Diel mercury concentration variations in a mercury-impacted stream

Filtered and particulate mercury (Hg) and methylmercury (MMHg), and associated water chemistry parameters, were evaluated bi-hourly for several 30 h periods during the summer and winter seasons at several distinct locations (downstream forested, midstream urban/suburban, upstream industrial) along a creek contaminated with high levels of inorganic Hg to determine if biogeochemical Hg and MMHg cycles respond to the daily photocycle. In summer particulate Hg and MMHg concentrations doubled overnight (excluding the upstream industrial site) concurrent with increases in turbidity and total suspended sediment; no such pattern was evident in winter. Seasonal and diel changes in the activity of macrobiota affecting the suspension of contaminated sediments are likely responsible for these patterns as other potential explanatory variables (e.g., instrument drift, pH, discharge) could not account for the range and timing of our observations. Diel patterns in filtered Hg (Hg_D) were significant only at locations and times of the year when channel shading was not present and daytime concentrations increased 22-89% above nighttime minima likely caused by direct and indirect photochemical reactions. Relationships between Hg_D and dissolved organic carbon (DOC) concentration or character were inconsistent between sites. Unlike Hg_D, there were significant diel patterns in filtered MMHg (MMHg_D) at all sites and times of year, with summer concentrations peaking in mid to late afternoon while the timing differed in winter, with concentrations peaking after sunset. Daily variability in MMHg_D concentration ranged between 25 and 75%. The results imply key controls on net methylation occur within the stream or on the stream bed and include factors such as small-scale temperature changes in the water column and photosynthetic activity of stream biofilm. With respect to stream monitoring, results from this study indicate (1) consistent timing in stream Hg and MMHg sampling is required for accurate assessment of long-term trends, (2) in situ measurements of turbidity can be used to quantify diel dynamics of both particulate Hg and MMHg concentrations, and (3) in situ fluorescing dissolved organic matter (FDOM), a potential proxy for DOC, was not capable of resolving diel dynamics of filtered Hg or MMHg.

Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.

Dissolved organic matter reduces the effectiveness of sorbents for mercury removal

Mercury (Hg) contamination of soils and sediments impacts numerous environments worldwide and constitutes a challenging remediation problem. In this study, we evaluate the impact of dissolved organic matter (DOM) on the effectiveness of eight sorbent materials considered for Hg remediation in soils and sediments. The materials include both engineered and unmodified materials based on carbon, clays, mesoporous silica and a copper alloy. Initially, we investigated the kinetics of Hg(II) complexation with DOM for a series of Hg:DOM ratios. Steady-state Hg-DOM complexation occurred within 48 to 120 h, taking longer time at higher Hg:DOC (dissolved organic carbon) molar ratios. In subsequent equilibrium experiments, Hg(II) was equilibrated with DOM at a defined Hg:DOC molar ratio (2.4 · 10^-6) for 170 h and used in batch experiments to determine the effect of DOM on Hg partition coefficients and sorption isotherms by comparing Hg(II) and Hg-DOM. Hg sorption capacities of all sorbents were severely limited in the presence of DOM as a competing ligand. Thiol-SAMMS®, SediMite™ and pine biochar were most effective in reducing Hg concentrations. While pine biochar and lignin-derived carbon processed at high temperatures released negligible amounts of anions into solution, leaching of sulfate and chloride was observed for most engineered sorbent materials. Sulfate may stimulate microbial communities harboring sulfate reducing bacteria, which are considered one of the primary drivers of microbial mercury methylation in the environment. The results highlight potential challenges arising from the application of sorbents for Hg remediation in the field.

Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets

RNA-seq is being used increasingly for gene expression studies and it is revolutionizing the fields of genomics and transcriptomics. However, the field of RNA-seq analysis is still evolving. Therefore, we specifically designed this study to contain large numbers of reads and four biological replicates per condition so we could alter these parameters and assess their impact on differential expression results. Bacillus thuringiensis strains ATCC10792 and CT43 were grown in two Luria broth medium lots on four dates and transcriptomics data were generated using one lane of sequence output from an Illumina HiSeq2000 instrument for each of the 32 samples, which were then analyzed using DESeq2. Genome coverages across samples ranged from 87 to 465X with medium lots and culture dates identified as major variation sources. Significantly differentially expressed genes (5% FDR, two-fold change) were detected for cultures grown using different medium lots and between different dates. The highly differentially expressed iron acquisition and metabolism genes, were a likely consequence of differing amounts of iron in the two media lots. Indeed, in this study RNA-seq was a tool for predictive biology since we hypothesized and confirmed the two LB medium lots had different iron contents (~two-fold difference). This study shows that the noise in data can be controlled and minimized with appropriate experimental design and by having the appropriate number of replicates and reads for the system being studied. We outline parameters for an efficient and cost effective microbial transcriptomics study.

Natural bacterial communities serve as quantitative geochemical biosensors

Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive.

IMPORTANCE

Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.

Influence of soil geochemical and physical properties on chromium(VI) sorption and bioaccessibility

The Department of Defense (DoD) is faced with the daunting task of possible remediation of numerous soil-Cr(VI) contaminated sites throughout the continental U.S. The primary risk driver at these sites is hand-to-mouth ingestion of contaminated soil by children. In the following study we investigate the impact of soil geochemical and physical properties on the sorption and bioaccessibility of Cr(VI) in a vast array of soils relevant to neighboring DoD sites. For the 35 soils used in this study, A-horizon soils typically sorbed significantly more Cr(VI) relative to B-horizon soils. Multiple linear regression analysis suggested that Cr(VI) sorption increased with increasing soil total organic C (TOC) and decreasing soil pH. The bioaccessibility of total Cr (CrT) and Cr(VI) on the soils decreased with increasing soil TOC content. As the soil TOC content approached 0.4%, the bioaccessibility of soil bound Cr systematically decreased from approximately 65 to 10%. As the soil TOC content increased from 0.4 to 4%, the bioaccessibility of Cr(VI) and CrT remained relatively constant at approximately 4% and 10%, respectively. X-ray absorption near edge structure (XANES) spectroscopy suggested that Cr(VI) reduction to Cr(III) was prevalent and that the redox transformation of Cr(VI) increased with increasing soil TOC. XANES confirmed that nearly all bioaccessible soil Cr was the Cr(VI) moiety. Multiple linear regression analysis suggested that the bioaccessibility of Cr(VI) and its reduced counterpart Cr(III), decreased with increasing soil TOC and increasing soil pH. This is consistent with the observation that the reduction reaction and formation of Cr(III) increased with increasing soil TOC and that Cr(III) was significantly less bioaccessible relative to Cr(VI). The model was found to adequately describe CrT bioaccessibility in soils from DoD facilities where Cr(VI) contaminated sites were present. The results of this study illustrate the importance of soil properties on Cr(VI) sorption and bioassessability and help define what soil types have the greatest risk associated with Cr(VI) exposure.

Decreasing lead bioaccessibility in industrial and firing range soils with phosphate-based amendments

In-situ stabilization using phosphate (P) amendments, such as P-based fertilizers and rock, are a potentially cost-effective and minimally disruptive alternative for stabilizing Pb in soils. We examined the effect of time (0-365 d), in vitro extraction pH (1.5 vs. 2.3), and dosage of three P-based amendments on the bioaccessibility (as a surrogate for oral bioavailability) of Pb in 10 soils from U.S. Department of Defense facilities. Initial untreated soil bioaccessibility consistently exceeded the U.S. Environmental Protection Agency default value of 60% relative bioavailability, with higher bioaccessibility consistently observed at an in vitro extraction pH of 1.5 vs. 2.3. Although P-based amendments statistically (P < 0.05) reduced bioaccessibility in many instances, with reductions dependent on the amendment and dosage, large amendment dosages (approximately 20-25% by mass to yield 5% P by mass) were required to reduce average bioaccessibility by approximately 25%. For most amendment combinations, reductions continued to occur for periods up to 1 yr, indicating that the observed reductions were not merely experimental artifacts of the in vitro extraction procedure. Although our results indicated that reductions in Pb bioaccessibility with P amendments are technically feasible, relatively large amendment masses were required to achieve relatively modest reductions in bioaccessibility. The cost and potential environmental implications of adding such large amounts of P may limit the practicality of in situ immobilization for some Pb-contaminated soils, industrial and firing range soils in particular.

