Stable isotope fractionation caused by glycyl radical enzymes during bacterial degradation of aromatic compounds

Quantification of biodegradation rate of hydrocarbons in a contaminated aquifer by CO2 δ13C monitoring at ground surface

Ground surface analysis of CO₂ emissions with δ¹³C determination is experimentally demonstrated to be a potential methodology to monitor, on line, the dynamics of petroleum-hydrocarbon biodegradation in soil aquifers, thanks to the improvement of the Isotopic Ratio Infra Red Spectroscopy technique. Biodegradation rate of remaining hydrocarbon substrates in groundwater can be quantified using basic application of the Rayleigh equations, by δ¹³C_CO2 analysis released at ground surface above the pollution plume instead of usual approaches based on groundwater hydrocarbons δ¹³C analysis, when physical and chemical properties for the contaminated site meet appropriate conditions. The validation approach for that gasoline contaminated specific site is discussed and verified by comparison of first order attenuation rate constant determined from δ¹³C_CO2 analysis emitted at ground surface and from δ¹³C_TOLUENE analysis in ground water. A kinetic fractionation factor α of 0.9979 (or ε value of -2.1 ± 0.5‰) is estimated for the biodegradation of the most reactive hydrocarbon substrates (TEX). The treatment of this Rayleigh equations by linear regression of δ¹³C_CO2 values along the predominant direction of groundwater flow leads to the following results and conclusions for that site: (i) first order biodegradation rate constants (and annual variation) are maximum after the activation of a Permeable Reactive Barrier (PRB) in May 2014: 0.92(+0.29-0.17) year^-1, and during July and October: 0.46(+0.14-0.09) year^-1 and minimum in mid-winter in February 2015: 0.17(+0.05-0.03) year^-1, given by the estimation range for ε. These results are in the lower range with reported in literature for similar contaminated sites (1.6-18 year^-1) considering natural attenuation under sulfate reducing conditions and (ii) the seasonal variation of the first order biodegradation rate constant is mainly correlated with the seasonal variation of the CO₂ flux, where maximum values are in summers and minimum values in winters. Both seasonal variations are mainly due to the annual cycle of the natural biodegradation activity at the scale of the pollution plume, rather than the activation of the PRB. This work demonstrates that δ¹³C_CO2 analysis released at ground surface from biodegradation of groundwater hydrocarbons could provide, under characterized and appropriate conditions, a non-intrusive (without soil samplings), fast, and low-cost online method to monitor and therefore to optimize soil remediation processes in real time. (Monitored Natural Attenuation or Enhanced Bioremediation).

Carbon and hydrogen stable isotope fractionation of sulfamethoxazole during anaerobic transformation catalyzed by Desulfovibrio vulgaris Hildenborough

The fate of antibiotics in aquatic environments is of high concern and approaches are needed to assess the transformation of antibiotics in wastewater treatment plants. Here we used the model organism Desulfovibrio vulgaris Hildenborough to analyze compound specific isotope fractionation associated with anaerobic transformation of the antibiotic sulfamethoxazole (SMX). The results show that the rearrangement of the isoxazole ring in SMX is leading to significant carbon and hydrogen isotopic fractionation (εC = -5.8 ± 0.7‰, εH = -34 ± 9‰) during anaerobic transformation. The observed carbon isotopic fractionation is significantly higher than the values reported for aerobic degradation (εC = -0.6 ± 0.1‰) or abiotic reactions (εC = -0.8 to -4.8‰ for photolysis, εC = -0.8 to -2.2‰ for advanced oxidation). This indicates that carbon isotope fractionation can be used as a parameter to differentiate reaction mechanisms of SMX transformation. The corresponding apparent kinetic isotope effect (AKIEC) for anaerobic transformation of SMX was 1.029 ± 0.003, suggesting that the mechanism for anaerobic transformation is distinct from the mechanism reported for microbial aerobic degradation (AKIEC = 1.006 ± 0.001). In addition, dual-element (C-H) isotope analysis of SMX was performed in the present study, which was achieved by utilizing gas chromatography (GC) as the separation method instead of routine liquid chromatography. This dual-element isotope analysis resulted in a Λ value of 4.5 ± 2.2. Overall, compound specific isotope analysis can be a feasible tool to monitor the mitigation of SMX in wastewater treatment plants.

