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Water resources, including groundwater and prominent rivers worldwide, are under duress because of excessive contaminant and nutrient loads. To help mitigate this problem, the United States Department of Energy (DOE) has supported research since the late 1980s to improve our fundamental knowledge of processes that could be used to help clean up challenging subsurface problems. Problems of interest have included subsurface radioactive waste, heavy metals, and metalloids (e.g. uranium, mercury, arsenic). Research efforts have provided insights into detailed groundwater biogeochemical process coupling and the resulting geochemical exports of metals and nutrients to surrounding environments. Recently, an increased focus has been placed on constraining the exchanges and fates of carbon and nitrogen within and across bedrock to canopy compartments of a watershed and in river-floodplain settings, because of their important role in driving biogeochemical interactions with contaminants and the potential of increased fluxes under changing precipitation regimes, including extreme events. While reviewing the extensive research that has been conducted at DOE's representative sites and testbeds (such as the Oyster Site in Virginia, Savannah River Site in South Carolina, Oak Ridge Reservation in Tennessee, Hanford in Washington, Nevada National Security Site in Nevada, Riverton in Wyoming, and Rifle and East River in Colorado), this review paper explores the nature and distribution of contaminants in the surface and shallow subsurface (i.e. the critical zone) and their interactions with carbon and nitrogen dynamics. We also describe state-of-the-art, scale-aware characterization approaches and models developed to predict contaminant fate and transport. The models take advantage of DOE leadership-class high-performance computers and are beginning to incorporate artificial intelligence approaches to tackle the extreme diversity of hydro-biogeochemical processes and measurements. Recognizing that the insights and capability developments are potentially transferable to many other sites, we also explore the scientific implications of these advances and recommend future research directions.

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.

Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH4+), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH4+ in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH4+ availability, with broad implications for comparisons of ecologically distinct populations.

Floodplains, heavily used for water supplies, housing, agriculture, mining, and industry, are important repositories of organic carbon, nutrients, and metal contaminants. The accumulation and release of these species is often mediated by redox processes. Understanding the physicochemical, hydrological, and biogeochemical controls on the distribution and variability of sediment redox conditions is therefore critical to developing conceptual and numerical models of contaminant transport within floodplains. The Upper Colorado River Basin (UCRB) is impacted by former uranium and vanadium ore processing, resulting in contamination by V, Cr, Mn, As, Se, Mo and U. Previous authors have suggested that sediment redox activity occurring within organic carbon-enriched bodies located below the groundwater level may be regionally important to the maintenance and release of contaminant inventories, particularly uranium. To help assess this hypothesis, vertical distributions of Fe and S redox states and sulfide mineralogy were assessed in sediment cores from three floodplain sites spanning a 250km transect of the central UCRB. The results of this study support the hypothesis that organic-enriched reduced sediments are important zones of biogeochemical activity within UCRB floodplains. We found that the presence of organic carbon, together with pore saturation, are the key requirements for maintaining reducing conditions, which were dominated by sulfate-reduction products. Sediment texture was found to be of secondary importance and to moderate the response of the system to external forcing, such as oxidant diffusion. Consequently, fine-grain sediments are relatively resistant to oxidation in comparison to coarser-grained sediments. Exposure to oxidants consumes precipitated sulfides, with a disproportionate loss of mackinawite (FeS) as compared to the more stable pyrite. The accompanying loss of redox buffering capacity creates the potential for release of sequestered radionuclides and metals. Because of their redox reactivity and stores of metals, C, and N, organic-enriched sediments are likely to be important to nutrient and contaminant mobility within UCRB floodplain aquifers.

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.

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.