Transport of Sr2+ and SrEDTA2- in partially-saturated and heterogeneous sediments

Strontium-90 has migrated deep into the unsaturated subsurface beneath leaking storage tanks in the Waste Management Areas (WMA) at the U.S. Department of Energy's (DOE) Hanford Reservation. Faster than expected transport of contaminants in the vadose zone is typically attributed to either physical hydrologic processes such as development of preferential flow pathways, or to geochemical processes such as the formation of stable, anionic complexes with organic chelates, e.g., ethylenediaminetetraacetic acid (EDTA). The goal of this paper is to determine whether hydrological processes in the Hanford sediments can influence the geochemistry of the system and hence control transport of Sr(2+) and SrEDTA(2-). The study used batch isotherms, saturated packed column experiments, and an unsaturated transport experiment in an undisturbed core. Isotherms and repacked column experiments suggested that the SrEDTA(2-) complex was unstable in the presence of Hanford sediments, resulting in dissociation and transport of Sr(2+) as a divalent cation. A decrease in sorption with increasing solid:solution ratio for Sr(2+) and SrEDTA(2-) suggested mineral dissolution resulted in competition for sorption sites and the formation of stable aqueous complexes. This was confirmed by detection of MgEDTA(2-), MnEDTA(2-), PbEDTA(2-), and unidentified Sr and Ca complexes. Displacement of Sr(2+) through a partially-saturated undisturbed core resulted in less retardation and more irreversible sorption than was observed in the saturated repacked columns, and model results suggested a significant reservoir (49%) of immobile water was present during transport through the heterogeneous layered sediments. The undisturbed core was subsequently disassembled along distinct bedding planes and subjected to sequential extractions. Strontium was unequally distributed between carbonates (49%), ion exchange sites (37%), and the oxide (14%) fraction. An inverse relationship between mass wetness and Sr suggested that sandy sediments of low water content constituted the immobile flow regime. Our results suggested that the sequestration of Sr(2+) in partially-saturated, heterogeneous sediments was most likely due to the formation of immobile water in drier regions having low hydraulic conductivities.

Distribution of uranium contamination in weathered fractured saprolite/shale and ground water

The objective of this study was to determine how structure, stratigraphy, and weathering influence fate and transport of contaminants (particularly U) in the ground water and geologic material at the Department of Energy (DOE) Environmental Remediation Sciences Department (ERSD) Field Research Center (FRC). Several cores were collected near four former unlined adjoining waste disposal ponds. The cores were collected, described, analyzed for U, and compared with ground water geochemistry from surrounding multilevel wells. At some locations, acidic U-contaminated ground water was found to preferentially flow in small remnant fractures weathering the surrounding shale (nitric acid extractable U [U(NA)] usually < 50 mg kg(-1)) into thin (<25 cm) Fe oxide-rich clayey seams that retain U (U(NA) 239 to 375 mg kg(-1)). However, greatest contaminant transport occurs in a 2 to 3 m thick more permeable stratigraphic transition zone located between two less permeable, and generally less contaminated zones consisting of (i) overlying unconsolidated saprolite (U(NA) < 0.01 to 200 mg kg(-1)) and (ii) underlying less-weathered bedrock (U(NA) generally < 0.01 to 7 mg kg(-1)). In this transition zone, acidic (pH < 4) U-enriched ground water (U of 38 mg L(-1)) has weathered away calcite veins resulting in greater porosity, higher hydraulic conductivity, and higher U contamination (U(NA) 106 to 745 mg kg(-1)) of the weathered interbedded shale and sandstone. These characteristics of the transition zone produce an interval with a high flux of contaminants that could be targeted for remediation.