Laboratory Experiments to Evaluate the Effectiveness of Persulfate to Oxidize BTEX in Saline Environment and at Elevated Temperature Using Stable Isotopes

In this study, batch experiments were carried out to investigate the effectiveness of persulfate (PS) as an oxidant agent to remediate benzene, toluene, ethylbenzene, and xylenes (BTEX) in saline environments and at high water temperatures (30 °C). This hydrological setting is quite common in contaminated groundwater aquifers in Middle Eastern countries. In general, increasing the system temperature from 10 to 30 °C greatly enhanced the effectiveness of PS, and resulted in a faster oxidation rate for the target contaminants. When PS was added to the reactor at 30 °C, the targeted contaminants were almost completely oxidized over a 98-day reaction period. During the chemical oxidation of the BTEX, carbon and hydrogen isotope fractionations were monitored and utilized as potential proof of contaminant degradation. The calculated carbon-enrichment values were −1.9‰ for benzene, −1.5‰ for ethylbenzene and toluene, −0.4‰ for ρ,m-xylene, and −1.4‰ for o-xylene, while the hydrogen enrichment values were −9.5‰, −6.8‰, −2.1‰, −6.9‰, and −9.1‰, respectively. In comparison with other processes, the hydrogen and carbon isotope fractionations during the chemical oxidation by PS were smaller than the isotope fractionations resulting from sulfate reduction and denitrification. This observation demonstrates the differences in the transformation pathways and isotope fractionations when compounds undergo chemical oxidation or biodegradation. The distinct trend observed on the dual isotope plot (Δδ13C vs. Δδ2H) suggests that compound-specific isotope analysis can be utilized to monitor the chemical oxidation of BTEX by PS, and to distinguish treatment zones where PS and biodegradation technologies are applied simultaneously.

Quantifying biodegradation rate constants of o-xylene by combining compound-specific isotope analysis and groundwater dating

The objective of this study is to estimate hydraulic conductivities and biodegradation rate constants in a coal-tar contaminated aquifer by compound-specific isotope analysis (CSIA) and tracer-based (³H-³He) groundwater dating (TGD). In two observation wells downgradient from the contaminant source in situ biodegradation of o-xylene, toluene and naphthalene under sulfate-reducing redox conditions could be demonstrated using CSIA. Median biodegradation rate constants for o-xylene ranging between 0.08 and 0.22 a^-1 were estimated. By using tracer-based groundwater dating in these two wells, hydraulic conductivities could be also estimated, which are in a similar range as k-values derived from sieve analysis, a pumping test and a calibrated groundwater flow model. These results clearly demonstrate the applicability of tracer-based groundwater dating for the determination of in situ hydraulic conductivities in aquifers without pumping contaminated groundwater. Finally, a sensitivity analysis is performed using a Monte Carlo simulation. These results indicate high sensitivities of the assumed effective porosity for the estimation of the hydraulic conductivity and the selected isotope enrichment factor for the biodegradation rate constant, respectively. Conversely, the outcome also evidently demonstrates the main limitations of the novel combined isotope approach for a successful implementation of monitored natural attenuation (MNA) at such field sites.

The dissolution and microbial degradation of mobile aromatic hydrocarbons from a Pintsch gas tar DNAPL source zone

