New Insights into Calcite Dissolution Mechanisms under Water, Proton, or Carbonic Acid-Dominated Conditions.

Carbonate minerals are ubiquitous in nature, and their dissolution impacts many environmentally relevant processes including preferential flow during geological carbon sequestration, pH buffering with climate-change induced ocean acidification, and organic carbon bioavailability in melting permafrost. In this study, we advance the atomic level understanding of calcite dissolution mechanisms to improve our ability to predict this complex process. We performed high pressure and temperature (1300 psi and 50 °C) batch experiments to measure transient dissolution of freshly cleaved calcite under H2O, H+, and H2CO3-dominated conditions, without and with an inhibitory anionic surfactant present. Before and after dissolution experiments, we measured dissolution etch-pit geometries using laser profilometry, and we used density functional theory to investigate relative adsorption energies of competing species that affect dissolution. Our results support the hypothesis that calcite dissolution is controlled by the ability of H2O to preferentially adsorb to surface Ca atoms over competing species, even when dissolution is dominated by H+ or H2CO3. More importantly, we identify for the first time that adsorbed H+ enhances the role of water by weakening surface Ca-O bonds. We also identify that H2CO3 undergoes dissociative adsorption resulting in adsorbed HCO3- and H+. Adsorbed HCO3- that competes with H2O for Ca acute edge sites inhibits dissolution, while adsorbed H+ at the neighboring surface of CO3 enhances dissolution. The net effect of the dissociative adsorption of H2CO3 is enhanced dissolution. These results will impact future efforts to more accurately model the impact of solutes in complex water matrices on carbonate mineral dissolution.

Tuning the Selectivity of Nitrate Reduction via Fine Composition Control of RuPdNP Catalysts.

Herein, aqueous nitrate (NO3 -) reduction is used to explore composition-selectivity relationships of randomly alloyed ruthenium-palladium nanoparticle catalysts to provide insights into the factors affecting selectivity during this and other industrially relevant catalytic reactions. NO3 - reduction proceeds through nitrite (NO2 -) and then nitric oxide (NO), before diverging to form either dinitrogen (N2) or ammonium (NH4 +) as final products, with N2 preferred in potable water treatment but NH4 + preferred for nitrogen recovery. It is shown that the NO3 - and NO starting feedstocks favor NH4 + formation using Ru-rich catalysts, while Pd-rich catalysts favor N2 formation. Conversely, a NO2 - starting feedstock favors NH4 + at ≈50 atomic-% Ru and selectivity decreases with higher Ru content. Mechanistic differences have been probed using density functional theory (DFT). Results show that, for NO3 - and NO feedstocks, the thermodynamics of the competing pathways for N-H and N-N formation lead to preferential NH4 + or N2 production, respectively, while Ru-rich surfaces are susceptible to poisoning by NO2 - feedstock, which displaces H atoms. This leads to a decrease in overall reduction activity and an increase in selectivity toward N2 production. Together, these results demonstrate the importance of tailoring both the reaction pathway thermodynamics and initial reactant binding energies to control overall reaction selectivity.

Modeling EDTA-facilitated cadmium migration in high- and low-permeability systems using MODFLOW and RT3D.

Cadmium (Cd) has impacted groundwater resources and can pose a serious threat to human health and the environment. Its fate in groundwater is complex and challenging to predict, as it is affected by adsorption to sediments, complexation with aqueous phase ligands, and variations in hydraulic conductivity. In this study, a 2D reactive transport model based on MODFLOW and RT3D is used to simulate published experimental results of cadmium migration without and with EDTA present in a flow cell containing high- and low-permeability zones (i.e., HPZs and LPZs). The model is then extended to conceptual flow cells with more complex LPZ configurations. Simulation results generally match the experimental data well, and analysis of experimental and simulated Cd effluent concentration profiles shows that EDTA enhances Cd removal from LPZs relative to water alone. Simulation results indicate that faster Cd removal is due to EDTA complexation with adsorbed Cd in LPZs, which enhances its solubilization and subsequent back diffusion. Lastly, simulation results show that with increasing LPZ heterogeneity more Cd is retained in flow cells, and EDTA is more effective in enhancing Cd removal relative to water alone; these results are attributed to more LPZ-HPZ interfaces that enhance Cd mass transfer into LPZs during contamination, and enhance EDTA mass transfer into LPZs to promote cleanup. Overall, the results highlight the promise of using EDTA to remove Cd from heterogeneous sites, but caution is advised due to model simplicity and lack of consideration of changes in solution pH, redox potential, or competing cations.

