Borgs are giant genetic elements with potential to expand metabolic capacity.

Anaerobic methane oxidation exerts a key control on greenhouse gas emissions1, yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins through studying groundwater, sediments and wetland soil where methane production and oxidation occur. Four curated, complete genomes are linear, up to approximately 1 Mb in length and share genome organization, including replichore structure, long inverted terminal repeats and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are highly divergent archaeal extrachromosomal elements with a distinct evolutionary origin. Gene sequence similarity, phylogeny and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as 'Borgs'. We identified at least 19 different Borg types coexisting with Methanoperedens spp. in four distinct ecosystems. Borgs provide methane-oxidizing Methanoperedens archaea access to genes encoding proteins involved in redox reactions and energy conservation (for example, clusters of multihaem cytochromes and methyl coenzyme M reductase). These data suggest that Borgs might have previously unrecognized roles in the metabolism of this group of archaea, which are known to modulate greenhouse gas emissions, but further studies are now needed to establish their functional relevance.

Unusual biology across a group comprising more than 15% of domain Bacteria.

A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments and are thought to mediate carbon and hydrogen cycles. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.

Phosphorus Speciation in Atmospherically Deposited Particulate Matter and Implications for Terrestrial Ecosystem Productivity.

Chemical forms of phosphorus (P) in airborne particulate matter (PM) are poorly known and do not correlate with solubility or extraction measurements commonly used to infer speciation. We used P X-ray absorption near-edge structure (XANES) and 31P nuclear magnetic resonance (NMR) spectroscopies to determine P species in PM collected at four mountain sites (Colorado and California). Organic P species dominated samples from high elevations, with organic P estimated at 65-100% of total P in bulk samples by XANES and 79-88% in extracted fractions (62-84% of total P) by NMR regardless of particle size (≥10 or 1-10 µm). Phosphorus monoester and diester organic species were dominant and present in about equal proportions, with low fractions of inorganic P species. By comparison, PM from low elevation contained mixtures of organic and inorganic P, with organic P estimated at 30-60% of total P. Intercontinental PM transport determined from radiogenic lead (Pb) isotopes varied from 0 to 59% (mean 37%) Asian-sourced Pb at high elevation, whereas stronger regional PM inputs were found at low elevation. Airborne flux of bioavailable P to high-elevation ecosystems may be twice as high as estimated by global models, which will disproportionately affect net primary productivity.

Isotopic Fingerprint of Uranium Accumulation and Redox Cycling in Floodplains of the Upper Colorado River Basin.

Uranium (U) groundwater contamination is a major concern at numerous former mining and milling sites across the Upper Colorado River Basin (UCRB), USA, where U(IV)-bearing solids have accumulated within naturally reduced zones (NRZs). Understanding the processes governing U reduction and oxidation within NRZs is critical for assessing the persistence of U in groundwater. To evaluate the redox cycling of uranium, we measured the U concentrations and isotopic compositions (δ238U) of sediments and pore waters from four study sites across the UCRB that span a gradient in sediment texture and composition. We observe that U accumulation occurs primarily within fine-grained (low-permeability) NRZs that show active redox variations. Low-permeability NRZs display high accumulation and low export of U, with internal redox cycling of U. In contrast, within high-permeability NRZs, U is remobilized under oxidative conditions, possibly without any fractionation, and transported outside the NRZs. The low δ238U of sediments outside of defined NRZs suggests that these reduced zones act as additional U sources. Collectively, our results indicate that fine-grained NRZs have a greater potential to retain uranium, whereas NRZs with higher permeability may constitute a more-persistent but dilute U source.

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.

Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads.

Uranium Retention in a Bioreduced Region of an Alluvial Aquifer Induced by the Influx of Dissolved Oxygen.

Reduced zones in the subsurface represent biogeochemically active hotspots enriched in buried organic matter and reduced metals. Within a shallow alluvial aquifer located near Rifle, CO, reduced zones control the fate and transport of uranium (U). Though an influx of dissolved oxygen (DO) would be expected to mobilize U, we report U immobilization. Groundwater U concentrations decreased following delivery of DO (21.6 mg O2/well/h). After 23 days of DO delivery, injection of oxygenated groundwater was paused and resulted in the rebound of groundwater U concentrations to preinjection levels. When DO delivery resumed (day 51), groundwater U concentrations again decreased. The injection was halted on day 82 again and resulted in a rebound of groundwater U concentrations. DO delivery rate was increased to 54 mg O2/well/h (day 95) whereby groundwater U concentrations increased. Planktonic cell abundance remained stable throughout the experiment, but virus-to-microbial cell ratio increased 1.8-3.4-fold with initial DO delivery, indicative of microbial activity in response to DO injection. Together, these results indicate that the redox-buffering capacity of reduced sediments can prevent U mobilization, but could be overcome as delivery rate or oxidant concentration increases, mobilizing U.