Source zones containing tar, a dense non-aqueous phase liquid (DNAPL), can contaminate groundwater for centuries. A common occurrence of tar is at former Pintsch gas factories. Little is known about the composition and fate of contaminants dissolving from Pintsch gas tar DNAPL. In this study, we determined the composition and water-soluble characteristics of mobile aromatic hydrocarbons and their biodegradation metabolites in the DNAPL contaminated groundwater at a former Pintsch gas tar plant. We assessed the factors that determine the fate of observed groundwater contaminants. Measured values of density (1.03-1.06 kg/m³) and viscosity (18.6-39.4 cP) were found to be relatively low compared to common coal tars. Analysis showed that unlike common coal tars phenanthrene is the primary component rather than naphthalene. Moreover, it was found that Pintsch gas tar contains a relatively high amount of light molecular aromatic hydrocarbon compounds, such as benzene, toluene, ethylbenzene and xylenes (BTEX). Less commonly reported components, such as styrene, ethyltoluenes, di-ethylbenzene, 1,2,4,5-tetramethylbenzene, were also detected in water extracts from Pintsch gas tar. Moreover, 46 relatively hydrophilic metabolites were found within the tar samples. Metabolites present within the tar suggest biodegradation of mobile aromatic Pintsch gas tar compounds occurred near the DNAPL. Based on eleven detected suspect metabolites, a novel anaerobic biodegradation pathway is proposed for indene. Overall, our findings indicate that Pintsch gas tar has higher invasive and higher flux properties than most coal tars due to its relatively low density, low viscosity and, high content of water-soluble compounds. The partitioning of contaminants from multi-component DNAPL into the aqueous phase and re-dissolution of their slightly less hydrophobic metabolites back from the aqueous phase into the DNAPL is feasible and demonstrates the complexity of assessing degradation processes within a source zone.

Nitrate attenuation in low-permeability sediments based on isotopic and microbial analyses

This study investigated nitrate attenuation in low-permeability sediments (LPS) in a multi-layer aquifer by integrating hydrochemical, isotopic and microbiological molecular techniques in a field site. In the meantime, the overlying high-permeability sediment (HPS) was also examined on the nitrate attenuation for the sake of comparison. Additionally, laboratory flow-through experiments were conducted to assess the overall nitrate reduction rate in the two types of sediment. The δ¹⁵N-NO₃^- and δ³⁴S-SO₄^2- values were more enriched by approximately 37‰ and 15‰ in the LPS than the overlying HPS associated with substantial reductions of the NO₃^- and SO₄^2- concentration, indicating the occurrence of strong bio-reductions in nitrate and sulfate. The microbial community diversity analyses showed a higher diversity of the denitrifiers encoding nirS- (Shannon Index SI=6.3) and nrf-type gene (SI=2.7), and the sulfate reduction bacteria (SRB) encoding the dsr gene (SI=6.4) in the LPS than in the HPS. The bacterial community structure was influenced by the groundwater hydrochemistry and the redox conditions. Due to the presence of anoxic groundwater with low levels of nutrients, the LPS featured higher abundances of nitrate reducers belonging to Alphaproteobacteria and SRB belonging to the strictly anaerobic class Clostridia relative to the HPS. Notably, chemolithotrophs were abundant in the LPS and likely coupled the reduction of nitrate with the oxidation of iron. Furthermore, the LPS was demonstrated to attenuate nitrate at a rate two times of the HPS in flow-through experiments, and denitrification accounted for approximately 93% of the nitrate reduction. The high nitrate reduction rate of the LPS was likely attributable to its high functional genes diversity. This study confirmed the occurrence of strong nitrate attenuation in the LPS. The LPS was found to play a significant role in protecting aquifers from anthropogenic contamination.

Relating Carbon and Nitrogen Isotope Effects to Reaction Mechanisms during Aerobic or Anaerobic Degradation of RDX (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine) by Pure Bacterial Cultures