Kinetics of Hydroxyl Radical Production from Oxygenation of Reduced Iron Minerals and Their Reactivity with Trichloroethene: Effects of Iron Amounts, Iron Species, and Sulfate Reducing Bacteria.

Reactive oxygen species generated during the oxygenation of different ferrous species have been documented at groundwater field sites, but their effect on pollutant destruction remains an open question. To address this knowledge gap, a kinetic model was developed to probe mechanisms of •OH production and reactivity with trichloroethene (TCE) and competing species in the presence of reduced iron minerals (RIM) and oxygen in batch experiments. RIM slurries were formed by combining different amounts of Fe(II) and sulfide (with Fe(II):S ratios from 1:1 to 50:1) or Fe(II) and sulfate with sulfate reducing bacteria (SRB) added. Extents of TCE oxidation and •OH production were both greater with RIM prepared under more reducing conditions (more added Fe(II)) and then amended with O2. Kinetic rate constants from modeling indicate that •OH production from free Fe(II) dominates •OH production from solid Fe(II) and that TCE competes for •OH with Fe(II) and organic matter (OM). Competition with OM only occurs in experiments with SRB, which include cells and their exudates. Experimental results indicate that cells and/or exudates also provide electron equivalents to reform Fe(II) from oxidized RIM. Our work provides new insights into mechanisms and environmental significance of TCE oxidation by •OH produced from oxygenation of RIM. However, further work is necessary to confirm the relative importance of reaction pathways identified here and to probe potentially unaccounted for mechanisms that affect abiotic TCE oxidation in natural systems.

Fate of pyrene on mineral surfaces during thermal remediation as a function of temperature.

There is evidence that contaminants can transform at the elevated temperatures of thermal remediation; however, the contribution of redox active minerals to transformation has not been investigated. Three redox active minerals (i.e., birnessite (MnO2), magnetite (Fe3O4), and hematite (Fe2O3)) and one redox inactive mineral (Ottawa sand (SiO2)) were spiked with pyrene and thermally treated. Under dry, anoxic conditions, 100%, 75% ± 3%, 70% ± 15%, and 14% ± 28% of the initial pyrene mass was removed with birnessite, magnetite, hematite, and Ottawa sand, respectively, after treatment at 250 °C for 30 min. Under wet, oxic conditions, 92% ± 8%, 86% ± 12%, 79% ± 4%, and 42% ± 7% was removed for the same minerals, respectively, after treatment at only 150 °C for 30 min. Baseline studies with Ottawa sand resulted in volatilization alone of pyrene with no transformation observed. Increased pyrene loading was used to evaluate potential transformation pathways based on identified by-products, demonstrating that both oxidative and reductive pathways were operative depending on the conditions. Reaction products in the presence of redox active minerals indicate transformation was dominated by reduction via hydrogenation in dry experiments, and by oxidation via hydroxyl radicals in wet experiments. The latter was unexpected, because only low hydroxyl radical concentrations have been detected in mineral-water systems at ambient temperature. These results indicate that understanding dominant reaction pathways and products is advantageous for the design of efficient and safe thermally enhanced treatment systems.

Contamination Assessment and Site-Management Tool (CAST): A Browser-Based Tool for Site Assessment.

Groundwater dependency is increasing globally, while millions of potentially contaminated sites are yet to be characterized for contamination levels. In particular, groundwater contamination due to light nonaqueous phase liquids (LNAPLs) continues to be a global challenge. Mathematical approaches (i.e., analytical, semi-analytical, empirical, numerical) are preferred for an initial site assessment to circumvent the high characterization costs and limited site data availability. However, the site-specific nature of contamination restricts the generalization of any single approach. Hence, the requirement is for an easy-to-use computing interface that provides site-specific data management, the selection and use of multiple-model interfaces for computing, and site characterization, with extension for the latest models as they become available. This work provides one such interface called CAST or Contamination Assessment and Site-management Tool. CAST is an open-source browser-based (online/offline) tool that provides an interface for six different analytical models (e.g., BIOSCREEN-AT), a MODFLOW based numerical model, and two empirical models (including a hybrid numerical-analytical model). Additionally, CAST includes interfaces for site data management, their evaluation, and scenario-based modeling. CAST's development is in a modular format, which simplifies the addition of new computing or data interfaces. Furthermore, the entire code-base of CAST is based on open-source (dominantly Python programming) libraries and standards. This further simplifies the modification or extension of this tool. This paper introduces CAST, its different computing, and data management interfaces and provides examples of the tool's functionality primarily for the initial evaluation of contaminated sites.

