function of depth. Although laboratory-determined values of maintenance power do a poor job of representing the amount of biomass in U1370 sediments, the number of cells per cm^-3 can be well-captured using a maintenance power, 190 zW cell^-1, two orders of magnitude lower than the lowest value reported in the literature. In addition, we have combined cell counts and calculated power supplies to determine that, on average, the microorganisms at Site U1370 require 50–3500 zW cell^-1, with most values under ∼300 zW cell^-1. Furthermore, we carried out an analysis of the absolute minimum power requirement for a single cell to remain viable to be on the order of 1 zW cell^-1.

Abstract

The subsurface evolution of shallow-sea hydrothermal fluids is a function of many factors including fluid–mineral equilibria, phase separation, magmatic inputs, and mineral precipitation, all of which influence discharging fluid chemistry and consequently associated seafloor microbial communities. Shallow-sea vent systems, however, are understudied in this regard. In order to investigate subsurface processes in a shallow-sea hydrothermal vent, and determine how these physical and chemical parameters influence the metabolic potential of the microbial communities, three shallow-sea hydrothermal vents associated with Panarea Island (Italy) were characterized. Vent fluids, pore fluids and gases at the three sites were sampled and analyzed for major and minor elements, redox-sensitive compounds, free gas compositions, and strontium isotopes. The corresponding data were used to 1) describe the subsurface geochemical evolution of the fluids and 2) to evaluate the catabolic potential of 61 inorganic redox reactions for in situ microbial communities. Generally, the vent fluids can be hot (up to 135 °C), acidic (pH 1.9–5.7), and sulfidic (up to 2.5 mM H₂S). Three distinct types of hydrothermal fluids were identified, each with higher temperatures and lower pH, Mg and SO₄, relative to seawater. Type 1 was consistently more saline than Type 2, and both were more saline than seawater. Type 3 fluids were similar to or slightly depleted in most major ions relative to seawater. End-member calculations of conservative elements indicate that Type 1 and Type 2 fluids are derived from two different sources, most likely 1) a deeper, higher salinity reservoir and 2) a shallower, lower salinity reservoir, respectively, in a layered hydrothermal system. The deeper reservoir records some of the highest end-member Cl concentrations to date, and developed as a result of recirculation of brine fluids with long term loss of steam and volatiles due to past phase separation. No strong evidence for ongoing phase separation is observed. Type 3 fluids are suggested to be mostly influenced by degassing of volatiles and subsequently dissolution of CO₂, H₂S, and other gases into the aqueous phase. Gibbs energies (ΔG_r) of redox reactions that couple potential terminal electron acceptors (O₂, NO₃⁻, Mn^IV, Fe^III, SO₄^2 −, S⁰, CO₂) with potential electron donors (H₂, NH₄⁺, Fe^2 +, Mn^2 +, H₂S, CH₄) were evaluated at in situ temperatures and compositions for each site and by fluid type. When Gibbs energies of reaction are normalized per kilogram of hydrothermal fluid, sulfur oxidation reactions are the most exergonic, while the oxidation of Fe^2 +, NH₄⁺, CH₄, and Mn^2 + is moderately energy yielding. The energetic calculations indicate that the most robust microbial communities in the Panarea hot springs combine H₂S from deep water–rock–gas interactions with O₂ that is entrained via seawater mixing to fuel their activities, regardless of site location or fluid type.

Abstract

The oceanic basaltic basement contains the largest aquifer on Earth and potentially plays an important role in the global carbon cycle as a net sink for dissolved organic carbon (DOC). However, few details of the organic matter cycling in the subsurface are known because great water depths and thick sediments typically hinder direct access to this environment. In an effort to examine the role of water–rock–microorganism interaction on organic matter cycling in the oceanic basaltic crust, basement fluid samples collected from three borehole observatories installed on the eastern flank of the Juan de Fuca Ridge were analyzed for dissolved amino acids. Our data show that dissolved free amino acids (1–13 nM) and dissolved hydrolyzable amino acids (43–89 nM) are present in the basement. The amino acid concentrations in the ridge-flank basement fluids are at the low end of all submarine hydrothermal fluids reported in the literature and are similar to those in deep seawater. Amino acids in recharging deep seawater, in situ amino acid production, and diffusional input from overlying sediments are potential sources of amino acids in the basement fluids. Thermodynamic modeling shows that amino acid synthesis in the basement can be sustained by energy supplied from inorganic substrates via chemolithotrophic metabolisms. Furthermore, an analysis of amino acid concentrations and compositions in basement fluids support the notion that heterotrophic activity is ongoing. Similarly, the enrichment of acidic amino acids and depletion of hydrophobic ones relative to sedimentary particulate organic matter suggests that surface sorption and desorption also alters amino acids in the basaltic basement. In summary, although the oceanic basement aquifer is a net sink for deep seawater DOC, similar amino acid concentrations in basement aquifer and deep seawater suggest that DOC is preferentially removed in the basement over dissolved amino acids. Our data also suggest that organic carbon cycling occurs in the oceanic basaltic basement, where an active subsurface biosphere is likely responsible for amino acid synthesis and degradation.

