Person: Douglas E. LaRowe

Abstract

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.

Abstract

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

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

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.

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

We report measurements of resolved ¹²CH₂D₂ and ¹³CH₃D at natural abundances in a variety of methane gases produced naturally and in the laboratory. The ability to resolve ¹²CH₂D₂ from ¹³CH₃D provides unprecedented insights into the origin and evolution of CH₄. The results identify conditions under which either isotopic bond order disequilibrium or equilibrium are expected. Where equilibrium obtains, concordant Δ¹²CH₂D₂ and Δ¹³CH₃D temperatures can be used reliably for thermometry. We find that concordant temperatures do not always match previous hypotheses based on indirect estimates of temperature of formation nor temperatures derived from CH₄/H₂ D/H exchange, underscoring the importance of reliable thermometry based on the CH₄ molecules themselves. Where Δ¹²CH₂D₂ and Δ¹³CH₃D values are inconsistent with thermodynamic equilibrium, temperatures of formation derived from these species are spurious. In such situations, while formation temperatures are unavailable, disequilibrium isotopologue ratios nonetheless provide novel information about the formation mechanism of the gas and the presence or absence of multiple sources or sinks. In particular, disequilibrium isotopologue ratios may provide the means for differentiating between methane produced by abiotic synthesis vs. biological processes. Deficits in ¹²CH₂D₂ compared with equilibrium values in CH₄ gas made by surface-catalyzed abiotic reactions are so large as to point towards a quantum tunneling origin. Tunneling also accounts for the more moderate depletions in ¹³CH₃D that accompany the low ¹²CH₂D₂ abundances produced by abiotic reactions. The tunneling signature may prove to be an important tracer of abiotic methane formation, especially where it is preserved by dissolution of gas in cool hydrothermal systems (e.g., Mars). Isotopologue signatures of abiotic methane production can be erased by infiltration of microbial communities, and Δ¹²CH₂D₂ values are a key tracer of microbial recycling.

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

The role of nitrogen cycling in submarine hydrothermal systems is far less studied than that of other biologically reactive elements such as sulfur and iron. In order to address this knowledge gap, we investigated nitrogen redox processes at Loihi Seamount, Hawaii, using a combination of biogeochemical and isotopic measurements, bioenergetic calculations and analysis of the prokaryotic community composition in venting fluids sampled during four cruises in 2006, 2008, 2009 and 2013. Concentrations of NH₄⁺ were positively correlated to dissolved Si and negatively correlated to NO₃^-+NO₂^-, while NO₂^- was not correlated to NO₃^-+NO₂^-, dissolved Si or NH₄⁺. This is indicative of hydrothermal input of NH₄⁺ and biological mediation influencing NO₂^-concentrations. The stable isotope ratios of NO₃^- (δ¹⁵N and δ¹⁸O) was elevated with respect to background seawater, with δ¹⁸O values exhibiting larger changes than corresponding δ¹⁵N values, reflecting the occurrence of both production and reduction of NO₃^- by an active microbial community. δ¹⁵N-NH₄⁺ values ranged from 0‰ to +16.7‰, suggesting fractionation during consumption and potentially N-fixation as well. Bioenergetic calculations reveal that several catabolic strategies involving the reduction of NO₃^- and NO₂^- coupled to sulfide and iron oxidation could provide energy to microbes in Loihi fluids, while 16S rRNA gene sequencing of Archaea and Bacteria in the fluids reveals groups known to participate in denitrification and N-fixation. Taken together, our data support the hypothesis that microbes are mediating N-based redox processes in venting hydrothermal fluids at Loihi Seamount.

Abstract

The deep marine biosphere hosts a rich microbial community whose dynamics are important analogues to oligotrophic and extra-terrestrial environments, and whose activity bears a major control on the burial of organic carbon and thus global climate. However, these environments are notoriously difficult to study because of their remoteness, limited sampling opportunities and limited material. Numerical models are useful in the context of geochemistry, but many do not explicitly resolve microbes, rather implicitly accounting for microbial processes. Thus, I propose to develop a new biogeochemical-evolutionary model. This research will develop the existing BRNS reaction/transport model and microbial populations will be explicitly resolved (with functionality-based classifications) and will drive geochemical reactions. The evolutionary model will include a trade-off based microbial functionality (similar to the DARWIN model). This research will provide a new tool to the scientific community, and act as a platform for collaboration between experimentalists, modellers, geochemists and microbiologists. Additionally, it will provide quantitate insight into microbial and geochemical coupling in deep marine sediments, with a focus on the Peru Margin, specifically addressing the role of geochemistry in selecting the microbial community, the role of the microbial community in driving geochemical gradients, and the activity of microbes in the sediment profile.

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

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

Sedimentary biomarker distributions can record ocean productivity and community structure, but their interpretation must consider alteration during organic matter (OM) export and burial. Large changes in the water column redox state are known to impact on the preservation of biomarkers, but more subtle variation in sediment redox conditions, characteristic of major modern ocean basins, have been less thoroughly investigated. Here we evaluate changes in biomarker distributions during sinking and burial across a nearshore to offshore transect in the southwestern Cape Basin (South East Atlantic), which includes a range of sedimentary environments. Biomarker concentrations and distributions in suspended particulate matter from the upper water column were determined and compared with underlying sedimentary biomarker accumulation rates and distributions. Biomarker distributions were similar in surface and subsurface waters, indicating that the OM signature is exported from the ocean mixed layer with minimal alteration. We show that, while export production (100 m) is similar along this transect, ²³⁰Th_xs-corrected biomarker accumulation rate varies by over an order of magnitude in sediments and is directly associated with sedimentary redox conditions, ranging from oxic to nitrogenous–ferruginous. Biomarker distributions were dominated by sterols in surface water, and by alkenones in underlying sediments, which we propose to be primarily the result of selective preservation. Notably, the difference in sediment O₂ penetration depth was associated with relative biomarker preservation. Subtle variation in sedimentary redox conditions has a dramatic impact on the distribution of preserved biomarkers. We discuss mechanisms for preferential degradation of specific biomarkers within this setting.

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

Temperature is one of the key constraints on the spatial extent, physiological and phylogenetic diversity, and biogeochemical function of subsurface life. A model system to explore these interrelationships should offer a suitable range of geochemical regimes, carbon substrates and temperature gradients under which microbial life can generate energy and sustain itself. In this theory and hypothesis article, we make the case for the hydrothermally heated sediments of Guaymas Basin in the Gulf of California as a suitable model system where extensive temperature and geochemical gradients create distinct niches for active microbial populations in the hydrothermally influenced sedimentary subsurface that in turn intercept and process hydrothermally generated carbon sources. We synthesize the evidence for high-temperature microbial methane cycling and sulfate reduction at Guaymas Basin – with an eye on sulfate-dependent oxidation of abundant alkanes – and demonstrate the energetic feasibility of these latter types of deep subsurface life in previously drilled Guaymas Basin locations of Deep-Sea Drilling Project 64.

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

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

Quantifying the rates of biogeochemical processes in marine sediments is essential for understanding global element cycles and climate change. Because organic matter degradation is the engine behind benthic dynamics, deciphering the impact that various forces have on this process is central to determining the evolution of the Earth system. Therefore, recent developments in the quantitative modeling of organic matter degradation in marine sediments are critically reviewed. The first part of the review synthesizes the main chemical, biological and physical factors that control organic matter degradation in sediments while the second part provides a general review of the mathematical formulations used to model these processes and the third part evaluates their application over different spatial and temporal scales. Key transport mechanisms in sedimentary environments are summarized and the mathematical formulation of the organic matter degradation rate law is described in detail. The roles of enzyme kinetics, bioenergetics, temperature and biomass growth in particular are highlighted. Alternative model approaches that quantify the degradation rate constant are also critically compared. In the third part of the review, the capability of different model approaches to extrapolate organic matter degradation rates over a broad range of temporal and spatial scales is assessed. In addition, the structure, functions and parameterization of more than 250 published models of organic matter degradation in marine sediments are analyzed. The large range of published model parameters illustrates the complex nature of organic matter dynamics, and, thus, the limited transferability of these parameters from one site to another. Compiled model parameters do not reveal a statistically significant correlation with single environmental characteristics such as water depth, deposition rate or organic matter flux. The lack of a generic framework that allows for model parameters to be constrained in data-poor areas seriously limits the quantification of organic matter degradation on a global scale. Therefore, we explore regional patterns that emerge from the compiled more than 250 organic matter rate constants and critically discuss them in their environmental context. This review provides an interdisciplinary view on organic matter degradation in marine sediments. It contributes to an improved understanding of global patterns in benthic organic matter degradation, and helps identify outstanding questions and future directions in the modeling of organic matter degradation in marine sediments.

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 vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).

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.