Abstract: We assess the role of septic systems as potential nitrogen (N) sources to coastal open water bodies. To quantify the potential role of septic tanks, we document the distribution pattern and functionality of septic tanks in McIntosh County in Georgia, USA, and examine factors governing the mitigation of septic N loading in coastal groundwater. Employing a field calibrated 2D variable-density reaction-transport model, we focus on the role of setback distance of a leaky septic source from the receiving surface waters, on transport and biogeochemical characteristics of the subsurface environment, and on leachate composition and reactivity. We conclude that the removal of bioavailable nitrogen via denitrification may be increased by increasing the septic system setback distance, in particular in brackish and saline coastal settings where sulfide produced in sulfate reduction can limit N2 production. Water Research

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Abstract: Within soils, biogeochemical processes controlling elemental cycling are heterogeneously distributed owing, in large part, to the physical complexity of the media. Here we quantify how diffusive mass-transfer limitation at the soil aggregate scale controls the biogeochemical processes governing ferrihydrite reductive dissolution and secondary iron mineral formation. Artificial cm-scale aggregates made of ferrihydrite-coated sand inoculated with iron-reducing bacteria were placed in flow-through reactors, mimicking macro- and micro-porous soil environments. A reactive transport model was developed to delineate diffusively and advectively controlled regions, identify reaction zones and estimate kinetic parameters. Simulated iron (Fe) breakthrough-curves show good agreement with experimental results for a wide-range of flow rates and input lactate concentrations, with only a limited amount (≤12%) of Fe lost in the reactor outflow over a 31 d period. Model simulations show substantial intra-aggregate, mm-scale radial variations in the secondary iron phase distributions, reproducing the trends observed experimentally where only limited transformation of ferrihydrite was found near the aggregate surface while extensive formation of goethite/lepidocrocite and minor amounts of magnetite and/or siderite were observed towards the aggregate center. Our study highlights the important control of variations in transport intensities on microbially-induced iron transformation at the soil aggregate scale. Environmental Science and Technology

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Abstract: Brine fluids that upwell from deep, hot reservoirs below the sea bed supply the sea floor with energy-rich substrates and nutrients that are used by diverse microbial ecosystems. Contemporary hypersaline environments formed by brine seeps may provide insights into the metabolism and distribution of microorganisms on the early Earth or on extraterrestrial bodies. Here we use geochemical and genetic analyses to characterize microbial community composition and metabolism in two seafloor brines in the Gulf of Mexico: an active mud volcano and a quiescent brine pool. Both brine environments are anoxic and hypersaline. However, rates of sulphate reduction and acetate production are much higher in the brine pool, whereas the mud volcano supports much higher rates of methane production. We find no evidence of anaerobic oxidation of methane, despite high methane fluxes at both sites. We conclude that the contrasting microbial community compositions and metabolisms are linked to differences in dissolved organic matter input from the deep subsurface and different fluid advection rates between the two sites. Nature Geoscience

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Abstract: Microbial activity governs elemental cycling and the transformation of many anthropogenic substances in aqueous environments. Through the development of a dynamic cell model of the well characterized, versatile and abundant Geobacter sulfurreducens, we showed that a kinetic representation of key components of cell metabolism matched microbial growth dynamics observed in chemostat experiments under varying environmental conditions and led to results similar to those from a comprehensive flux balance model. Coupling the kinetic cell model to its environment by expressing substrate uptake rates depending on intra- and extracellular substrate concentrations, 2D reactive transport simulations of an aquifer were performed. They illustrated that a proper representation of growth efficiency as a function of substrate availability is a determining factor for the spatial distribution of microbial populations in a porous medium. It was shown that simplified model representations of microbial dynamics in the subsurface that only depended on extracellular conditions could be derived by properly parameterizing emerging properties of the kinetic cell model. Applied and Environmental Microbiology

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Abstract: Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth’s marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2 , formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal was examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species causes the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), none of the potential intermediates considered here is able to support metabolic activity matching the measured rates. Biogeosciences