Abstract

A facultatively anaerobic bacterium, designated strain 1MBB1^T, was isolated from basaltic breccia collected from 341 m below the seafloor by seafloor drilling of Rigil Guyot during Integrated Ocean Drilling Program Expedition 330. The cells were straight rods, 0.5 μm wide and 1–3 μm long, that occurred singly and in chains. Strain 1MBB1^T stained Gram-positive. Catalase and oxidase were produced. The isolate grew optimally at 30 °C and pH 7.5, and could grow with up to 12 % (w/v) NaCl. The DNA G+C content was 40.5 mol%. The major cellular fatty acids were C_16:1ω11c (26.5 %), anteiso-C_15:0 (19.5 %), C_16:0 (18.7 %) and iso-C_15:0 (10.4 %), and the cell-wall diamino acid was meso-diaminopimelic acid. Endospores of strain 1MBB1^T oxidized Mn(II) to Mn(IV), and siderophore production by vegetative cells was positive. Phylogenetic analysis of the 16S rRNA gene indicated that strain 1MBB1^T was a member of the family Bacillaceae, with Bacillus foraminis CV53^T and Bacillus novalis LMG 21837^T being the closest phylogenetic neighbours (96.5 and 96.2 % similarity, respectively). This is the first novel species described from deep subseafloor basaltic crust. On the basis of our polyphasic analysis, we conclude that strain 1MBB1^T represents a novel species of the genus Bacillus, for which we propose the name Bacillus rigiliprofundi sp. nov. The type strain is 1MBB1^T ( = NCMA B78^T = LMG 28275^T).

Abstract

Shallow-sea (5 m depth) hydrothermal venting off Milos Island provides an ideal opportunity to target transitions between igneous abiogenic sulfide inputs and biogenic sulfide production during microbial sulfate reduction. Seafloor vent features include large (>1 m²) white patches containing hydrothermal minerals (elemental sulfur and orange/yellow patches of arsenic-sulfides) and cells of sulfur oxidizing and reducing microorganisms. Sulfide-sensitive film deployed in the vent and non-vent sediments captured strong geochemical spatial patterns that varied from advective to diffusive sulfide transport from the subsurface. Despite clear visual evidence for the close association of vent organisms and hydrothermalism, the sulfur and oxygen isotope composition of pore fluids did not permit delineation of a biotic signal separate from an abiotic signal. Hydrogen sulfide (H₂S) in the free gas had uniform δ³⁴S values (2.5±0.28‰, n=€‰4) that were nearly identical to pore water H₂S (2.7±€‰0.36‰, n€‰=21). In pore water sulfate, there were no paired increases in δ³⁴S_SO4 and δ¹⁸O_SO4 as expected of microbial sulfate reduction. Instead, pore water δ³⁴S_SO4 values decreased (from approximately 21€° to 17€°) as temperature increased (up to 97.4°C) across each hydrothermal feature. We interpret the inverse relationship between temperature and δ³⁴S_SO4 as a mixing process between oxic seawater and ³⁴S-depleted hydrothermal inputs that are oxidized during seawater entrainment. An isotope mass balance model suggests secondary sulfate from sulfide oxidation provides at least 15% of the bulk sulfate pool. Coincident with this trend in δ³⁴S_SO4, the oxygen isotope composition of sulfate tended to be ¹⁸O-enriched in low pH (<5), high temperature (>75°C) pore waters. The shift toward high δ¹⁸O_SO4 is consistent with equilibrium isotope exchange under acidic and high temperature conditions. The source of H₂S contained in hydrothermal fluids could not be determined with the present dataset; however, the end-member δ³⁴S value of H₂S discharged to the seafloor is consistent with equilibrium isotope exchange with subsurface anhydrite veins at a temperature of ~300°C. Any biological sulfur cycling within these hydrothermal systems is masked by abiotic chemical reactions driven by mixing between low-sulfate, H₂S-rich hydrothermal fluids and oxic, sulfate-rich seawater.

