Signature metabolites attesting to the in situ attenuation of alkylbenzenes in anaerobic environments

The formation, reactivity, and fate of oxygen-containing organic compounds in petroleum-contaminated groundwaters: A state of the science review and future research directions

Hydrocarbon (HC) contamination in groundwater (GW) is a widespread environmental issue. Dissolved hydrocarbons in water are commonly utilized as an energy source by natural microbial communities, which can produce water soluble intermediate metabolite compounds, herein referred to as oxygen containing organic compounds (OCOCs), before achieving complete mineralization. This review aims to provide a comprehensive assessment of the literature focused on the state of the science for OCOCs detected and measured in GW samples collected from petroleum contaminated aquifers. In this review, we discuss and evaluate two hypotheses investigating OCOC formation, which are major points of contention in the freshwater oil spill community that need to be addressed. We reviewed over 150 articles compiling studies investigating OCOC formation and persistence to uncover knowledge gaps in the literature and studies that recommend quantitative and qualitative measurements of OCOCs in petroleum-contaminated aquifers. This review is essential because no consensus exists regarding specific compounds and related concerns. We highlight the knowledge gaps to progressing the discussion of hydrocarbon conversion products.

Anaerobic degradation of benzene and other aromatic hydrocarbons in a tar-derived plume: Nitrate versus iron reducing conditions

The anaerobic degradation of aromatic hydrocarbons in a plume originating from a Pintsch gas tar-DNAPL zone was investigated using molecular, isotopic- and microbial analyses. Benzene concentrations diminished at the relatively small meter scale dimensions of the nitrate reducing plume fringe. The ratio of benzene to toluene, ethylbenzene, xylenes and naphthalene (BTEXN) in the fringe zone compared to the plume zone, indicated relatively more loss of benzene in the fringe zone than TEXN. This was substantiated by changes in relative concentrations of BTEXN, and multi-element compound specific isotope analysis for δ²H and δ¹³C. This was supported by the presence of (abcA) genes, indicating the presumed benzene carboxylase enzyme in the nitrate-reducing plume fringe. Biodegradation of most hydrocarbon contaminants at iron reducing conditions in the plume core, appears to be quantitatively of greater significance due to the large volume of the plume core, rather than relatively faster biodegradation under nitrate reducing conditions at the smaller volume of the plume fringe. Contaminant concentration reductions by biodegradation processes were shown to vary distinctively between the source, plume (both iron-reducing) and fringe (nitrate-reducing) zones of the plume. High anaerobic microbial activity was detected in the plume zone as well as in the dense non aqueous phase liquid (DNAPL) containing source zone. Biodegradation of most, if not all, other water-soluble Pintsch gas tar aromatic hydrocarbon contaminants occur at the relatively large dimensions of the anoxic plume core. The highest diversity and concentrations of metabolites were detected in the iron-reducing plume core, where the sum of parent compounds of aromatic hydrocarbons was greater than 10 mg/L. The relatively high concentrations of metabolites suggest a hot spot for anaerobic degradation in the core of the plume downgradient but relatively close to the DNAPL containing source zone.

Simultaneous detection of transcribed functional assA gene and the corresponding metabolites of linear alkanes (C4, C5, and C7) in production water of a low-temperature oil reservoir

Methanogenic hydrocarbon degradation is an important biogeochemical process in oil reservoirs; however, genomic DNA-based analysis of microorganisms and metabolite detection are not conclusive for identification of the ongoing nature of this bioprocess. In this study, a suite of analyses, involving the study of microbial community and selective gene quantification of both genomic DNA and RNA together with signature metabolites, were performed to comprehensively advance the understanding of the methanogenic biodegradation of hydrocarbons in a low-temperature oilfield. The fumarate addition products for alkanes-C₄, C₅, and C₇-alkylsuccinates-and transcribed assA and mcrA genes were simultaneously detected in the production water sample, providing robust and convincing evidence for both the initial activation of n-alkanes and methane metabolism in this oilfield. The clone library of assA gene transcripts showed that Smithella was active and most likely responsible for the addition of fumarate to n-alkanes, whereas Methanoculleus and Methanothrix were the dominant and active methane-producers via CO₂ reduction and acetoclastic pathways, respectively. Additionally, qPCR results of assA and mcrA genes and their transcribed gene copy numbers revealed a roughly similar transcriptional activity in both n-alkanes-degraders and methane producers, implying that they were the major participants in the methanogenic degradation of n-alkanes in this oilfield. To the best of our knowledge, this is the first report presenting sufficient speculation, through detection of signature intermediates, corresponding gene quantification at transcriptional levels, and microbial community analysis, of methanogenic degradation of n-alkanes in production water of an oil reservoir.

Biological Effects of Hydrocarbon Degradation Intermediates: Is the Total Petroleum Hydrocarbon Analytical Method Adequate for Risk Assessment?

In crude oil contaminant plumes, the dissolved organic carbon (DOC) is mainly hydrocarbon degradation intermediates only partly quantified by the diesel range total petroleum hydrocarbon (TPHd) method. To understand potential biological effects of degradation intermediates, we tested three fractions of DOC: (1) solid-phase extract (HLB); (2) dichloromethane (DCM-total) extract used in TPHd; and (3) DCM extract with hydrocarbons isolated by silica gel cleanup (DCM-SGC). Bioactivity of extracts from five wells spanning a range of DOC was tested using an in vitro multiplex reporter system that evaluates modulation of the activity of 46 transcription factors; extracts were evaluated at concentrations equivalent to the well water samples. The aryl hydrocarbon receptor (AhR) and pregnane X receptor (PXR) transcription factors showed the greatest upregulation, with HLB exceeding DCM-total, and no upregulation in the hydrocarbon fraction (DCM-SGC). The HLB extracts were further studied with HepG2 chemically activated luciferase expression (CALUX) in vitro assays at nine concentrations ranging from 40 to 0.01 times the well water concentrations. Responses decreased with distance from the source but were still present at two wells without detectable hydrocarbons. Thus, our in vitro assay results indicate that risks associated with degradation intermediates of hydrocarbons in groundwater will be underestimated when protocols that remove these chemicals are employed.

Evaluation of the anaerobic biodegradation of linear alkylbenzene sulfonates (LAS) using OECD 308 water/sediment systems

Linear alkylbenzene sulfonates (LAS) are the most widely used anionic surfactants in household detergents and cleaning products. We have evaluated LAS anaerobic degradation in sediments following OECD 308 guidelines. Four different classes of sediments were collected from non-polluted areas and tested to check the influence of: fine and coarse texture, low and high organic carbon content, and freshwater and marine origin. The concentrations of LAS and possible degradation metabolites in sediment and water phases were monitored by high resolution mass spectrometry over an incubation period of 160 days. LAS removal was between 0 and 63%, depending on the sediment used, and it was accompanied by formation of sulfophenyl carboxylic acids (SPCs). The best results were observed for marine sediments having low organic carbon and silt + clay contents (0.5% and 13%, respectively), whereas degradation was negligible in freshwater sediments. The large differences in degradation observed across the sediments tested were attributed to their physicochemical properties influencing LAS bioavailability and the heterogeneity of microbial communities. Further research is also needed to address some shortcomings observed during the application of the OECD 308 and to ensure that test results obtained with these guidelines model anaerobic biodegradation under realistic environmental conditions.

Predicted and measured acute toxicity and developmental abnormalities in zebrafish embryos produced by exposure to individual aromatic acids

Petroleum acids, often called 'Naphthenic Acids' (NA), enter the environment in complex mixtures from numerous sources. These include from Produced and Process-Affected waters discharged from some oil industry activities, and from the environmental weathering of spilled crude oil hydrocarbons. Here, we test the hypothesis that individual NA within the complex mixtures can induce developmental abnormalities in fish, by screening a range of individual acids, with known chemical structures. Sixteen aromatic NA were tested using a Thamnocephalus platyrus (beavertail fairyshrimp) assay, to establish acute toxicity. Toxicities ranged from 568 to 8 μM, with the methylbiphenyl acid, 4-(p-tolyl)benzoic acid, most toxic. Next, five of the most toxic monoacids and for comparison, a diacid, were assayed using Danio rerio (zebrafish) embryos to test for lethality and developmental abnormalities. The toxicities were also predicted using Admet predictor™ software. Exposure to the five monoacids produced deformities in zebrafish embryos in a dose-dependent manner. Thus, exposure to 4-(p-tolyl)benzoic acid produced abnormalities in >90% of the embryos at concentrations of <1 μM; exposure to dehydroabietic acid caused pericardial edema and stunted growth in 100% of the embryos at 6 μM and exposure to pyrene-1-carboxylic acid caused 80% of embryos to be affected at 3 μM. The findings of this preliminary study therefore suggest that some aromatic acids are targets for more detailed mechanistic studies of mode of action. The results should help to focus on those NA which may be important for monitoring in oil industry wastewaters and polluted environmental samples.

Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment

Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is the assumption that the aerobic degradation is more energetically favorable than degradation under strictly anaerobic conditions. Certain aerobically recalcitrant contaminants, however, are biodegraded under strictly anaerobic conditions and little is known about the organisms and enzymatic processes involved in their degradation. This review provides a comprehensive survey of characteristic anaerobic biotransformation reactions for a variety of well-studied, structurally rather simple contaminants (SMOCs) bearing one or a few different functional groups/structural moieties. Furthermore it summarizes anaerobic degradation studies of more complex contaminants with several functional groups (CMCs), in soil, sediment and wastewater treatment. While strictly anaerobic conditions are able to promote the transformation of several aerobically persistent contaminants, the variety of observed reactions is limited, with reductive dehalogenations and the cleavage of ether bonds being the most prevalent. Thus, it becomes clear that the transferability of degradation mechanisms deduced from culture studies of SMOCs to predict the degradation of CMCs, such as EOCs, in environmental matrices is hampered due the more complex chemical structure bearing different functional groups, different environmental conditions (e.g. matrix, redox, pH), the microbial community (e.g. adaptation, competition) and the low concentrations typical for EOCs.

Microbial transformation of the Deepwater Horizon oil spill-past, present, and future perspectives

The Deepwater Horizon blowout, which occurred on April 20, 2010, resulted in an unprecedented oil spill. Despite a complex effort to cap the well, oil and gas spewed from the site until July 15, 2010. Although a large proportion of the hydrocarbons was depleted via natural processes and human intervention, a substantial portion of the oil remained unaccounted for and impacted multiple ecosystems throughout the Gulf of Mexico. The depth, duration and magnitude of this spill were unique, raising many questions and concerns regarding the fate of the hydrocarbons released. One major question was whether or not microbial communities would be capable of metabolizing the hydrocarbons, and if so, by what mechanisms and to what extent? In this review, we summarize the microbial response to the oil spill as described by studies performed during the past four years, providing an overview of the different responses associated with the water column, surface waters, deep-sea sediments, and coastal sands/sediments. Collectively, these studies provide evidence that the microbial response to the Deepwater Horizon oil spill was rapid and robust, displaying common attenuation mechanisms optimized for low molecular weight aliphatic and aromatic hydrocarbons. In contrast, the lack of evidence for the attenuation of more recalcitrant hydrocarbon components suggests that future work should focus on both the environmental impact and metabolic fate of recalcitrant compounds, such as oxygenated oil components.

Can two-dimensional gas chromatography/mass spectrometric identification of bicyclic aromatic acids in petroleum fractions help to reveal further details of aromatic hydrocarbon biotransformation pathways?

RATIONALE

The identification of key acid metabolites ('signature' metabolites) has allowed significant improvements to be made in our understanding of the biodegradation of petroleum hydrocarbons, in reservoir and in contaminated natural systems, such as aquifers and seawater. On this basis, anaerobic oxidation is now more widely accepted as one viable mechanism, for instance. However, identification of metabolites in the complex acid mixtures from petroleum degradation is challenging and would benefit from use of more highly resolving analytical methods.

METHODS

Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GCxGC/TOFMS) with both nominal mass and accurate mass measurement was used to study the complex mixtures of aromatic acids (as methyl esters) in petroleum fractions.

RESULTS

Numerous mono- and di-aromatic acid isomers were identified in a commercial naphthenic acids fraction from petroleum and in an acids fraction from a biodegraded petroleum. In many instances, compounds were identified by comparison of mass spectral and retention time data with those of authentic compounds.

CONCLUSIONS

The identification of a variety of alkyl naphthalene carboxylic and alkanoic and alkyl tetralin carboxylic and alkanoic acids, plus identifications of a range of alkyl indane acids, provides further evidence for 'signature' metabolites of biodegradation of aromatic petroleum hydrocarbons. Identifications such as these now offer the prospect of better differentiation of metabolites of bacterial processes (e.g. aerobic, methanogenic, sulphate-reducing) in polar petroleum fractions.

Non-targeted analysis of petroleum metabolites in groundwater using GC×GC-TOFMS

Groundwater at fuel release sites often contains nonpolar hydrocarbons that originate from both the fuel release and other environmental sources, as well as polar metabolites of petroleum biodegradation. These compounds, along with other polar artifacts, can be quantified as "total petroleum hydrocarbons" using USEPA Methods 3510/8015B, unless a silica gel cleanup step is used to separate nonpolar hydrocarbons from polar compounds prior to analysis. Only a limited number of these metabolites have been identified by traditional GC-MS methods, because they are difficult to resolve using single-column configurations. Additionally, the targeted use of derivatization limits the detection of many potential metabolites of interest. The objective of this research was to develop a nontargeted GC×GC-TOFMS approach to characterize petroleum metabolites in environmental samples gathered from fuel release sites. The method tentatively identified more than 760 unique polar compounds, including acids/esters, alcohols, phenols, ketones, and aldehydes, from 22 groundwater samples collected at five sites. Standards for 28 polar compounds indicate that effective limits of quantitation for most of these compounds in the groundwater samples range from 1 to 11 μg/L.

Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill

Marine subsurface environments such as deep-sea sediments, house abundant and diverse microbial communities that are believed to influence large-scale geochemical processes. These processes include the biotransformation and mineralization of numerous petroleum constituents. Thus, microbial communities in the Gulf of Mexico are thought to be responsible for the intrinsic bioremediation of crude oil released by the Deepwater Horizon (DWH) oil spill. While hydrocarbon contamination is known to enrich for aerobic, oil-degrading bacteria in deep-seawater habitats, relatively little is known about the response of communities in deep-sea sediments, where low oxygen levels may hinder such a response. Here, we examined the hypothesis that increased hydrocarbon exposure results in an altered sediment microbial community structure that reflects the prospects for oil biodegradation under the prevailing conditions. We explore this hypothesis using metagenomic analysis and metabolite profiling of deep-sea sediment samples following the DWH oil spill. The presence of aerobic microbial communities and associated functional genes was consistent among all samples, whereas, a greater number of Deltaproteobacteria and anaerobic functional genes were found in sediments closest to the DWH blowout site. Metabolite profiling also revealed a greater number of putative metabolites in sediments surrounding the blowout zone relative to a background site located 127 km away. The mass spectral analysis of the putative metabolites revealed that alkylsuccinates remained below detection levels, but a homologous series of benzylsuccinates (with carbon chain lengths from 5 to 10) could be detected. Our findings suggest that increased exposure to hydrocarbons enriches for Deltaproteobacteria, which are known to be capable of anaerobic hydrocarbon metabolism. We also provide evidence for an active microbial community metabolizing aromatic hydrocarbons in deep-sea sediments of the Gulf of Mexico.

Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium

Carbon flow in a model methanogenic consortium capable of hydrocarbon degradation was investigated using a combination of stable isotope fractionation, protein-based stable isotope probing, and metaproteomics. Overall δ(13) C enrichment for methane and CO2 in the presence and absence of oil suggests that complex microbial interactions occur during methanogenic hydrocarbon mineralization. Specifically, the Δδ(13) C of CO2 was statistically identical in all incubations irrespective of oil presence, but the Δδ(13) C for methane was greater in the presence of oil compared with fatty acids alone. In addition, carbon from uniformly ((13) C) labelled n-fatty acids was distributed evenly among consortium members in the presence of oil, but used by relatively few community members when provided alone. In all incubations, aceticlastic and hydrogenotrophic methanogens were labelled to an equal extent, suggesting that no pathway is overwhelmingly dominant during methane production by the model consortium. Protein-based stable isotope probing identified key enzymes responsible for methanogenesis from CO2 and acetate labelled with 78.0 ± 4.4% and 73.3 ± 1.0% (13) C respectively. Results suggest that acetate was used directly by methanogens in the presence of n-fatty acids alone, and that methanogenesis from CO2 was a secondary process. Proteins capable of catalysing hydrocarbon activation by addition to fumarate were not found. Collectively, this study demonstrates that significant microbial cooperation is required to recover hydrocarbons as methane.

Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin

The bioconversion of coal to methane in the San Juan Basin, New Mexico, was investigated. Production waters were analyzed via enrichment studies, metabolite-profiling, and culture-independent methods. Analysis of 16S rRNA gene sequences indicated the presence of methanogens potentially capable of acetoclastic, hydrogenotrophic, and methylotrophic metabolisms, predominantly belonging to the Methanosarcinales and Methanomicrobiales. Incubations of produced water and coal readily produced methane, but there was no correlation between the thermal maturity and methanogenesis. Coal methanogenesis was greater when samples with a greater richness of Firmicutes were utilized. A greater archaeal diversity was observed in the presence of several aromatic and short-chain fatty acid metabolites. Incubations amended with lactate, hydrogen, formate, and short-chain alcohols produced methane above un-amended controls. Methanogenesis from acetate was not observed. Metabolite profiling showed the widespread occurrence of putative aromatic ring intermediates including benzoate, toluic acids, phthalic acids, and cresols. The detection of saturated and unsaturated alkylsuccinic acids indicated n-alkane and cyclic alkane/alkene metabolism. Microarray analysis complemented observations based on hybridization to functional genes related to the anaerobic metabolism of aromatic and aliphatic substrates. These data suggest that coal methanogenesis is unlikely to be limited by methanogen biomass, but rather the activation and degradation of coal constituents.

Intrinsic biodegradation potential of aromatic hydrocarbons in an alluvial aquifer--potentials and limits of signature metabolite analysis and two stable isotope-based techniques

Three independent techniques were used to assess the biodegradation of monoaromatic hydrocarbons and low-molecular weight polyaromatic hydrocarbons in the alluvial aquifer at the site of a former cokery (Flémalle, Belgium). Firstly, a stable carbon isotope-based field method allowed quantifying biodegradation of monoaromatic compounds in situ and confirmed the degradation of naphthalene. No evidence could be deduced from stable isotope shifts for the intrinsic biodegradation of larger molecules such as methylnaphthalenes or acenaphthene. Secondly, using signature metabolite analysis, various intermediates of the anaerobic degradation of (poly-) aromatic and heterocyclic compounds were identified. The discovery of a novel metabolite of acenaphthene in groundwater samples permitted deeper insights into the anaerobic biodegradation of almost persistent environmental contaminants. A third method, microcosm incubations with 13C-labeled compounds under in situ-like conditions, complemented techniques one and two by providing quantitative information on contaminant biodegradation independent of molecule size and sorption properties. Thanks to stable isotope labels, the sensitivity of this method was much higher compared to classical microcosm studies. The 13C-microcosm approach allowed the determination of first-order rate constants for 13C-labeled benzene, naphthalene, or acenaphthene even in cases when degradation activities were only small. The plausibility of the third method was checked by comparing 13C-microcosm-derived rates to field-derived rates of the first approach. Further advantage of the use of 13C-labels in microcosms is that novel metabolites can be linked more easily to specific mother compounds even in complex systems. This was achieved using alluvial sediments where 13C-acenaphthyl methylsuccinate was identified as transformation product of the anaerobic degradation of acenaphthene.

Co-metabolic conversion of toluene in anaerobic n-alkane-degrading bacteria

Diverse microorganisms have been described to degrade petroleum hydrocarbons anaerobically. Strains able to utilize n-alkanes do not grow with aromatic hydrocarbons, whereas strains able to utilize aromatic hydrocarbons do not grow with n-alkanes. To investigate this specificity in more detail, three anaerobic n-alkane degraders (two denitrifying, one sulfate-reducing) and eight anaerobic alkylbenzene degraders (five denitrifying, three sulfate-reducing) were incubated with mixtures of n-alkanes and toluene. Whereas the toluene degradationers formed only the characteristic toluene-derived benzylsuccinate and benzoate, but no n-alkane-derived metabolites, the n-alkane degraders formed toluene-derived benzylsuccinate, 4-phenylbutanoate, phenylacetate and benzoate besides the regular n-alkane-derived (1-methylalkyl)succinates and methyl-branched alkanoates. The co-metabolic conversion of toluene by anaerobic n-alkane degraders to the level of benzoate obviously follows the anaerobic n-alkane degradation pathway with C-skeleton rearrangement and decarboxylation rather than the β-oxidation pathway of anaerobic toluene metabolism. Hence, petroleum-derived aromatic metabolites detectable in anoxic environments may not be exclusively formed by genuine alkylbenzene degraders. In addition, the hitherto largely unexplored fate of fumarate hydrogen during the activation reactions was examined with (2,3-(2) H(2) )fumarate as co-substrate. Deuterium was completely exchanged with hydrogen at the substituted carbon atom (C-2) of the succinate adducts of n-alkanes, whereas it is retained in toluene-derived benzylsuccinate, regardless of the type of enzyme catalysing the fumarate addition reaction.

Field metabolomics and laboratory assessments of anaerobic intrinsic bioremediation of hydrocarbons at a petroleum-contaminated site

Field metabolomics and laboratory assays were used to assess the in situ anaerobic attenuation of hydrocarbons in a contaminated aquifer underlying a former refinery. Benzene, ethylbenzene, 2-methylnaphthalene, 1,2,4- and 1,3,5-trimethylbenzene were targeted as contaminants of greatest regulatory concern (COC) whose intrinsic remediation has been previously reported. Metabolite profiles associated with anaerobic hydrocarbon decay revealed the microbial utilization of alkylbenzenes, including the trimethylbenzene COC, PAHs and several n-alkanes in the contaminated portions of the aquifer. Anaerobic biodegradation experiments designed to mimic in situ conditions showed no loss of exogenously amended COC; however, a substantive rate of endogenous electron acceptor reduction was measured (55 ± 8 µM SO(4) day(-1)). An assessment of hydrocarbon loss in laboratory experiments relative to a conserved internal marker revealed that non-COC hydrocarbons were being metabolized. Purge and trap analysis of laboratory assays showed a substantial loss of toluene, m- and o-xylene, as well as several alkanes (C(6)-C(12)). Multiple lines of evidence suggest that benzene is persistent under the prevailing site anaerobic conditions. We could find no in situ benzene intermediates (phenol or benzoate), the parent molecule proved recalcitrant in laboratory assays and low copy numbers of Desulfobacterium were found, a genus previously implicated in anaerobic benzene biodegradation. This study also showed that there was a reasonable correlation between field and laboratory findings, although with notable exception. Thus, while the intrinsic anaerobic bioremediation was clearly evident at the site, non-COC hydrocarbons were preferentially metabolized, even though there was ample literature precedence for the biodegradation of the target molecules.

