Declining carbohydrate content of Sitka-spruce treesdying from seawater exposure.

Increasing sea levels associated with climate change threaten the survival of coastal forests, yet the mechanisms by which seawater exposure causes tree death remain poorly understood. Despite the potentially crucial role of nonstructural carbohydrate (NSC) reserves in tree survival, their dynamics in the process of death under seawater exposure are unknown. Here we monitored progressive tree mortality and associated NSC storage in Sitka-spruce (Picea sitchensis) trees dying under ecosystem-scale increases in seawater exposure in western Washington, USA. All trees exposed to seawater, because of monthly tidal intrusion, experienced declining crown foliage during the sampling period, and individuals with a lower percentage of live foliated crown (PLFC) died faster. Tree PLFC was strongly correlated with subsurface salinity and needle ion contents. Total NSC concentrations in trees declined remarkably with crown decline, and reached extremely low levels at tree death (2.4% and 1.6% in leaves and branches, respectively, and 0.4% in stems and roots). Starch in all tissues was almost completely consumed, while sugars remained at a homeostatic level in foliage. The decreasing NSC with closer proximity to death and near zero starch at death are evidences that carbon starvation occurred during Sitka-spruce mortality during seawater exposure. Our results highlight the importance of carbon storage as an indicator of tree mortality risks under seawater exposure.

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.

Evaluation of a genome-scale in silico metabolic model for Geobacter metallireducens by using proteomic data from a field biostimulation experiment.

Accurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within an in silico model using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model of Geobacter metallireducens-specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.

Uranium removal from groundwater via in situ biostimulation: Field-scale modeling of transport and biological processes.

During 2002 and 2003, bioremediation experiments in the unconfined aquifer of the Old Rifle UMTRA field site in western Colorado provided evidence for the immobilization of hexavalent uranium in groundwater by iron-reducing Geobacter sp. stimulated by acetate amendment. As the bioavailable Fe(III) terminal electron acceptor was depleted in the zone just downgradient of the acetate injection gallery, sulfate-reducing organisms came to dominate the microbial community. In the present study, we use multicomponent reactive transport modeling to analyze data from the 2002 field experiment to identify the dominant transport and biological processes controlling uranium mobility during biostimulation, and determine field-scale parameters for these modeled processes. The coupled process simulation approach was able to establish a quantitative characterization of the principal flow, transport, and reaction processes based on the 2002 field experiment, that could be applied without modification to describe the 2003 field experiment. Insights gained from this analysis include field-scale estimates of the bioavailable Fe(III) mineral threshold for the onset of sulfate reduction, and rates for the Fe(III), U(VI), and sulfate terminal electron accepting processes.

Enhanced radionuclide immobilization and flow path modifications by dissolution and secondary precipitates.

Caustic radioactive wastes that have leaked at Hanford Site (Richland, WA) induce mineral dissolution and subsequent secondary precipitation that influence the fate and transport of contaminants present in the waste solutions. The effects of secondary mineral precipitates, formed after contacting solids with simulated caustic wastes, on the flow path changes and radionuclide immobilization were investigated by reacting quartz, a mixture of quartz and biotite, and a Hanford sediment (Warden soil: coarse-silty, mixed, superactive, mesic Xeric Haplocambids) with simulated caustic tank waste solution. Continuous Si dissolution and concomitant secondary mineral precipitation were the principal reactions observed in both batch and flow-through tests. Nitrate-cancrinite was the dominant secondary precipitate on mineral surfaces after 3- to 10-d reaction times in batch experiments. X-ray microtomography images of a reacted quartz column revealed that secondary precipitates cemented quartz grains together and modified pore geometry in the center of the column. Along the circumference of the packed column, however, quartz dissolution continuously occurred, suggesting that wastes that leaked from buried tanks in the past likely did not migrate vertically as modeled in risk assessments but rather the pathways likely changed to be dominantly horizontal on precipitation of secondary precipitate phases in the Hanford vadose zone. Based on batch equilibrium sorption results on the reacted sediments, the dominant secondary precipitates (cancrinites) on the mineral surfaces enhanced the sorption capacity of typical Hanford sediment for radionuclides 129I(-I), 79Se(VI), 99Tc(VII), and 90Sr(II), all of which are of major concern at the Hanford Site.

Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment.

Three-dimensional, coupled variably saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport and biogeochemical reactions controlling uranium behavior under pulsed acetate amendment, seasonal water table variation, spatially variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. While the simulation of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado was generally consistent with behaviors identified in previous field experiments at the Rifle IFRC site, the additional process and property detail provided several new insights. A principal conclusion from this work is that uranium bioreduction is most effective when acetate, in excess of the sulfate-reducing bacteria demand, is available to the metal-reducing bacteria. The inclusion of an initially small population of slow growing sulfate-reducing bacteria identified in proteomic analyses led to an additional source of Fe(II) from the dissolution of Fe(III) minerals promoted by biogenic sulfide. The falling water table during the experiment significantly reduced the saturated thickness of the aquifer and resulted in reactants and products, as well as unmitigated uranium, in the newly unsaturated vadose zone. High permeability sandy gravel structures resulted in locally high flow rates in the vicinity of injection wells that increased acetate dilution. In downgradient locations, these structures created preferential flow paths for acetate delivery that enhanced local zones of TEAP reactivity and subsidiary reactions. Conversely, smaller transport rates associated with the lower permeability lithofacies (e.g., fine) and vadose zone were shown to limit acetate access and reaction. Once accessed by acetate, however, these same zones limited subsequent acetate dilution and provided longer residence times that resulted in higher concentrations of TEAP reaction products when terminal electron donors and acceptors were not limiting. Finally, facies-based porosity and reactive surface area variations were shown to affect aqueous uranium concentration distributions with localized effects of the fine lithofacies having the largest impact on U(VI) surface complexation. The ability to model the comprehensive biogeochemical reaction network, and spatially and temporally variable processes, properties, and conditions controlling uranium behavior during engineered bioremediation in the naturally complex Rifle IFRC subsurface system required a subsurface simulator that could use the large memory and computational performance of a massively parallel computer. In this case, the eSTOMP simulator, operating on 128 processor cores for 12h, was used to simulate the 110-day field experiment and 50 days of post-biostimulation behavior.

Oxidation of H2S by iron oxides in unsaturated conditions.

Previous studies have demonstrated that gas-phase H2S can immobilize certain redox-sensitive contaminants (e.g., Cr, U, Tc) in vadose zone environments. A key issue for effective and efficient delivery of H2S in these environments is the reactivity of the gas with indigenous iron oxides. To elucidate the factors that control the transport of H2S in the vadose zone, laboratory column experiments were conducted to identify reaction mechanisms and measure rates of H2S oxidation by iron oxide-coated sands using several carrier gas compositions (N2, air, and O2) and flow rates. Most experiments were conducted using ferrihydrite-coated sand. Additional studies were conducted with goethite- and hematite-coated sand and a natural sediment. Selective extractions were conducted at the end of each column experiment to determine the mass balance of the reaction products. XPS was used to confirm the presence of the reaction products. For column experiments in which ferrihydrite-coated sand was the substrate and N2 was the carrier gas, the major H2S oxidation products were FeS and elemental sulfur (mostly S8(0), represented as S(0) for simplicity) at ratios that were consistent with the stoichiometry of the postulated reactions. When air or O2 were used as the carrier gas, S(0) became the dominant reaction product along with FeS2 and smaller amounts of FeS, sulfate, and thiosulfate. A mathematical model of reactive transport was used to test the hypothesis that S(0) forming on the iron oxide surfaces reduces access of H2S to the reactive surface. Several conceptual models were assessed in the context of the postulated reactions with the final model based on a linear surface poisoning model and fitted reaction rates. These results indicate that carrier gas selection is a critical consideration with significant tradeoffs for remediation objectives.