Abstract

The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown. Low-temperature (<100°C) fluid samples were investigated from two borehole observatories in the Juan de Fuca Ridge (JFR) flank, representing a range of upper oceanic basement thermal and geochemical properties. Microbial sulfate reduction rates (SRR) were measured in laboratory incubations with ³⁵S-sulfate over a range of temperatures and the identity of the corresponding sulfate-reducing microorganisms (SRM) was studied by analyzing the sequence diversity of the functional marker dissimilatory (bi)sulfite reductase (dsrAB) gene. We found that microbial sulfate reduction was limited by the decreasing availability of organic electron donors in higher temperature, more altered fluids. Thermodynamic calculations indicate energetic constraints for metabolism, which together with relatively higher cell-specific SRR reveal increased maintenance requirements, consistent with novel species-level dsrAB phylotypes of thermophilic SRM. Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling.

Abstract

The deep subsurface is an enormous repository of microbial life. However, the metabolic capabilities of these microorganisms and the degree to which they are dependent on surface processes are largely unknown. Due to the logistical difficulty of sampling and inherent heterogeneity, the microbial populations of the terrestrial subsurface are poorly characterized. In an effort to better understand the biogeochemistry of deep terrestrial habitats, we evaluate the energetic yield of chemolithotrophic metabolisms and microbial diversity in the Sanford Underground Research Facility (SURF) in the former Homestake Gold Mine, SD, USA. Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment. SURF provides access into an iron-rich Paleoproterozoic metasedimentary deposit that contains deeply circulating groundwater. Geochemical analyses of subsurface fluids reveal enormous geochemical diversity ranging widely in salinity, oxidation state (ORP 330 to −328 mV), and concentrations of redox sensitive species (e.g., Fe²⁺ from near 0 to 6.2 mg/L and Σ S^2- from 7 to 2778μg/L). As a direct result of this compositional buffet, Gibbs energy calculations reveal an abundance of energy for microorganisms from the oxidation of sulfur, iron, nitrogen, methane, and manganese. Pyrotag DNA sequencing reveals diverse communities of chemolithoautotrophs, thermophiles, aerobic and anaerobic heterotrophs, and numerous uncultivated clades. Extrapolated across the mine footprint, these data suggest a complex spatial mosaic of subsurface primary productivity that is in good agreement with predicted energy yields. Notably, we report Gibbs energy normalized both per mole of reaction and per kg fluid (energy density) and find the later to be more consistent with observed physiologies and environmental conditions. Further application of this approach will significantly expand our understanding of the deep terrestrial biosphere.

Abstract

Directly assessing the impact of subsurface microbial activity on global element cycles is complicated by the inaccessibility of most deep biospheres and the difficulty of growing representative cultivars in the laboratory. In order to constrain the rates of biogeochemical processes in such settings, a quantitative relationship between rates of microbial catalysis, energy supply and demand and population size has been developed that complements the limited biogeochemical data describing subsurface environments. Within this formulation, rates of biomass change are determined as a function of the proportion of catabolic power that is converted into anabolism—either new microorganisms or the replacement of existing cell components—and the amount of energy that is required to synthesize biomass. Catabolic power is related to biomass through an energy-based yield coefficient that takes into account the constraints that different environments impose on biomolecule synthesis; this method is compared to other approaches for determining yield coefficients. Furthermore, so-called microbial maintenance energies that have been reported in the literature, which span many orders of magnitude, are reviewed. The equations developed in this study are used to demonstrate the interrelatedness of catabolic reaction rates, Gibbs energy of reaction, maintenance energy, biomass yield coefficients, microbial population sizes and doubling/replacement times. The number of microorganisms that can be supported by particular combinations of energy supply and demand is illustrated as a function of the catabolic rates in marine environments. Replacement/doubling times for various population sizes are shown as well. Finally, cell count and geochemical data describing two marine sedimentary environments in the South Pacific Gyre and the Peru Margin are used to constrain in situ metabolic and catabolic rates. The formulations developed in this study can be used to better define the limits and extent of life because they are valid for any metabolism under any set of conditions.

Abstract

The origin, evolution, and distribution of life throughout the universe can be better understood by determining the limits to life on Earth. A broad range of many of the physical and chemical constraints that determine the limits to life, such as temperature, pressure, physical space, water content, and the availability of energy and nutrients, are found in subseafloor environments. In fact, several expeditions (Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP: now International Ocean Discovery Program)) have been at least partially motivated by the desire to explore the boundaries between the habitable and the uninhabitable parts of the subseafloor. In this chapter, the possible subseafloor environments and their physical and chemical characteristics that could signify the limits of the biosphere, particularly the hydrothermally active subseafloor environments, are reviewed. Although the nature and distribution of extreme or fringe biospheres are unknown, previous ODP- and IODP-expedition-based microbiological investigations have shown that the subseafloor hydrothermal systems with relatively abundant energy supplies (sediment-derived organic compounds and serpentinization-derived H₂) provide targets for seeking the limits (boundary conditions) in subseafloor environments. Here, we also discuss predicted patterns of the abundance and composition of potential microbial catabolisms in the fringe microbial communities of subseafloor hydrothermal fluids based on the thermodynamic potential of particular catabolic strategies and the computed cost of anabolism in these settings.