Kinetic isotopic fractionation of carbon and nitrogen during RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) biodegradation was investigated with pure bacterial cultures under aerobic and anaerobic conditions. Relatively large bulk enrichments in (15)N were observed during biodegradation of RDX via anaerobic ring cleavage (ε(15)N = -12.7‰ ± 0.8‰) and anaerobic nitro reduction (ε(15)N = -9.9‰ ± 0.7‰), in comparison to smaller effects during biodegradation via aerobic denitration (ε(15)N = -2.4‰ ± 0.2‰). (13)C enrichment was negligible during aerobic RDX biodegradation (ε(13)C = -0.8‰ ± 0.5‰) but larger during anaerobic degradation (ε(13)C = -4.0‰ ± 0.8‰), with modest variability among genera. Dual-isotope ε(13)C/ε(15)N analyses indicated that the three biodegradation pathways could be distinguished isotopically from each other and from abiotic degradation mechanisms. Compared to the initial RDX bulk δ(15)N value of +9‰, δ(15)N values of the NO2 (-) released from RDX ranged from -7‰ to +2‰ during aerobic biodegradation and from -42‰ to -24‰ during anaerobic biodegradation. Numerical reaction models indicated that N isotope effects of NO2 (-) production were much larger than, but systematically related to, the bulk RDX N isotope effects with different bacteria. Apparent intrinsic ε(15)N-NO2 (-) values were consistent with an initial denitration pathway in the aerobic experiments and more complex processes of NO2 (-) formation associated with anaerobic ring cleavage. These results indicate the potential for isotopic analysis of residual RDX for the differentiation of degradation pathways and indicate that further efforts to examine the isotopic composition of potential RDX degradation products (e.g., NOx) in the environment are warranted.

IMPORTANCE

This work provides the first systematic evaluation of the isotopic fractionation of carbon and nitrogen in the organic explosive RDX during degradation by different pathways. It also provides data on the isotopic effects observed in the nitrite produced during RDX biodegradation. Both of these results could lead to better understanding of the fate of RDX in the environment and help improve monitoring and remediation technologies.

Modeling of the Reaction Mechanism of Enzymatic Radical C-C Coupling by Benzylsuccinate Synthase

Molecular modeling techniques and density functional theory calculations were performed to study the mechanism of enzymatic radical C–C coupling catalyzed by benzylsuccinate synthase (BSS). BSS has been identified as a glycyl radical enzyme that catalyzes the enantiospecific fumarate addition to toluene initiating its anaerobic metabolism in the denitrifying bacterium Thauera aromatica, and this reaction represents the general mechanism of toluene degradation in all known anaerobic degraders. In this work docking calculations, classical molecular dynamics (MD) simulations, and DFT+D2 cluster modeling was employed to address the following questions: (i) What mechanistic details of the BSS reaction yield the most probable molecular model? (ii) What is the molecular basis of enantiospecificity of BSS? (iii) Is the proposed mechanism consistent with experimental observations, such as an inversion of the stereochemistry of the benzylic protons, syn addition of toluene to fumarate, exclusive production of (R)-benzylsuccinate as a product and a kinetic isotope effect (KIE) ranging between 2 and 4? The quantum mechanics (QM) modeling confirms that the previously proposed hypothetical mechanism is the most probable among several variants considered, although C–H activation and not C–C coupling turns out to be the rate limiting step. The enantiospecificity of the enzyme seems to be enforced by a thermodynamic preference for binding of fumarate in the pro(R) orientation and reverse preference of benzyl radical attack on fumarate in pro(S) pathway which results with prohibitively high energy barrier of the radical quenching. Finally, the proposed mechanism agrees with most of the experimental observations, although the calculated intrinsic KIE from the model (6.5) is still higher than the experimentally observed values (4.0) which suggests that both C–H activation and radical quenching may jointly be involved in the kinetic control of the reaction.

Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons

Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.

Characterization of phenol and cresol biodegradation by compound-specific stable isotope analysis

Microbial degradation of phenol and cresols can occur under oxic and anoxic conditions by different degradation pathways. One recent technique to take insight into reaction mechanisms is compound-specific isotope analysis (CSIA). While enzymes and reaction mechanisms of several degradation pathways have been characterized in (bio)chemical studies, associated isotope fractionation patterns have been rarely reported, possibly due to constraints in current analytical methods. In this study, carbon enrichment factors and apparent kinetic isotope effects (AKIEc) of the initial steps of different aerobic and anaerobic phenol and cresols degradation pathways were analyzed by isotope ratio mass spectrometry connected with liquid chromatography (LC-IRMS). Significant isotope fractionation was detected for aerobic ring hydroxylation, anoxic side chain hydroxylation, and anoxic fumarate addition, while anoxic carboxylation reactions produced small and inconsistent fractionation. The results suggest that several microbial degradation pathways of phenol and cresols are detectable in the environment by CSIA.

