Integration of stable carbon isotope, microbial community, dissolved hydrogen gas, and ²HH₂O tracer data to assess bioaugmentation for chlorinated ethene degradation in fractured rocks

Use of isotopic (C, Cl) and molecular biology tools to assess biodegradation in a source area of chlorinated ethenes after biostimulation with Emulsified Vegetable Oil (EVO)

Enhanced In Situ Bioremediation (EISB) using Emulsified Vegetable Oil (EVO) as a long-term electron donor has gained prominence for the treatment of groundwater contaminated with chlorinated ethenes (CEs). This study explores the potential of isotopic and molecular biology tools (MBT) to investigate the CEs (PCE, TCE and cis-DCE) bioremediation using EVO in a contaminated site. A multiple approach using C and Cl-CSIA, quantification of Dehalococcoides (Dhc) and specific reductive dechlorination (RD) gene population, and hydrochemical data in microcosm experiments and field samples was applied. Despite the high partitioning of CEs into the EVO phase, the carbon isotopic values of the remaining CEs fraction in the aqueous phase did not exhibit significant changes caused by phase partitioning in laboratory experiments. Both microcosm experiments and field data revealed a rapid RD of PCE and TCE, resulting in the transient accumulation of cis-DCE, which was slowly degraded to vinyl chloride (VC). These results agreed with the presence of Dhc populations and a shift to stronger reducing conditions in the field: i) RD functional genes (tceA, vcrA and bvcA) exhibited a trend to higher values and ii) a substantial increase in Dhc populations (up to 30% of the total bacterial populations) was observed over time. The dual-element isotope slope ΛC-Cl for RD of cis-DCE obtained from field data (ΛC - Cl = 5 ± 3) was similar to the one determined from the microcosm experiments under controlled anoxic conditions (ΛC - Cl = 4.9 ± 0.8). However, ΛC-Cl values differ from those reported so far for laboratory studies with Dhc strains and mixed cultures containing Dhc, i.e., between 8.3 and 17.8. This observation underscores the potential variety of reductive dehalogenases involved during cis-DCE RD and the importance of determining site-specific Λ and ɛ values in order to improve the identification and quantification of transformation processes in the field.

Microbial Community Response to a Bioaugmentation Test to Degrade Trichloroethylene in a Fractured Rock Aquifer, Trenton, N.J

Bioaugmentation is a promising strategy for enhancing trichloroethylene (TCE) degradation in fractured rock. However, slow or incomplete biodegradation can lead to stalling at degradation byproducts such as 1,2-dichloroethene (cis-DCE) and vinyl chloride (VC). Over the course of 7 years, we examined the response of groundwater microbial populations in a bioaugmentation test where an emulsified vegetable oil solution (EOS®) and a dechlorinating consortium (KB-1®), containing the established dechlorinator Dehalococcoides, were injected into a TCE-contaminated fractured rock aquifer. Indigenous microbial communities responded within 2 days to added substrate and outcompeted KB-1®, and over the years of monitoring, several other notable turnover events were observed. Concentrations of ethene, the end product in reductive dechlorination, had the strongest correlations (p< 0.05) with members of Candidatus Colwellbacteria but their involvement in reductive dechlorination is unknown and warrants further investigation. Dehalococcoides never exceeded 0.6% relative abundance of groundwater microbial communities, despite its previously presumed importance at the site. Increased concentrations of carbon dioxide, acetic acid, and methane were positively correlated with increasing ethene concentrations; however, concentrations of cis-DCE and VC remained high by the end of the monitoring period suggesting preferential enrichment of indigenous partial dechlorinators over bioaugmented complete dechlorinators. This study highlights the importance of characterizing in situ microbial populations to understand how they can potentially enhance or inhibit augmented TCE degradation.

Got acetylene: a personal research retrospective

In research, sometimes sheer happenstance and serendipity make for an unexpected discovery. Once revealed and if interesting enough, such a finding and its follow-up investigations can lead to advances by others that leave its originators 'scooped' and mulling about what next to do with their unpublished data, specifically what journals could it still be published in and be perceived as original. This is what occurred with us nearly 40 years ago with regard to our follow-up observations of acetylene fermentation and led us to concoct a 'cock-and-bull' story. We hypothesized about a plausible role for acetylene metabolism in the primordial biogeochemistry of Earth and the possibility of acetylene serving as a key life-sustaining substrate for alien microbes dwelling in the orbs of the outer solar system. With the passage of time, advances were made in whole-genome sequencing coupled with major in silico progress in bioinformatics. In parallel came the results of explorations of the outer solar system (i.e. the Cassini mission to Saturn and its moons). It now appears that these somewhat harebrained ideas of ours, arisen at first out of a sense of desperation, actually ring true in fact, and particularly well in song: 'Tell a tale of cock and bull, Of convincing detail full Tale tremendous, Heav'n defend us! What a tale of cock and bull!' From 'The Yeoman of the Guard' by Gilbert & Sullivan.