Abstract

Quantification of global biogeochemical cycles requires knowledge of the rates at which microorganisms catalyze chemical reactions. In order for models that describe these processes to capture global patterns of change, the underlying formulations in them must account for biogeochemical transformations over seasonal and millennial time scales in environments characterized by different energy levels. Building on existing models, a new thermodynamic limiting function is introduced. With only one adjustable parameter, this function that can be used to model microbial metabolism throughout the range of conditions in which organisms are known to be active. The formulation is based on a comparison of the amount of energy available from any redox reaction to the energy required to maintain a membrane potential, a proxy for the minimum amount of energy required by an active microorganism. This function does not require species- or metabolism-specific parameters, and can be used to model metabolisms that capture any amount of energy. The utility of this new thermodynamic rate limiting term is illustrated by applying it to three low-energy processes: fermentation, methanogenesis and sulfate reduction. The model predicts that the rate of fermentation will be reduced by half once the Gibbs energy of the catalyzed reaction reaches −12 kJ (mol e⁻)⁻¹, and then slowing exponentially until the energy yield approaches zero. Similarly, the new model predicts that the low energy yield of methanogenesis, −4 to −0.5 kJ (mol e⁻)⁻¹, for a partial pressure of H₂ between 11 and 0.6 Pa decreases the reaction rate by 95–99%. Finally, the new function’s utility is illustrated through its ability to accurately model sulfate concentration data in an anoxic marine sediment.

Abstract

This study is the first to investigate the microbial ecology of the Tutum Bay (Papua New Guinea) shallow-sea hydrothermal system. The subsurface environment was sampled by SCUBA using push cores, which allowed collection of sediments and pore fluids. Geochemical analysis of sediments and fluids along a transect emanating from a discrete venting environment, about 10 mbsl, revealed a complex fluid flow regime and mixing of hydrothermal fluid with seawater within the sediments, providing a continuously fluctuating redox gradient. Vent fluids are highly elevated in arsenic, up to ∼1 ppm, serving as a “point source” of arsenic to this marine environment. 16S rRNA gene and FISH (fluorescence in situ hybridization) analyses revealed distinct prokaryotic communities in different sediment horizons, numerically dominated by Bacteria. 16S rRNA gene diversity at the genus level is greater among the Bacteria than the Archaea. The majority of taxa were similar to uncultured Crenarchaea, Chloroflexus, and various heterotrophic Bacteria. The archaeal community did not appear to increase significantly in number or diversity with depth in these sediments. Further, the majority of sequences identifying with thermophilic bacteria were found in the shallower section of the sediment core. No 16S rRNA genes of marine Crenarchaeota or Euryarchaeota were identified, and none of the identified Crenarchaeota have been cultured. Both sediment horizons also hosted “Korarchaeota”, which represent 2–5% of the 16S rRNA gene clone libraries. Metabolic functions, especially among the Archaea, were difficult to constrain given the distant relationships of most of the community members from cultured representatives. Identification of phenotypes and key ecological processes will depend on future culturing, identification of arsenic cycling genes, and RNA-based analyses.

Abstract

The shallow submarine hydrothermal systems of Tutum Bay, Papua New Guinea, are an ideal opportunity to study the influence of arsenic on a marine ecosystem. Previous reports have demonstrated that the hydrothermal vents in Tutum Bay release arsenic in reduced hydrothermal fluids into the marine environment at the rate of 1.5 kg of arsenic/day. Aqueous arsenite is oxidized and adsorbed onto hydrous ferric oxides [HFOs] surrounding the venting area. We demonstrate here that microorganisms are key in both the oxidation of Fe^II and As^III in the areas immediately surrounding the vent source. Surveys of community diversity in biofilms and in vent fluid indicate the presence of zeta-Proteobacteria, alpha-Proteobacteria, Persephonella, and close relatives of the archaeon Nitrosocaldus. The iron oxidizing zeta-Proteobacteria are among the first colonizers of solid substrates near the vents, where they appear to be involved in the precipitation of the hydrous ferric oxides (HFOs). Further, the biofilm communities possess the genetic capacity for the oxidation of arsenite. The resulting arsenate is adsorbed onto the HFOs, potentially removing the arsenic from the immediate marine system. No evidence was found for dissimilatory arsenate reduction, but the arsenate may be remobilized by detoxification mechanisms. This is the first demonstration of the genetic capacity for arsenic cycling in high temperature, shallow-sea vent communities, supporting recent culture-based findings in similar systems in Greece (Handley et al., 2010). These reports extend the deep-sea habitat of the zeta-Proteobacteria to shallow submarine hydrothermal systems, and together implicate biological oxidation of both iron and arsenite as primary biogeochemical processes in these systems, providing a mechanism for the partial removal of aqueous arsenic from the marine environment surrounding the vents.

