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.

Natural bacterial communities serve as quantitative geochemical biosensors.

UNLABELLED: 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.

A limited microbial consortium is responsible for extended bioreduction of uranium in a contaminated aquifer.

Subsurface amendments of slow-release substrates (e.g., emulsified vegetable oil [EVO]) are thought to be a pragmatic alternative to using short-lived, labile substrates for sustained uranium bioimmobilization within contaminated groundwater systems. Spatial and temporal dynamics of subsurface microbial communities during EVO amendment are unknown and likely differ significantly from those of populations stimulated by soluble substrates, such as ethanol and acetate. In this study, a one-time EVO injection resulted in decreased groundwater U concentrations that remained below initial levels for approximately 4 months. Pyrosequencing and quantitative PCR of 16S rRNA from monitoring well samples revealed a rapid decline in groundwater bacterial community richness and diversity after EVO injection, concurrent with increased 16S rRNA copy levels, indicating the selection of a narrow group of taxa rather than a broad community stimulation. Members of the Firmicutes family Veillonellaceae dominated after injection and most likely catalyzed the initial oil decomposition. Sulfate-reducing bacteria from the genus Desulforegula, known for long-chain fatty acid oxidation to acetate, also dominated after EVO amendment. Acetate and H(2) production during EVO degradation appeared to stimulate NO(3)(-), Fe(III), U(VI), and SO(4)(2-) reduction by members of the Comamonadaceae, Geobacteriaceae, and Desulfobacterales. Methanogenic archaea flourished late to comprise over 25% of the total microbial community. Bacterial diversity rebounded after 9 months, although community compositions remained distinct from the preamendment conditions. These results demonstrated that a one-time EVO amendment served as an effective electron donor source for in situ U(VI) bioreduction and that subsurface EVO degradation and metal reduction were likely mediated by successive identifiable guilds of organisms.

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.

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.