Assessment of chlorinated ethenes degradation after field scale injection of activated carbon and bioamendments: Application of isotopic and microbial analyses

Over the last decade, activated carbon amendments have successfully been applied to retain chlorinated ethene subsurface contamination. The concept of this remediation technology is that activated carbon and bioamendments are injected into aquifer systems to enhance biodegradation. While the scientific basis of the technology is established, there is a need for methods to characterise and quantify the biodegradation at field scale. In this study, an integrated approach was applied to assess in situ biodegradation after the establishment of a cross sectional treatment zone in a TCE plume. The amendments were liquid activated carbon, hydrogen release donors and a Dehalococcoides containing culture. The integrated approach included spatial and temporal evaluations on flow and transport, redox conditions, contaminant concentrations, biomarker abundance and compound-specific stable isotopes. This is the first study applying isotopic and microbial techniques to assess field scale biodegradation enhanced by liquid activated carbon and bioamendments. The injection enhanced biodegradation from TCE to primarily cis-DCE. The Dehalococcoides abundances facilitated characterisation of critical zones with insufficient degradation and possible explanations. A conceptual model of isotopic data together with distribution and transport information improved process understanding; the degradation of TCE was insufficient to counteract the contaminant input by inflow into the treatment zone and desorption from the sediment. The integrated approach could be used to document and characterise the in situ degradation, and the isotopic and microbial data provided process understanding that could not have been gathered from conventional monitoring tools. However, quantification of degradation through isotope data was restricted for TCE due to isotope masking effects. The combination of various monitoring tools, applied frequently at high-resolution, with system understanding, was essential for the assessment of biodegradation in the complex, non-stationary system. Furthermore, the investigations revealed prospects for future research, which should focus on monitoring contaminant fate and microbial distribution on the sediment and the activated carbon.

Strategies for Managing Risk due to Back Diffusion

Back diffusion of contaminants from secondary sources may hamper site remediation if it is not properly addressed in the remedial design. A review of all reported technologies and strategies that have been or could be applied to address plume persistence due to back diffusion as published in the peer-reviewed literature is provided. We classify these into four major categories. The first category consists of those approaches that do not include active measures to specifically address contamination in the low permeable zones (LPZs) and can therefore be considered passive LPZ management approaches. A disadvantage of these approaches is the long duration that may be required to meet acceptable endpoints; however, this allows degradation to potentially play a significant part even at modest rates. The remaining three categories all use approaches to specifically address contaminants in the LPZ. The second category consists of strategies that promote contaminant destruction through the forward diffusion of amendments into the LPZ. A variety of laboratory tests indicate concentration or flux reductions range from no improvement, to reductions as high as four orders-of-magnitude depending on the evaluation metric. The third category consists of strategies that alter physical characteristics of the secondary source, and includes viscosity modification, fracturing, and soil mixing. Each of these offer unique advantages and are often used to deliver one or more amendments for contaminant treatment. The final category consists of thermal and electrokinetic remediation, both less susceptible to permeability contrast limitations. However, they are not routinely used for secondary-source treatment.

The Spatial Distribution of the Microbial Community in a Contaminated Aquitard below an Industrial Zone

The industrial complex Neot Hovav, in Israel, is situated above an anaerobic fractured chalk aquitard, which is polluted by a wide variety of hazardous organic compounds. These include volatile and non-volatile, halogenated, organic compounds. In this study, we characterized the indigenous bacterial population in 17 boreholes of the groundwater environment, while observing the spatial variations in the population and structure as a function of distance from the polluting source. In addition, the de-halogenating potential of the microbial groundwater population was tested through a series of lab microcosm experiments, thus exemplifying the potential and limitations for bioremediation of the site. In all samples, the dominant phylum was Proteobacteria. In the production plant area, the non-obligatory organo-halide respiring bacteria (OHRB) Firmicutes Phylum was also detected in the polluted water, in abundancies of up to 16 %. Non-metric multidimensional scaling (NMDS) analysis of the microbial community structure in the groundwater exhibited clusters of distinct populations following the location in the industrial complex and distance from the polluting source. Dehalogenation of halogenated ethylene was demonstrated in contrast to the persistence of brominated alcohols. Persistence is likely due to the chemical characteristics of brominated alcohols, and not because of the absence of active de-halogenating bacteria.