Abstract

Phase separation is a ubiquitous process in seafloor hydrothermal vents, creating a large range of salinities. Toxic elements (e.g., arsenic) partition into the vapor phase, and thus can be enriched in both high and low salinity fluids. However, investigations of microbial diversity at sites associated with phase separation are rare. We evaluated prokaryotic diversity in arsenic-rich shallow-sea vents off Milos Island (Greece) by comparative analysis of 16S rRNA clone sequences from two vent sites with similar pH and temperature but marked differences in salinity. Clone sequences were also obtained for aioA-like functional genes (AFGs). Bacteria in the surface sediments (0–1.5 cm) at the high salinity site consisted of mainly Epsilonproteobacteria (Arcobacter sp.), which transitioned to almost exclusively Firmicutes (Bacillus sp.) at ~10 cm depth. However, the low salinity site consisted of Bacteroidetes (Flavobacteria) in the surface and Epsilonproteobacteria (Arcobacter sp.) at ~10 cm depth. Archaea in the high salinity surface sediments were dominated by the orders Archaeoglobales and Thermococcales, transitioning to Thermoproteales and Desulfurococcales (Staphylothermus sp.) in the deeper sediments. In contrast, the low salinity site was dominated by Thermoplasmatales in the surface and Thermoproteales at depth. Similarities in gas and redox chemistry suggest that salinity and/or arsenic concentrations may select for microbial communities that can tolerate these parameters. Many of the archaeal 16S rRNA sequences contained inserts, possibly introns, including members of the Euryarchaeota. Clones containing AFGs affiliated with either Alpha– or Betaproteobacteria, although most were only distantly related to published representatives. Most clones (89%) originated from the deeper layer of the low salinity, highest arsenic site. This is the only sample with overlap in 16S rRNA data, suggesting arsenotrophy as an important metabolism in similar environments.

Abstract

Active deep-sea hydrothermal vents are hosted by a range of different rock types, including basalt, peridotite, and felsic rocks. The associated hydrothermal fluids exhibit substantial chemical variability, which is largely attributable to compositional differences among the underlying host rocks. Numerical models were used to evaluate the energetics of seven inorganic redox reactions (potential catabolisms of chemolithoautotrophs) and numerous biomolecule synthesis reactions (anabolism) in a representative sampling of these systems, where chemical gradients are established by mixing hydrothermal fluid with seawater. The wide ranging fluid compositions dictate demonstrable differences in Gibbs energies (ΔG_r) of these catabolic and anabolic reactions in three peridotite-hosted, six basalt-hosted, one troctolite-basalt hybrid, and two felsic rock-hosted systems. In peridotite-hosted systems at low to moderate temperatures (<∼45 °C) and high seawater:hydrothermal fluid (SW:HF) mixing ratios (>10), hydrogen oxidation yields the most catabolic energy, but the oxidation of methane, ferrous iron, and sulfide can also be moderately exergonic. At higher temperatures, and consequent SW:HF mixing ratios <10, anaerobic processes dominate the energy landscape; sulfate reduction and methanogenesis are more exergonic than any of the aerobic respiration reactions. By comparison, in the basalt-hosted and felsic rock-hosted systems, sulfide oxidation was the predominant catabolic energy source at all temperatures (and SW:HF ratios) considered. The energetics of catabolism at the troctolite-basalt hybrid system were intermediate to these extremes. Reaction energetics for anabolism in chemolithoautotrophs—represented here by the synthesis of amino acids, nucleotides, fatty acids, saccharides, and amines—were generally most favorable at moderate temperatures (22–32 °C) and corresponding SW:HF mixing ratios (∼15). In peridotite-hosted and the troctolite-basalt hybrid systems, ΔG_r for primary biomass synthesis yielded up to ∼900 J per g dry cell mass. The energetics of anabolism in basalt- and felsic rock-hosted systems were far less favorable. The results suggest that in peridotite-hosted (and troctolite-basalt hybrid) systems, compared with their basalt (and felsic rock) counterparts, microbial catabolic strategies—and consequently variations in microbial phylotypes—may be far more diverse and some biomass synthesis may yield energy rather than imposing a high energetic cost.