Assessing in situ rates of anaerobic hydrocarbon bioremediation

Identifying metabolites associated with anaerobic hydrocarbon biodegradation is a reliable way to garner evidence for the intrinsic bioremediation of problem contaminants. While such metabolites have been detected at numerous sites, the in situ rates of anaerobic hydrocarbon decay remain largely unknown. Yet, realistic rate information is critical for predicting how long individual contaminants will persist and remain environmental threats. Here, single‐well push–pull tests were conducted at two fuel‐contaminated aquifers to determine the in situ biotransformation rates of a suite of hydrocarbons added as deuterated surrogates, including toluene‐d₈, o‐xylene‐d₁₀, m‐xylene‐d₁₀, ethylbenzene‐d₅ (or ‐d₁₀), 1, 2, 4‐trimethylbenzene‐d₁₂, 1, 3, 5‐trimethylbenzene‐d₁₂, methylcyclohexane‐d₁₄ and n‐hexane‐d₁₄. The formation of deuterated fumarate addition and downstream metabolites was quantified and found to be somewhat variable among wells in each aquifer, but generally within an order of magnitude. Deuterated metabolites formed in one aquifer at rates that ranged from 3 to 50 µg l⁻¹ day⁻¹, while the comparable rates at another aquifer were slower and ranged from 0.03 to 15 µg l⁻¹ day⁻¹. An important observation was that the deuterated hydrocarbon surrogates were metabolized in situ within hours or days at both sites, in contrast to many laboratory findings suggesting that long lag periods of weeks to months before the onset of anaerobic biodegradation are typical. It seems clear that highly reduced conditions are not detrimental to the intrinsic bioremediation of fuel‐contaminated aquifers.

Dual biomarkers of anaerobic hydrocarbon degradation in historically contaminated groundwater

This study reports that ongoing in situ anaerobic hydrocarbon biodegradation at a manufactured gas plant impacted site is occurring, 9 years after the initial investigation. Groundwater samples from the site monitoring wells (MW) were analyzed for biomarkers by GC-MS, end-point PCR, and quantitative PCR (qPCR). Metabolic biomarkers included specific intermediates of anaerobic naphthalene and/or 2-methylnaphthalene degradation: 2-naphthoic acid (2-NA); 5,6,7,8-tetrahydro-2-NA (TH-2-NA); hexahydro-2-NA (HH-2-NA); and carboxylated-2-methylnaphthalene (MNA). The analogues of gene bssA, encoding alpha subunit of enzyme benzylsuccinate synthase, were used as a genetic biomarker. Results indicate 1-2 orders of magnitude higher abundance of total bacteria in the impacted wells than in the unimpacted wells. End-point PCR analysis of bssA gene, with degenerate primers, indicated the presence of hydrocarbon degrading bacteria within the plume. In qPCR analysis, using primers based on toluene-degrading denitrifying or sulfate-reducing/methanogenic bacteria, bssA genes were detected only in MW-24, located downstream from the source. Metabolic biomarkers were detected in multiple wells. The highest abundance of 2-NA (6.7 μg/L), TH-2-NA (2.6 μg/L), HH-2-NA, and MNA was also detected in MW-24. The distribution of two independent biomarkers indicates that the site is enriched for anaerobic hydrocarbon biodegradation and provides strong evidence in support of natural attenuation.

Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

To understand how sulphate-reducing bacteria respond to oxidative stresses, the responses of Desulfovibrio vulgaris Hildenborough to H(2)O(2)-induced stresses were investigated with transcriptomic, proteomic and genetic approaches. H(2)O(2) and induced chemical species (e.g. polysulfide, ROS) and redox potential shift increased the expressions of the genes involved in detoxification, thioredoxin-dependent reduction system, protein and DNA repair, and decreased those involved in sulfate reduction, lactate oxidation and protein synthesis. A gene coexpression network analysis revealed complicated network interactions among differentially expressed genes, and suggested possible importance of several hypothetical genes in H(2)O(2) stress. Also, most of the genes in PerR and Fur regulons were highly induced, and the abundance of a Fur regulon protein increased. Mutant analysis suggested that PerR and Fur are functionally overlapped in response to stresses induced by H(2)O(2) and reaction products, and the upregulation of thioredoxin-dependent reduction genes was independent of PerR or Fur. It appears that induction of those stress response genes could contribute to the increased resistance of deletion mutants to H(2)O(2)-induced stresses. In addition, a conceptual cellular model of D. vulgaris responses to H(2)O(2) stress was constructed to illustrate that this bacterium may employ a complicated molecular mechanism to defend against the H(2)O(2)-induced stresses.

Metabolites indicate hot spots of biodegradation and biogeochemical gradients in a high-resolution monitoring well

Anaerobic degradation processes play an important role in contaminated aquifers. To indicate active biodegradation processes signature metabolites can be used. In this study field samples from a high-resolution multilevel well in a tar oil-contaminated, anoxic aquifer were analyzed for metabolites by liquid chromatography-tandem mass spectrometry and time-of-flight mass spectrometry. In addition to already known specific degradation products of toluene, xylenes, and naphthalenes, the seldom reported degradation products benzothiophenemethylsuccinic acid (BTMS), benzofuranmethylsuccinic acid (BFMS), methylnaphthyl-2-methylsuccinic acid (MNMS), and acenaphthene-5-carboxylic acid (AC) could be identified (BFMS, AC) and tentatively identified (BTMS, MNMS). The occurrence of BTMS and BFMS clearly show that the fumarate addition pathway, known for toluene and methylnaphthalene, is also important for the anaerobic degradation of heterocyclic contaminants in aquifers. The molar concentration ratios of metabolites and their related parent compounds differ over a wide range which shows that there is no simple and consistent quantitative relation. However, generally higher ratios were found for the more recalcitrant compounds, which are putatively cometabolically degraded (e.g., 2-carboxybenzothiophene and acenaphthene-5-carboxylic acid), indicating an accumulation of these metabolites. Vertical concentration profiles of benzylsuccinic acid (BS) and methyl-benzylsuccinic acid (MBS) showed distinct peaks at the fringes of the toluene and xylene plume indicating hot spots of biodegradation activity and supporting the plume fringe concept. However, there are some compounds which show a different vertical distribution with the most prominent concentrations where also the precursor compounds peaked.