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Abstract: A two-dimensional (2D) reactive transport model is used to investigate the controls on nutrient (NO3-, NH4+, PO4) dynamics in a coastal aquifer. The model couples density-dependent flow to a reaction network which includes oxic degradation of organic matter, denitrification, iron oxide reduction, nitrification, Fe2+ oxidation and sorption of PO4 onto iron oxides. Porewater measurements from a well transect at Waquoit Bay, MA, USA indicate the presence of a reducing plume with high Fe2+, NH4+, DOC (dissolved organic carbon) and PO4 concentrations overlying a more oxidizing NO3--rich plume. These two plumes travel nearly conservatively until they start to overlap in the intertidal coastal sediments prior to discharge into the bay. In this zone, the aeration of the surface beach sediments drives nitrification and allows the precipitation of iron oxide, which leads to the removal of PO4 through sorption. Model simulations suggest that removal of NO3- through denitrification is inhibited by the limited overlap between the two freshwater plumes, as well as by the refractory nature of terrestrial DOC. Submarine groundwater discharge is a significant source of NO3- to the bay. Geochimica Cosmochimica Acta

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Abstract: Sulfur isotope composition (δ34S) profiles in sediment pore waters often show an offset between sulfate and sulfide (∆δ34SSO4-H2S) much greater in magnitude than S isotope fractionations observed in pure cultures. A number of workers have invoked an additional reaction, microbial disproportionation of sulfur intermediates, to explain the offset between experimental and natural systems. Here, we present an alternative explanation based on modeling of pore water sulfate and sulfide concentrations and stable isotope data from the Cariaco Basin (ODP Leg 165, Site 1002B). The use of unique diffusion coefficients for 32SO42- and 34SO42-, based on their unequal molecular masses, resulted in an increase in the computed fractionation by almost 10‰, when compared to the common assumption of equal diffusion coefficients for the two species. These small differences in diffusion coefficients yield calculated isotopic offsets between coeval sediment pore water sulfate and sulfide without disproportionation (up to 53.4‰) that exceed the largest fractionations observed in experimental cultures. Furthermore, the diffusion of sulfide within sediment pore waters leads to ∆δ34SSO4-H2S values that are even greater than those predicted by our model for sulfate reduction with unique diffusion coefficients. These diffusive effects on the sulfur isotope composition of pore water sulfate and sulfide can impact our interpretations of geologic records of sulfate and sulfide minerals, and should be considered in future studies. Geochimica Cosmochimica Acta

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Abstract: A reaction-transport model is used to interpret 13 data sets of in situ O2 and pH microelectrode profiles measured in deep-sea sediments from 5 oceanic regions. The model includes a mechanistic description of the major early diagenetic redox transformations, as well as solid and solute transport processes, pore water acid-base equilibria, and calcite dissolution. Four different dependencies of the calcite dissolution rate on the degree of pore water saturation are considered. The results of the systematic and data-driven approach indicate that consideration of two pools of reactive organic carbon is sufficient to reproduce the oxygen data; that the more reactive pool dominates the organic carbon deposition flux; and that suboxic degradation pathways play a non-negligible role at the majority of sites. Estimation of the calcite related parameters, however, yields only 9 successful simulations of the pH profiles. The dissolution rate expressions with the higher rate orders tested (2 and 4.5) are generally more successful in reproducing the in situ pH profiles. While the pore water pH profiles cannot constrain the calcite deposition flux, robust estimates of the depth-integrated calcite dissolution rates can be obtained. These correlate positively with the benthic oxygen uptake fluxes, although sites overlain with undersaturated and supersaturated bottom waters exhibit separate trends. Geochimica Cosmochimica Acta