Organic matter decomposition in soils and terrestrial sediments has a prominent role in the global carbon cycle. Carbon stocks in anoxic environments, such as wetlands and the subsurface of floodplains, are large and presumed to decompose slowly. The degree of microbial respiration in anoxic environments is typically thought to depend on the energetics of available terminal electron acceptors such as nitrate or sulfate; microbes couple the reduction of these compounds to the oxidation of organic carbon. However, it is also possible that the energetics of the organic carbon itself can determine whether it is decomposed. Here we examined water-soluble organic carbon by Fourier-transform ion-cyclotron-resonance mass spectrometry to compare the chemical composition and average nominal oxidation state of carbon-A metric reflecting whether microbial oxidation of organic matter is thermodynamically favourable-in anoxic (sulfidic) and oxic (non-sulfidic) floodplain sediments. We observed distinct minima in the average nominal oxidation state of water-soluble carbon in sediments exhibiting anoxic, sulfate-reducing conditions, suggesting preservation of carbon compounds with nominal oxidation states below the threshold that makes microbial sulfate reduction thermodynamically favourable. We conclude that thermodynamic limitations constitute an important complement to other mechanisms of carbon preservation, such as enzymatic restrictions and mineral association, within anaerobic environments.

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.

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.

Highly active catalysts for the oxygen evolution reaction (OER) are required for the development of photoelectrochemical devices that generate hydrogen efficiently from water using solar energy. Here, we identify the origin of a 500-fold OER activity enhancement that can be achieved with mixed (Ni,Fe)oxyhydroxides (Ni(1-x)Fe(x)OOH) over their pure Ni and Fe parent compounds, resulting in one of the most active currently known OER catalysts in alkaline electrolyte. Operando X-ray absorption spectroscopy (XAS) using high energy resolution fluorescence detection (HERFD) reveals that Fe(3+) in Ni(1-x)Fe(x)OOH occupies octahedral sites with unusually short Fe-O bond distances, induced by edge-sharing with surrounding [NiO6] octahedra. Using computational methods, we establish that this structural motif results in near optimal adsorption energies of OER intermediates and low overpotentials at Fe sites. By contrast, Ni sites in Ni(1-x)Fe(x)OOH are not active sites for the oxidation of water.

In mountainous watersheds, floodplain sediments are typically characterized by gravel bed layers capped by an overlying soil unit that serves as a hotspot for biogeochemical reactivity. However, the influence of soil biogeochemistry on gravel bed underflow composition remains unclear, especially during hydrological transitions that alter the vertical connectivity between overlaying soils and the underlying gravel bed. This study investigates these dynamics by measuring hydraulic gradients and water compositions over three hydrological years in a typical mountainous, low‐order stream floodplain in the Upper Colorado River Basin. Results indicate that the timing of hydrological conditions strongly influences the vertical exchanges that control water quality. Specifically, during flooding events such as beaver ponding, that induce downward flushing of the soil, anoxic conditions prevalent in the biogeochemically active soil are transferred downstream via gravel bed underflow. Conversely, snowmelt and drought conditions increase oxic conditions in the gravel bed due to diminished hydrological connectivity with the overlying soil. To compare water quality response to hydrological transitions across similar floodplain environments, we propose a conceptual model that quantifies the inundation‐induced flushing of soil porewater to measure solute exchange efficiency with the gravel bed solute convergence efficiency (SCE). This model provides a framework for quantifying biogeochemical processes in hydrological underflow systems, which is critical for water and elemental budgets in these globally important mountainous ecosystems. Plain Language Summary: Mountains are important sources of freshwater for humans and ecosystems. They are however increasingly impacted by climate change. In this paper, we investigate how changes in water availability (droughts, snowmelt, inundations) can cascade into changes in water quality (concentrations of dissolved chemical elements). We show that in mountain valleys, the zone of contact between the soil and the underlying gravel bed aquifer is important for water quality. Chemical elements from the soil can be flushed down into the gravel bed aquifer, then transported by groundwater to the stream. Chemical elements from the soil can also react with chemical elements present in the aquifer. Our research can be used to better predict the water and elemental budgets in these important mountainous systems. Key Points: Soil / gravel bed connectivity in floodplains is important for water qualitySnowmelt and drought both reduce soil / gravel bed connectivityBeaver ponding increases downward flushing to gravel bed unit [ABSTRACT FROM AUTHOR]

The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick x 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-A basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn-Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mn oxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments.