Chemistry of iron sulfides.

Our work was motivated by discoveries of prokaryotic communities that survive with little nutrient in ice and permafrost, with implications for past or present microbial life in Martian permafrost and Europan ice. We compared the temperature dependence of metabolic rates of microbial communities in permafrost, ice, snow, clouds, oceans, lakes, marine and freshwater sediments, and subsurface aquifer sediments. Metabolic rates per cell fall into three groupings: (i) a rate, μg(T), for growth, measured in the laboratory at in situ temperatures with minimal disturbance of the medium; (ii) a rate, μm(T), sufficient for maintenance of functions but for a nutrient level too low for growth; and (iii) a rate, μs(T), for survival of communities imprisoned in deep glacial ice, subsurface sediment, or ocean sediment, in which they can repair macromolecular damage but are probably largely dormant. The three groups have metabolic rates consistent with a single activation energy of ≈110 kJ and that scale as μg(T):μm(T):μs(T) ≈ 106:103:1. There is no evidence of a minimum temperature for metabolism. The rate at -40°C in ice corresponds to ≈10 turnovers of cellular carbon per billion years. Microbes in ice and permafrost have metabolic rates similar to those in water, soil, and sediment at the same temperature. This finding supports the view that, far below the freezing point, liquid water inside ice and permafrost is available for metabolism. The rate μs(T) for repairing molecular damage by means of DNA-repair enzymes and protein-repair enzymes such as methyltransferase is found to be comparable to the rate of spontaneous molecular damage.

https://www.pnas.org/content/pnas/101/13/4631.full.pdf

Temperature dependence of metabolic rates for microbial growth, maintenance, and survival.

Thermophilic and hyperthermophilic Archaea and Bacteria have been isolated from marine hydrothermal systems, heated sediments, continental solfataras, hot springs, water heaters, and industrial waste They catalyze a tremendous array of widely varying metabolic processes As determined in the laboratory, electron donors in thermophilic and hyperthermophilic microbial redox reactions include H2, Fe(2+), H2S, S, S2O3(2-), S4O6(2-), sulfide minerals, CH4, various mono-, di-, and hydroxy-carboxylic acids, alcohols, amino acids, and complex organic substrates; electron acceptors include O2, Fe(3+), CO2, CO, NO3(-), NO2(-), NO, N2O, SO4(2-), SO3(2-), S2O3(2-), and S Although many assimilatory and dissimilatory metabolic reactions have been identified for these groups of microorganisms, little attention has been paid to the energetics of these reactions In this review, standard molal Gibbs free energies (DeltaGr(0)) as a function of temperature to 200 degrees C are tabulated for 370 organic and inorganic redox, disproportionation, dissociation, hydrolysis, and solubility reactions directly or indirectly involved in microbial metabolism To calculate values of DeltaGr(0) for these and countless other reactions, the apparent standard molal Gibbs free energies of formation (DeltaG(0)) at temperatures to 200 degrees C are given for 307 solids, liquids, gases, and aqueous solutes It is shown that values of DeltaGr(0) for many microbially mediated reactions are highly temperature dependent, and that adopting values determined at 25 degrees C for systems at elevated temperatures introduces significant and unnecessary errors The metabolic processes considered here involve compounds that belong to the following chemical systems: H-O, H-O-N, H-O-S, H-O-N-S, H-O-C(inorganic), H-O-C, H-O-N-C, H-O-S-C, H-O-N-S-C(amino acids), H-O-S-C-metals/minerals, and H-O-P For four metabolic reactions of particular interest in thermophily and hyperthermophily (knallgas reaction, anaerobic sulfur and nitrate reduction, and autotrophic methanogenesis), values of the overall Gibbs free energy (DeltaGr) as a function of temperature are calculated for a wide range of chemical compositions likely to be present in near-surface and deep hydrothermal and geothermal systems