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Abstract Non-conservative behaviour of dissolved inorganic phosphate (DIP) upon groundwater salinization is generally ascribed to desorption from iron (hydr)oxides. We assess this hypothesis by incorporating the reversible adsorption of phosphate onto a model oxide (goethite) in a two-dimensional, density-dependent groundwater flow model. The model is then applied to simulate the transient behaviour of DIP during seawater intrusion in a coastal freshwater aquifer. Two different approaches are used to simulate phosphate adsorption: (1) a surface complexation model (SCM), which accounts for the changes in aqueous and surface-bound speciation of phosphate with variable pH and salinity, and (2) a linear adsorption isotherm (Kd), in which the partition coefficient Kd is assumed to remain constant. In the latter case, a typical Kd value for freshwater aquifer conditions is imposed. The seawater intrusion scenario is implemented using a set of aquifer settings similar to the Henry saltwater intrusion benchmark problem. In addition, the evolution of the pH distribution is computed assuming conservative mixing of dissolved inorganic carbon and alkalinity between the groundwater and seawater. The results show that, as the saltwater wedge advances, DIP is released and progressively dispersed at the freshwater–seawater interface. The released DIP is flushed out with the discharging groundwater, giving rise to a final, steady state DIP concentration distribution that follows a conservative mixing curve with respect to salinity. Use of a freshwater end-member Kd value over¬estimates the overall release of DIP. In general, however, the salinity-induced phosphate mobilization predicted by the SCM and Kd models is lower than that observed in coastal aquifers, implying that other factors besides pH and salinity gradients are likely to contribute to DIP release observed upon saltwater intrusion.

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Abstract: A two-dimensional density-dependent reactive transport model, which couples groundwater flow and biogeochemical reactions, is used to investigate the fate of nutrients (NO3-, NH4+ and PO4) in idealized subterranean estuaries representing four end members of oxic/anoxic aquifer and seawater redox conditions. Results from the simplified model representations show that the prevalent flow characteristics and redox conditions in the freshwater-seawater mixing zone determine the extent of nutrient removal and the input of nitrogen and phosphorus to coastal waters. At low to moderate groundwater velocities, simultaneous nitrification and denitrification can lead to a reversal in the depth of freshwater NO3- and NH4+-PO4 plumes, compared to their original positions at the landward source. Model results suggest that autotrophic denitrification pathways with Fe2+ or FeS2 may provide an important, often overlooked link between nitrogen and phosphorus biogeochemistry through the precipitation of iron oxides and subsequent binding of phosphorus. Simulations also highlight that deviations of nutrient data from conservative mixing curves do not necessarily indicate nutrient removal. Water Resources Research

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Abstract: Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a Type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, DMSP demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation. Applied and Environmental Microbiology

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Abstract: Seagrasses provide a physical connection between the water column and sediments by transporting photosynthetic- and seawater-derived oxygen to their roots and rhizomes. In this paper, we present a single-shoot reaction-transport model that incorporates the biological, chemical and physical processes in the water column, seagrass plant, and sediments and that simulates oxygen and hydrogen sulfide dynamics in the system. The model reproduces oxygen and sulfide patterns observed in laboratory manipulations and field measurements of Thalassia testudinum and Zostera marina. Model results reinforce experimental conclusions that (1) meristem oxygen is tightly coupled to water column oxygen and diel patterns of sunlight, (2) sediment sulfide enters the plant when plant tissues are hypoxic, and (3) internal sulfide is rapidly depleted once oxic seawaters are re-established or with the onset of photosynthesis. Sensitivity analysis further emphasizes that water column oxygen concentration has a strong influence on the minimum oxygen concentration and maximum sulfide concentration in the meristem at night. The model indicates that diffusion is the dominant transport process in the lacunae, though advective mass flow can account for nearly a quarter of oxygen transport during periods of increasing sunlight. In the model, biological sulfide oxidation and plant dissolved organic carbon exudation both play significant roles in determining patterns of sediment oxygen consumption and sulfide intrusion into the plant. Ecological Modeling