A nested-cell approach for in situ remediation

We characterize the hydraulics of an extraction-injection well pair in arbitrarily oriented regional flow by the recirculation ratio, area, and average residence time in the recirculation zone. Erratic regional flow conditions may compromise the performance of the reactor between a single well pair. We propose an alternative four-well system: two downgradient extraction and two upgradient injection wells creating an inner cell nested within an outer cell. The outer cell protects the inner cell from the influence of regional flow. Compared to a two-well system, the proposed four-well system has several advantages: (1) the recirculation ratio within the nested inner cell is less sensitive to the regional flow direction; (2) a transitional recirculation zone between the inner and outer cells can capture flow leakage from the inner cell, minimizing the release of untreated contaminants; and (3) the size of the recirculation zone and residence times can be better controlled within the inner cell by changing the pumping rates. The system is applied at the Field Research Center in Oak Ridge, Tennessee, where experiments on microbial in situ reduction of uranium (VI) are under way.

A parametric transfer function methodology for analyzing reactive transport in nonuniform flow

We analyze reactive transport during in-situ bioremediation in a nonuniform flow field, involving multiple extraction and injection wells, by the method of transfer functions. Gamma distributions are used as parametric models of the transfer functions. Apparent parameters of classical transport models may be estimated from those of the gamma distributions by matching temporal moments. We demonstrate the method by application to measured data taken at a field experiment on bioremediation conducted in a multiple-well system in Oak Ridge, TN. Breakthrough curves (BTCs) of a conservative tracer (bromide) and a reactive compound (ethanol) are measured at multi-level sampling (MLS) wells and in extraction wells. The BTCs of both compounds are jointly analyzed to estimate the first-order degradation rate of ethanol. To quantify the tracer loss, we compare the approaches of using a scaling factor and a first-order decay term. Results show that by including a scaling factor both gamma distributions and inverse-Gaussian distributions (transfer functions according to the advection-dispersion equation) are suitable to approximate the transfer functions and estimate the reactive rate coefficients for both MLS and extraction wells. However, using a first-order decay term for tracer loss fails to describe the BTCs at the extraction well, which is affected by the nonuniform distribution of travel paths.

Mass-transfer limitations for nitrate removal in a uranium-contaminated aquifer

A field test on in situ subsurface bioremediation of uranium(VI) is underway at the Y-12 National Security Complex in the Oak Ridge Reservation, Oak Ridge, TN. Nitrate has a high concentration at the site, which prevents U(VI) reduction, and thus must be removed. An acidic-flush strategy for nitrate removal was proposed to create a treatment zone with low levels of accessible nitrate. The subsurface at the site contains highly interconnected fractures surrounded by matrix blocks of low permeability and high porosity and is therefore subject to preferential flow and matrix diffusion. To identify the heterogeneous mass transfer properties, we performed a novel forced-gradient tracer test, which involved the addition of bromide, the displacement of nitrate, and the rebound of nitrate after completion of pumping. The simplest conceptualization consistent with the data is that the pore-space consists of a single mobile domain, as well as a fast and a slowly reacting immobile domain. The slowly reacting immobile domain (shale matrix) constitutes over 80% of the pore volume and acts as a long-term reservoir of nitrate. According to simulations, the nitrate stored in the slowly interacting immobile domain in the fast flow layer, at depths of about 12.2-13.7 m, will be reduced by an order of magnitude over a period of about a year. By contrast, the mobile domain rapidly responds to flushing, and a low average nitrate concentration can be maintained if the nitrate is removed as soon as it enters the mobile domain. A field-scale experiment in which the aquifer was flushed with acidic solution confirmed our understanding of the system. For the ongoing experiments on microbial U(VI) reduction, nitrate concentrations must be low in the mobile domain to ensure U(VI) reducing conditions. We therefore conclude that the nitrate leaching out of the immobile pore space must continuously be removed by in situ denitrification to maintain favorable conditions.