The complex spatial distribution of trichloroethene and the probability of NAPL occurrence in the rock matrix of a mudstone aquifer

Methanol extractions for chloroethene analyses are conducted on rock samples from seven closely spaced coreholes in a mudstone aquifer that was subject to releases of the nonaqueous phase liquid (NAPL) form of trichloroethene (TCE) between the 1950's and 1990's. Although TCE concentration in the rock matrix over the length of coreholes is dictated by proximity to subhorizontal bedding plane fractures, elevated TCE concentrations in the rock matrix are not continuous along the most permeable bedding plane fractures. A complex configuration of subvertical and subhorizontal fractures appears to be responsible for the TCE distribution from prior TCE releases at land surface. Phase partitioning calculations of TCE in the rock matrix show that most TCE is adsorbed to solid surfaces because of the large fraction of organic carbon (f_oc) in the mudstone. Large TCE content in some cores indicate the likely presence of the NAPL form of TCE in the rock matrix. Using average values of porosity (n) and f_oc in phase partitioning calculations identifies a number of locations of possible NAPL occurrence in the rock matrix. Samples of mudstone analyzed for n and f_oc show variability in these properties over several orders of magnitude. Accounting for this variability in phase partitioning calculations identifies a probability of NAPL occurrence, P_NAPL. The spatial variability of P_NAPL along coreholes identifies a configuration that may be attributed to a TCE source zone that has evolved after emplacement due to NAPL dissolution, adsorption, and matrix diffusion.

Acetylenotrophy: a hidden but ubiquitous microbial metabolism?

Acetylene (IUPAC name: ethyne) is a colorless, gaseous hydrocarbon, composed of two triple bonded carbon atoms attached to hydrogens (C2H2). When microbiologists and biogeochemists think of acetylene, they immediately think of its use as an inhibitory compound of certain microbial processes and a tracer for nitrogen fixation. However, what is less widely known is that anaerobic and aerobic microorganisms can degrade acetylene, using it as a sole carbon and energy source and providing the basis of a microbial food web. Here, we review what is known about acetylene degrading organisms and introduce the term 'acetylenotrophs' to refer to the microorganisms that carry out this metabolic pathway. In addition, we review the known environmental sources of acetylene and postulate the presence of an hidden acetylene cycle. The abundance of bacteria capable of using acetylene and other alkynes as an energy and carbon source suggests that there are energy cycles present in the environment that are driven by acetylene and alkyne production and consumption that are isolated from atmospheric exchange. Acetylenotrophs may have developed to leverage the relatively high concentrations of acetylene in the pre-Cambrian atmosphere, evolving later to survive in specialized niches where acetylene and other alkynes were produced.

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.

Bioremediation in Fractured Rock: 2. Mobilization of Chloroethene Compounds from the Rock Matrix

A mass balance is formulated to evaluate the mobilization of chlorinated ethene compounds (CE) from the rock matrix of a fractured mudstone aquifer under pre- and postbioremediation conditions. The analysis relies on a sparse number of monitoring locations and is constrained by a detailed description of the groundwater flow regime. Groundwater flow modeling developed under the site characterization identified groundwater fluxes to formulate the CE mass balance in the rock volume exposed to the injected remediation amendments. Differences in the CE fluxes into and out of the rock volume identify the total CE mobilized from diffusion, desorption, and nonaqueous phase liquid dissolution under pre- and postinjection conditions. The initial CE mass in the rock matrix prior to remediation is estimated using analyses of CE in rock core. The CE mass mobilized per year under preinjection conditions is small relative to the total CE mass in the rock, indicating that current pump-and-treat and natural attenuation conditions are likely to require hundreds of years to achieve groundwater concentrations that meet regulatory guidelines. The postinjection CE mobilization rate increased by approximately an order of magnitude over the 5 years of monitoring after the amendment injection. This rate is likely to decrease and additional remediation applications over several decades would still be needed to reduce CE mass in the rock matrix to levels where groundwater concentrations in fractures achieve regulatory standards.