Abiotic dechlorination in the presence of ferrous minerals.

Laboratory batch experiments were performed to assess the reduction of trichloroethene (TCE) and oxygen via natural ferrous minerals. TCE reduction under anoxic conditions was measured via the generation of reduced gases, while oxygen reduction via the generation of hydroxyl radicals was measured as a surrogate for potential TCE oxidation. Results showed that TCE reduction under anoxic conditions was observed for ankerite, siderite, and illite, but not for biotite; acetylene was the primary identified dechlorination product. With the exception of biotite, first-order dechlorination rate constants increased with increasing ferrous content of the mineral, with rate constants ranging from 3.1 × 10-8 to 4.8 10-7 L g-1 d-1. Measured reduction potentials (mV vs SHE) ranged from -104 for illite to +84 for biotite. When normalizing measured first-order dechlorination rate constants to the estimated ferrous iron mineral specific surface area (where surface area was based on nitrogen adsorption analysis of the minerals), TCE dechlorination rate constants increased with increasing reduction potentials. Under oxic conditions, hydroxyl radicals were generated with each of the four minerals. However, mineral activity showed no readily apparent correlation to ferrous content or mineral surface area. In terms of TCE and oxygen reduced per mole of ferrous iron initially present in each mineral, illite was the most reactive of the four minerals. Together, these results suggest that several ferrous minerals may contribute to abiotic dechlorination in the natural environment, and (at least for TCE reduction under anoxic conditions) measurement of ferrous mineral content and reduction potential may serve as useful tools for estimating TCE first-order abiotic dechlorination rate constants.

Impact of antibiotic concentration gradients on nitrate reduction and antibiotic resistance in a microfluidic gradient chamber.

In order to explore the impact of antibiotics on the bacterial metabolic cycling of nitrate within contaminated soil and groundwater environments, we compared the effects of polymyxin B (PMB) and ciprofloxacin (CIP) concentration gradients on the distribution and activity of a wild type (WT) and a flagella deficient mutant (Δflag) of Shewanella oneidensis MR-1 in a microfluidic gradient chamber (MGC). Complementary batch experiments were performed to measure bacteriostatic versus bactericidal concentrations of the two antibiotics, as well as their effect on nitrate reduction. Prior work demonstrated that PMB disrupts cell membranes while CIP inhibits DNA synthesis. Consistent with these modes of action, batch results from this work show that PMB is bactericidal at lower concentrations than CIP relative to their respective minimum inhibitory concentrations (MICs) (≥5× MICPMB vs. ≥20× MICCIP). Concentration gradients from 0 to 50× the MIC of both antibiotics were established in the MGC across a 2-cm interconnected pore network, with nutrients injected at both concentration boundaries. The WT cells could only access and reduce nitrate in regions of the MGC with PMB at <18× MICPMB, whereas this occurred with CIP up to 50× MICCIP; and cells extracted from these MGCs showed no antibiotic resistance. The distribution of Δflag cells was further limited to lower antibiotic concentrations (≤1× MICPMB, ≤43× MICCIP) due to inability of movement. These results indicate that S. oneidensis access and reduce nitrate in bactericidal regions via chemotactic migration without development of antibiotic resistance, and that this migration is inhibited by acutely lethal bactericidal levels of antibiotics.

The role of chemotaxis and efflux pumps on nitrate reduction in the toxic regions of a ciprofloxacin concentration gradient.