Carbon isotopic fractionation during biodegradation of phthalate esters in anoxic condition

Here we evaluate the quantitative relationship between carbon isotopic fractionation and anoxic biodegradation of phthalate esters (PAEs), a kind of endocrine disruptors. The stable carbon isotope delta values (δ(13)C) of 4 PAEs, i.e. di-methyl phthalate (DMP), di-ethyl phthalate (DEP), di-n-butyl phthalate (DBP), and di-iso-butyl phthalate (DiBP), were analyzed during biodegradation by a pure bacteria strain isolated from the shallow aquifer sediment in anoxic condition. Results showed that the carbon isotopic fractionation in the initial degradation of PAEs was well-described by the Rayleigh equation model with R(2) from 0.8885 to 0.9821. The carbon isotopic fractionation (ε) for DMP and DEP were -4.6±0.4‰ and -2.9±0.1‰, respectively, while DBP and DiBP showed limited isotopic fractionation. A linear relationship between ε values and the total carbon atoms present in straight-carbon-chain PAE molecules with R(2) of 0.9918. The apparent kinetic isotope effects (AKIEs) were calculated for proposed 4 initial transformation pathways of PAEs. The high carbon AKIEs of 1.048 and 1.036 were obtained for single enzymatic hydrolysis of DMP and DEP, respectively, and fell in the expected KIE range of 1.03-1.09. However, the intrinsic carbon isotope effects for enzymatic hydrolysis of DBP and DiBP might be masked.

C & N isotope analysis of diclofenac to distinguish oxidative and reductive transformation and to track commercial products

Although diclofenac is frequently found in aquatic systems, its degradability in the environment remains imperfectly understood. On the one hand, evidence from concentration analysis alone is inconclusive if an unknown hydrology impedes a distinction between degradation and dilution. On the other hand, not all transformation products may be detectable. As a new approach, we therefore developed GC-IRMS (gas chromatography-isotope-ratio mass-spectrometry) analysis for carbon and nitrogen isotope measurements of diclofenac. The method uses a derivatization step that can be conducted either online or offline, for optimized throughput or sensitivity, respectively. In combination with on-column injection, the latter method enables determination of diclofenac isotope ratios down to the sub-μgL(-1) range in environmental samples. Degradation in an aerobic sediment-water system showed strong nitrogen isotope fractionation (εN = -7.1‰), whereas reductive diclofenac dechlorination was associated with significant carbon isotope fractionation (εC = -2.0‰). Hence dual element isotope analysis bears potential not only to detect diclofenac degradation, but even to distinguish both transformation pathways in the environment. In an explorative survey, analysis of commercial diclofenac products showed significant differences in carbon and nitrogen isotope ratios, demonstrating a further potential to track, and potentially even to authenticate, commercial production batches.

Evidence for benzylsuccinate synthase subtypes obtained by using stable isotope tools

We studied the benzylsuccinate synthase (Bss) reaction mechanism with respect to the hydrogen-carbon bond cleavage at the methyl group of toluene by using different stable isotope tools. Λ values (slopes of linear regression curves for carbon and hydrogen discrimination) for two-dimensional compound-specific stable isotope analysis (2D-CSIA) of toluene activation by Bss-containing cell extracts (in vitro studies) were found to be similar to previously reported data from analogous experiments with whole cells (in vivo studies), proving that Λ values generated by whole cells are caused by Bss catalysis. The Bss enzymes of facultative anaerobic bacteria produced smaller Λ values than those of obligate anaerobes. In addition, a partial exchange of a single deuterium atom in benzylsuccinate with hydrogen was observed in experiments with deuterium-labeled toluene. In this study, the Bss enzymes of the tested facultative anaerobes showed 3- to 8-fold higher exchange probabilities than those for the enzymes of the tested obligate anaerobic bacteria. The phylogeny of the Bss variants, determined by sequence analyses of BssA, the gene product corresponding to the α subunit of Bss, correlated with the observed differences in Λ values and hydrogen exchange probabilities. In conclusion, our results suggest subtle differences in the reaction mechanisms of Bss isoenzymes of facultative and obligate anaerobes and show that the putative isoenzymes can be differentiated by 2D-CSIA.

Insight on RDX degradation mechanism by Rhodococcus strains using 13C and 15N kinetic isotope effects

The explosive Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is known to be degraded aerobically by various isolates of the Rhodococcus species, with denitration being the key step, mediated by Cytochrome P450. Our study aimed at gaining insight into the RDX degradation mechanism by Rhodococcus species and comparing isotope effects associated with RDX degradation by distinct Rhodococcus strains. For these purposes, enrichment in (13)C and (15)N isotopes throughout RDX denitration was studied for three distinct Rhodococcus strains, isolated from soil and groundwater in an RDX-contaminated site. The observable (15)N enrichment throughout the reaction, together with minor (13)C enrichment, suggests that N-N bond cleavage is likely to be the key rate-limiting step in the reaction. The similarity in the kinetic (15)N isotope effect between the three tested strains suggests that either isotope-masking effects are negligible, or are of a similar extent for all tested strains. The lack of variability in the kinetic (15)N isotope effect allows the interpretation of environmental studies with greater confidence.

Pathway of diethyl phthalate photolysis in sea-water determined by gas chromatography-mass spectrometry and compound-specific isotope analysis

The degradation mechanism of diethyl phthalate (DEP) in natural seawater under UV irradiation was investigated using a combination of intermediates detection and determination of stable carbon isotopic fractionation. Typical intermediates identified with gas chromatography-mass spectrometry (GC-MS) were mono-ethyl phthalate (MEP) and phthalic anhydride. Stable carbon isotope signature was determined by gas chromatography coupled with isotope ratio mass spectrometry through a combustion interface (GC-C-IRMS). A profound (13)C enrichment, with a δ(13)C isotope shift of 12.3±0.3‰ (f=0.09) in residual DEP molecule, was clearly an indicator to its photolysis. The reactive position isotope enrichment factor (ε(reactive position)) and apparent kinetic isotope effects (AKIE) were -35.25±2.26‰ and 1.075, respectively, indicating that the initial reaction step was cleavage of a CO bond in DEP photolysis. Based on these observations, a degradation pathway was proposed. First, a CO bond in DEP molecule was broken to form MEP. Then, MEP was further degraded to phthalic anhydride. Our work demonstrates that compound-specific isotope analysis (CSIA), when combined with intermediates analysis, is a reliable measure to deduce the mechanism of DEP photolysis. This approach might be extended as a reference for mechanism investigation in complicated environment systems.

Stable isotope fractionation to investigate natural transformation mechanisms of organic contaminants: principles, prospects and limitations

Gas chromatography-isotope ratio mass spectrometry (GC-IRMS) has made it possible to analyze natural stable isotope ratios (e.g., (13)C/(12)C, (15)N/(14)N, (2)H/(1)H) of individual organic contaminants in environmental samples. They may be used as fingerprints to infer contamination sources, and may demonstrate, and even quantify, the occurrence of natural contaminant transformation by the enrichment of heavy isotopes that arises from degradation-induced isotope fractionation. This review highlights an additional powerful feature of stable isotope fractionation: the study of environmental transformation mechanisms. Isotope effects reflect the energy difference of isotopologues (i.e., molecules carrying a light versus a heavy isotope in a particular molecular position) when moving from reactant to transition state. Measuring isotope fractionation, therefore, essentially allows a glimpse at transition states! It is shown how such position-specific isotope effects are "diluted out" in the compound average measured by GC-IRMS, and how a careful evaluation in mechanistic scenarios and by dual isotope plots can recover the underlying mechanistic information. The mathematical framework for multistep isotope fractionation in environmental transformations is reviewed. Case studies demonstrate how isotope fractionation changes in the presence of mass transfer, enzymatic commitment to catalysis, multiple chemical reaction steps or limited bioavailability, and how this gives information about the individual process steps. Finally, it is discussed how isotope ratios of individual products evolve in sequential or parallel transformations, and what mechanistic insight they contain. A concluding session gives an outlook on current developments, future research directions and the potential for bridging the gap between laboratory and real world systems.