Evidence of rock matrix back-diffusion and abiotic dechlorination using a field testing approach

An in situ field demonstration was performed in fractured rock impacted with trichloroethene (TCE) and cis-1,2-dichloroethene (DCE) to assess the impacts of contaminant rebound after removing dissolved contaminants within hydraulically conductive fractures. Using a bedrock well pair spaced 2.4m apart, TCE and DCE were first flushed with water to create a decrease in dissolved contaminant concentrations. While hydraulically isolating the well pair from upgradient contaminant impacts, contaminant rebound then was observed between the well pair over 151days. The magnitude, but not trend, of TCE rebound was reasonably described by a matrix back-diffusion screening model that employed an effective diffusion coefficient and first-order abiotic TCE dechlorination rate constant that was based on bench-scale testing. Furthermore, a shift in the TCE:DCE ratio and carbon isotopic enrichment was observed during the rebound, suggesting that both biotic and abiotic dechlorination were occurring within the rock matrix. The isotopic data and back-diffusion model together served as a convincing argument that matrix back-diffusion was the mechanism responsible for the observed contaminant rebound. Results of this field demonstration highlight the importance and applicability of rock matrix parameters determined at the bench-scale, and suggest that carbon isotopic enrichment can be used as a line of evidence for abiotic dechlorination within rock matrices.

Detection of Diazotrophy in the Acetylene-Fermenting Anaerobe Pelobacter sp. Strain SFB93

Acetylene (C₂H₂) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during C₂H₂ block assays of N₂O reductase, and Pelobacter acetylenicus was shown to grow on C₂H₂ via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (N₂ase), is specific for acetylene. Acetylene fermentation is a rare metabolic process that is well characterized only in P. acetylenicus DSM3246 and DSM3247 and Pelobacter sp. strain SFB93. To better understand the genetic controls for AH activity, we sequenced the genomes of the three acetylene-fermenting Pelobacter strains. Genome assembly and annotation produced three novel genomes containing gene sequences for AH, with two copies being present in SFB93. In addition, gene sequences for all five compulsory genes for iron-molybdenum N₂ase were also present in the three genomes, indicating the cooccurrence of two acetylene transformation pathways. Nitrogen fixation growth assays showed that DSM3426 could ferment acetylene in the absence of ammonium, but no ethylene was produced. However, SFB93 degraded acetylene and, in the absence of ammonium, produced ethylene, indicating an active N₂ase. Diazotrophic growth was observed under N₂ but not in experimental controls incubated under argon. SFB93 exhibits acetylene fermentation and nitrogen fixation, the only known biochemical mechanisms for acetylene transformation. Our results indicate complex interactions between N₂ase and AH and suggest novel evolutionary pathways for these relic enzymes from early Earth to modern days.IMPORTANCE Here we show that a single Pelobacter strain can grow via acetylene fermentation and carry out nitrogen fixation, using the only two enzymes known to transform acetylene. These findings provide new insights into acetylene transformations and adaptations for nutrient (C and N) and energy acquisition by microorganisms. Enhanced understanding of acetylene transformations (i.e., extent, occurrence, and rates) in modern environments is important for the use of acetylene as a potential biomarker for extraterrestrial life and for degradation of anthropogenic contaminants.

Porosity and pore size distribution in a sedimentary rock: Implications for the distribution of chlorinated solvents

Characterizing properties of the rock matrix that control retention and release of chlorinated solvents is essential in evaluating the extent of contamination and the application of remediation technologies in fractured rock. Core samples from seven closely spaced boreholes in a mudstone subject to trichloroethene (TCE) contamination were analyzed using Mercury Intrusion Porosimetry to investigate porosity and pore size distribution as a function of mudstone characteristics, and depth and lateral extent in the aquifer; organic carbon content was also evaluated to identify the potential for adsorption. Porosity and retardation factor varied over two orders of magnitude, with the largest porosities and largest retardation factors associated with carbon-rich mudstone layers. Larger porosities were also measured in the shallow rock that has been subject to enhanced groundwater flow. Porosity also varied over more than an order of magnitude in spatially continuous mudstone layers. The analyses of the rock cores indicated that the largest pore diameters may be accessible to entry of the nonaqueous form of TCE. Although the porosity associated with the largest pore diameters is small (~0.1%), that volume of TCE can significantly affect the total TCE that is retained in the rock matrix. The dimensions of the largest pore diameters may also be accessible to microbes responsible for reductive dechlorination; however, the small percentage of the pore space that can accommodate microbes may limit the extent of reductive dechlorination in the rock matrix.

Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation

Organohalides are recalcitrant pollutants that have been responsible for substantial contamination of soils and groundwater. Organohalide-respiring bacteria (ORB) provide a potential solution to remediate contaminated sites, through their ability to use organohalides as terminal electron acceptors to yield energy for growth (i.e., organohalide respiration). Ideally, this process results in non- or lesser-halogenated compounds that are mostly less toxic to the environment or more easily degraded. At the heart of these processes are reductive dehalogenases (RDases), which are membrane bound enzymes coupled with other components that facilitate dehalogenation of organohalides to generate cellular energy. This review focuses on RDases, concentrating on those which have been purified (partially or wholly) and functionally characterized. Further, the paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases. Finally, the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed.

High-resolution delineation of chlorinated volatile organic compounds in a dipping, fractured mudstone: Depth- and strata-dependent spatial variability from rock-core sampling

Synthesis of rock-core sampling and chlorinated volatile organic compound (CVOC) analysis at five coreholes, with hydraulic and water-quality monitoring and a detailed hydrogeologic framework, was used to characterize the fine-scale distribution of CVOCs in dipping, fractured mudstones of the Lockatong Formation of Triassic age, of the Newark Basin in West Trenton, New Jersey. From these results, a refined conceptual model for more than 55years of migration of CVOCs and depth- and strata-dependent rock-matrix contamination was developed. Industrial use of trichloroethene (TCE) at the former Naval Air Warfare Center (NAWC) from 1953 to 1995 resulted in dense non-aqueous phase liquid (DNAPL) TCE and dissolved TCE and related breakdown products, including other CVOCs, in underlying mudstones. Shallow highly weathered and fractured strata overlie unweathered, gently dipping, fractured strata that become progressively less fractured with depth. The unweathered lithology includes black highly fractured (fissile) carbon-rich strata, gray mildly fractured thinly layered (laminated) strata, and light-gray weakly fractured massive strata. CVOC concentrations in water samples pumped from the shallow weathered and highly fractured strata remain elevated near residual DNAPL TCE, but dilution by uncontaminated recharge, and other natural and engineered attenuation processes, have substantially reduced concentrations along flow paths removed from sources and residual DNAPL. CVOCs also were detected in most rock-core samples in source areas in shallow wells. In many locations, lower aqueous concentrations, compared to rock core concentrations, suggest that CVOCs are presently back-diffusing from the rock matrix. Below the weathered and highly fractured strata, and to depths of at least 50 meters (m), groundwater flow and contaminant transport is primarily in bedding-plane-oriented fractures in thin fissile high-carbon strata, and in fractured, laminated strata of the gently dipping mudstones. Despite more than 18 years of pump and treat (P&T) remediation, and natural attenuation processes, CVOC concentrations in aqueous samples pumped from these deeper strata remain elevated in isolated intervals. DNAPL was detected in one borehole during coring at a depth of 27 m. In contrast to core samples from the weathered zone, concentrations in core samples from deeper unweathered and unfractured strata are typically below detection. However, high CVOC concentrations were found in isolated samples from fissile black carbon-rich strata and fractured gray laminated strata. Aqueous-phase concentrations were correspondingly high in samples pumped from these strata via short-interval wells or packer-isolated zones in long boreholes. A refined conceptual site model considers that prior to P&T remediation groundwater flow was primarily subhorizontal in the higher-permeability near surface strata, and the bulk of contaminant mass was shallow. CVOCs diffused into these fractured and weathered mudstones. DNAPL and high concentrations of CVOCs migrated slowly down in deeper unweathered strata, primarily along isolated dipping bedding-plane fractures. After P&T began in 1995, using wells open to both shallow and deep strata, downward transport of dissolved CVOCs accelerated. Diffusion of TCE and other CVOCs from deeper fractures penetrated only a few centimeters into the unweathered rock matrix, likely due to sorption of CVOCs on rock organic carbon. Remediation in the deep, unweathered strata may benefit from the relatively limited migration of CVOCs into the rock matrix. Synthesis of rock core sampling from closely spaced boreholes with geophysical logging and hydraulic testing improves understanding of the controls on CVOC delineation and informs remediation design and monitoring.