Spatial concentration gradients of antibiotics are prevalent in the natural environment. Yet, the microbial response in these heterogeneous systems remains poorly understood. We used a microfluidic reactor to create an artificial microscopic ecosystem that generates diffusive gradients of solutes across interconnected microenvironments. With this reactor, we showed that chemotaxis toward a soluble electron acceptor (nitrate) allowed Shewanella oneidensis MR-1 to inhabit and sustain metabolic activity in highly toxic regions of the antibiotic ciprofloxacin (>80× minimum inhibitory concentration, MIC). Acquired antibiotic resistance was not observed for cells extracted from the reactor, so we explored the role of transient adaptive resistance by probing multidrug resistance (MDR) efflux pumps, ancient elements that are important for bacterial physiology and virulence. Accordingly, we constructed an efflux pump deficient mutant (∆mexF) and used resistance-nodulation-division (RND) efflux pump inhibitors (EPIs). While batch results showed the importance of RND efflux pumps for microbial survival, microfluidic studies indicated that these pumps were not necessary for survival in antibiotic gradients. Our work contributes to an emerging body of knowledge deciphering the effects of antibiotic spatial heterogeneity on microorganisms and highlights differences of microbial response in these systems versus well-mixed batch conditions.

Using MODFLOW and RT3D to simulate diffusion and reaction without discretizing low permeability zones.

Low permeability zones (LPZs) are major sources of groundwater contamination after active remediation to remove pollutants in adjacent high permeability zones (HPZs). Slow back diffusion from LPZs to HPZs can extend management of polluted sites by decades. Numerical models are often used to simulate back diffusion, estimate cleanup times, and develop site management strategies. Sharp concentration gradients of pollutants are present at the interface between HPZs and LPZs, and hence accurate simulation requires fine grid sizes resulting in high computational burden. Since the MODFLOW family of codes is widely used in practice, we develop a new approach for modeling pollutant back diffusion using MODFLOW/RT3D that eliminates the need for fine discretization of the LPZ. Instead, the LPZ is treated as an impermeable region in MODFLOW, while in RT3D the LPZ is conceptualized as a series of immobile zones coupled with a mobile zone at the HPZ/LPZ interface. Finite volume discretization of diffusion and reaction within the LPZ is then modeled as mass transfer and reaction among several immobile species. This results in a simulation domain with significantly fewer grid cells compared to that required if all LPZs are discretized, providing potential for improved computational efficiency. Cases, including a layer of HPZ over an LPZ, a thin/thick lens of LPZ embedded in HPZ, and multiple lens of LPZs embedded in HPZ are tested by the new approach for tracer and reactive scenarios.

Towards predicting DNAPL source zone formation to improve plume assessment: Using robust laboratory and numerical experiments to evaluate the relevance of retention curve characteristics.

We conducted multiple laboratory trials in a robust and repeatable experimental layout to study dense non-aqueous phase liquid (DNAPL) source zone formation. We extended an image processing and analysis framework to derive DNAPL saturation distributions from reflective optical imaging data, with volume balance deviations < 5.07%. We used a multiphase flow model to simulate source zone formation in a Monte Carlo approach, where the parameter space was defined by the variation of retention curve parameters. Integral and geometric measures were used to characterize the source zones and implemented into a multi-criteria objective function. The latter showed good agreement between observation data and simulation results for effective DNAPL saturation values > 0.04, especially for early stages of DNAPL migration. The common hypothesis that parameters defining the DNAPL-water retention curves are constant over time was not confirmed. Once DNAPL pooling started, the optimal fit in the parameter space was significantly different compared to the earlier DNAPL migration stages. We suspect more complex processes (e.g., capillary hysteresis, adsorption) to become relevant during pool formation. Our results reveal deficits in the grayscale-DNAPL saturation relationship definition and laboratory estimation of DNAPL-water retention curve parameters to overcome current limitations to describe DNAPL source zone formation.

Adaptive Evolution of Escherichia coli to Ciprofloxacin in Controlled Stress Environments: Contrasting Patterns of Resistance in Spatially Varying versus Uniformly Mixed Concentration Conditions.