Field Application of 238U/235U Measurements To Detect Reoxidation and Mobilization of U(IV).

Biostimulation to induce reduction of soluble U(VI) to relatively immobile U(IV) is an effective strategy for decreasing aqueous U(VI) concentrations in contaminated groundwater systems. If oxidation of U(IV) occurs following the biostimulation phase, U(VI) concentrations increase, challenging the long-term effectiveness of this technique. However, detecting U(IV) oxidation through dissolved U concentrations alone can prove difficult in locations with few groundwater wells to track the addition of U to a mass of groundwater. We propose the 238U/235U ratio of aqueous U as an independent, reliable tracer of U(IV) remobilization via oxidation or mobilization of colloids. Reduction of U(VI) produces 238U-enriched U(IV), whereas remobilization of solid U(IV) should not induce isotopic fractionation. The incorporation of remobilized U(IV) with a high 238U/235U ratio into the aqueous U(VI) pool produces an increase in 238U/235U of aqueous U(VI). During several injections of nitrate to induce U(IV) oxidation, 238U/235U consistently increased, suggesting 238U/235U is broadly applicable for detecting mobilization of U(IV).

Correlative Cryogenic Spectromicroscopy to Investigate Selenium Bioreduction Products.

Accurate mapping of the composition and structure of minerals and associated biological materials is critical in geomicrobiology and environmental research. Here, we have developed an apparatus that allows the correlation of cryogenic transmission electron microscopy (cryo-TEM) and synchrotron hard X-ray microprobe (SHXM) data sets to precisely determine the distribution, valence state, and structure of selenium in biofilms sampled from a contaminated aquifer near Rifle, CO. Results were replicated in the laboratory via anaerobic selenate-reducing enrichment cultures. 16S rRNA analyses of field-derived biofilm indicated the dominance of Betaproteobacteria from the Comamonadaceae family and uncultivated members of the Simplicispira genus. The major product in field and culture-derived biofilms is ∼25-300 nm red amorphous Se0 aggregates of colloidal nanoparticles. Correlative analyses of the cultures provided direct evidence for the microbial dissimilatory reduction of Se(VI) to Se(IV) to Se0. Extended X-ray absorption fine-structure spectroscopy showed red amorphous Se0 with a first shell Se-Se interatomic distance of 2.339 ± 0.003 Å. Complementary scanning transmission X-ray microscopy revealed that these aggregates are strongly associated with a protein-rich biofilm matrix. These findings have important implications for predicting the stability and mobility of Se bioremediation products and understanding of Se biogeochemical cycling. The approach, involving the correlation of cryo-SHXM and cryo-TEM data sets from the same specimen area, is broadly applicable to biological and environmental samples.

Oxidative Uranium Release from Anoxic Sediments under Diffusion-Limited Conditions.

Uranium (U) contamination occurs as a result of mining and ore processing; often in alluvial aquifers that contain organic-rich, reduced sediments that accumulate tetravalent U, U(IV). Uranium(IV) is sparingly soluble, but may be mobilized upon exposure to nitrate (NO3-) and oxygen (O2), which become elevated in groundwater due to seasonal fluctuations in the water table. The extent to which oxidative U mobilization can occur depends upon the transport properties of the sediments, the rate of U(IV) oxidation, and the availability of inorganic reductants and organic electron donors that consume oxidants. We investigated the processes governing U release upon exposure of reduced sediments to artificial groundwater containing O2 or NO3- under diffusion-limited conditions. Little U was mobilized during the 85-day reaction, despite rapid diffusion of groundwater within the sediments and the presence of nonuraninite U(IV) species. The production of ferrous iron and sulfide in conjunction with rapid oxidant consumption suggested that the sediments harbored large concentrations of bioavailable organic carbon that fueled anaerobic microbial respiration and stabilized U(IV). Our results suggest that seasonal influxes of O2 and NO3- may cause only localized mobilization of U without leading to export of U from the reducing sediments when ample organic carbon is present.

Production of Hydrogen Peroxide in Groundwater at Rifle, Colorado.