Abstract

During the past decade, the IODP (International Ocean Discovery Program) has fostered a significant increase in deep biosphere investigations in the marine sedimentary and crustal environments, and scientists are well-poised to continue this momentum into the next phase of the IODP. The goals of this workshop were to evaluate recent findings in a global context, synthesize available biogeochemical data to foster thermodynamic and metabolic activity modeling and measurements, identify regional targets for future targeted sampling and dedicated expeditions, foster collaborations, and highlight the accomplishments of deep biosphere research within IODP. Twenty-four scientists from around the world participated in this one-day workshop sponsored by IODP-MI and held in Florence, Italy, immediately prior to the Goldschmidt 2013 conference. A major topic of discussion at the workshop was the continued need for standard biological sampling and measurements across IODP platforms. Workshop participants renew the call to IODP operators to implement recommended protocols.

Abstract

Thermodynamic modelling of organic synthesis has largely been focused on deep-sea hydrothermal systems. When seawater mixes with hydrothermal fluids, redox gradients are established that serve as potential energy sources for the formation of organic compounds and biomolecules from inorganic starting materials. This energetic drive, which varies substantially depending on the type of host rock, is present and available both for abiotic (outside the cell) and biotic (inside the cell) processes. Here, we review and interpret a library of theoretical studies that target organic synthesis energetics. The biogeochemical scenarios evaluated include those in present-day hydrothermal systems and in putative early Earth environments. It is consistently and repeatedly shown in these studies that the formation of relatively simple organic compounds and biomolecules can be energy-yielding (exergonic) at conditions that occur in hydrothermal systems. Expanding on our ability to calculate biomass synthesis energetics, we also present here a new approach for estimating the energetics of polymerization reactions, specifically those associated with polypeptide formation from the requisite amino acids.

Abstract

The fluids emanating from active submarine hydrothermal vent chimneys provide a window into subseafloor processes and, through mixing with seawater, are responsible for steep thermal and compositional gradients that provide the energetic basis for diverse biological communities. Although several models have been developed to better understand the dynamic interplay of seawater, hydrothermal fluid, minerals and microorganisms inside chimney walls, none provide a fully integrated approach to quantifying the biogeochemistry of these hydrothermal systems. In an effort to remedy this, a fully coupled biogeochemical reaction-transport model of a hydrothermal vent chimney has been developed that explicitly quantifies the rates of microbial catalysis while taking into account geochemical processes such as fluid flow, solute transport and oxidation–reduction reactions associated with fluid mixing as a function of temperature. The metabolisms included in the reaction network are methanogenesis, aerobic oxidation of hydrogen, sulfide and methane and sulfate reduction by hydrogen and methane. Model results indicate that microbial catalysis is generally fastest in the hottest habitable portion of the vent chimney (77–102 °C), and methane and sulfide oxidation peak near the seawater-side of the chimney. The fastest metabolisms are aerobic oxidation of H₂ and sulfide and reduction of sulfate by H₂ with maximum rates of 140, 900 and 800 pmol cm⁻³ d⁻¹, respectively. The maximum rate of hydrogenotrophic methanogenesis is just under 0.03 pmol cm⁻³ d⁻¹, the slowest of the metabolisms considered. Due to thermodynamic inhibition, there is no anaerobic oxidation of methane by sulfate (AOM). These simulations are consistent with vent chimney metabolic activity inferred from phylogenetic data reported in the literature. The model developed here provides a quantitative approach to describing the rates of biogeochemical transformations in hydrothermal systems and can be used to constrain the role of microbial activity in the deep subsurface.

Abstract

This study examines the potential for the biologically mediated anaerobic oxidation of methane (AOM) coupled to sulfate reduction on ancient Mars. Seven distinct fluids representative of putative martian groundwater were used to calculate Gibbs energy values in the presence of dissolved methane under a range of atmospheric CO₂ partial pressures. In all scenarios, AOM is exergonic, ranging from −31 to −135 kJ/mol CH₄. A reaction transport model was constructed to examine how environmentally relevant parameters such as advection velocity, reactant concentrations, and biomass production rate affect the spatial and temporal dependences of AOM reaction rates. Two geologically supported models for ancient martian AOM are presented: a sulfate-rich groundwater with methane produced from serpentinization by-products, and acid-sulfate fluids with methane from basalt alteration. The simulations presented in this study indicate that AOM could have been a feasible metabolism on ancient Mars, and fossil or isotopic evidence of this metabolic pathway may persist beneath the surface and in surface exposures of eroded ancient terrains.

