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Previous work has shown that about 10% of total clay-bound Fe(III) in unaltered nontronite NAu-1 is bioreducible, although it remains unclear how much of the bioreducible Fe pool persists after repeated oscillations between anoxic and oxic conditions. Here, we report on results from an experiment where we monitored the abundance of bioreducible Fe(III) in NAu-1 over three consecutive redox cycles using chemical extractions and Fe isotope analysis to document the changes in the nature and extent of Fe atom exchange. During each cycle, NAu-1 was reduced biotically by Shewanella oneidensis MR-1 and then re-oxidized abiotically by O2 via aeration. By the third reduction period (RP3), the bacteria were only able to reduce 5.7% of the total clay Fe, that is, 40% less than during the first reduction period (RP1). The decrease in bioreducible Fe(III) is attributed to preferential reductive dissolution of Fe(III) from the finest clay particles. Extrapolation of the observed trend implies that, once the reducible Fe of the finest clay particles is removed, around 4% of the total Fe of the clay remains permanently redox-active, presumably as Fe atoms within the octahedral mineral structure that are accessible to the bacteria. The proposed particle size-dependent evolution of bioreducible Fe(III) from RP1 to RP3 is supported by the observed increasing crystalline domain size, preferential Fe dissolution from the smallest aggregates, and decreasing Fe isotope fractionation factors between aqueous Fe(II) and structural Fe(III) and between solid-bound Fe(II) and structural Fe(III). Our results imply that, in redox dynamic environments, the fraction of insoluble clay-bound Fe that is potentially renewable for use by Fe-reducing bacteria is a function of the evolving size distribution of the clay particles.

A correlation between methanogenesis and dolomite formation has been reported; however, the mechanism underlying this association is not fully understood. In this study, we conducted forced carbonate precipitation experiments at room temperature in calcite-seeded Ca/Mg carbonate solutions containing either purified non-living biomass or bound extracellular polymeric substances (EPS) of the methanogen Methanosarcina barkeri. Purified non-living biomass and bound EPS was used so as to avoid the possible influence of the complex components of the growing microbial culture on carbonate crystallization. Our results demonstrated that non-living biomass of M. Barkeri can enhance the Mg incorporation into calcitic structure and induce the crystallization of disordered dolomite. In the presence of ~113 mg L–1 of non-living biomass, disordered dolomite with ~41 and 45 mol% of MgCO3 was precipitated in solutions with initial Mg:Ca ratios of 5:1 and 8:1, respectively. A systematic increase in the MgCO3 contents of the precipitated Ca-Mg carbonates was also observed with the increased non-living biomass concentration. Bound EPS was shown to be the component of non-living biomass that catalyzed the precipitation of disordered dolomite. At only ~25 mg L–1 of bound EPS, disordered dolomite with ~47 and 48 mol% of MgCO3 was precipitated in solutions with initial Mg:Ca ratios of 5:1 and 8:1, respectively. We propose that adsorption of bound EPS to growing carbonate surfaces through hydrogen bonding is the key to catalyzing disordered dolomite crystallization, and that this mechanism is also applicable to natural EPS-induced dolomite formation. This study provides significant insight into the formation mechanism of microbial-induced dolomite with high δ13C values.

Extracellular electron transfer (EET) by electroactive bacteria in anoxic soils and sediments is an intensively researched subject, but EET’s function in planktonic ecology has been less considered. Following the discovery of an unexpectedly high prevalence of EET genes in a bog lake’s bacterioplankton, we hypothesized that the redox capacities of dissolved organic matter (DOM) enrich for electroactive bacteria by mediating redox chemistry. We developed the bioinformatics pipeline FEET (Find EET) to identify and summarize EET proteins from metagenomics data. We then applied FEET to several bog and thermokarst lakes and correlated EET protein occurrence values with environmental data to test our predictions. Our results provide evidence that DOM participates in EET by bacterioplankton. We found a similarly high prevalence of EET genes in most of these lakes, where oxidative EET strongly correlated with DOM. Numerous novel clusters of multiheme cytochromes that may enable EET were identified. Taxa previously not considered EET-capable were found to carry EET genes. We conclude that EET and DOM interactions are of major ecological importance to bacterioplankton in small boreal lakes, and that EET, particularly by methylotrophs and phototrophs, should be further studied and incorporated into both conceptual and quantitative methane emission models of melting permafrost.

Oxidative weathering of pyrite plays an important role in the biogeochemical cycling of Fe and S in terrestrial environments. While the mechanism and occurrence of biologically accelerated pyrite oxidation under acidic conditions are well established, much less is known about microbially mediated pyrite oxidation at circumneutral pH. Recent work (Percak-Dennett et al., 2017, Geobiology, 15, 690) has demonstrated the ability of aerobic chemolithotrophic microorganisms to accelerate pyrite oxidation at circumneutral pH and proposed two mechanistic models by which this phenomenon might occur. Here, we assess the potential relevance of aerobic microbially catalyzed circumneutral pH pyrite oxidation in relation to subsurface shale weathering at Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) in Pennsylvania, USA. Specimen pyrite mixed with native shale was incubated in groundwater for 3 months at the inferred depth of in situ pyrite oxidation. The colonized materials were used as an inoculum for pyrite-oxidizing enrichment cultures. Microbial activity accelerated the release of sulfate across all conditions. 16S rRNA gene sequencing and metagenomic analysis revealed the dominance of a putative chemolithoautotrophic sulfur-oxidizing bacterium from the genus Thiobacillus in the enrichment cultures. Previously proposed models for aerobic microbial pyrite oxidation were assessed in terms of physical constraints, enrichment culture geochemistry, and metagenomic analysis. Although we conclude that subsurface pyrite oxidation at SSCHZO is largely abiotic, this work nonetheless yields new insight into the potential pathways by which aerobic microorganisms may accelerate pyrite oxidation at circumneutral pH. We propose a new "direct sulfur oxidation" pathway, whereby sulfhydryl-bearing outer membrane proteins mediate oxidation of pyrite surfaces through a persulfide intermediate, analogous to previously proposed mechanisms for direct microbial oxidation of elemental sulfur. The action of this and other direct microbial pyrite oxidation pathways have major implications for controls on pyrite weathering rates in circumneutral pH sedimentary environments where pore throat sizes permit widespread access of microorganisms to pyrite surfaces.