A microfluidic gradient chamber (MGC) and a homogeneous batch culturing system were used to evaluate whether spatial concentration gradients of the antibiotic ciprofloxacin allow development of greater antibiotic resistance in Escherichia coli strain 307 (E. coli 307) compared to exclusively temporal concentration gradients, as indicated in an earlier study. A linear spatial gradient of ciprofloxacin and Luria-Bertani broth (LB) medium was established and maintained by diffusion over 5 days across a well array in the MGC, with relative concentrations along the gradient of 1.7-7.7× the original minimum inhibitory concentration (MICoriginal). The E. coli biomass increased in wells with lower ciprofloxacin concentrations, and only a low level of resistance to ciprofloxacin was detected in the recovered cells (∼2× MICoriginal). Homogeneous batch culture experiments were performed with the same temporal exposure history to ciprofloxacin concentration, the same and higher initial cell densities, and the same and higher nutrient (i.e., LB) concentrations as in the MGC. In all batch experiments, E. coli 307 developed higher ciprofloxacin resistance after exposure, ranging from 4 to 24× MICoriginal in all replicates. Hence, these results suggest that the presence of spatial gradients appears to reduce the driving force for E. coli 307 adaptation to ciprofloxacin, which suggests that results from batch experiments may over predict the development of antibiotic resistance in natural environments.

Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats.

The evolutionarily ancient Aquificales bacterium Sulfurihydrogenibium spp. dominates filamentous microbial mat communities in shallow, fast-flowing, and dysoxic hot-spring drainage systems around the world. In the present study, field observations of these fettuccini-like microbial mats at Mammoth Hot Springs in Yellowstone National Park are integrated with geology, geochemistry, hydrology, microscopy, and multi-omic molecular biology analyses. Strategic sampling of living filamentous mats along with the hot-spring CaCO3 (travertine) in which they are actively being entombed and fossilized has permitted the first direct linkage of Sulfurihydrogenibium spp. physiology and metabolism with the formation of distinct travertine streamer microbial biomarkers. Results indicate that, during chemoautotrophy and CO2 carbon fixation, the 87-98% Sulfurihydrogenibium-dominated mats utilize chaperons to facilitate enzyme stability and function. High-abundance transcripts and proteins for type IV pili and extracellular polymeric substances (EPSs) are consistent with their strong mucus-rich filaments tens of centimeters long that withstand hydrodynamic shear as they become encrusted by more than 5 mm of travertine per day. Their primary energy source is the oxidation of reduced sulfur (e.g., sulfide, sulfur, or thiosulfate) and the simultaneous uptake of extremely low concentrations of dissolved O2 facilitated by bd-type cytochromes. The formation of elevated travertine ridges permits the Sulfurihydrogenibium-dominated mats to create a shallow platform from which to access low levels of dissolved oxygen at the virtual exclusion of other microorganisms. These ridged travertine streamer microbial biomarkers are well preserved and create a robust fossil record of microbial physiological and metabolic activities in modern and ancient hot-spring ecosystems.

Contributions of biotic and abiotic pathways to anaerobic trichloroethene transformation in low permeability source zones.

Low permeability source zones sustain long-term trichloroethene (TCE) groundwater contamination. In anaerobic environments, TCE is transformed by both biological reductive dechlorination and abiotic reactions with reactive minerals. Little is known about the relative contribution of these two pathways as TCE diffuses from low permeability zones (LPZs) into high permeability zones (HPZs). This study combines a flow cell experiment, batch experiments, and a diffusion-reaction model to evaluate the contributions of biotic and abiotic TCE transformation in LPZs. Natural clay (LPZ) and sand (HPZ) from a former Air Force base were used in all experiments. In batch, the LPZ material transformed TCE and cis-1,2-dichloroethene (cis-DCE) to acetylene with pseudo first-order rate constants of 8.57 × 10-6 day-1 and 1.02 × 10-6 day-1, respectively. Biotic and abiotic pathways were then evaluated together in a bench-scale flow cell (16.5 cm × 2 cm × 16.5 cm) that contained a LPZ layer, with a source of TCE at the base, overlain by a HPZ continuously purged with lactate-amended groundwater. Diffusion controlled mass transfer in the LPZ, while advection controlled migration in the HPZ. The mass discharge rate of TCE and its biotic (cis-DCE and vinyl chloride) and abiotic (acetylene) transformation products were measured over 180 days in the flow cell effluent. Depth profiles of these compounds through the LPZ were determined after terminating the experiment. A one-dimensional diffusion-reaction model was used to interpret the effluent and depth profile data and constrain reaction parameters. Abiotic transformation rate constants for TCE to acetylene, normalized to in situ solids loading, were approximately 13 times greater in batch than in the flow cell. Slower transformation rates in the flow cell indicate elevated TCE concentration and/or further degradation of acetylene to other reduced gas compounds in the flow cell LPZ (thereby partially masking TCE abiotic transformation). Biotic and abiotic parameters used to interpret the flow cell data were then used to simulate a field site with a 300 cm thick LPZ. Abiotic processes contributed to a 2% reduction in TCE flux after 730 days. When abiotic rate constants were changed to that observed in batch, or to rate constants previously reported for a pyrite rich mudstone, the TCE flux reduction was 21% and 53%, respectively, after 730 days. Though biotic processes dominated TCE transformation in the flow cell experiment, the simulations indicate that abiotic processes have potential to significantly contribute to TCE attenuation in electron donor limited environments provided suitable reactive minerals are present.