Diversity of benzyl- and alkylsuccinate synthase genes in hydrocarbon-impacted environments and enrichment cultures

Hydrocarbon-degrading microorganisms play an important role in the natural attenuation of spilled petroleum in a variety of anoxic environments. The role of benzylsuccinate synthase (BSS) in aromatic hydrocarbon degradation and its use as a biomarker for field investigations are well documented. The recent discovery of alkylsuccinate synthase (ASS) allows the opportunity to test whether its encoding gene, assA, can serve as a comparable biomarker of anaerobic alkane degradation. Degenerate assA- and bssA-targeted PCR primers were designed in order to survey the diversity of genes associated with aromatic and aliphatic hydrocarbon biodegradation in petroleum-impacted environments and enrichment cultures. DNA was extracted from an anaerobic alkane-degrading isolate (Desulfoglaeba alkenexedens ALDC), hydrocarbon-contaminated river and aquifer sediments, a paraffin-degrading enrichment, and a propane-utilizing mixed culture. Partial assA and bssA genes were PCR amplified, cloned, and sequenced, yielding several novel clades of assA genes. These data expand the range of alkane-degrading conditions for which relevant gene sequences are available and indicate that considerable diversity of assA genes can be found in hydrocarbon-impacted environments. The detection of genes associated with anaerobic alkane degradation in conjunction with the in situ detection of alkylsuccinate metabolites was also demonstrated. Comparable molecular signals of assA/bssA were not found when environmental metagenome databases of uncontaminated sites were searched. These data confirm that the assA gene is a useful biomarker for anaerobic alkane metabolism.

Current approaches for the assessment of in situ biodegradation

Considering the high costs and technical difficulties associated with conventional remediation strategies, in situ biodegradation has become a promising approach for cleaning up contaminated aquifers. To verify if in situ biodegradation of organic contaminants is taking place at a contaminated site and to determine if these processes are efficient enough to replace conventional cleanup technologies, a comprehensive characterization of site-specific biodegradation processes is essential. In recent years, several strategies including geochemical analyses, microbial and molecular methods, tracer tests, metabolite analysis, compound-specific isotope analysis, and in situ microcosms have been developed to investigate the relevance of biodegradation processes for cleaning up contaminated aquifers. In this review, we outline current approaches for the assessment of in situ biodegradation and discuss their potential and limitations. We also discuss the benefits of research strategies combining complementary methods to gain a more comprehensive understanding of the complex hydrogeological and microbial interactions governing contaminant biodegradation in the field.

Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities

Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon, with standard treatment methods targeting mesophilic sulfate-reducing bacteria. In assessing biocorrosion potential at an Alaskan North Slope oil field, we identified thermophilic hydrogen-using methanogens, syntrophic bacteria, peptide- and amino acid-fermenting bacteria, iron reducers, sulfur/thiosulfate-reducing bacteria, and sulfate-reducing archaea. These microbes can stimulate metal corrosion through production of organic acids, CO2, sulfur species, and via hydrogen oxidation and iron reduction, implicating many more types of organisms than are currently targeted. Micromolar quantities of putative anaerobic metabolites of C1-C4 n-alkanes in pipeline fluids were detected, implying that these low molecular weight hydrocarbons, routinely reinjected into reservoirs for oil recovery purposes, are biodegraded and can provide biocorrosive microbial communities with an important source of nutrients.

Polarizability and spin density correlate with the relative anaerobic biodegradability of alkylaromatic hydrocarbons

Polarizability ((alpha) and spin density (SD) of benzyl radical intermediates calculated using Gaussian O3 were correlated with the extent of anaerobic biodegradation for 17 C1 to C4 parent alkylbenzenes. The percent anaerobic biodegradation of the hydrocarbon series was determined in a previous study using an inoculum from a gas condensate-contaminated aquifer incubated under sulfate-reducing conditions. Many of the parent compounds are known to be biodegraded in the absence of oxygen by fumarate addition reactions. Percent biodegradation over a 100 day incubation (predicted) = -1.044 <alpha> + 908.271SD - 586.197 (R2 = 0.839; all p-values < or = 0.058). This correlation suggests that compounds forming more stable alkylbenzyl radical intermediates biodegrade by fumarate addition more slowly than their counterparts forming less stable radicals. More highly substituted molecules including isopropylbenzene, 1-ethyl-2,6-dimethylbenzene and 1-ethyl-3,4-dimethylbenzene did not fit the model. The assumption of biodegradation by fumarate addition reaction was independently verified with several substrates. These findings help form a basis for predicting the relative rate of alkylbenzene metabolism in anaerobic environments.

Comparative assessments of benzene, toluene, and xylene natural attenuation by quantitative polymerase chain reaction analysis of a catabolic gene, signature metabolites, and compound-specific isotope analysis

A controlled-release study conducted at Vandenberg Air Force Base involved the injection of anaerobic groundwater amended with benzene, toluene, and o-xylene (BToX; 1-3 mg/L each) in two parallel lanes: lane A injectate contained no ethanol, whereas lane B injectate contained approximately 500 mg/L ethanol. As reported previously by Mackay and co-workers, ethanol led to slower BToX disappearance in lane B. Here, we report on assessments of BToX natural attenuation by three independent and specific monitoring approaches: signature metabolites diagnostic of anaerobic TX metabolism (benzysuccinates), compound-specific isotope analysis (CSIA), and quantitative polymerase chain reaction (qPCR) analysis of a catabolic gene involved in anaerobic TX degradation (bssA). In combination, the three monitoring methods provided strong evidence of in situ TX biodegradation in both lanes A and B; however, no single method provided strong evidence for TX biodegradation in both lanes. Benzylsuccinates were detected almost exclusively in lane B, where slower TX degradation and higher residual TX concentrations led to higher metabolite concentrations. In contrast, CSIA provided evidence of TX biodegradation almost exclusively in lane A, as greater degradation rates led to more pronounced isotopic enrichment. qPCR analyses of bssA were more complex. Evidence of increases in bssA copy number (up to 200-fold) after the release started was stronger in lane A, but higher absolute bssA copy number (and bacterial abundance, based on 16S rRNA genes) was observed in lane B, where bacteria genetically capable of anaerobic TX degradation may have been growing primarily on ethanol or its metabolites rather than TX.

Bioenergy production via microbial conversion of residual oil to natural gas

World requirements for fossil energy are expected to grow by more than 50% within the next 25 years, despite advances in alternative technologies. Since conventional production methods retrieve only about one-third of the oil in place, either large new fields or innovative strategies for recovering energy resources from existing fields are needed to meet the burgeoning demand. The anaerobic biodegradation of n-alkanes to methane gas has now been documented in a few studies, and it was speculated that this process might be useful for recovering energy from existing petroleum reservoirs. We found that residual oil entrained in a marginal sandstone reservoir core could be converted to methane, a key component of natural gas, by an oil-degrading methanogenic consortium. Methane production required inoculation, and rates ranged from 0.15 to 0.40 micromol/day/g core (or 11 to 31 micromol/day/g oil), with yields of up to 3 mmol CH(4)/g residual oil. Concomitant alterations in the hydrocarbon profile of the oil-bearing core revealed that alkanes were preferentially metabolized. The consortium was found to produce comparable amounts of methane in the absence or presence of sulfate as an alternate electron acceptor. Cloning and sequencing exercises revealed that the inoculum comprised sulfate-reducing, syntrophic, and fermentative bacteria acting in concert with aceticlastic and hydrogenotrophic methanogens. Collectively, the cells generated methane from a variety of petroliferous rocks. Such microbe-based methane production holds promise for producing a clean-burning and efficient form of energy from underutilized hydrocarbon-bearing resources.

Evidence for in situ degradation of mono-and polyaromatic hydrocarbons in alluvial sediments based on microcosm experiments with 13C-labeled contaminants

A microcosm study was conducted to investigate the degradation of mono- and polyaromatic hydrocarbons under in situ-like conditions using alluvial sediments from the site of a former cokery. Benzene, naphthalene, or acenaphthene were added to the sediments as (13)C-labeled substrates. Based on the evolution of (13)C-CO(2) determined by gas chromatography isotope-ratio mass spectrometry (GC-IRMS) it was possible to prove mineralization of the compound of interest in the presence of other unknown organic substances of the sediment material. This new approach was suitable to give evidence for the intrinsic biodegradation of benzene, naphthalene, and acenaphthene under oxic and also under anoxic conditions, due to the high sensitivity and reproducibility of (13)C/(12)C stable isotope analysis. This semi-quantitative method can be used to screen for biodegradation of any slowly degrading, strongly sorbing compound in long-term experiments.