http://rcn.montana.edu/Resources/LRES555/Manuscripts/energetics.pdf

Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria

Characterization of redox conditions in groundwater contaminant plumes

Microbial communities from a subseafloor sediment core from the southwestern Sea of Okhotsk were evaluated by performing both cultivation-dependent and cultivation-independent (molecular) analyses. The core, which extended 58.1 m below the seafloor, was composed of pelagic clays with several volcanic ash layers containing fine pumice grains. Direct cell counting and quantitative PCR analysis of archaeal and bacterial 16S rRNA gene fragments indicated that the bacterial populations in the ash layers were approximately 2 to 10 times larger than those in the clays. Partial sequences of 1,210 rRNA gene clones revealed that there were qualitative differences in the microbial communities from the two different types of layers. Two phylogenetically distinct archaeal assemblages in the Crenarchaeota, the miscellaneous crenarchaeotic group and the deep-sea archaeal group, were the most predominant archaeal 16S rRNA gene components in the ash layers and the pelagic clays, respectively. Clones of 16S rRNA gene sequences from members of the gamma subclass of the class Proteobacteria dominated the ash layers, whereas sequences from members of the candidate division OP9 and the green nonsulfur bacteria dominated the pelagic clay environments. Molecular (16S rRNA gene sequence) analysis of 181 isolated colonies revealed that there was regional proliferation of viable heterotrophic mesophiles in the volcanic ash layers, along with some gram-positive bacteria and actinobacteria. The porous ash layers, which ranged in age from tens of thousands of years to hundreds of thousands of years, thus appear to be discrete microbial habitats within the coastal subseafloor clay sediment, which are capable of harboring microbial communities that are very distinct from the communities in the more abundant pelagic clays.

https://aem.asm.org/content/aem/69/12/7224.full.pdf

Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk

Deep subsurface microbial communities1 are believed to be supported by organic matter that was either deposited with the formation sediments or which migrated from the surface along groundwater flowpaths. Investigation has therefore focused on the existence of microorganisms in recently deposited or highly permeable sediments2,3. Fewer reports have focused on consolidated rocks4–7. These findings have often been limited by inadequate tracer methodology or non-sterile sampling techniques. Here we present evidence for the presence of spatially discrete microbial communities in Cretaceous rocks and advance a mechanism for the long-term survival of these subterranean communities. Samples were collected using aseptic methods and sensitive tracers8. Our results indicate that the main energy source for these communities is organic material trapped within shales. Microbial activity in shales appears to be greatly reduced, presumably because of their restrictive pore size9. However, organic material or its fermentation products could diffuse into adjacent, more permeable sandstones, where microbial activity was much more abundant. This process resulted in the presence of microbial communities at sandstone–shale interfaces. These microorganisms presumably ferment organic matter and carry out sulphate reduction and acetogenesis.

Confined subsurface microbial communities in Cretaceous rock

A simplified passive extraction procedure for quantifying reduced inorganic sulfur compounds from sediments and water is presented. This method may also be used for the estimation of sulfate reduction rates. Efficient extraction of FeS, FeS(inf2), and S(sup2-) was obtained with this procedure; however, the efficiency for S(sup0) depended on the form that was tested. Passive extraction can be used with samples containing up to 20 mg of reduced sulfur. We demonstrated the utility of this technique in a determination of both sulfate reduction rates and reduced inorganic sulfur pools in marine and freshwater sediments. A side-by-side comparison of the passive extraction method with the established single-step distillation technique yielded comparable results with a fraction of the effort.

A Rapid and Simple Method for Estimating Sulfate Reduction Activity and Quantifying Inorganic Sulfides

A combined geochemical and microbiological approach was needed to delineate the biogeochemical processes occurring in an aquifer contaminated by landfill leachate in Norman, OK, where the important microbially mediated reactions in an anoxic plume were iron reduction, sulfate reduction, and methanogenesis. The highest rates of sulfate reduction (13.2 μM/day) were detected near the water table where sulfate levels were maximal (up to 4.6 mM). The enrichment of 34S in the sulfate pools (δ34S of SO42- was 67−69‰), and dissolved hydrogen measurements provided additional support for the importance of sulfate reduction near the water table. Methane was detected in the center of the plume where sulfate was depleted. Microbial incubations demonstrated concomitant sulfate reduction and methanogenesis in the anoxic portion of the plume. Although high concentrations of soluble reduced iron were detected throughout the aquifer and H2 levels were indicative of iron reduction under steady-state conditions, microbiologi...