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Abstract: Seeded calcite growth experiments were conducted at fixed pH (10.2) and two degrees of supersaturation (Ω = 5, 16), while varying the Ca2+ to solution ratio over several orders of magnitude. The calcite growth rate and the incorporation of Sr in the growing crystals strongly depended on the solution stoichiometry. At a constant degree of supersaturation, the growth rate was highest when the solution concentration ratio, r = [Ca2+]/[CO32-], equaled one, and decreased symmetrically with increasing or decreasing values of r. This behavior is consistent with the kink growth rate theory for non-Kossel crystals, assuming that the frequency factors for attachment to kink sites are the same for the cation and anion. Measured Sr partition coefficients, DSr, ranged from 0.02 to 0.12, and correlated positively with the calcite growth rate. Geochimica et Cosmochimica Acta

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Abstract: A 1D reactive transport model (RTM) is used to obtain a mechanistic understanding of the fate of wastewater-derived phosphorus (P) in two oxic, electron donor-poor, sandy Canadian aquifers with contrasting sediment characteristics (calcareous versus non-calcareous). After around 10 years of nutrient loading, wastewater P is effectively attenuated mainly through fast sorption onto calcite (Cambridge) and Fe oxides (Muskoka) within up to 10 m downgradient of the source. Slow, kinetic sorption contributes further to the P removal while precipitation of P-bearing minerals (strengite, hydroxyapatite) is quantitatively unimportant. Nitrogen (N) dynamics are also considered, but nitrate behaves essentially as a conservative tracer in both systems. The gradual advancement of the P plume upon continued wastewater discharge predicted by the model is in line with field observations and is more pronounced at the calcareous Cambridge site. Model results suggest that, upon removal of the wastewater source, the P plume at both sites will persist for at least 20 years, owing to the desorption of P from aquifer solids and the slow rate of P mineral precipitation. Sensitivity analyses for the non-calcareous Muskoka site demonstrate the importance of the sorption capacity of the aquifer solids for P in modulating groundwater N:P ratios in oxic groundwater. Breakthrough of groundwater with high P concentrations and low N:P ratios is observed within 17 years at 20 m from the source in aquifers with low sorption capacities (less than 0.02 % w/w Fe(OH)3). In general, denitrification plays a minor role in lowering the N:P ratios, since in this type of system it is limited by the availability of a labile dissolved organic carbon (DOC) pool. Journal of Contaminant Hydrology

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Abstract: Flow-through reactors (FTR) provide a means to measure reaction rates on undisturbed sediment slices. Because in this approach the porous structure and the spatial arrangements of particle-bound constituents, including microorganisms, are preserved, kinetic parameters are obtained whose values are representative of in situ conditions. The theory and application of FTRs is reviewed here using data on sulfate and nitrate reduction in a number of nearshore sediments. In particular, we focus on the determination of maximum potential reduction rates (Rmax) and half-saturation constants (Km) of the terminal electron acceptors. Alternative methods for extracting these kinetic parameters from time-series outflow concentration measurements are compared. To deal with the uncertainties associated with temporal and spatial variations in solute concentrations within the FTR, a novel method is presented, based on a continuous reactive transport model representation of the FTR system. Potential biases related to the loss of dissolved organic substrates via the outflow are addressed by analyzing the results of variable flow nitrate reduction experiments. For sediment intervals on which both nitrate and sulfate reduction rates have been measured, Rmax values (in units of C equivalents) are systematically higher for nitrate reduction. In addition, the relative difference in Rmax between the two terminal electron accepting processes increases with decreasing mineralization rates. Marine Chemistry