Anaerobic biodegradation of 4-alkylphenols in a paddy soil microcosm supplemented with nitrate

Anaerobic degradation of phenol, p-cresol, 4-n-propylphenol (n-PP), 4-i-propylphenol (i-PP), 4-n-butylphenol (n-BP) and 4-sec-butylphenol (sec-BP) was observed in a paddy soil supplemented with nitrate. We detected the metabolites 4'-hydroxypropiophenone (HPP) from n-PP, 4-i-propenylphenol from i-PP, and 4-(1-butenyl)phenol and 4'-hydroxybutyrophenone (HBP) from n-BP. Compared with the original soils, Betaproteobacteria became predominant in the microcosm during the degradation of phenol and p-cresol whereas no remarkable change was observed in the community degrading propylphenols and butylphenols. The microcosm, however, did not degrade 4-t-butylphenol (t-BP), 4-t-octylphenol (t-OP) and 4-n-octylphenol (n-OP). Paddy soil supplemented with sulfate or iron (III) as electron acceptors did not degrade phenol and 4-alkylphenols with the exception of the degradation of p-cresol in sulfate-reducing conditions. It was demonstrated for the first time that anaerobic microbial degradation of alkylphenols, in a paddy soil supplemented with nitrate as an electron acceptor, occurred via oxidation of the alpha carbon in the alkyl chain.

Bioremediation and monitoring of aromatic-polluted habitats

Bioremediation may restore contaminated soils through the broad biodegradative capabilities evolved by microorganisms towards undesirable organic compounds. Understanding bioremediation and its effectiveness is rapidly advancing, bringing available molecular approaches for examining the presence and expression of the key genes involved in microbial processes. These methods are continuously improving and require further development and validation of primer- and probe-based analyses and expansion of databases for alternative microbial markers. Phylogenetic marker approaches provide tools to determine which organisms are present or generally active in a community; functional gene markers provide only information concerning the distribution or transcript levels (deoxyribonucleic acid [DNA]- or messenger ribonucleic acid [mRNA]-based approaches) of specific gene populations across environmental gradients. Stable isotope probing methods offer great potential to identify microorganisms that metabolize and assimilate specific substrates in environmental samples, incorporating usually a rare isotope (i.e., (13)C) into their DNA and RNA. DNA and RNA in situ characterization allows the determination of the species actually involved in the processes being measured. DNA microarrays may analyze the expression of thousands of genes in a soil simultaneously. A global analysis of which genes are being expressed under various conditions in contaminated soils will reveal the metabolic status of microorganisms and indicate environmental modifications accelerating bioremediation.

Anaerobic degradation of linear alkylbenzene sulfonates in coastal marine sediments

This research shows for the first time the degradation of linear alkylbenzene sulfonates (LAS) under anaerobic conditions, together with the presence of metabolites and the identification of microorganisms involved in this process. This compound is the most widely used surfactant and its main environmental concern is related to its persistence in the absence of oxygen as LAS accumulates in anaerobic sediments and sewage sludges. Laboratory experiments performed with anoxic marine sediments spiked with 10-50 ppm of LAS demonstrated, however, that its degradation reached 79% in 165 days via the generation of sulfophenyl carboxylic acids (SPCs). Almost all of the added LAS (>99%) was found to be attached to the sediment while the less hydrophobic SPCs were predominant in solution, as their concentration increased progressively up to 3 ppm during the full course of the experiment. Average half-life for LAS has been estimated to be 90 days, although higher values should be expected when the LAS concentration exceeds 20 ppm, due to inhibition of the microbial community. Sulfate-reducing and methanogenic activities proved to be intense during the experiment. Several sulfate-reducing bacteria and firmicutes/clostridia have been identified as possible candidates for effecting this degradation. Our results imply that the persistence of LAS in anoxic compartments, such as marine sediments, should be reconsidered when evaluating its environmental risk.

Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms

In spite of their chemical inertness, hydrocarbons are degraded by microorganisms in the complete absence of oxygen. As all known aerobic hydrocarbon degradation pathways start with oxygen-dependent reactions, hydrocarbon catabolism in anaerobes must be initiated by novel biochemical reactions. In recent years, the enzymes catalyzing oxygen-independent activation of several hydrocarbons have been identified. Surprisingly, a variety of reactions seems to be employed to overcome the activation barrier of different hydrocarbons. This review presents the current understanding on some of these reactions and the associated degradation pathways: oxygen-independent hydroxylation as employed in ethylbenzene metabolism, fumarate addition to methyl or methylene carbons in toluene or alkane degradation, and only recently discovered reactions such as methylation of naphthalene or anaerobic methane oxidation via reverse methanogenesis.

Anaerobic cometabolic transformation of polycyclic and heterocyclic aromatic hydrocarbons: evidence from laboratory and field studies

The sulfate-reducing enrichment culture N47 can grow on naphthalene or 2-methylnaphthalene as the sole carbon and energy source. Here we show that the culture can furthermore cometabolicallytransform a variety of polycyclic and heteroaromatic compounds with naphthalene or methylnaphthalene as the auxiliary substrate. Most of the cosubstrates were converted to the corresponding carboxylic acids, frequently to several isomers. The mass spectra of specific metabolites that were extracted from supernatants of cultures containing the cosubstrates benzothiophene, benzofuran, and 1-methylnaphthalene resembled known intermediates of the anaerobic naphthalene and 2-methylnaphthalene degradation pathways (i.e., naphthyl-2-methylsuccinic acid and naphthyl-2-methylenesuccinic acid). This indicates that some of the tested compounds were first methylated and then transformed to the corresponding methylsuccinic acids by a fumarate addition to the methyl group. For some of the cosubstrates, a partial or total inhibition of growth on the auxiliary substrate was observed. This was not caused by the toxicity of the individual cosubstrate itself, but by a specific combination of auxiliary substrate and cosubstrate. None of the cosubstrates tested could be utilized as the sole carbon source and electron donor by the enrichment culture N47. Field investigations at the tar-oil-contaminated aquifer, where strain N47 originated, revealed the presence of a number of metabolites similar to the ones identified in batch culture supernatants. Our findings suggest that aromatic hydrocarbons and heterocyclic compounds can be converted by aquifer organisms and produce a variety of polar compounds that become mobile in groundwater.

Methylation is the initial reaction in anaerobic naphthalene degradation by a sulfate-reducing enrichment culture

The sulfate-reducing culture N47 can utilize naphthalene or 2-methylnaphthalene as the sole carbon source and electron donor. Here we show that the initial reaction in the naphthalene degradation pathway is a methylation to 2-methylnaphthalene which then undergoes the subsequent oxidation to the central metabolite 2-naphthoic acid, ring reduction and cleavage. Specific metabolites occurring exclusively during anaerobic degradation of 2-methylnaphthalene were detected during growth on naphthalene, i.e. naphthyl-2-methyl-succinate and naphthyl-2-methylene-succinate. Additionally, all three enzymes involved in anaerobic degradation of 2-methylnaphthalene to 2-naphthoic acid that could be measured in vitro so far, i.e. naphthyl-2-methyl-succinate synthase, succinyl-CoA:naphthyl-2-methyl-succinate CoA-transferase and naphthyl-2-methyl-succinyl-CoA dehydrogenase were also detected in naphthalene-grown cells with similar activities. Induction experiments were performed to study the growth behaviour of the cell when transferred from naphthalene to 2-methylnaphthalene or vice versa. When the cells were transferred from naphthalene to 2-methylnaphthalene they grew immediately, indicating that no new enzymes had to be induced. On the contrary, the transfer of cells from 2-methylnaphthalene to naphthalene caused a lag-phase of almost 100 days demonstrating that an additional catabolic enzyme has to be activated in this case. We propose the methylation as a novel general mechanism of activation reactions in anaerobic degradation of unsubstituted aromatic hydrocarbons.

