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Methanogenic archaea in subsurface coal seams are biogeographically distinct: An analysis of metagenomically-derived mcrA sequences

The production of methane as an end-product of organic matter degradation in the absence of other terminal electron acceptors is common, and has often been studied in environments such as animal guts, soils, and wetlands due to its potency as a greenhouse gas. To date however, the study of the biogeographic distribution of methanogens across coal seam environments has been minimal. Here, we show that coal seams are host to a diverse range of methanogens, which are distinctive to each geological basin. Based on comparisons to close relatives from other methanogenic environments, the dominant methanogenic pathway in these basins is hydrogenotrophic, with acetoclastic being a second major pathway in the Surat Basin. Finally, mcrA and 16S rRNA gene primer biases were predominantly seen to affect the detection of Methanocellales, Methanomicrobiales and Methanosarcinales taxa in this study. Subsurface coal methanogenic community distributions and pathways presented here provide insights into important metabolites and bacterial partners for in situ coal biodegradation.

Environmental Microbiology

Bioremediation in fractured rock: 1. Modeling to inform design, monitoring, and expectations

Field characterization of a trichloroethene (TCE) source area in fractured mudstones produced a detailed understanding of the geology, contaminant distribution in fractures and the rock matrix, and hydraulic and transport properties. Groundwater flow and chemical transport modeling that synthesized the field characterization information proved critical for designing bioremediation of the source area. The planned bioremediation involved injecting emulsified vegetable oil and bacteria to enhance the naturally occurring biodegradation of TCE. The flow and transport modeling showed that injection will spread amendments widely over a zone of lower‐permeability fractures, with long residence times expected because of small velocities after injection and sorption of emulsified vegetable oil onto solids. Amendments transported out of this zone will be diluted by groundwater flux from other areas, limiting bioremediation effectiveness downgradient. At nearby pumping wells, further dilution is expected to make bioremediation effects undetectable in the pumped water. The results emphasize that in fracture‐dominated flow regimes, the extent of injected amendments cannot be conceptualized using simple homogeneous models of groundwater flow commonly adopted to design injections in unconsolidated porous media (e.g., radial diverging or dipole flow regimes). Instead, it is important to synthesize site characterization information using a groundwater flow model that includes discrete features representing high‐ and low‐permeability fractures. This type of model accounts for the highly heterogeneous hydraulic conductivity and groundwater fluxes in fractured‐rock aquifers, and facilitates designing injection strategies that target specific volumes of the aquifer and maximize the distribution of amendments over these volumes.

Groundwater

Examining the extraction efficiency of petroleum-derived dissolved organic matter in contaminated groundwater plumes

The extraction efficiency of petroleum-derived dissolved organic matter (DOM) was examined for groundwater samples from an aquifer contaminated with crude oil. Four different types of extraction were used to determine which method is best suited for the analysis of potentially toxic petroleum-derived DOM. The four types were a liquid-liquid extraction (LLE) with dichloromethane (EPA method 3510C), and three solid-phase extraction (SPE) stationary phases that are routinely used for extraction of polar analytes from water. For the LLE, that is selective for non-polar compounds, the extraction efficiency of petroleum-derived DOM decreased downgradient as the petroleum-derived DOM becomes increasingly polar due to biodegradation. In contrast, the average extraction efficiency by the SPE methods was greater than 65 % across the gradient. The results showed that SPE is more efficient for extracting petroleum-derived DOM at hydrocarbon-contaminated sites. The use of a method with greater extraction efficiency for partially-oxidized hydrocarbons may prove useful in determining relationships between their composition and structure and potential for risks to human health or the environment.

Ground Water Monitoring and Remediation

Understanding the evolution of groundwater-contaminant plume chemistry emanating from legacy contaminant sources: An example from a long-term crude oil spill

Understanding the evolution of plumes emanating from residual hydrocarbon contaminant sources requires evaluating how changes in source compositions over time cause changes in dissolved plume chemistry as residual sources age. This study investigates such changes at the site of a 1979 crude-oil pipeline spill and is the first comprehensive look at groundwater chemistry associated with a residual hydrocarbon source zones in different stages of aging. The data show a direct relationship between concentrations of benzene and naphthalene in the residual oil and those measured in water samples collected below the oil. Groundwater associated with oil near the spill site had different chemical composition compared with water associated with oil that had spread downgradient from the spill zone, indicating a shift in biodegradation reactions. These results emphasize that source zone processes are spatially and temporally heterogeneous and should be accounted for in natural attenuation studies where residual source zones persist.