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Abstract: Denitrifying activity in a sediment from the freshwater part of a polluted estuary in northwest Europe was quantified using two independent approaches. High-resolution N2O microprofiles were recorded for sediment cores to which acetylene was added to the overlying water and injected laterally into the sediment. The vertical distribution of the rate of denitrification supported by nitrate uptake from the overlying water was then derived from the time series N2O concentration profiles. The rates obtained for the core incubations were compared to the rates predicted by a forward reactive transport model, which included rate expression for denitrification calibrated with potential rate measurements obtained in flowthrough reactors containing undisturbed, 1-cm- thick sediment slices. The two approaches yielded comparable rate profiles, with a near-surface, 2- to 3-mm narrow zone of denitrification and maximum in situ rates on the order of 200 to 300 nmol cm3 h1. The maximum in situ rates were about twofold lower than the maximum potential rate for the 0- to 1-cm depth interval of the sediment, indicating that in situ denitrification was nitrate limited. The experimentally and model-derived rates of denitrification implied that there was nitrate uptake by the sediment at a rate that was on the order of 50 ( 10) nmol cm2 h1, which agreed well with direct nitrate flux measurements for core incubations. Reactive transport model calculations showed that benthic uptake of nitrate at the site is particularly sensitive to the nitrate concentration in the overlying water and the maximum potential rate of denitrification in the sediment. AEM

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Abstract: Elemental turnover in porous media depends on substrate concentrations at the pore-scale. In this study, the effect of small scale variability in concentration fields on reaction rate estimates and the validity of the continuum approximation in reactive transport models are investigated via a pore-scale numerical model. Artificial porous media are generated using an identical overlapping sphere algorithm. By comparison between explicit pore-scale simulations and macroscopic continuum approximations, it is shown that inhomogeneous solute distribution within the pores can affect estimates of elemental turnover rates. The error associated with large scale rate estimates depends on the type of reaction, pore geometry, reaction kinetics and macroscopic concentration gradient. A correction term that involves a phenomenological parameter which can be evaluated numerically and macroscopic concentration gradients is introduced to improve the accuracy of upscaled homogeneous reaction rates. Implications for macroscopic descriptions of surface processes and surface attached microbial populations are discussed and it is shown that pore-scale heterogeneity can substantially affect estimates of heterogeneous reactions, while for homogeneous reactions, the error amounts to only a couple of percents. AWR

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Abstract: A stochastic particle tracking approach is used to compute particulate age distributions and oxygen exposure times (OETs) in bioturbated marine sediments. Simulations representative of abyssal plain, continental slope, and continental shelf sediments indicate that within the mixed zone, the variability in particle age is of the same order of magnitude as the average age itself. This spreading of particle age by bioturbation complicates the interpretation of sedimentary archives. The results further show that average and median ages of particle-bound constituents undergoing decay during early diagenesis deviate from those of inert tracers. Similarly, OETs depend on the biological mixing and biogeochemical reactivity of particulate constituents. Hence ratios of the O2 penetration depth (LO2) and the linear sedimentation rate (w) may not offer reliable measures of actual OETs. Taking into account biodiffusional particle mixing and preferential degradation of organic matter under oxygenated conditions, the stochastic model predicts a global inverse relationship between the burial efficiency and the OET of organic carbon in ocean sediments. The relationship, however, differs significantly from that proposed by Hartnett et al. (1998), who used O2 penetration depths divided by linear sedimentation rates (LO2/w) to estimate OETs. Global Biogeochemical Cycles

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Abstract: In one-dimensional (1D) early diagenetic models, bioirrigation is typically represented by a nonlocal mass transfer or bioirrigation coefficient, alpha. Usually, all pore water species are assigned the same alpha. Here, we show that this assumption can lead to significant errors in estimates of bioirrigation intensities. Using a simplified early diagenetic reaction network, we compute the 3D concentration fields of major pore water species around a vertical burrow, as well as the solute fluxes across the burrow wall. From these results, corresponding 1D vertical alpha profiles are derived. The alpha profiles show pronounced differences from one solute to another. Dissolved O2 systematically exhibits the highest alpha values, while fast oxygenation kinetics near the burrow wall result in near-zero alpha values for aqueous Fe2+. For nitrate, use of a species-averaged alpha profile may even lead to an erroneous prediction of the direction of the irrigation flux across the water-sediment interface. The large differences in alpha profiles reflect the variable effects of biogeochemical processes on pore water concentration fields of reactive solutes near the burrow wall. Even for inert solutes, however, determination of alpha can be ambiguous. Transient simulations mimicking the intrusion into the sediment of an inert tracer during an incubation experiment yield apparent mixing intensities that depend on the incubation time. JMR