Long-term (2–3 months) batch U(VI) sorption-desorption experiments were conducted to understand the long-term sorption-desorption behavior of U(VI) in saprolite subsoils from Oak Ridge Field Research Center (ORFRC), Tennessee, which contained naturally occurring nanoporous goethite. Three subsoil samples containing a range of dithionite-citrate-bicarbonate (DCB) extractable Fe oxide content (7138, 11,161, and 22,582 mg Fe/kg) were used for the experiments. Sorption of 50 μM U(VI) to the subsoils in the presence of Ca2+ and HCO3− at circumneutral pH occurred rapidly during the first 2 days, after which slow U(VI) sorption continued over 3 months. U(VI) desorption from the soils by 10 mM NaHCO3 solution exhibited an initial fast desorption step during the first 24 h, followed by slower desorption over a week. Sorption of 50 μM U(VI) for 1 day to 3 months in the presence or absence of Ca2+ consistently resulted in higher U(VI) sorption to saprolite soil with higher amount of nanoporous goethite, while desorption of U(VI) for 1 week to 2 months was consistently lower in saprolite soil with higher amount of nanoporous goethite. Saprolite subsoils containing higher amounts of nanoporous goethite exhibited more resistant U(VI) desorption, and the proportions of irreversible U(VI) sorption increased with longer residence time with soils. These results indicates that more U(VI) became bound to the internal surfaces of nanoporous iron oxides during long-term sorption. This study suggests that naturally occurring nanoporous goethite may exert a significant role in controlling the mobility and transport of U(VI) in historically contaminated sites that have existed over decades.

Chocolate Pots hot spring (CP) is an Fe-rich, circumneutral-pH geothermal spring in Yellowstone National Park. Relic hydrothermal systems have been identified on Mars, and modern hydrothermal environments such as CP are useful for gaining insight into potential pathways for generation of biosignatures of ancient microbial life on Earth and Mars. Fe isotope fractionation is recognized as a signature of dissimilatory microbial iron oxide reduction (DIR) in both the rock record and modern sedimentary environments. Previous studies in CP have demonstrated the presence of DIR in vent pool deposits and show aqueous-/solid-phase Fe isotope variations along the hot spring flow path that may be linked to this process. In this study, we examined the geochemistry and stable Fe isotopic composition of spring water and sediment core samples collected from the vent pool and along the flow path, with the goal of evaluating whether Fe isotopes can serve as a signature of past or present DIR activity. Bulk sediment Fe redox speciation confirmed that DIR is active within the hot spring vent pool sediments (but not in more distal deposits), and the observed Fe isotope fractionation between Fe(II) and Fe(III) is consistent with previous studies of DIR-driven Fe isotope fractionation. However, modeling of sediment Fe isotope distributions indicates that DIR does not produce a unique Fe isotopic signature of DIR in the vent pool environment. Because of rapid chemical and isotopic communication between the vent pool fluid and sediment, sorption of Fe(II) to Fe(III) oxides would produce an isotopic signature similar to DIR despite DIR-driven generation of large quantities of isotopically light solid-associated Fe(II). The possibility exists, however, for preservation of specific DIR-derived Fe(II) minerals such as siderite (which is present in the vent pool deposits), whose isotopic composition could serve as a long-term signature of DIR in relic hot spring environments.

Geosphere, June 2006, v. 2, p. 220-235, doi: 10.1130/GES00029.1. Animation 1 - Animation of simulation results for U(VI) contamination period (22 yr) for the Geophys2 case. Upper panel—sorbed U(VI); lower panel—aqueous U(VI). All concentrations are in molar units (M). The file size is 1.4 MB.

Recent studies have suggested the potential for release of iron (Fe) oxide-bound organic carbon (OC) during dissimilatory iron oxide reduction (DIR). However, the stability of Fe (hydr)oxide-bound OC in the presence of a natural microbial consortium capable of driving both OC metabolism and DIR has not been resolved. Pure ferrihydrite (Fhy) and Fhy-humic acid coprecipitates (Fhy-HA) were inoculated with a small quantity of freshwater sediment and incubated under anoxic conditions in the presence and absence of H(2) or glucose as electron donors for DIR. H(2) promoted DIR led to release of ca. 1 mM dissolved organic carbon (DOC). However, comparable amounts of DOC were released from both pure Fhy and Fhy-HA, similar to DOC levels in mineral-free, inoculum only controls. These results suggest that the observed DOC release during H(2)-promoted DIR originated from OC contained in the inoculum as opposed to the much larger pool (ca. 38 mM) of OC in the Fhy-HA. Thus, DIR preferentially released sorbed OC with low aromaticity (inoculum OC) versus highly aromatic OC (HA) coprecipitated with Fe oxide. Our findings provide new insight into the extent and mechanisms by which DIR is likely to influence aqueous/solid-phase OC partitioning in anoxic soils and sediments.

Growth substrates that maximize energy yield are widely thought to be utilized preferentially by microorganisms. However, observed distributions of microorganisms and their activities often deviate from predictions based solely on thermodynamic considerations of substrate energy supply. Here we present observations of the bioenergetics and growth yields of a metabolically flexible, thermophilic strain of the archaeon Acidianus when grown autotrophically on minimal medium with hydrogen (H2) or elemental sulfur (S°) as an electron donor, and S° or ferric iron (Fe3+) as an electron acceptor. Thermodynamic calculations indicate that S°/Fe3+ and H2/Fe3+ yield three- and four-fold more energy per mol electron transferred, respectively, than the H2/S° couple. However, biomass yields in Acidianus cultures provided with H2/S° were eight-fold greater than when provided S°/Fe3+ or H2/Fe3+, indicating the H2/S° redox couple is preferred. Indeed, cells provided with all three growth substrates (H2, Fe3+, and S°) grew preferentially by reduction of S° with H2. We conclude that substrate preference is dictated by differences in the energy demand of electron transfer reactions in Acidianus when grown with different substrates, rather than substrate energy supply.

Growth substrates that maximize energy yield are widely thought to be utilized preferentially by microorganisms. However, observed distributions of microorganisms and their activities often deviate from predictions based solely on thermodynamic considerations of substrate energy supply. Here we present observations of the bioenergetics and growth yields of a metabolically flexible, thermophilic strain of the archaeon Acidianus when grown autotrophically on minimal medium with hydrogen (H2) or elemental sulfur (S°) as an electron donor, and S° or ferric iron (Fe3+) as an electron acceptor. Thermodynamic calculations indicate that S°/Fe3+ and H2/Fe3+ yield three- and four-fold more energy per mol electron transferred, respectively, than the H2/S° couple. However, biomass yields in Acidianus cultures provided with H2/S° were eight-fold greater than when provided S°/Fe3+ or H2/Fe3+, indicating the H2/S° redox couple is preferred. Indeed, cells provided with all three growth substrates (H2, Fe3+, and S°) grew preferentially by reduction of S° with H2. We conclude that substrate preference is dictated by differences in the energy demand of electron transfer reactions in Acidianus when grown with different substrates, rather than substrate energy supply.

Pyrite (FeS2) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite-bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin–Benson–Bassham CO2 fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30–50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X-ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro-organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral-pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite-associated metals.

The flux of solutes from the chemical weathering of the continental crust supplies a steady supply of essential nutrients necessary for the maintenance of Earth’s biosphere. Promotion of weathering by microorganisms is a well-documented phenomenon and is most often attributed to heterotrophic microbial metabolism for the purposes of nutrient acquisition. Here, we demonstrate the role of chemolithotrophic ferrous iron [Fe(II)]-oxidizing bacteria in biogeochemical weathering of subsurface Fe(II)-silicate minerals at the Luquillo Critical Zone Observatory in Puerto Rico. Under chemolithotrophic growth conditions, mineral-derived Fe(II) in the Rio Blanco Quartz Diorite served as the primary energy source for microbial growth. An enrichment in homologs to gene clusters involved in extracellular electron transfer was associated with dramatically accelerated rates of mineral oxidation and adenosine triphosphate generation relative to sterile diorite suspensions. Transmission electron microscopy and energy-dispersive spectroscopy revealed the accumulation of nanoparticulate Fe–oxyhydroxides on mineral surfaces only under biotic conditions. Microbially oxidized quartz diorite showed greater susceptibility to proton-promoted dissolution, which has important implications for weathering reactions in situ. Collectively, our results suggest that chemolithotrophic Fe(II)-oxidizing bacteria are likely contributors in the transformation of rock to regolith.

Microbial dissimilatory iron reduction (DIR) is a deeply rooted metabolism in the Bacteria and Archaea. In the Archean and Proterozoic, the most likely electron acceptor for DIR in marine environments was Fe(III)–Si gels. It has been recently suggested that the Fe and Si cycles were coupled through sorption of aqueous Si to iron oxides/hydroxides, and through release of Si during DIR. Evidence for the close association of the Fe and Si cycles comes from banded iron formations (BIFs), which consist of alternating bands of Fe-bearing minerals and quartz (chert). Although there has been extensive study of the stable Fe isotope fractionations produced by DIR of Fe(III)–Si gels, as well as studies of stable Fe isotope fractionations in analogous abiologic systems, no studies to date have investigated stable Si isotope fractionations produced by DIR. In this study, the stable Si isotope fractionations produced by microbial reduction of Fe(III)–Si gels were investigated in simulated artificial Archean seawater (AAS), using the marine iron-reducing bacterium Desulfuromonas acetoxidans . Microbial reduction produced very large 30 Si/ 28 Si isotope fractionations between the solid and aqueous phase at ∼23 °C, where Δ 30 Si solid–aqueous isotope fractionations of −3.35 ± 0.16‰ and −3.46 ± 0.09‰ were produced in two replicate experiments at 32% Fe(III) reduction (solid-phase Fe(II)/Fe Total = 0.32). This isotopic fractionation was substantially greater than that observed in two abiologic controls that had solid-phase Fe(II)/Fe Total = 0.02–0.03, which produced Δ 30 Si solid–aqueous isotope fractionations of −2.83 ± 0.24‰ and −2.65 ± 0.28‰. In a companion study, the equilibrium Δ 30 Si solid–aqueous isotope fractionation was determined to be −2.3‰ for solid-phase Fe(II)/Fe Total = 0. Collectively, these results highlight the importance of Fe(II) in Fe–Si gels in producing large changes in Si isotope fractionations. These results suggest that DIR should produce highly negative δ 30 Si values in quartz that is the product of diagenetic reactions associated with Fe–Si gels. Such Si isotope compositions would be expected to be associated with Fe-bearing minerals that contain Fe(II), indicative of reduction, such as magnetite. Support for this model comes from recent in situ Si isotope studies of oxide-facies BIFs, where quartz in magnetite-rich samples have significantly more negative δ 30 Si values than quartz in hematite-rich samples.