Minnesota

A comparison of zero-order, first-order, and monod biotransformation models

Under some conditions, a first-order kinetic model is a poor representation of biodegradation in contaminated aquifers. Although it is well known that the assumption of first-order kinetics is valid only when substrate concentration, S, is much less than the half-saturation constant, K(s), this assumption is often made without verification of this condition. We present a formal error analysis showing that the relative error in the first-order approximation is S/K(S) and in the zero-order approximation the error is K(s)/S. We then examine the problems that arise when the first-order approximation is used outside the range for which it is valid. A series of numerical simulations comparing results of first- and zero-order rate approximations to Monod kinetics for a real data set illustrates that if concentrations observed in the field are higher than K(s), it may better to model degradation using a zero-order rate expression. Compared with Monod kinetics, extrapolation of a first-order rate to lower concentrations under-predicts the biotransformation potential, while extrapolation to higher concentrations may grossly over-predict the transformation rate. A summary of solubilities and Monod parameters for aerobic benzene, toluene, and xylene (BTX) degradation shows that the a priori assumption of first-order degradation kinetics at sites contaminated with these compounds is not valid. In particular, out of six published values of KS for toluene, only one is greater than 2 mg/L, indicating that when toluene is present in concentrations greater than about a part per million, the assumption of first-order kinetics may be invalid. Finally, we apply an existing analytical solution for steady-state one-dimensional advective transport with Monod degradation kinetics to a field data set.A formal error analysis is presented showing that the relative error in the first-order approximation is S/KS and in the zero-order approximation the error is KS/S where S is the substrate concentration and KS is the half-saturation constant. The problems that arise when the first-order approximation is used outside the range for which it is valid are examined. A series of numerical simulations comparing results of first- and zero-order rate approximations to Monod kinetics for a real data set illustrates that if concentrations observed in the field are higher than KS, it may be better to model degradation using a zero-order rate expression.

Ground Water

Bacterial transport experiments in fractured crystalline bedrock

The efficiency of contaminant biodegradation in ground water depends, in part, on the transport properties of the degrading bacteria. Few data exist concerning the transport of bacteria in saturated bedrock, particularly at the field scale. Bacteria and microsphere tracer experiments were conducted in a fractured crystalline bedrock under forced-gradient conditions over a distance of 36 m. Bacteria isolated from the local ground water were chosen on the basis of physicochemical and physiological differences (shape, cell-wall type, motility), and were differentially stained so that their transport behavior could be compared. No two bacterial strains transported in an identical manner, and microspheres produced distinctly different breakthrough curves than bacteria. Although there was insufficient control in this field experiment to completely separate the effects of bacteria shape, reaction to Gram staining, cell size, and motility on transport efficiency, it was observed that (1) the nonmotile, mutant strain exhibited better fractional recovery than the motile parent strain; (2) Gram-negative rod-shaped bacteria exhibited higher fractional recovery relative to the Gram-positive rod-shaped strain of similar size; and (3) coccoidal (spherical-shaped) bacteria transported better than all but one strain of the rod-shaped bacteria. The field experiment must be interpreted in the context of the specific bacterial strains and ground water environment in which they were conducted, but experimental results suggest that minor differences in the physical properties of bacteria can lead to major differences in transport behavior at the field scale.

Ground Water

Evaluation of volatilization as a natural attenuation pathway for MTBE

Volatilization and diffusion through the unsaturated zone can be an important pathway for natural attenuation remediation of methyl tert-butyl ether (MTBE) at gasoline spill sites. The significance of this pathway depends primarily on the distribution of immiscible product within the unsaturated zone and the relative magnitude of aqueous-phase advection (ground water recharge) to gaseous-phase diffusion. At a gasoline spill site in Laurel Bay, South Carolina, rates of MTBE volatilization from ground water downgradient from the source are estimated by analyzing the distribution of MTBE in the unsaturated zone above a solute plume. Volatilization rates of MTBE from ground water determined by transport modeling ranged from 0.0020 to 0.0042 g m- 2 /year, depending on the assumed rate of ground water recharge. Although diffusive conditions at the Laurel Bay site are favorable for volatilization, mass loss of MTBE is insignificant over the length (230 m) of the solute plume. Based on this analysis, significant volatilization of MTBE from ground water downgradient from source areas at other sites is not likely. In contrast, model results indicate that volatilization coupled with diffusion to the atmosphere could be a significant mass loss pathway for MTBE in source areas where residual product resides above the capillary zone. Although not documented, mass loss of MTBE at the Laurel Bay site due to volatilization and diffusion to the atmosphere are predicted to be two to three times greater than mass loading of MTBE to ground water due to dissolution and recharge. This result would imply that volatilization in the source zone may be the critical natural attenuation pathway for MTBE at gasoline spill sites, especially when considering capillary zone limitations on volatilization of MTBE from ground water and the relative recalcitrance of MTBE to biodegradation.