Analysis of anaerobic BTX biodegradation in a subarctic aquifer using isotopes and benzylsuccinates

In situ biodegradation of benzene, toluene, and xylenes in a petroleum hydrocarbon contaminated aquifer near Fairbanks, Alaska was assessed using carbon and hydrogen compound specific isotope analysis (CSIA) of benzene and toluene and analysis of signature metabolites for toluene (benzylsuccinate) and xylenes (methylbenzylsuccinates). Carbon and hydrogen isotope ratios of benzene were between -25.9 per thousand and -26.8 per thousand for delta13C and -119 per thousand and -136 per thousand for delta2H, suggesting that biodegradation of benzene is unlikely at this site. However, biodegradation of both xylenes and toluene were documented in this subarctic aquifer. Biodegradation of xylenes was indicated by the presence of methylbenzylsuccinates with concentrations of 17-50 microg/L in three wells. Anaerobic toluene biodegradation was also indicated by benzylsuccinate concentrations of 10-49 microg/L in the three wells with the highest toluene concentrations (1500-5000 microg/L toluene). Since benzylsuccinate typically accounts for a very small fraction of the toluene present in groundwater (generally <1 mol%), the signature metabolite approach works best at higher toluene concentrations when it is not constrained by detection limits. In wells with lower toluene concentrations (410-640 microg/L), carbon and hydrogen isotopic values were enriched by up to approximately 2 per thousand for delta13C and approximately 70 per thousand for delta2H. This evidence of isotopic fractionation verifies the effects of biodegradation in these low concentration wells where metabolites may already be below detection limits. The combined use of signature metabolite and CSIA data is particularly valuable given the challenge of verifying biodegradation in subarctic environments where degradation rates are typically much slower than in temperate environments.

Anaerobic Degradation of p-Xylene by a Sulfate-Reducing Enrichment Culture

A strictly anaerobic enrichment culture was obtained with p-xylene as organic substrate and sulfate as electron acceptor from an aquifer at a former gasworks plant contaminated with aromatic hydrocarbons. p-Xylene was completely oxidized to CO(2). The enrichment culture depended on Fe(II) in the medium as a scavenger of the produced sulfide. 4-Methylbenzylsuccinic acid and 4-methylphenylitaconic acid were identified in supernatants of cultures indicating that degradation of p-xylene was initiated by fumarate addition to one of the methyl groups. Therefore, p-xylene degradation probably proceeds analogously to toluene degradation by Thauera aromatica or anaerobic degradation pathways for o- and m-xylene.

In situ assessment of biodegradation potential using biotraps amended with 13C-labeled benzene or toluene

Stable isotope fractionation analysis of an aquifer heavily contaminated with benzene (up to 850 mg L(-1)) and toluene (up to 50 mg L(-1)) at a former hydrogenation plant in Zeitz (Saxonia, Germany) has suggested that significant biodegradation of toluene was occurring. However, clear evidence of benzene biodegradation has been lacking at this site. Determining the fate of benzene is often a determining factor in regulatory approval of a risk-based management strategy. The objective of the work described here was the demonstration of a new tool that can be used to provide proof of biodegradation of benzene or other organics by indigenous microorganisms under actual aquifer conditions. Unique in situ biotraps containing Bio-Sep beads, amended with 13C-labeled or 12C nonlabeled benzene and toluene, were deployed at the Zeitz site for 32 days in an existing groundwater monitoring well and used to collect and enrich microbial biofilms. Lipid biomarkers or remaining substrate was extracted from the beads and analyzed by mass spectrometry and molecular methods. Isotopic analysis of the remaining amounts of 13C-labeled contaminants (about 15-18% of the initial loading) showed no alteration of the 12C/13C ratio during incubation. Therefore, no measurable exchange of labeled compounds in the beads by the nonlabeled compounds in the aquifer materials occurred. Isotopic ratio analysis of microbial lipid fatty acids (as methyl ester derivatives) from labeled benzene- and toluene-amended biotraps showed 13C enrichment in several fatty acids of up to delta (13C) 13400%o, clearly verifying benzene and toluene biodegradation and the transformation of the labeled carbon into biomass by indigenous organisms under aquifer conditions. Fatty acid profiles of total lipid fatty acids and the phospholipid fatty acid fraction and their isotopic composition showed significant differences between benzene- and toluene-amended biotraps, suggesting that different microbial communities were involved in the biodegradation of the two compounds.

Propylphenols are metabolites in the anaerobic biodegradation of propylbenzene under iron-reducing conditions

The metabolism of monoaromatic hydrocarbons by an iron-reducing bacterial enrichment culture originating from diesel-contaminated groundwater was examined using d7-propylbenzene as a model hydrocarbon. Sequence analysis of the 16S rDNA gene showed that the dominant part (10 of 10 clones) of the enrichment culture consisted of a bacterium closely related to clones found in benzene-contaminated groundwater and to the iron-reducing beta-proteobacterium, Rhodoferax ferrireducens (similarity values were 99.5% and 98.3%, respectively). In degradation studies conducted over 18 weeks, d7-propylphenols were detected by gas chromatography-mass spectrometry (GC/MS) as intra-cellular metabolites concomitant with cell growth in the cultures. The amount of propylphenols increased during the exponential growth phase, and by the end of this phase 4 x 10(-14) moles of ferric iron were reduced and 3 x 10(-15) moles propylphenol produced for every cell formed. During the stationary growth phase the cell density was approximately 10(7) ml(-1), with significantly correlated amounts of propylphenols. Succinate derivates of propylbenzene or phenylpropanol previously shown to be the initial metabolites in the anaerobic degradation of alkylbenzenes could not be identified. This study is the first to report that oxidation of propylbenzene to propylphenols can initiate anaerobic propylbenzene degradation and that iron-reducing bacteria are responsible for this process. In addition, the study shows the importance of taking account of the metabolites adhering to solid phases when determining the extent of biodegradation, so as not to underestimate the extent of the process.

Determination of microbial carbon sources in petroleum contaminated sediments using molecular 14C analysis

Understanding microbial carbon sources is fundamental to elucidating the role of microbial communities in carbon cycling and in the biodegradation of organic contaminants. Because the majority of anthropogenic contaminants are either directly or indirectly derived from fossil fuels that are devoid of 14C, radiocarbon can be used as a natural inverse tracer of contaminant carbon in the contemporary environment. Here, 14C analysis of individual microbial phospholipid fatty acids (PLFA) was used to characterize the carbon sources utilized bythe active microbial community in salt marsh sediments contaminated by the Florida oil spill of 1969 in Wild Harbor, West Falmouth, MA. A specific goal was to determine whether this community is actively degrading petroleum residues that persist in these sediments. The delta14C values of microbial PLFA in all sediment horizons (contaminated and noncontaminated) matched the delta14C of the total sedimentary organic carbon after petroleum removal, indicating that no measurable metabolism of petroleum residues was occurring. This result agrees with ancillary data such as the delta13C content and distribution of PLFA, and the residual hydrocarbon composition determined by comprehensive two-dimensional gas chromatography (GCxGC) analysis. We hypothesize that microbes have chosen to respire the natural organic matter rather than the residual petroleum hydrocarbons because the former is more labile. Future efforts directed at determining indices of microbial degradation of petroleum hydrocarbons should consider competition with natural organic matter.