Abstract

Although it is becoming clear that microorganisms are abundant in marine deep sediments [1–8], it is unclear what percentage of cells are active, how fast they are growing or what controls their diversity and population size [9]. Addressing these issues is a formidable task due to the relative inaccessibility of these environments, the difficulty of cultivating representative microorganisms and the long time scales associated with some of their lifestyles [2, 10–12]. However, quantitative limits on life in the subsurface can be determined by using the physiochemical data that describe their habitats. In particular, the chemical composition can be used to constrain likely metabolic strategies and rates in a given setting. This is accomplished by calculating values of Gibbs energy available from reactions containing different combinations of the electron donors and acceptors that are found in these environments. Not only can Gibbs energies of reaction reveal which catabolic strategies are thermodynamically possible, but they can also help determine which geochemical variables (e.g. temperature, pressure, pH, salinity, composition) are controlling microbial activity. When reduced to an environmentally-appropriate common factor, the energetic potential of all biogeochemical environments can be directly compared to assess how energy limitations affect the amount and type of biomass in them. In the present chapter, geochemical data obtained from sediment cores taken from the Peru Margin, South Pacific Gyre and Juan de Fuca Ridge are used to assess the Gibbs energies of plausible catabolic strategies including, but not limited to, the oxidation of organic matter, methane and hydrogen by a variety of electron acceptors. In conjunction with cell-count data, the results of these calculations illustrate the importance of normalizing energy availability to the limiting substrate and how geochemical data can be used to better understand the distribution of life deep in marine sediments.

Abstract

The permeable rocks of the upper oceanic basement contain seawater-sourced fluids estimated to be ~ 2% of the global ocean volume. This represents a very large potential subsurface biosphere supported by chemosynthesis. Recent collection of high integrity samples of basement fluid from the sedimented young basaltic basement on the Juan de Fuca Ridge flanks, off the coasts of Vancouver Island (Canada) and Washington (USA), and subsequent chemical analyses permit numerical modeling of metabolic redox reaction energetics. Here, values of Gibbs free energy for potential chemolithotrophic net reactions were calculated in basement fluid and in zones where basement fluid and entrained seawater may mix; the energy yields are reported both on a per mole electrons transferred and on a per kg of basement fluid basis. In pure basement fluid, energy yields from the anaerobic respiration processes investigated are anemic, releasing < 0.3 J/kg basement fluid for all reactions except methane oxidation by ferric iron, which releases ~ 0.6 J/kg basement fluid. In mixed solutions, aerobic oxidation of hydrogen, methane, and sulfide is the most exergonic on a per mole electron basis. Per kg of basement fluid, the aerobic oxidation of ammonia is by far the most exergonic at low temperature and high seawater:basement fluid ratio, decreasing by more than two orders of magnitude at the highest temperature (63 °C) and lowest seawater:basement fluid ratio investigated. Compared with mixing zones in deep-sea hydrothermal systems, oceanic basement aquifers appear to be very low energy systems, but because of their expanse, may support what has been labeled the ‘starving majority’.

Abstract

The permeable upper oceanic basement serves as a plausible habitat for a variety of microbial communities. There is growing evidence suggesting a substantial subseafloor biosphere. Here new time series data are presented on key inorganic species, methane, hydrogen and dissolved organic carbon (DOC) in ridge flank fluids obtained from subseafloor observatory CORKs (Circulation Obviation Retrofit Kits) at Integrated Ocean Drilling Program (IODP) boreholes 1301A and 1026B. These data show that the new sampling methods (Cowen et al., 2012) employed at 1301A result in lower contamination than earlier studies. Furthermore, sample collection methods permitted most chemical analyses to be performed from aliquots of single large volume samples, thereby allowing more direct comparison of the data. The low phosphate concentrations (0.06–0.2 μM) suggest that relative to carbon and nitrogen, phosphorus could be a limiting nutrient in the basement biosphere. Coexisting sulfate (17–18 mM), hydrogen sulfide (∼0.1 μM), hydrogen (0.3–0.7 μM) and methane (1.5–2 μM) indicates that the basement aquifer at 1301A either draws fluids from multiple flow paths with different redox histories or is a complex environment that is not thermodynamically controlled and may allow co-occurring metabolic pathways including sulfate reduction and methanogenesis. The low DOC concentrations (11–18 μM) confirm that ridge flank basement is a net DOC sink and ultimately a net carbon sink. Based on the net amounts of DOC, oxygen, nitrate and sulfate removed (∼30 μM, ∼80 μM, ∼40 μM and ∼10 mM, respectively) from entrained bottom seawater, organic carbon may be aerobically or anaerobically oxidized in biotic and/or abiotic processes.

Abstract

Sulfate reducing microorganisms (SRM) may play a significant role altering upper oceanic crustal fluids when suitable electron donors, such as hydrogen or organic matter, are available. The habitability of such an environment with respect to sulfate reduction depends on the competition of microbial communities for substrates, which is largely dictated by the energetics of catabolic and anabolic processes. Although sulfate reduction has been observed in fluids taken from the upper ocean crust in Juan de Fuca Ridge flanks, the electron donors (EDs) used by SRM have not been identified, nor has the energy required for organic synthesis been determined. As a result, a collaboration is underway to characterize the EDs that are plausible candidates for the SRM in the Juan de Fuca system and to quantify the amount of energy these microorganisms require to synthesize biomolecules. This is accomplished by carrying out thermodynamic calculations that take into account the physicochemical properties of the resident fluids. Specifically, the Gibbs energy of reactions describing the reduction of sulfate by various EDs and the synthesis of amino acids from inorganic precursors is being calculated at the temperature, pressure and compositional conditions prevailing in particular Juan de Fuca sample site locations.