Groundwater

Long-term changes in ground water chemistry at a phytoremediation demonstration site

A field-scale demonstration project was conducted to evaluate the capability of eastern cottonwood trees ( Populus deltoides ) to attenuate trichloroethene (TCE) contamination of ground water. By the middle of the sixth growing season, trees planted where depth to water was <3 m delivered enough dissolved organic carbon to the underlying aquifer to lower dissolved oxygen concentrations, to create iron-reducing conditions along the plume centerline and sulfate-reducing or methanogenic conditions in localized areas, and to initiate in situ reductive dechlorination of TCE. Apparent biodegradation rate constants for TCE along the centerline of the plume beneath the phytoremediation system increased from 0.0002/d to 0.02/d during the first six growing seasons. The corresponding increase in natural attenuation capacity of the aquifer along the plume centerline, from 0.0004/m to 0.024/m, is associated with a potential decrease in plume-stabilization distance from 9680 to 160 m. Demonstration results provide insight into the amount of vegetation and time that may be needed to achieve cleanup objectives at the field scale.

Ground Water

Biochemical indicators for the bioavailability of organic carbon in ground water

The bioavailability of total organic carbon (TOC) was examined in ground water from two hydrologically distinct aquifers using biochemical indicators widely employed in chemical oceanography. Concentrations of total hydrolyzable neutral sugars (THNS), total hydrolyzable amino acids (THAA), and carbon‐normalized percentages of TOC present as THNS and THAA (referred to as “yields”) were assessed as indicators of bioavailability. A shallow coastal plain aquifer in Kings Bay, Georgia, was characterized by relatively high concentrations (425 to 1492 μM; 5.1 to 17.9 mg/L) of TOC but relatively low THNS and THAA yields (∼0.2%–1.0%). These low yields are consistent with the highly biodegraded nature of TOC mobilized from relatively ancient (Pleistocene) sediments overlying the aquifer. In contrast, a shallow fractured rock aquifer in West Trenton, New Jersey, exhibited lower TOC concentrations (47 to 325 μM; 0.6 to 3.9 mg/L) but higher THNS and THAA yields (∼1% to 4%). These higher yields were consistent with the younger, and thus more bioavailable, TOC being mobilized from modern soils overlying the aquifer. Consistent with these apparent differences in TOC bioavailability, no significant correlation between TOC and dissolved inorganic carbon (DIC), a product of organic carbon mineralization, was observed at Kings Bay, whereas a strong correlation was observed at West Trenton. In contrast to TOC, THNS and THAA concentrations were observed to correlate with DIC at the Kings Bay site. These observations suggest that biochemical indicators such as THNS and THAA may provide information concerning the bioavailability of organic carbon present in ground water that is not available from TOC measurements alone.

Ground Water

Biogeochemical evolution of a landfill leachate plume, Norman, Oklahoma

Leachate from municipal landfills can create groundwater contaminant plumes that may last for decades to centuries. The fate of reactive contaminants in leachate-affected aquifers depends on the sustainability of biogeochemical processes affecting contaminant transport. Temporal variations in the configuration of redox zones downgradient from the Norman Landfill were studied for more than a decade. The leachate plume contained elevated concentrations of nonvolatile dissolved organic carbon (NVDOC) (up to 300 mg/L), methane (16 mg/L), ammonium (650 mg/L as N), iron (23 mg/L), chloride (1030 mg/L), and bicarbonate (4270 mg/L). Chemical and isotopic investigations along a 2D plume transect revealed consumption of solid and aqueous electron acceptors in the aquifer, depleting the natural attenuation capacity. Despite the relative recalcitrance of NVDOC to biodegradation, the center of the plume was depleted in sulfate, which reduces the long-term oxidation capacity of the leachate-affected aquifer. Ammonium and methane were attenuated in the aquifer relative to chloride by different processes: ammonium transport was retarded mainly by physical interaction with aquifer solids, whereas the methane plume was truncated largely by oxidation. Studies near plume boundaries revealed temporal variability in constituent concentrations related in part to hydrologic changes at various time scales. The upper boundary of the plume was a particularly active location where redox reactions responded to recharge events and seasonal water-table fluctuations. Accurately describing the biogeochemical processes that affect the transport of contaminants in this landfill-leachate-affected aquifer required understanding the aquifer's geologic and hydrodynamic framework.