The commonly held assumption that photodependent processes dominate H2O2 production in natural waters has been recently questioned. Here, we present evidence for the unrecognized and light-independent generation of H2O2 in groundwater of an alluvial aquifer adjacent to the Colorado River near Rifle, CO. In situ detection using a sensitive chemiluminescent method suggests H2O2 concentrations ranging from lower than the detection limit (<1 nM) to 54 nM along the vertical profiles obtained at various locations across the aquifer. Our results also suggest dark formation of H2O2 is more likely to occur in transitional redox environments where reduced elements (e.g., reduced metals and NOM) meet oxygen, such as oxic-anoxic interfaces. A simplified kinetic model involving interactions among iron, reduced NOM, and oxygen was able to reproduce roughly many, but not all, of the features in our detected H2O2 profiles, and therefore there are other minor biological and/or chemical controls on H2O2 steady-state concentrations in such aquifer. Because of its transient nature, the widespread presence of H2O2 in groundwater suggests the existence of a balance between H2O2 sources and sinks, which potentially involves a cascade of various biogeochemically important processes that could have significant impacts on metal/nutrient cycling in groundwater-dependent ecosystems, such as wetlands and springs. More importantly, our results demonstrate that reactive oxygen species are not only widespread in oceanic and atmospheric systems but also in the subsurface domain, possibly the least understood component of biogeochemical cycles.

Redox Controls over the Stability of U(IV) in Floodplains of the Upper Colorado River Basin.

Aquifers in the Upper Colorado River Basin (UCRB) exhibit persistent uranium (U) groundwater contamination plumes originating from former ore processing operations. Previous observations at Rifle, Colorado, have shown that fine grained, sulfidic, organic-enriched sediments accumulate U in its reduced form, U(IV), which is less mobile than oxidized U(VI). These reduced sediment bodies can subsequently act as secondary sources, releasing U back to the aquifer. There is a need to understand if U(IV) accumulation in reduced sediments is a common process at contaminated sites basin-wide, to constrain accumulated U(IV) speciation, and to define the biogeochemical factors controlling its reactivity. We have investigated U(IV) accumulation in organic-enriched reduced sediments at three UCRB floodplains. Noncrystalline U(IV) is the dominant form of accumulated U, but crystalline U(IV) comprises up to ca. 30% of total U at some locations. Differing susceptibilities of these species to oxidative remobilization can explain this variability. Particle size, organic carbon content, and pore saturation, control the exposure of U(IV) to oxidants, moderating its oxidative release. Further, our data suggest that U(IV) can be mobilized under deeply reducing conditions, which may contribute to maintenance and seasonal variability of U in groundwater plumes in the UCRB.

Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain.

Three-dimensional variably saturated flow and multicomponent biogeochemical reactive transport modeling, based on published and newly generated data, is used to better understand the interplay of hydrology, geochemistry, and biology controlling the cycling of carbon, nitrogen, oxygen, iron, sulfur, and uranium in a shallow floodplain. In this system, aerobic respiration generally maintains anoxic groundwater below an oxic vadose zone until seasonal snowmelt-driven water table peaking transports dissolved oxygen (DO) and nitrate from the vadose zone into the alluvial aquifer. The response to this perturbation is localized due to distinct physico-biogeochemical environments and relatively long time scales for transport through the floodplain aquifer and vadose zone. Naturally reduced zones (NRZs) containing sediments higher in organic matter, iron sulfides, and non-crystalline U(IV) rapidly consume DO and nitrate to maintain anoxic conditions, yielding Fe(II) from FeS oxidative dissolution, nitrite from denitrification, and U(VI) from nitrite-promoted U(IV) oxidation. Redox cycling is a key factor for sustaining the observed aquifer behaviors despite continuous oxygen influx and the annual hydrologically induced oxidation event. Depth-dependent activity of fermenters, aerobes, nitrate reducers, sulfate reducers, and chemolithoautotrophs (e.g., oxidizing Fe(II), S compounds, and ammonium) is linked to the presence of DO, which has higher concentrations near the water table.

Transport and humification of dissolved organic matter within a semi-arid floodplain.

In order to understand the transport and humification processes of dissolved organic matter (DOM) within sediments of a semi-arid floodplain at Rifle, Colorado, fluorescence excitation-emission matrix (EEM) spectroscopy, humification index (HIX) and specific UV absorbance (SUVA) at 254nm were applied for characterizing depth and seasonal variations of DOM composition. Results revealed that late spring snowmelt leached relatively fresh DOM from plant residue and soil organic matter down into the deeper vadose zone (VZ). More humified DOM is preferentially adsorbed by upper VZ sediments, while non- or less-humified DOM was transported into the deeper VZ. Interestingly, DOM at all depths undergoes rapid biological humification process evidenced by the products of microbial by-product-like (i.e., tyrosine-like and tryptophan-like) matter in late spring and early summer, particularly in the deeper VZ, resulting in more humified DOM (e.g., fulvic-acid-like and humic-acid-like substances) at the end of year. This indicates that DOM transport is dominated by spring snowmelt, and DOM humification is controlled by microbial degradation, with seasonal variations. It is expected that these relatively simple spectroscopic measurements (e.g., EEM spectroscopy, HIX and SUVA) applied to depth- and temporally-distributed pore-water samples can provide useful insights into transport and humification of DOM in other subsurface environments as well.