Diffusion-Based Recycling of Flavins Allows Shewanella oneidensis MR-1 To Yield Energy from Metal Reduction Across Physical Separations.

We fabricated a microfluidic reactor with a nanoporous barrier to characterize electron transport between Shewanella oneidensis MR-1 and the metal oxide birnessite across a physical separation. Real-time quantification of electron flux across this barrier by strains with different electron transfer capabilities revealed that this bacterium exports flavins to its surroundings when faced with no direct physical access to an electron acceptor, allowing it to reduce metals at distances exceeding 60 µm. An energy balance indicates that flavins must be recycled for S. oneidensis MR-1 to yield energy from lactate oxidation coupled to flavin reduction. In our system, we find that flavins are recycled between 24 and 60 times depending on flow conditions. This energy saving strategy, which until now had not been systematically tested or captured in environmentally relevant systems, suggests that electron shuttling microorganisms have the capacity to access and reduce metals in physically distant or potentially toxic microenvironments (i.e., pores with soluble and transiently sorbed toxins) where direct contact is limited or unfavorable. Our results challenge the prediction that diffusion-based electron shuttling is only effective across short distances and may lead to improved bioremediation strategies or advance biogeochemical models of electron transfer in anaerobic sediments.

Motility of Shewanella oneidensis MR-1 Allows for Nitrate Reduction in the Toxic Region of a Ciprofloxacin Concentration Gradient in a Microfluidic Reactor.

Subsurface environments often contain mixtures of contaminants in which the microbial degradation of one pollutant may be inhibited by the toxicity of another. Agricultural settings exemplify these complex environments, where antimicrobial leachates may inhibit nitrate bioreduction, and are the motivation to address this fundamental ecological response. In this study, a microfluidic reactor was fabricated to create diffusion-controlled concentration gradients of nitrate and ciprofloxacin under anoxic conditions in order to evaluate the ability of Shewanella oneidenisis MR-1 to reduce the former in the presence of the latter. Results show a surprising ecological response, where swimming motility allow S. oneidensis MR-1 to accumulate and maintain metabolic activity for nitrate reduction in regions with toxic ciprofloxacin concentrations (i.e., 50× minimum inhibitory concentration, MIC), despite the lack of observed antibiotic resistance. Controls with limited nutrient flux and a nonmotile mutant (Δ flag) show that cells cannot colonize antibiotic rich microenvironments, and this results in minimal metabolic activity for nitrate reduction. These results demonstrate that under anoxic, nitrate-reducing conditions, motility can control microbial habitability and metabolic activity in spatially heterogeneous toxic environments.

Mechanisms for Abiotic Dechlorination of Trichloroethene by Ferrous Minerals under Oxic and Anoxic Conditions in Natural Sediments.

Bench-scale experiments were performed on natural sediments to assess abiotic dechlorination of trichloroethene (TCE) under both aerobic and anaerobic conditions. In the absence of oxygen (<26 µM), TCE dechlorination proceeded via a reductive pathway generating acetylene and/or ethene. Reductive dechlorination rate constants up to 3.1 × 10-5 d-1 were measured, after scaling to in situ solid:water ratios. In the presence of oxygen greater than 120 µM, TCE dechlorination proceeded via an oxidative pathway generating formic/glyoxylic and glycolic/acetic acids, and oxidative dechlorination rate constants (again scaled to in situ conditions) up to 7.4 × 10-3 d-1 were measured. These rates correspond to half-lives of 60 and 0.25 years for abiotic TCE dechlorination under anaerobic and aerobic conditions, respectively, indicating the potentially large impact of aerobic TCE oxidation in the field. For both reductive and oxidative TCE dechlorination pathways, measured first-order rate constants increased with increasing ferrous iron content, suggesting the role of iron oxidation. Hydroxyl radical formation was measured and increased with increasing oxygen and ferrous iron content. Rate constants associated with TCE oxidation products increased with increasing hydroxyl radical generation rates, and were zero in the presence of a hydroxyl radical scavenger, suggesting that oxidative TCE dechlorination is a hydroxyl radical driven process.