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Abstract: The construction and ventilation of macrofaunal burrows can fundamentally alter biogeochemical processes in marine sediments. Burrowing benthic organisms produce lateral heterogeneity, intensify the cycling of redox-sensitive elements, and create ecological niches for microbial life. To quantify the increased solute transport, termed bioirrigation, resulting from macrofaunal activities, a variety of models, such as the Aller tubemodel and the one-dimensional nonlocal exchange model, have been developed. These models have been successful at reproducing some of the effects of burrow ventilation at early diagenetic scales. This chapter reviews the progress made in using existing and emerging reactive transport models to quantify the effects of bioirrigation and identifies current challenges to developing improved models. In particular, multidimensional models that account for reactive transport processes at the burrow–sediment interface, and the hydraulics associated with burrow ventilation, hold great promise for a more accurate representation of the role of benthic macrofauna in modern and ancient marine environments.

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Abstract: Mono Lake is a closed-basin, alkaline, hypersaline lake located at the western edge of the Great Basin in eastern California. We studied the distribution of arsenic (As) species in the water column of Mono Lake between February and November, 2002. This period captured the seasonal progression from winter mixing, through summer thermal stratification, to autumn overturn. Arsenic speciation was determined by ion chromatography-inductively coupled-plasma-mass spectrometry of samples preserved in the field by flash-freezing in liquid nitrogen. We found that arsenic speciation was dominated (>90%) by arsenate when oxygen levels fell below 6 umol/L O2, arsenic speciation shifted to dominance by reduced species. Arsenate and arsenite co-occurred in a transition zone immediately below the base of the oxycline and low but significant concentrations of arsenate were occasionally detected in sulfidic hypolimnion samples. Thio-arsenic species were the dominant form of As found in sulfidic waters. Maxima of thio-arsenic species with stoichiometries consistent with mono-, di- and trithio-arsenic occurred in succession as sulfide concentration increased. A compound with a stoichiometry consistent with trithio-arsenic was the dominant As species (~50% of total As) in high sulfide (2 mmol/L) bottom water. Lower concentrations of total As in bottom water relative to surface water suggest precipitation of As/S mineral phases in response to sulfide accumulation during prolonged anoxia. Geochimica et Cosmochimica Acta

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Abstract: The hydroelectric reservoir of Petit Saut, French Guiana, was created in 1994–1995 by flooding 350 km2 of tropical forest. When sampled in 1999, the lake exhibited a permanent stratification separating the 3–5 m thick, oxygenated epilimnion from the anoxic hypolimnion. The rate of anaerobic organic carbon mineralization below the oxycline was on the order of 1 lmol C m-2 s-1 and did not show a pronounced difference between wet and dry seasons. Methanogenesis accounted for 76–83% of anaerobic carbon mineralization, with lesser contributions of sulfate reduction and dissimilatory iron reduction. Upward mixing of reduced inorganic solutes explained 90% of the water column O2 demand during the dry season, while most O2 consumption during the wet season was coupled to aerobic respiration of organic matter synthesized in the surface waters. Inorganic mercury species represented 10–40% of total dissolved mercury in the epilimnion, but were of relatively minor importance (<= 10%) in the anoxic portion of the water column. Net production of soluble organic mercury compounds in the flooded soils and anoxic water column did not vary significantly between wet and dry seasons. Methylmercury accounted for about 15% of total dissolved mercury below the oxycline. Its estimated net production rate, 0.04 mg m-2 yr-1, is of the same order of magnitude as values reported for contaminated lakes and flooded terrestrial ecosystems. AqCh