Abstract

The goal of this postdoctoral fellowship was to quantify the types and amounts energy that are available to microorganisms in the subsurface, with particular emphasis on the main C-DEBI Focus Study Sites. Not only has this objective been achieved, but a number of related research activities have also been undertaken throughout and beyond the funding period (April 1, 2012 – March 31/2014). Published research directly related to the proposed research goal includes quantitative analyses of the energy available to microorganisms in sediments located near the Juan de Fuca ridge, South Pacific Gyre, Peru Margin (LaRowe and Amend, 2014), deep Guaymas Basin (Teske et al., 2014) and Cape Basin (southeastern Atlantic) (Hernández-Sánchez et al., 2014) and crustal fluids from the Juan de Fuca Ridge (Robador et al., 2015). In closely related work, a model linking the energetics and rates of microbially catalyzed reactions in low-energy environments has been applied to calculate the rates of microbial activity in a hydrothermal vent chimney wall (LaRowe et al., 2014). In a related project, a quantitative relationship between rates of microbial catalysis, energy supply and demand and population size has been developed that complements the limited biogeochemical data describing subsurface environments has been published (LaRowe andAmend, 2015). In addition, collaborations with several other C-DEBI-funded scientists has results in a series of review papers concerning rates of microbial activity in the deep biosphere (Orcutt et al., 2013), an overview and catalogue of IODP sampling that has resulted in microbiological sampling (Orcutt et al., 2014) and a summary of extreme life research that has resulted from the last decade of IODP-sponsored activities (Takai et al., 2014). Furthermore, several ongoing projects are focused on the bioenergetics of shallow Guaymas Basin sediments (McKay et al.), and diffuse hydrothermal fluids emanating from the Loihi seamount (Sylvan et al.). In addition to the research summarized above, the results of a number of other scientific endeavors concerning themes related to C-DEBI goals have also been published. These include a review and synthesis of the energetics of organic synthesis inside and outside of cells (Amend et al., 2013), the possibility of anaerobic oxidation of methane on ancient Mars (Marlow et al., 2014), chemolithotrophy in the continental deep subsurface (Osburn et al., 2014) and the geochemistry and bioenergetic potential of a shallow-sea hydrothermal vent system (Price et al., 2015). Along with these papers, several more have been published concerning the fate or organic matter. In particular, peer-reviewed publications on the anthropogenic perturbation of carbon from land to ocean (Regnier et al., 2013) and a review and synthesis paper on the degradation of organic carbon in marine sediments (Arndt et al., 2013). Furthermore, several more projects related to quantifying the microbial degradation of organic carbon in marine sediments on a global scale are underway.

Abstract

The Strytan Hydrothermal Field (SHF; Eyjafjord, northern Iceland) exhibits alkaline (pH ~ 10), hot (up to 78°C), submarine hydrothermal venting, resulting in the formation of numerous saponite towers. We performed a detailed geochemical and microbiological characterization of hydrothermal fluids and precipitates from the site. End-member calculations revealed elevated concentrations of many major and trace elements (e.g., 2.4 mM Na, 3 to 27 μM K, 40 to 120 μM Ca, 10 to 25 μM B, and overall high concentrations of trace elements). We hypothesize that recharge of meteoric water occurs in the mountains south of Eyjafjord, and low temperature alteration of plagioclase, pyroxene and olivine in basalt, and precipitation of calcite, occurs in a closed system. This explains the observed high pH, variable Ca concentrations, and low DIC. CH₄, H₂, and CO concentrations were all elevated relative to normal seawater (up to 1.41, 5.19, and 0.13 μM, respectively), and a range of δ¹³C-CH₄ was measured. Weathering of pyroxene may produce H₂, which combines with CO₂ to form abiotic CH₄. The abiotic production of H₂ and CH₄ in a site such as the SHF broadens the range of potential origin of life environments significantly. Intact polar lipids indicate Bacteria dominated all samples except one. Up to 50% of the lipids at this site were archaeal. Bacterial clone sequences were dominated by betaproteobacteria (Dechloromonas sp.), followed by deltaproteobacteria (Desulfovibrio sp.) Archaeal results indicate a dominance of Crenarchaeota, particularly Thermoproteales, followed by Desulfurococcales. More detailed analysis of microbial communities is currently underway.