Oklahoma

Relative vulnerability of public supply wells to VOC contamination in hydrologically distinct regional aquifers

A process-based methodology was used to compare the vulnerability of public supply wells tapping seven study areas in four hydrologically distinct regional aquifers to volatile organic compound (VOC) contamination. This method considers (1) contributing areas and travel times of groundwater flowpaths converging at individual supply wells, (2) the oxic and/or anoxic conditions encountered along each flowpath, and (3) the combined effects of hydrodynamic dispersion and contaminant- and oxic/anoxic-specific biodegradation. Contributing areas and travel times were assessed using particle tracks generated from calibrated regional groundwater flow models. These results were then used to estimate VOC concentrations relative to an unspecified initial concentration (C/C0) at individual public supply wells. The results show that the vulnerability of public supply wells to VOC contamination varies widely between different regional aquifers. Low-recharge rates, long travel times, and the predominantly oxic conditions characteristic of Basin and Range aquifers in the western United States leads to lower vulnerability to VOCs, particularly to petroleum hydrocarbons such as benzene and toluene. On the other hand, high recharge rates and short residence times characteristic of the glacial aquifers of the eastern United States leads to greater vulnerability to VOCs. These differences lead to distinct patterns of C/C0 values estimated for public supply wells characteristic of each aquifer, information that can be used by resource managers to develop monitoring plans based on relative vulnerability, to locate new public supply wells, or to make land-use management decisions.

Ground Water Monitoring and Remediation

Microbial mineralization of dichloroethene and vinyl chloride under hypoxic conditions

Mineralization of 14C-radiolabled vinyl chloride ([1,2-14C] VC) and cis-dichloroethene ([1,2-14C] cis-DCE) under hypoxic (initial dissolved oxygen (DO) concentrations about 0.1 mg/L) and nominally anoxic (DO minimum detection limit = 0.01 mg/L) was examined in chloroethene-exposed sediments from two groundwater and two surface water sites. The results show significant VC and dichloroethene (DCE) mineralization under hypoxic conditions. All the sample treatments exhibited pseudo-first-order kinetics for DCE and VC mineralization over an extended range of substrate concentrations. First-order rates for VC mineralization were approximately 1 to 2 orders of magnitude higher in hypoxic groundwater sediment treatments and at least three times higher in hypoxic surface water sediment treatments than in the respective anoxic treatments. For VC, oxygen-linked processes accounted for 65 to 85% of mineralization at DO concentrations below 0.1 mg/L, and 14CO2 was the only degradation product observed in VC treatments under hypoxic conditions. Because the lower detection limit for DO concentrations measured in the field is typically 0.1 to 0.5 mg/L, these results indicate that oxygen-linked VC and DCE biodegradation can be significant under field conditions that appear anoxic. Furthermore, because rates of VC mineralization exceeded rates of DCE mineralization under hypoxic conditions, DCE accumulation without concomitant accumulation of VC may not be evidence of a DCE degradative “stall” in chloroethene plumes. Significantly, mineralization of VC above the level that could reasonably be attributed to residual DO contamination was also observed in several nominally anoxic (DO minimum detection limit = 0.01 mg/L) microcosm treatments.

Georgia

Potentially bioavailable natural organic carbon and hydrolyzable amino acids in aquifer sediments

This study evaluated the relationship between concentrations of operationally defined potentially bioavailable organic -carbon (PBOC) and hydrolyzable amino acids (HAAs) in sediments collected from a diverse range of chloroethene--contaminated sites. Concentrations of PBOC and HAA were measured using aquifer sediment samples collected at six selected study sites. Average concentrations of total HAA and PBOC ranged from 1.96 ± 1.53 to 20.1 ± 25.6 mg/kg and 4.72 ± 0.72 to 443 ± 65.4 mg/kg, respectively. Results demonstrated a statistically significant positive relationship between concentrations of PBOC and total HAA present in the aquifer sediment (p < 0.05). Higher levels of HAA were consistently observed at sites with greater levels of PBOC and first-order decay rates. Because amino acids are known to be readily biodegradable carbon compounds, this relationship suggests that the sequential chemical extraction procedure used to measure PBOC is a useful indicator of bioavailable carbon in aquifer sediments. This, in turn, is consistent with the interpretation that PBOC measurements can be used for estimating the amount of natural organic carbon available for driving the reductive dechlorination of chloroethenes in groundwater systems.