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Abstract: Despite growing concerns about potential enhancement of global warming and slope failure by methane produced by gas hydrate dissociation, much uncertainty surrounds estimates of gas hydrate reservoir sizes, as well as methane fluxes and oxidation rates at the sea floor. For cold seep sediments of the eastern Mediterranean Sea, depth-dependent methane concentrations and rates of anaerobic oxidation of methane (AOM) are constrained by modeling the measured pore-water sulfate profile. The calculated dissolved methane distribution and flux are sensitive to the advective flow velocity, which is estimated from the depth distributions of conservative pore-water constituents (Na, B). Near-complete anaerobic oxidation of the upward methane flux of ~6.0 mol m-2 yr-1 is supported by the depth distributions of indicative biomarkers, and the carbon isotopic compositions of organic matter and dissolved inorganic carbon. Pore-water and solid-phase data are consistent with a narrow depth interval of AOM, 14-18 cm below the sediment-water interface. Based on an isotopic mass balance, the biomass of the microbial population carrying out oxidation of methane coupled to sulfate reduction at the given methane flux represents ~20% of the total organic carbon, which is a significant pool of in situ formed organic matter. Model results indicate that the asymptotic methane concentration is reached a few meters below the sediment surface. The predicted asymptotic concentration is close to the in situ saturation value with respect to gas hydrate, suggesting that the rate of shallow gas hydrate formation is controlled by the ascending methane flux. The proposed model approach can be used to predict the formation of gas hydrate, and to quantify methane fluxes plus transformation rates in surface sediments where fluid advection is an important transport mechanism. EPSL

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Abstract: Existing reactive transport models represent aquatic sediments as one-dimensional systems. These models account for the predominantly vertical chemical gradients recorded by traditional pore water and solid sediment sampling techniques (e.g., cores, dialysis samplers). However, advances in sampling techniques, including the rapid development of in situ microprofilers, are providing increasingly detailed data sets, which highlight the laterally heterogeneous nature of the water – sediment interface. In particular, coastal sediments inhabited by macrofauna exhibit large horizontal gradients in chemical composition and microbial communities. The availability of comprehensive and multidimensional data sets, along with our growing conceptual understanding of the complex biogeochemical dynamics in sediments, requires more sophisticated reactive transport models that explicitly account for the heterogeneity of aquatic sediments. Here, we present a model that explicitly calculates the effect of flushing of macrofaunal burrows on dissolved chemical species distributions. JGE

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Abstract: Seasonal variations in anaerobic respiration pathways were investigated at three saltmarsh sites using chemical data, sulfate reduction rate measurements, enumerations of culturable populations of anaerobic iron-reducing bacteria (FeRB), and quantification of in situ 16S rRNA hybridization signals targeted for sulfate-reducing bacteria (SRB). Bacterial sulfate reduction in the sediments followed seasonal changes in temperature and primary production of the saltmarsh, with activity levels lowest in winter and highest in summer. In contrast, a dramatic decrease in the FeRB population size was observed during summer at all sites. The collapse of FeRB populations during summer was ascribed to high rates of sulfide production by SRB, resulting in abiotic reduction of bioavailable Fe(III) (hydr)oxides. To test this hypothesis, sediment slurry incubations at 10, 20 and 30 °C were carried out. Increases in temperature and labile organic carbon availability (acetate or lactate additions) increased rates of sulfate reduction while decreasing the abundance of culturable anaerobic FeRB. These trends were not reversed by the addition of amorphous Fe(III) (hydr)oxides to the slurries. However, when sulfate reduction was inhibited by molybdate, no decline in FeRB growth was observed with increasing temperature. Addition of dissolved sulfide adversely impacted propagation of FeRB whether molybdate was added or not. Both field and laboratory data therefore support a sulfide-mediated limitation of microbial iron respiration by SRB. When total sediment respiration rates reach their highest levels during summer, SRB force a decline in the FeRB populations. As sulfate reduction activity slows down after the summer, the FeRB are able to recover. BGC