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages.

Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by the intersecting activities of microbial community members, yet the organisms responsible are largely unknown. Metagenomic methods can identify organisms and functions, but genome recovery is often precluded by data complexity. To address this limitation, we developed subsampling assembly methods to re-construct high-quality draft genomes from complex samples. We applied these methods to evaluate the interlinked roles of the most abundant organisms in biogeochemical cycling in the aquifer sediment. Community proteomics confirmed these activities. The eight most abundant organisms belong to novel lineages, and two represent phyla with no previously sequenced genome. Four organisms are predicted to fix carbon via the Calvin-Benson-Bassham, Wood-Ljungdahl or 3-hydroxyproprionate/4-hydroxybutarate pathways. The profiled organisms are involved in the network of denitrification, dissimilatory nitrate reduction to ammonia, ammonia oxidation and sulfate reduction/oxidation, and require substrates supplied by other community members. An ammonium-oxidizing Thaumarchaeote is the most abundant community member, despite low ammonium concentrations in the groundwater. This organism likely benefits from two other relatively abundant organisms capable of producing ammonium from nitrate, which is abundant in the groundwater. Overall, dominant members of the microbial community are interconnected through exchange of geochemical resources.

Iron and Carbon Dynamics during Aging and Reductive Transformation of Biogenic Ferrihydrite.

Natural organic matter is often associated with Fe(III) oxyhydroxides, and may be stabilized as a result of coprecipitation or sorption to their surfaces. However, the significance of this association in relation to Fe and C dynamics and biogeochemical cycling, and the mechanisms responsible for organic matter stabilization as a result of interaction with minerals under various environmental conditions (e.g., pH, Eh, etc.) are not entirely understood. The preservation of mineral-bound OM may be affected by OM structure and mineral identity, and bond types between OM and minerals may be central to influencing the stability, transformation and composition of both organic and mineral components under changing environmental conditions. Here we use bulk and submicron-scale spectroscopic synchrotron methods to examine the in situ transformation of OM-bearing, biogenic ferrihydrite stalks (Gallionella ferruginea-like), which formed following injection of oxygenated groundwater into a saturated alluvial aquifer at the Rifle, CO field site. A progression from oxidizing to reducing conditions during an eight-month period triggered the aging and reductive transformation of Gallionella-like ferrihydrite stalks to Fe (hydroxy)carbonates and Fe sulfides, as well as alteration of the composition and amount of OM. Spectromicroscopic measurements showed a gradual decrease in reduced carbon forms (aromatic/alkene, aliphatic C), a relative increase in amide/carboxyl functional groups and a significant increase in carbonate in the stalk structures, and the appearance of organic globules not associated with stalk structures. Biogenic stalks lost ∼30% of their initial organic carbon content. Conversely, a significant increase in bulk organic matter accompanied these transformations. The character of bulk OM changed in parallel with mineralogical transformations, showing an increase in aliphatic, aromatic and amide functional groups. These changes likely occurred as a result of an increase in microbial activity, or biomass production under anoxic conditions. By the end of this experiment, a substantial fraction of organic matter remained in identifiable Fe containing stalks, but carbon was also present in additional pools, for example, organic matter globules and iron carbonate minerals.

Physico-Chemical Heterogeneity of Organic-Rich Sediments in the Rifle Aquifer, CO: Impact on Uranium Biogeochemistry.

The Rifle alluvial aquifer along the Colorado River in west central Colorado contains fine-grained, diffusion-limited sediment lenses that are substantially enriched in organic carbon and sulfides, as well as uranium, from previous milling operations. These naturally reduced zones (NRZs) coincide spatially with a persistent uranium groundwater plume. There is concern that uranium release from NRZs is contributing to plume persistence or will do so in the future. To better define the physical extent, heterogeneity and biogeochemistry of these NRZs, we investigated sediment cores from five neighboring wells. The main NRZ body exhibited uranium concentrations up to 100 mg/kg U as U(IV) and contains ca. 286 g of U in total. Uranium accumulated only in areas where organic carbon and reduced sulfur (as iron sulfides) were present, emphasizing the importance of sulfate-reducing conditions to uranium retention and the essential role of organic matter. NRZs further exhibited centimeter-scale variations in both redox status and particle size. Mackinawite, greigite, pyrite and sulfate coexist in the sediments, indicating that dynamic redox cycling occurs within NRZs and that their internal portions can be seasonally oxidized. We show that oxidative U(VI) release to the aquifer has the potential to sustain a groundwater contaminant plume for centuries. NRZs, known to exist in other uranium-contaminated aquifers, may be regionally important to uranium persistence.