Geobiology reveals how human kidney stones dissolve in vivo.

More than 10% of the global human population is now afflicted with kidney stones, which are commonly associated with other significant health problems including diabetes, hypertension and obesity. Nearly 70% of these stones are primarily composed of calcium oxalate, a mineral previously assumed to be effectively insoluble within the kidney. This has limited currently available treatment options to painful passage and/or invasive surgical procedures. We analyze kidney stone thin sections with a combination of optical techniques, which include bright field, polarization, confocal and super-resolution nanometer-scale auto-fluorescence microscopy. Here we demonstrate using interdisciplinary geology and biology (geobiology) approaches that calcium oxalate stones undergo multiple events of dissolution as they crystallize and grow within the kidney. These observations open a fundamentally new paradigm for clinical approaches that include in vivo stone dissolution and identify high-frequency layering of organic matter and minerals as a template for biomineralization in natural and engineered settings.

Critical Review: DNA Aptasensors, Are They Ready for Monitoring Organic Pollutants in Natural and Treated Water Sources?

There is a growing need to monitor anthropogenic organic contaminants detected in water sources. DNA aptamers are synthetic single-stranded oligonucleotides, selected to bind to target contaminants with favorable selectivity and sensitivity. These aptamers can be functionalized and are used with a variety of sensing platforms to develop sensors, or aptasensors. In this critical review, we (1) identify the state-of-the-art in DNA aptamer selection, (2) evaluate target and aptamer properties that make for sensitive and selective binding and sensing, (3) determine strengths and weaknesses of alternative sensing platforms, and (4) assess the potential for aptasensors to quantify environmentally relevant concentrations of organic contaminants in water. Among a suite of target and aptamer properties, binding affinity is either directly (e.g., organic carbon partition coefficient) or inversely (e.g., polar surface area) correlated to properties that indicate greater target hydrophobicity results in the strongest binding aptamers, and binding affinity is correlated to aptasensor limits of detection. Electrochemical-based aptasensors show the greatest sensitivity, which is similar to ELISA-based methods. Only a handful of aptasensors can detect organic pollutants at environmentally relevant concentrations, and interference from structurally similar analogs commonly present in natural waters is a yet-to-be overcome challenge. These findings lead to recommendations to improve aptasensor performance.

Intracellular versus extracellular accumulation of Hexavalent chromium reduction products by Geobacter sulfurreducens PCA.

Hexavalent chromium (Cr(VI)) reduction by Geobacter sulfurreducens PCA was evaluated in batch experiments, and the form and amounts of intracellular and extra-cellular Cr(VI) reduction products were determined over time. The first-order Cr(VI) reduction rate per unit mass of cells was consistent for different initial cell concentrations, and approximately equal to (2.065 ±â€¯0.389) x 10-9 mL CFU-1 h-1. A portion of the reduced Cr(VI) products precipitated on Geobacter cell walls as Cr(III) and was bound via carboxylate functional groups, a portion accumulated inside Geobacter cells, and another portion existed as soluble Cr(III) or organo-Cr(III) released to solution. A mass balance analysis of total chromium in aqueous media, on cell walls, and inside cells was determined as a function of time, and with different initial cell concentrations. Mass balances were between 92% and 98%, and indicated Cr(VI) reduction products accumulate more on cell walls and inside cells with time and with increasing initial cell concentration, as opposed to particulates in aqueous solution. Reduced Cr(VI) products both in solution and on cell surfaces appear to form organo-Cr(III) complexes, and our results suggest that such complexes are more stable to reoxidation than aqueous Cr(III) or Cr(OH)3. Chromium inside cells is also likely more stable to reoxidation, both because it can form organic complexes, and it is separated by the cell membrane from solution conditions. Hence, Cr(VI) reduction products in groundwater during bioremediation may become more stable against re-oxidation, and may pose a lower risk to human health, over time and with greater initial biomass densities.