Monitoring in situ biodegradation of benzene and toluene by stable carbon isotope fractionation

Intrinsic biodegradation of benzene and toluene in a heavily contaminated aquifer at the site of a former hydrogenation plant was investigated by means of isotope fractionation processes. The carbon isotope compositions of benzene and toluene were monitored in two campaigns within a time period of 12 months to assess the extent of the in situ biodegradation and the stability of the plume over time. The Rayleigh model, applied to calculate the extent of biodegradation and residual theoretical concentrations of toluene, showed that in situ biodegradation was a relevant attenuation process. The biodegradation rate constant for toluene was estimated to be k = 5.7+/-0.5 microM/d in the groundwater flow path downstream of the source area. The spatial distribution of the carbon isotope composition of benzene indicated that in situ biodegradation occurred at marginal zones of the plume where concentrations were lower than 30 mg/L. The vertical structure of the benzene plume provided evidence for in situ degradation processes at the upper and lower fringes of the plume. The results show that isotope fractionation can be used to quantify the extent of microbial in situ degradation in contaminated aquifers and to develop conceptual models for natural attenuation approaches.

Stable isotope fractionation analysis as a tool to monitor biodegradation in contaminated acquifers

The assessment of biodegradation in contaminated aquifers has become an issue of increasing importance in the recent years. To some extent, this can be related to the acceptance of intrinsic bioremediation or monitored natural attenuation as a means to manage contaminated sites. Among the few existing methods to detect biodegradation in the subsurface, stable isotope fractionation analysis (SIFA) is one of the most promising approaches which is pronounced by the drastically increasing number of applications. This review covers the recent laboratory and field studies assessing biodegradation of contaminants via stable isotope analysis. Stable isotope enrichment factors have been found that vary from no fractionation for dioxygenase reactions converting aromatic hydrocarbons over moderate fractionation by monooxygenase reactions (epsilon=-3 per thousand) and some anaerobic studies on microbial degradation of aromatic hydrocarbons (epsilon=-1.7 per thousand) to larger fractionations by anaerobic dehalogenation reactions of chlorinated solvents (epsilon=between -5 per thousand and -30 per thousand). The different isotope enrichment factors can be related to the respective biochemical reactions. Based on that knowledge, we discuss under what circumstances SIFA can be used for a qualitative or even a quantitative assessment of biodegradation in the environment. In a steadily increasing number of cases, it was possible to explain biodegradation processes in the field based on isotope enrichment factors obtained from laboratory experiments with pure cultures and measured isotope values from the field. The review will focus on the aerobic and anaerobic degradation of aromatic hydrocarbons and chlorinated solvents as the major contaminants of groundwater. Advances in the instrumental development for stable isotope analysis are only mentioned if it is important for the understanding of the application.

Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs

Biodegradation of crude oil in subsurface petroleum reservoirs is an important alteration process with major economic consequences. Aerobic degradation of petroleum hydrocarbons at the surface is well documented and it has long been thought that the flow of oxygen- and nutrient-bearing meteoric waters into reservoirs was necessary for in-reservoir petroleum biodegradation. The occurrence of biodegraded oils in reservoirs where aerobic conditions are unlikely, together with the identification of several anaerobic microorganisms in oil fields and the discovery of anaerobic hydrocarbon biodegradation mechanisms, suggests that anaerobic degradation processes could also be responsible. The extent of anaerobic hydrocarbon degradation processes in the world's deep petroleum reservoirs, however, remains strongly contested. Moreover, no organism has yet been isolated that has been shown to degrade hydrocarbons under the conditions found in deep petroleum reservoirs. Here we report the isolation of metabolites indicative of anaerobic hydrocarbon degradation from a large fraction of 77 degraded oil samples from both marine and lacustrine sources from around the world, including the volumetrically important Canadian tar sands. Our results therefore suggest that anaerobic hydrocarbon degradation is a common process in biodegraded subsurface oil reservoirs.

Determination of alkylbenzene metabolites in groundwater by solid-phase extraction and liquid chromatography–tandem mass spectrometry

Benzylsuccinate (BSA), methylbenzylsuccinate (methylBSA), and ethylbenzylsuccinate (ethylBSA) are unambiguous anaerobic biotransformation products from toluene, xylenes, and ethylbenzene decay, respectively, and may be used to indicate intrinsic bioremediation is occurring at hydrocarbon-contaminated sites. In order to improve upon current methods that detect and quantify anaerobic hydrocarbon metabolites in field samples, solid-phase extraction (SPE) and direct sample injection methods coupled with liquid chromatography-tandem mass spectrometry (LC-MS-MS) were evaluated. In laboratory studies, recoveries of authentic standards of non-deuterated or deuterated benzylsuccinates and toluates ranged from 80 to 106% with relative standard errors ranging from 2 to 4%. The method detection limits for these analytes using SPE-LC-MS-MS ranged from 0.006 to 0.029 microg/L whereas those for direct injection-LC-MS-MS ranged from 0.61 to 1.5 microg/L. Given the increased sensitivity of using SPE coupled with LC-MS-MS, this technique was then used to analyze for the presence of putative anaerobic alkylbenzene metabolites in groundwater from a hydrocarbon-contaminated site where single-well push-pull tests were conducted using deuterated aromatic hydrocarbons. Both deuterated and non-deuterated benzylsuccinates and toluates were successfully detected and quantified in field samples using this method.

Survey of archaeal diversity reveals an abundance of halophilic Archaea in a low-salt, sulfide- and sulfur-rich spring

The archaeal community in a sulfide- and sulfur-rich spring with a stream water salinity of 0.7 to 1.0% in southwestern Oklahoma was studied by cloning and sequencing of 16S rRNA genes. Two clone libraries were constructed from sediments obtained at the hydrocarbon-exposed source of the spring and the microbial mats underlying the water flowing from the spring source. Analysis of 113 clones from the source library and 65 clones from the mat library revealed that the majority of clones belonged to the kingdom Euryarchaeota, while Crenarchaeota represented less than 10% of clones. Euryarchaeotal clones belonged to the orders Methanomicrobiales, Methanosarcinales, and Halobacteriales, as well as several previously described lineages with no pure-culture representatives. Those within the Halobacteriales represented 36% of the mat library and 4% of the source library. All cultivated members of this order are obligately aerobic halophiles. The majority of halobacterial clones encountered were not affiliated with any of the currently described genera of the family Halobacteriaceae. Measurement of the salinity at various locations at the spring, as well as along vertical gradients, revealed that soils adjacent to spring mats have a much higher salinity (NaCl concentrations as high as 32%) and a lower moisture content than the spring water, presumably due to evaporation. By use of a high-salt-plus-antibiotic medium, several halobacterial isolates were obtained from the microbial mats. Analysis of 16S rRNA genes indicated that all the isolates were members of the genus Haloferax. All isolates obtained grew at a wide range of salt concentrations, ranging from 6% to saturation, and all were able to reduce elemental sulfur to sulfide. We reason that the unexpected abundance of halophilic Archaea in such a low-salt, highly reduced environment could be explained by their relatively low salt requirement, which could be satisfied in specific locations of the shallow spring via evaporation, and their ability to grow under the prevalent anaerobic conditions in the spring, utilizing zero-valent sulfur compounds as electron acceptors. This study demonstrates that members of the Halobacteriales are not restricted to their typical high-salt habitats, and we propose a role for the Halobacteriales in sulfur reduction in natural ecosystems.