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.

Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.

Reactivity of Uranium and Ferrous Iron with Natural Iron Oxyhydroxides.

Determining key reaction pathways involving uranium and iron oxyhydroxides under oxic and anoxic conditions is essential for understanding uranium mobility as well as other iron oxyhydroxide mediated processes, particularly near redox boundaries where redox conditions change rapidly in time and space. Here we examine the reactivity of a ferrihydrite-rich sediment from a surface seep adjacent to a redox boundary at the Rifle, Colorado field site. Iron(II)-sediment incubation experiments indicate that the natural ferrihydrite fraction of the sediment is not susceptible to reductive transformation under conditions that trigger significant mineralogical transformations of synthetic ferrihydrite. No measurable Fe(II)-promoted transformation was observed when the Rifle sediment was exposed to 30 mM Fe(II) for up to 2 weeks. Incubation of the Rifle sediment with 3 mM Fe(II) and 0.2 mM U(VI) for 15 days shows no measurable incorporation of U(VI) into the mineral structure or reduction of U(VI) to U(IV). Results indicate a significantly decreased reactivity of naturally occurring Fe oxyhydroxides as compared to synthetic minerals, likely due to the association of impurities (e.g., Si, organic matter), with implications for the mobility and bioavailability of uranium and other associated species in field environments.

Long-term in situ oxidation of biogenic uraninite in an alluvial aquifer: impact of dissolved oxygen and calcium.

Oxidative dissolution controls uranium release to (sub)oxic pore waters from biogenic uraninite produced by natural or engineered processes, such as bioremediation. Laboratory studies show that uraninite dissolution is profoundly influenced by dissolved oxygen (DO), carbonate, and solutes such as Ca(2+). In complex and heterogeneous subsurface environments, the concentrations of these solutes vary in time and space. Knowledge of dissolution processes and kinetics occurring over the long-term under such conditions is needed to predict subsurface uranium behavior and optimize the selection and performance of uraninite-based remediation technologies over multiyear periods. We have assessed dissolution of biogenic uraninite deployed in wells at the Rifle, CO, DOE research site over a 22 month period. Uraninite loss rates were highly sensitive to DO, with near-complete loss at >0.6 mg/L over this period but no measurable loss at lower DO. We conclude that uraninite can be stable over decadal time scales in aquifers under low DO conditions. U(VI) solid products were absent over a wide range of DO values, suggesting that dissolution proceeded through complexation and removal of oxidized surface uranium atoms by carbonate. Moreover, under the groundwater conditions present, Ca(2+) binds strongly to uraninite surfaces at structural uranium sites, impacting uranium fate.

The complete genome sequence for putative H2- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome.

We reconstructed the complete 2.4 Mb-long genome of a previously uncultivated epsilonproteobacterium, Candidatus Sulfuricurvum sp. RIFRC-1, via assembly of short-read shotgun metagenomic data using a complexity reduction approach. Genome-based comparisons indicate the bacterium is a novel species within the Sulfuricurvum genus, which contains one cultivated representative, S. kujiense. Divergence between the species appears due in part to extensive genomic rearrangements, gene loss and chromosomal versus plasmid encoding of certain (respiratory) genes by RIFRC-1. Deoxyribonucleic acid for the genome was obtained from terrestrial aquifer sediment, in which RIFRC-1 comprised ∼ 47% of the bacterial community. Genomic evidence suggests RIFRC-1 is a chemolithoautotrophic diazotroph capable of deriving energy for growth by microaerobic or nitrate-/nitric oxide-dependent oxidation of S°, sulfide or sulfite or H2oxidation. Carbon may be fixed via the reductive tricarboxylic acid cycle. Consistent with these physiological attributes, the local aquifer was microoxic with small concentrations of available nitrate, small but elevated concentrations of reduced sulfur and NH(4)(+) /NH3-limited. Additionally, various mechanisms for heavy metal and metalloid tolerance and virulence point to a lifestyle well-adapted for metal(loid)-rich environments and a shared evolutionary past with pathogenic Epsilonproteobacteria. Results expand upon recent findings highlighting the potential importance of sulfur and hydrogen metabolism in the terrestrial subsurface.