Iron oxide nanoparticles in natural soils and sediments can be nanoporous due to the aggregation of nanoparticles. Nanopores can greatly affect the sorption-desorption as well as reduction-oxidation behavior of U(VI) because of their high internal surface area and nanopore confinement effects. Batch U(VI) sorption-desorption experiments were conducted to understand the role of nano-goethite in controlling U(VI) sorption-desorption behavior in saprolite subsoil from Oak Ridge Field Research Center (ORFRC), Tennessee, a premier field research site for environmental remediation. The subsoil samples from ~ 6.5–8.5 m depth were nearly homogeneous in mineral composition (quartz, illite and smectite) and particle size distribution. The subsoil samples were characterized by a range of dithionite-citrate-bicarbonate (DCB) extractable Fe(III) oxide content (127–404 μM/g), BET surface area (25–38 m2/g), and nanoporosity (pore size

Dissimilatory microbial reduction of solid-phase Fe(III)-oxides and Fe(III)-bearing phyllosilicates (Fe(III)-phyllosilicates) is an important process in anoxic soils, sediments and subsurface materials. Although various studies have documented the relative extent of microbial reduction of single-phase Fe(III)-oxides and Fe(III)-phyllosilicates, detailed information is not available on interaction between these two processes in situations where both phases are available for microbial reduction. The goal of this research was to use the model dissimilatory iron-reducing bacterium (DIRB) Geobacter sulfurreducens to study Fe(III)-oxide vs. Fe(III)-phyllosilicate reduction in a range of subsurface materials and Fe(III)-oxide stripped versions of the materials. Low-temperature (12 K) Mossbauer spectroscopy was used to infer changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) (Fe(II) phyllosilicate). A Fe partitioning model was employed to anal...

Precambrian Si-rich sedimentary rocks, including cherts and banded iron formations (BIFs), record a >7‰ spread in 30Si/28Si ratios (δ30Si values), yet interpretation of this large variability has been hindered by the paucity of data on Si isotope exchange kinetics and equilibrium fractionation factors in systems that are pertinent to Precambrian marine conditions. Using the three-isotope method and an enriched 29Si tracer, a series of experiments were conducted to constrain Si isotope exchange kinetics and fractionation factors between amorphous Fe(III)–Si gel, a likely precursor to Precambrian jaspers and BIFs, and aqueous Si in artificial Archean seawater under anoxic conditions. Experiments were conducted at room temperature, and in the presence and absence of aqueous Fe(II) (Fe(II)aq). Results of this study demonstrate that Si solubility is significantly lower for Fe–Si gel than that of amorphous Si, indicating that seawater Si concentrations in the Precambrian may have been lower than previous estimates. The experiments reached ∼70–90% Si isotope exchange after a period of 53–126 days, and the highest extents of exchange were obtained where Fe(II)aq was present, suggesting that Fe(II)–Fe(III) electron-transfer and atom-exchange reactions catalyze Si isotope exchange through breakage of Fe–Si bonds. All experiments except one showed little change in the instantaneous solid–aqueous Si isotope fractionation factor with time, allowing extraction of equilibrium Si isotope fractionation factors through extrapolation to 100% isotope exchange. The equilibrium 30Si/28Si fractionation between Fe(III)–Si gel and aqueous Si (Δ30Sigel–aqueous) is −2.30 ± 0.25‰ (2σ) in the absence of Fe(II)aq. In the case where Fe(II)aq was present, which resulted in addition of ∼10% Fe(II) in the final solid, creating a mixed Fe(II)–Fe(III) Si gel, the equilibrium fractionation between Fe(II)–Fe(III)–Si gel and aqueous Si (Δ30Sigel–aqueous) is −3.23 ± 0.37‰ (2σ). Equilibrium Si isotope fractionation for Fe–Si gel systems is significantly larger in magnitude than estimates of a near-zero solid–aqueous fractionation factor between pure Si gel and aqueous Si, indicating a major influence of Fe atoms on Si–O bonds, and hence the isotopic properties, of Fe–Si gel. Larger Si isotope fractionation in the Fe(II)-bearing systems may be caused by incorporation of Fe(II) into the solid structure, which may further weaken Fe–Si bonds and thus change the Si isotope fractionation factor. The relatively large Si isotope fractionation for Fe–Si gel, relative to pure Si gel, provides a new explanation for the observed contrast in δ30Si values in the Precambrian BIFs and cherts, as well as an explanation for the relatively negative δ30Si values in BIFs, in contrast to previous proposals that the more negative δ30Si values in BIFs reflect hydrothermal sources of Si or sorption to Fe oxides/hydroxides.