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Abstract: Pore-water solute transport processes acting in addition to molecular diffusion affect sediment biogeochemistry and benthic exchange fluxes. Given the relatively few direct measurements of enhanced transport intensities, there is a need for predictive relationships to calculate enhanced transport parameters from more readily available information. Here, enhanced diffusion coefficients and nonlocal mass transfer coefficients are obtained by comparing total and molecular diffusion fluxes of oxygen across the sediment–water interface. Semiempirical relationships for these coefficients are derived as functions of benthic oxygen uptake. According to these relationships, enhanced solute transport significantly affects sediment–water column exchanges in regions with large benthic oxygen fluxes, typically on the continental shelves. On a global scale, enhanced transport contributes approximately one third of the total benthic flux of oxygen and more than half of that of phosphate. L&O

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Abstract: Irrigation by benthic macrofauna has a major influence on the biogeochemistry and microbial community structure of sediments. Existing quantitative models of bioirrigation rely primarily on chemical, rather than ecological, information and the depth-dependence of bioirrigation intensity is either imposed or constrained through a data fitting procedure. In this study, stochastic simulations of 3D burrow networks are used to calculate mean densities, volumes and wall surface areas of burrows, as well as their variabilities, as a function of sediment depth. Burrow networks of the following model organisms are considered: the polychaete worms Nereis diversicolor and Schizocardium sp., the shrimp Callianassa subterranea, the echiuran worm Maxmuelleria lankesteri, the fiddler crabs Uca minax, U. pugnax and U. pugilator, and the mud crabs Sesarma reticulatum and Eurytium limosum. Consortia of these model organisms are then used to predict burrow networks in a shallow water carbonate sediment at Dry Tortugas, FL, and in two intertidal saltmarsh sites at Sapelo Island, GA. Solute-specific nonlocal bioirrigation coefficients are calculated from the depth-dependent burrow surface areas and the radial diffusive length scale around the burrows. Bioirrigation coefficients for sulfate obtained from network simulations, with the diffusive length scales constrained by sulfate reduction rate profiles, agree with independent estimates of bioirrigation coefficients based on pore water chemistry. Bioirrigation coefficients for O2 derived from the stochastic model, with the diffusion length scales constrained by O2 microprofiles measured at the sediment/water interface, are larger than irrigation coefficients based on vertical pore water chemical profiles. This reflects, in part, the rapid attenuation with depth of the O2 concentration within the burrows, which reduces the driving force for chemical transfer across the burrow walls. Correction for the depletion of O2 in the burrows results in closer agreement between stochastically-derived and chemically-derived irrigation coefficient profiles. GT

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Abstract: An inverse model was developed to quantify the depth distributions of bioirrigation intensities in sediments based on measured solute concentration and reaction rate profiles. The model computes statistically optimal bioirrigation coefficient profiles; that is, profiles that best represent measured data with the least number of adjustable parameters. A parameter reduction routine weighs the goodness-of-fit of calculated concentration profiles against the number of adjustable parameters by performing statistical F-tests, whereas Monte Carlo simulations reduce the effects of spatial correlation and help avoid local minima encountered by the downhill simplex optimization algorithm. A quality function allows identification of depth inter vals where bioirrigation coefficients are not well constrained. The inverse model was applied to four different depositional environments (Sapelo Island, Georgia; Buzzards Bay, Massachusetts; Washington Shelf; Svalbard, Norway) using total CO2 production, sulfate reduction, and 222Rn/226Ra disequilibrium data. Calculated bioirrigation coefficients generally decreased rapidly as a function of depth, but distinct subsurface maxima were observed for sites in Buzzards Bay and along the Washington Shelf. Irrigation fluxes of O2 computed with the model-derived bioirrigation coefficients were in good agreement with those obtained by difference between total benthic O2 fluxes measured with benthic chambers and diffusive fluxes calculated from O2 microprofiles. L&O