Geochemical and microbiological methods for evaluating anaerobic processes in an aquifer contaminated by landfill leachate.

Microbiological, geochemical, and isotopic analyses of sediment and water samples from the unconsolidated Yegua formation in east-central Texas were used to assess microbial processes in the terrestrial subsurface. Previous geochemical studies suggested that sulfide oxidation at shallow depths may provide sulfate for sulfate-reducing bacteria (SRB) in deeper aquifer formations. The present study further examines this possibility, and provides a more detailed evaluation of the relationship between microbial activity, lithology, and the geochemical environment on meter-to-millimeter scales. Sediment of varied lithology (sands, silts, clays, lignite) was collected from two boreholes, to depths of 30 m. Our findings suggest that pyrite oxidation strongly influences the geochemical environment in shallow sediments (∼5 m), and produces acidic waters (pH 3.8) that are rich in sulfate (28 mM) and ferrous iron (0.3 mM). Sulfur and iron-oxidizing bacteria are readily detected in shallow sediments; they likely play an indirect role in pyrite oxidation. In consistent fashion, there is a relative paucity of pyrite in shallow sediments and a low 34S/32S-sulfate ratio (0.2‰) (reflecting contributions from 34S-depleted sulfides) in shallow regions. Pyrite oxidation likely provides a sulfate source for both oxic and anoxic aquifers in the region. A variety of assays and direct-imaging techniques of 35S-sulfide production in sediment cores indicates that sulfate reduction occurs in both the oxidizing and reducing portions of the sediment profile, with a high degree of spatial variability. Narrow zones of activity were detected in sands that were juxtaposed to clay or lignite-rich sediments. The fermentation of organic matter in the lignite-rich laminae provides small molecular weight organic acids to support sulfate reduction in neighboring sands. Consequently, sulfur cycling in shallow sediments, and sulfate transport represent important mechanisms for commensal interaction among subsurface microorganisms by providing electron donors for chemoautotrophic bacteria and electron acceptors for SRB. The activity of SRB is linked to the availability of suitable electron donors from spatially distinct zones.

Sulfur Cycling in the Terrestrial Subsurface: Commensal Interactions, Spatial Scales, and Microbial Heterogeneity

Field and laboratory techniques were used to identify the biogeochemical factors affecting sulfate reduction in a shallow, unconsolidated alluvial aquifer contaminated with landfill leachate. Depth profiles of 35S-sulfate reduction rates in aquifer sediments were positively correlated with the concentration of dissolved sulfate. Manipulation of the sulfate concentration in samples revealed a Michaelis−Menten-like relationship with an apparent Km and Vmax of approximately 80 and 0.83 μM SO4-2·day-1, respectively. The concentration of sulfate in the core of the leachate plume was well below 20 μM and coincided with very low reduction rates. Thus, the concentration and availability of this anion could limit in situ sulfate-reducing activity. Three sulfate sources were identified, including iron sulfide oxidation, barite dissolution, and advective flux of sulfate. The relative importance of these sources varied with depth in the alluvium. The relatively high concentration of dissolved sulfate at the water tab...

Glenn A. Ulrich

Papers

Confined subsurface microbial communities in Cretaceous rock

A Rapid and Simple Method for Estimating Sulfate Reduction Activity and Quantifying Inorganic Sulfides

Geochemical and microbiological methods for evaluating anaerobic processes in an aquifer contaminated by landfill leachate.

Sulfur Cycling in the Terrestrial Subsurface: Commensal Interactions, Spatial Scales, and Microbial Heterogeneity

Sources of sulfate supporting anaerobic metabolism in a contaminated aquifer.