Fe(III)-oxides and Fe(III)-bearing phyllosilicates are the two major iron sources utilized as electron acceptors by dissimilatory iron-reducing bacteria (DIRB) in anoxic soils and sediments. Although there have been many studies on microbial Fe(III)-oxide and Fe(III)-phyllosilicate reduction with both natural and specimen materials, no controlled experimental information is available on the interaction between these two phases when both are available for microbial reduction. In this study, the model DIRB Geobacter sulfurreducens was used to examine the pathways of Fe(III) reduction in Fe(III)-oxide stripped subsurface sediment that was coated with different amounts of synthetic high surface area (HSA) goethite. Cryogenic (12K) 57Fe Mossbauer spectroscopy was used to determine changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) [Fe(II)-phyllosilicate] in bioreduced samples. Analogous Mossbauer analyses were performed on samples from abio...

Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458–1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family Gallionellaceae , and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochrome c system identified in neutrophilic microaerobic Fe(II)-oxidizing Sideroxydans lithotrophicus ES-1] in a Gallionellaceae sp., and findings of other putative genes involving cytochrome c and multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this Gallionellaceae sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration.

In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.

Humic lakes and ponds receive large amounts of terrestrial carbon and are important components of the global carbon cycle, yet how their redox cycling influences the carbon budget is not fully understood. Here we compared metagenomes obtained from a humic bog and a clear-water eutrophic lake and found a much larger number of genes that might be involved in extracellular electron transfer (EET) for iron redox reactions and humic substance (HS) reduction in the bog than in the clear-water lake, consistent with the much higher iron and HS levels in the bog., Humic lakes and ponds receive large amounts of terrestrial carbon and are important components of the global carbon cycle, yet how their redox cycling influences the carbon budget is not fully understood. Here we compared metagenomes obtained from a humic bog and a clear-water eutrophic lake and found a much larger number of genes that might be involved in extracellular electron transfer (EET) for iron redox reactions and humic substance (HS) reduction in the bog than in the clear-water lake, consistent with the much higher iron and HS levels in the bog. These genes were particularly rich in the bog’s anoxic hypolimnion and were found in diverse bacterial lineages, some of which are relatives of known iron oxidizers or iron-HS reducers. We hypothesize that HS may be a previously overlooked electron acceptor and that EET-enabled redox cycling may be important in pelagic respiration and greenhouse gas budget in humic-rich freshwater lakes.

Chocolate Pots hot springs (CP) is a circumneutral-pH Fe-rich geothermal feature located in Yellowstone National Park. Previous Fe(III)-reducing enrichment culture studies with CP sediments identified close relatives of known dissimilatory Fe(III)-reducing bacterial (FeRB) taxa, including Geobacter and Melioribacter . However, the abundances and activities of such organisms in the native microbial community are unknown. Here, we used stable isotope probing experiments combined with 16S rRNA gene amplicon and shotgun metagenomic sequencing to gain an understanding of the in situ Fe(III)-reducing microbial community at CP. Fe-Si oxide precipitates collected near the hot spring vent were incubated with unlabeled and 13 C-labeled acetate to target active FeRB. We searched reconstructed genomes for homologs of genes involved in known extracellular electron transfer (EET) systems to identify the taxa involved in Fe redox transformations. Known FeRB taxa containing putative EET systems ( Geobacter , Ignavibacteria ) increased in abundance under acetate-amended conditions, whereas genomes related to Ignavibacterium and Thermodesulfovibrio that contained putative EET systems were recovered from incubations without electron donor. Our results suggest that FeRB play an active role in Fe redox cycling within Fe-Si oxide-rich deposits located at the hot spring vent. IMPORTANCE The identification of past near-surface hydrothermal environments on Mars emphasizes the importance of using modern Earth environments, such as CP, to gain insight into potential Fe-based microbial life on other rocky worlds, as well as ancient Fe-rich Earth ecosystems. By combining stable carbon isotope probing techniques and DNA sequencing technology, we gained insight into the pathways of microbial Fe redox cycling at CP. The results suggest that microbial Fe(III) oxide reduction is prominent in situ , with important implications for the generation of geochemical and stable Fe isotopic signatures of microbial Fe redox metabolism within Fe-rich circumneutral-pH thermal spring environments on Earth and Mars.

The thermoacidophilic Acidianus strain DS80 displays versatility in its energy metabolism and can grow autotrophically and heterotrophically with elemental sulfur (S°), ferric iron (Fe3+ ) or oxygen (O2 ) as electron acceptors. Here, we show that autotrophic and heterotrophic growth with S° as the electron acceptor is obligately dependent on hydrogen (H2 ) as electron donor; organic substrates such as acetate can only serve as a carbon source. In contrast, organic substrates such as acetate can serve as electron donor and carbon source for Fe3+ or O2 grown cells. During growth on S° or Fe3+ with H2 as an electron donor, the amount of CO2 assimilated into biomass decreased when cultures were provided with acetate. The addition of CO2 to cultures decreased the amount of acetate mineralized and assimilated and increased cell production in H2 /Fe3+ grown cells but had no effect on H2 /S° grown cells. In acetate/Fe3+ grown cells, the presence of H2 decreased the amount of acetate mineralized as CO2 in cultures compared to those without H2 . These results indicate that electron acceptor availability constrains the variety of carbon sources used by this strain. Addition of H2 to cultures overcomes this limitation and alters heterotrophic metabolism.

Dissimilatory iron-reducing bacteria (DIRB) are known to use humic substances (HS) as electron shuttles for dissimilatory iron reduction (DIR) by transferring electrons to HS-quinone moieties, which in turn rapidly reduce Fe(III) oxides. However, the potential for HS to serve as a source of organic carbon (OC) that can donate electrons for DIR is unknown. We studied whether humic acids (HA) and humins (HM) recovered from peat soil by sodium pyrophosphate extraction could serve as both electron shuttles and electron donors for DIR by freshwater sediment microorganisms. Both HA and HM served as electron shuttles in cultures amended with glucose. However, only HA served as an electron donor for DIR. Metagenomes from HA-containing cultures had an overrepresentation of genes involved in polysaccharide and to a lesser extent aromatic compound degradation, suggesting complex OC metabolism. Genomic searches for the porin-cytochrome complex involved in DIR resulted in matches to Ignavibacterium/Melioribacter, DIRB capable of polymeric OC metabolism. These results indicate that such taxa may have played a role in both DIR and decomposition of complex OC. Our results suggest that decomposition of HS coupled to DIR and other anaerobic pathways could play an important role in soil and sediment OC metabolism.

Basaltic glass (BG) is an amorphous ferrous iron [Fe(II)]-containing material present in basaltic rocks, which are abundant on rocky planets such as Earth and Mars. Previous research has suggested that Fe(II) in BG can serve as an energy source for chemolithotrophic microbial metabolism, which has important ramifications for potential past and present microbial life on Mars. However, to date there has been no direct demonstration of microbially catalyzed oxidation of Fe(II) in BG. In this study, three different culture systems were used to investigate the potential for microbial oxidation of Fe(II) in BG, including (1) the chemolithoautotrophic Fe(II)-oxidizing, nitrate-reducing "Straub culture"; (2) the mixotrophic Fe(II)-oxidizing, nitrate-reducing organism Desulfitobacterium frappieri strain G2; and (3) indigenous microorganisms from a streambed Fe seep in Wisconsin. The BG employed consisted of clay and silt-sized particles of freshly quenched lava from the TEB flow in Kilauea, Hawaii. Soluble Fe(II) or chemically reduced NAu-2 smectite (RS) were employed as positive controls to verify Fe(II) oxidation activity in the culture systems. All three systems demonstrated oxidation of soluble Fe(II) and/or structural Fe(II) in RS, whereas no oxidation of Fe(II) in BG material was observed. The inability of the Straub culture to oxidize Fe(II) in BG was particularly surprising, as this culture can oxidize other insoluble Fe(II)-bearing minerals such as biotite, magnetite, and siderite. Although the reason for the resistance of the BG toward enzymatic oxidation remains unknown, it seems possible that the absence of distinct crystal faces or edge sites in the amorphous glass renders the material resistant to such attack. These findings have implications with regard to the idea that Fe(II)-Si-rich phases in basalt rocks could provide a basis for chemolithotrophic microbial life on Mars, specifically in neutral-pH environments where acid-promoted mineral dissolution and utilization of dissolved Fe(II) as an energy source is not likely to take place.

Because of its rare occurrence in modern sediments, as well as the difficulty in synthesizing it under low-temperature conditions in the laboratory, the origin of sedimentary dolomite has remained a long-standing enigma, often referred to as the “dolomite problem.” Recently, anaerobic microorganisms, such as sulfate-reducing bacteria and methanogens, have been recognized for mediating dolomite precipitation. However, the exact role of microorganisms in dolomite crystallization is still under debate and the possible involvement of anaerobic fermenting bacteria has not been studied. In this study, we characterized the effect of purified non-metabolizing biomass and bound extracellular polymeric substances (EPS) of a natural consortium of anaerobic microorganisms dominated by fermenting bacteria and sulfate-reducing bacteria on Ca-Mg carbonate precipitation. This natural consortium was enriched from sediments of Deep Springs Lake, California, where dolomite is still precipitating. Our data show that disordered dolomite, a precursor of some sedimentary stoichiometric ordered dolomite, can be precipitated in calcite-seeded Ca-Mg carbonate solutions containing purified non-metabolizing consortium biomass. Bound EPS extracted from the consortium culture were shown to be the active component that triggered the crystallization of disordered dolomite. Further experiments show that purified non-metabolizing biomass from pure cultures of both anaerobic fermenting and sulfate-reducing bacteria closely related to those organisms present in the consortium could also catalyze the precipitation of disordered dolomite. This study contributes to the understanding of the “dolomite problem” by revealing (1) the catalytic effect of bound EPS on Ca-Mg carbonate crystallization and (2) the possible involvement of anaerobic fermenting bacteria in sedimentary dolomite formation, which has not been reported previously.

Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities ( in situ colonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding” with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection during in situ colonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition. IMPORTANCE The influence of river water-groundwater mixing on hyporheic zone microbial community structure and function is an important but poorly understood component of riverine biogeochemistry. This study employed an experimental approach to gain insight into how such mixing might be expected to influence the biomass, respiration, and composition of hyporheic zone microbial communities. Colonized sands from three different habitats (groundwater, river water, and hyporheic) were “cross-fed” with either groundwater, river water, or DOC-free artificial fluids. We expected that the colonization history would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. By contrast, the major observation was that the riverbed communities had much higher biomass and respiration, as well as a distinct community structure compared with those of the hyporheic and groundwater colonized sands. These results highlight the importance of riverbed microbial metabolism in organic carbon processing in hyporheic corridors.