Influence of soil geochemical and physical properties on the sorption and bioaccessibility of chromium(III)

There are numerous Cr(III)-contaminated sites on Department of Defense (DoD) and Department of Energy (DOE) lands that are awaiting possible clean up and closure. Ingestion of contaminated soil by children is the risk driver that generally motivates the likelihood of site remediation. The purpose of this study was to develop a simple statistical model based on common soil properties to estimate the hioaccessibility of Cr(III)-contaminated soil upon ingestion. Thirty-five uncontaminated soils from seven major soil orders, whose properties were similar to numerous U.S. DoD contaminated sites, were treated with Cr(III) and aged. Statistical analysis revealed that Cr(III) sorption (e.g., adsorption and surface precipitation) by the soils was strongly correlated with the clay content, total inorganic C, pH, and the cation exchange capacity of the soils. Soils with higher quantities of clay, inorganic C (i.e., carbonates), higher pH, and higher cation exchange capacity generally sequestered more Cr(III). The amount of Cr(III) bioaccessible from the treated soils was determined with a physiologically based extraction test (PBET) that was designed to simulate the digestive process of the stomach. The bioaccessibility of Cr(III) varied widely as a function of soil type with most soils limiting bioaccessibility to <45 and <30% after I and 100 d soil-Cr aging, respectively. Statistical analysis showed the bioaccessibility of Cr(III) on soil was again related to the clay and total inorganic carbon (TIC) content of the soil. Bioaccessibility decreased as the soil TIC content increased and as the clay content decreased. The model yielded an equation based on common soil properties that could be used to predict the Cr(III) bioaccessibility in soils with a reasonable level of confidence.

Influence of hydrological and geochemical processes on the transport of chelated metals and chromate in fractured shale bedrock

Field-scale processes governing the transport of chelated radionuclides in groundwater remain conceptually unclear for highly structured, heterogeneous environments. The objectives of this research were to provide an improved understanding and predictive capability of the hydrological and geochemical mechanisms that control the transport behavior of chelated radionuclides and metals in anoxic subsurface environments that are complicated by fracture flow and matrix diffusion. Our approach involved a long-term, steady-state natural gradient field experiment where nonreactive Br- and reactive 57Co(II)EDTA2- 109CdEDTA2-, and 51Cr(VI) were injected into a fracture zone of a contaminated fractured shale bedrock. The spatial and temporal distribution of the tracer and solutes was monitored for 500 days using an array of groundwater sampling wells instrumented within the fast-flowing fracture regime and a slower flowing matrix regime. The tracers were preferentially transported along strike-parallel fractures coupled with the slow diffusion of significant tracer mass into the bedrock matrix. The chelated radionuclides and metals were significantly retarded by the solid phase with the mechanisms of retardation largely due to redox reactions and sorption coupled with mineral-induced chelate-radionuclide dissociation. The formation of significant Fe(III)EDTA byproduct that accompanied the dissociation of the radionuclide-chelate complexes was believed to be the result of surface interactions with biotite which was the only Fe(III)-bearing mineral phase present in these Fe-reducing environments. These results counter current conceptual models that suggest chelated contaminants move conservatively through Fe-reducing environments since they are devoid of Fe-oxyhydroxides that are known to aggressively compete for chelates in oxic regimes. Modeling results further demonstrated that chelate-radionuclide dissociation reactions were most prevalent along fractures where accelerated weathering processes are expected to expose more primary minerals than the surrounding rock matrix. The findings of this study suggest that physical retardation mechanisms (i.e. diffusion) are dominant within the matrix regime, whereas geochemical retardation mechanisms are dominant within the fracture regime.