Ground Water Monitoring and Remediation

Oil and ice in the Arctic Ocean: Possible large-scale interactions

The diffusion and transport mechanisms generated by the pack ice dynamics of the Beaufort Sea, combined with the slow rate of biodegradation of oil under Arctic conditions, would combine to diffuse an oil spill over the sea and eventually deposit the oil on the ice surface, where it would lower the natural albedo over a large area.

Science

Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities

The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C 3 H 6 BrNO 4 ). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills.

Applied and Environmental Microbiology

Paleofluid-flow circulation within a Triassic rift basin: Evidence from oil inclusions and thermal histories

The migration of subsurface fluid flow within continental rift basins has been increasingly recognized to significantly affect the thermal history of sediments and petroleum formation. To gain insight into these paleofluid flow effects, the thermal history of the Taylorsville basin in Virginia was reconstructed from fluid-inclusion studies, apatite fission-track data, and vitrinite reflectance data. Models of thermal history indicate that the basin was buried to the thermal maximum at 200 Ma; a cooling event followed during which the eastern side of the basin cooled earlier and faster than the western side, suggesting that there was a differential uplift and topographically driven fluid flow. This hypothesis is supported by analyses of secondary oil and aqueous inclusions trapped in calcite and quartz veins during the uplift stage. Gas chromatograms of inclusion oils exhibit variable but extensive depletion of light molecular-weight hydrocarbons. The relative abundance of n-alkanes, petrographic observations, and the geological data indicate that the alteration process on these inclusion oils was probably neither phase separation nor biodegradation, but water washing. Water:oil ratios necessary to produce the observed alteration are much greater than 10000:1. These exceedingly high ratios are consistent with the migration of inclusion oils along with fluid flow during the early stages of basin evolution. The results provide significant evidence about the role of a subsurface flow system in modifying the temperature structure of the basin and the composition of petroleum generated within the basin.

Geological Society of America Bulletin

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 10 6 reads revealed >3 × 10 6 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 10 6 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria , predominantly Comamonadaceae . The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae , pathogenic Pseudomonadaceae , and ‘ Vibrionales' ) and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.

Virginia

Source rock contributions to the Lower Cretaceous heavy oil accumulations in Alberta: a basin modeling study

The origin of the immense oil sand deposits in Lower Cretaceous reservoirs of the Western Canada sedimentary basin is still a matter of debate, specifically with respect to the original in-place volumes and contributing source rocks. In this study, the contributions from the main source rocks were addressed using a three-dimensional petroleum system model calibrated to well data. A sensitivity analysis of source rock definition was performed in the case of the two main contributors, which are the Lower Jurassic Gordondale Member of the Fernie Group and the Upper Devonian&ndash;Lower Mississippian Exshaw Formation. This sensitivity analysis included variations of assigned total organic carbon and hydrogen index for both source intervals, and in the case of the Exshaw Formation, variations of thickness in areas beneath the Rocky Mountains were also considered. All of the modeled source rocks reached the early or main oil generation stages by 60 Ma, before the onset of the Laramide orogeny. Reconstructed oil accumulations were initially modest because of limited trapping efficiency. This was improved by defining lateral stratigraphic seals within the carrier system. An additional sealing effect by biodegraded oil may have hindered the migration of petroleum in the northern areas, but not to the east of Athabasca. In the latter case, the main trapping controls are dominantly stratigraphic and structural. Our model, based on available data, identifies the Gordondale source rock as the contributor of more than 54% of the oil in the Athabasca and Peace River accumulations, followed by minor amounts from Exshaw (15%) and other Devonian to Lower Jurassic source rocks. The proposed strong contribution of petroleum from the Exshaw Formation source rock to the Athabasca oil sands is only reproduced by assuming 25 m (82 ft) of mature Exshaw in the kitchen areas, with original total organic carbon of 9% or more.

Alberta