Naturally occurring porous minerals as adsorbents for the remediation of environmental pollution has been one of the hot topics in environmental science and material science. In this study, the adsorption of iodate (IO3−) on two nanosized tubular halloysite samples (HBHal and SCHal, from Hubei and Sichuan Province, China, respectively) were investigated for the first time. To evaluate the impact of nanopore of halloysite on the adsorption of IO3−, chemically similar platy kaolinite was used for comparative studies in the batch experiments. The adsorption of IO3− on HBHal reached equilibrium within 36 h, and the adsorption kinetics and isotherm fitted the pseudo-second-order and Langmuir equation well, respectively. Both HBHal and SCHal exhibited high adsorption capability to IO3−, with distribution coefficients (Kd's) of 131.6 ± 14.6 and 126.6 ± 3.1 mL/g, respectively, which were >30 times higher than that for kaolinite (4.2 ± 2.3 mL/g). The specific surface area normalized Kd values on halloysite samples were >13.5-fold higher than that on kaolinite. In addition, halloysite had high selectivity to IO3−, and the adsorption capacities on the two halloysite samples were slightly affected by the concurrent anions, such as SO42−, NO3−, or ClO3−. It was proposed that the curved octahedral sheet caused geometry match between three oxygen atoms in the iodate and three OH above the vacant site of the octahedral sheet. This work also gave insight into the potential application of halloysite on the adsorption of radioactive iodate in natural and engineering environments.

A committee of the Mars Exploration Program Analysis Group (MEPAG) has reviewed and updated the description of Special Regions on Mars as places where terrestrial organisms might replicate (per the COSPAR Planetary Protection Policy). This review and update was conducted by an international team (SR-SAG2) drawn from both the biological science and Mars exploration communities, focused on understanding when and where Special Regions could occur. The study applied recently available data about martian environments and about terrestrial organisms, building on a previous analysis of Mars Special Regions (2006) undertaken by a similar team. Since then, a new body of highly relevant information has been generated from the Mars Reconnaissance Orbiter (launched in 2005) and Phoenix (2007) and data from Mars Express and the twin Mars Exploration Rovers (all 2003). Results have also been gleaned from the Mars Science Laboratory (launched in 2011). In addition to Mars data, there is a considerable body of new data regarding the known environmental limits to life on Earth-including the potential for terrestrial microbial life to survive and replicate under martian environmental conditions. The SR-SAG2 analysis has included an examination of new Mars models relevant to natural environmental variation in water activity and temperature; a review and reconsideration of the current parameters used to define Special Regions; and updated maps and descriptions of the martian environments recommended for treatment as "Uncertain" or "Special" as natural features or those potentially formed by the influence of future landed spacecraft. Significant changes in our knowledge of the capabilities of terrestrial organisms and the existence of possibly habitable martian environments have led to a new appreciation of where Mars Special Regions may be identified and protected. The SR-SAG also considered the impact of Special Regions on potential future human missions to Mars, both as locations of potential resources and as places that should not be inadvertently contaminated by human activity.

Pliocene-aged reduced lacustrine sediment from below a subsurface redox transition zone at the 300 Area of the Hanford site (southeastern Washington) was used in a study of the geochemical response to introduction of oxygen or nitrate in the presence or absence of microbial activity. The sediments contained large quantities of reduced Fe in the form of Fe(II)-bearing phyllosilicates, together with smaller quantities of siderite and pyrite. A loss of ca. 50% of 0.5 M HCl-extractable Fe(II) [5-10 mmol Fe(II) L(-1)] and detectable generation of sulfate (ca. 0.2 mM, equivalent to 10% of the reduced inorganic sulfur pool) occurred in sterile aerobic reactors. In contrast, no systematic loss of Fe(II) or production of sulfate was observed in any of the other oxidant-amended sediment suspensions. Detectable Fe(II) accumulation and sulfate consumption occurred in non-sterile oxidant-free reactors. Together, these results indicate the potential for heterotrophic carbon metabolism in the reduced sediments, consistent with the proliferation of known heterotrophic taxa (e.g., Pseudomonadaceae, Burkholderiaceae, and Clostridiaceae) inferred from 16S rRNA gene pyrosequencing. Microbial carbon oxidation by heterotrophic communities is likely to play an important role in maintaining the redox boundary in situ, i.e., by modulating the impact of downward oxidant transport on Fe/S redox speciation. Diffusion-reaction simulations of oxygen and nitrate consumption coupled to solid-phase organic carbon oxidation indicate that heterotrophic consumption of oxidants could maintain the redox boundary at its current position over millennial time scales.

Immobilization of iodide (I−) from groundwater and soils is a challenging subject due to the large size and low charge of I−. Clay minerals and (hydr)oxides generally exhibit very low adsorption capacity due to anion exclusion or weak attraction. For the first time, the adsorption of I− by chrysotile bundles (Chry-B) was investigated and a characteristic mechanism was established by comparing the adsorption of I− on Chry-B with dispersed chrysotile single nanotubes, lizardite and brucite. The adsorption of I− by Chry-B reached equilibrium with 24 h, and Chry-B exhibited very strong adsorption to I−, with a distribution coefficient (Kd) of 179.24 mL/g, which is two orders of magnitude higher than those for previously reported clay minerals. The Langmuir adsorption capacity of Chry-B was 4.13 mg/g. The wedge-shaped nanopores among the neighboring nanotubes in Chry-B proved to be the primary adsorption sites for I−. The I− at end of the wedge sites was strongly bonded by the nanopores due to the severe superposition of electric potentials from the charged walls of the narrowing wedges. These results demonstrated that chrysotile bundles were a promising candidate for adsorption of I−, and that the shape of nanopore geometry was crucial in I− adsorption.

The oxidation state of the atmosphere and oceans on the early Earth remains controversial. Although it is accepted by many workers that the Archean atmosphere and ocean were anoxic, hematite in the 3.46 billion-year-old (Ga) Marble Bar Chert (MBC) from Pilbara Craton, NW Australia has figured prominently in arguments that the Paleoarchean atmosphere and ocean was fully oxygenated. In this study, we report the Fe isotope compositions and U concentrations of the MBC, and show that the samples have extreme heavy Fe isotope enrichment, where δ56Fe values range between +1.5‰ and +2.6‰, the highest δ56Fe values for bulk samples yet reported. The high δ56Fe values of the MBC require very low levels of oxidation and, in addition, point to a Paleoarchean ocean that had high aqueous Fe(II) contents. A dispersion/reaction model indicates that O2 contents in the photic zone of the ocean were less than 10−3 μM, which suggests that the ocean was essentially anoxic. An independent test of anoxic conditions is provided by U–Th–Pb isotope systematics, which show that U contents in the Paleoarchean ocean were likely below 0.02 ppb, two orders-of-magnitude lower than the modern ocean. Collectively, the Fe and U data indicate a reduced, Fe(II)-rich, U-poor environment in the Archean oceans at 3.46 billion years ago. Given the evidence for photosynthetic communities provided by broadly coeval stromatolites, these results suggests that an important photosynthetic pathway in the Paleoarchean oceans may have been anoxygenic photosynthetic Fe(II) oxidation.

It has been observed that the metabolism of sulfate-reducing bacteria can overcome the energy barrier to Mg 2+ incorporation into growing Ca–Mg carbonates and enhance dolomite precipitation, although the role of SRB in dolomite formation is still under debate. In this study, we presented in situ AFM observations of Ca–Mg carbonate {1 0 4} surface growing from supersaturated solutions. Our data showed that not only can Mg 2+ modify the morphology of the polygonal growth hillocks and impede step growth, but it can also inhibit 1-D step nucleation, resulting in the inability for spirals to continue their vertical growth. However, in the presence of dissolved sulfide, both the 1-D step nucleation and step growth which had been retarded by Mg 2+ ions were significantly enhanced. For example, in the presence as low as 0.13 mM dissolved sulfide, the step velocity can be increased by more than 9 times compared to that in contact with solutions containing Mg 2+ ions but no dissolved sulfide. The Ca–Mg carbonate growth hillock in contact with dissolved sulfide-bearing growth solutions eventually developed a micromosaic-like structure. Based on our observations, we propose that the overall catalytic effect of dissolved sulfide may be twofold, one to stabilize the critical nuclei during 1-D step nucleation by the adsorption of dissolved sulfide on Ca–Mg carbonate surfaces and two to facilitate the dehydration of surface Mg 2+ –water complexes during growth. We hypothesize that dissolved sulfide may adsorb on crystal faces through hydrogen bonding between the H in HS − /H 2 S and the O in calcite CO 3 2 - to weaken the rigid Mg 2+ hydration shell, resulting in an elevated activation entropy for particle attachment and hence a larger kinetic coefficient for step growth. Together with previous studies on disorder dolomite precipitation induced by dissolved sulfide, we demonstrate the catalysis role of dissolved sulfide in sedimentary dolomite formation associate with SRB, which may shed new light on the long-standing “dolomite problem”.

The redox balance of the Archean atmosphere–ocean system is among the most significant uncertainties in our understanding of the earliest history of Earth's surface zone. Most workers agree that oxygen did not constitute a significant proportion of the atmosphere until after ca. 2.45 Ga, after the Great Oxidation Event, but there is less agreement on when O2 production began, and how this may have been consumed by reduced species such as Fe(II) in the oceans. The Fe redox cycle through time has been traced using banded iron formations (BIFs), and Fe isotopes are increasingly used to constrain the conditions of Earth's paleoenvironments, including the pathways of formation of BIFs. Iron isotope analyses of BIFs from the 3.7 to 3.8 Ga Isua Supracrustal Belt (ISB), obtained by micro-sampling of magnetite-rich layers and conventional analysis, as well as by in situ femtosecond laser ablation (fs-LA-ICP-MS), indicate a consistently narrow range of non-zero δ56Fe values. Analysis of magnetite by fs-LA-ICP-MS allows for precise and accurate micron-scale analyses without the problems of orientation effects that are associated with secondary ion mass spectrometry (SIMS) analyses. Magnetite δ56Fe values range from +0.4‰ to +1.1‰ among different bands, but within individual layers magnetite grains are mostly homogeneous. Although these BIFs have been metamorphosed to amphibolite-facies, the metamorphism can neither explain the range in Fe isotope compositions across bands, nor that between hand samples. The isotopic compositions therefore reflect “primary”, low-temperature sedimentary values. The positive δ56Fe values measured from the ISB magnetites are best explained by deposition of Fe(III)-oxides produced by partial oxidation of Fe(II)-rich ocean water. A dispersion/reaction model, which accounts for rates of hydrothermal Fe(II)aq input, rates of oxidation, and rates of Fe(OH)3 settling suggests exceptionally low O2 contents

We measured mercury methylation potentials and a suite of related biogeochemical parameters in sediment cores and porewater from two geochemically distinct sites in the Allequash Creek wetland, northern Wisconsin, USA. We found a high degree of spatial variability in the methylation rate potentials but no significant differences between the two sites. We identified the primary geochemical factors controlling net methylmercury production at this site to be acid-volatile sulfide, dissolved organic carbon, total dissolved iron, and porewater iron(II). Season and demethylation rates also appear to regulate net methylmercury production. Our equilibrium speciation modeling demonstrated that sulfide likely regulated methylation rates by controlling the speciation of inorganic mercury and therefore its bioavailability to methylating bacteria. We found that no individual geochemical parameter could explain a significant amount of the observed variability in mercury methylation rates, but we found significant multivariate relationships, supporting the widely held understanding that net methylmercury production is balance of several simultaneously occurring processes.