Carbon isotope fractionation during dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin by a Dehalococcoides-containing culture

Carbon isotope fractionation was observed during dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) by a mixed culture containing Dehalococcoides ethenogenes strain 195. Fractionation was examined when 1,2,3,4-TeCDD was added as the only chlorinated compound and when 1,2,3,4-TeCDD was added with a known growth substrate, tetrachloroethene (PCE). The 1,2,3,4-TeCDD was dechlorinated to 1,2,4-trichlorodibenzo-p-dioxin (1,2,4-TrCDD) which was enriched in (13)C relative to 1,2,3,4-TeCDD with isotope separation factors, epsilon(C), of 1.3+/-0.2 per thousand and 1.7+/-0.4 per thousand (average+/-95% confidence interval (CI)) in cultures with and without PCE, respectively. The 1,2,4-TrCDD was further dechlorinated to 1,3-dichlorodibenzo-p-dioxin (1,3-DCDD) which was depleted in (13)C relative to 1,2,4-TrCDD with epsilon(C) of -2.4+/-0.4 per thousand and -2.9+/-0.8 per thousand (average+/-95% CI) in cultures with and without PCE, respectively. This demonstrates carbon isotope fractionation during sequential reductive dechlorination of PCDDs, where isotope fractionation during dechlorination of the intermediate was substantial and a (13)C depleted lightly chlorinated PCDD congener was ultimately formed during dechlorination of more highly chlorinated PCDD congeners. Despite reproducible, statistically significant differences between isotope compositions of the parent, 1,2,3,4-TeCDD and daughter, 1,2,4-TrCDD and 1,3-DCDD congeners in triplicate bottles of both treatments, fractionation factors for 1,2,3,4-TeCDD could not be determined for all replicates by regression analysis of the plot of the Rayleigh equation. It is possible that dissolution of 1,2,3,4-TeCDD imposed a kinetic limitation on dechlorination, thus masking isotope fractionation during its dechlorination.

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.

Characterization of anaerobic xylene biodegradation by two-dimensional isotope fractionation analysis

We determined stable carbon and hydrogen isotope fractionation factors for anaerobic degradation of xylene isomers by several pure and mixed cultures. All cultures initiated xylene degradation by the addition of fumarate to a methyl moiety, as is known from the literature or verified by the presence of methylbenzylsuccinates as metabolic intermediates. Additionally, the A subunit of benzylsuccinate synthase (bssA) was identified in the majority of the cultures by bssA-targeted primers. Xylene degradation was always coupled to a significant carbon and hydrogen isotope fractionation. The values of the apparent kinetic isotope effect (AKIE) for carbon and hydrogen indicate that the cleavage of a carbon-hydrogen bond is an isotope-sensitive step during fumarate addition to xylene isomers. The slopes of the linear regression for hydrogen (Δδ(2) H) versus carbon (Δδ(13) C) discrimination (Λ = Δδ(2) H/Δδ(13) C ≈ εHbulk /εCbulk ) ranged from 12 ± 4 to 29 ± 5 and were comparable to Λ values previously determined for anaerobic toluene degradation. The results suggest that combined carbon and hydrogen isotope fractionation analyses can be used to monitor anaerobic xylene degradation at contaminated sites.

Biogeochemical and isotopic gradients in a BTEX/PAH contaminant plume: model-based interpretation of a high-resolution field data set

A high spatial resolution data set documenting carbon and sulfur isotope fractionation at a tar oil-contaminated, sulfate-reducing field site was analyzed with a reactive transport model. Within a comprehensive numerical model, the study links the distinctive observed isotope depth profiles with the degradation of various monoaromatic and polycyclic aromatic hydrocarbon compounds (BTEX/PAHs) under sulfate-reducing conditions. In the numerical model, microbial dynamics were simulated explicitly and isotope fractionation was directly linked to the differential microbial uptake of lighter and heavier carbon isotopes during microbial growth. Measured depth profiles from a multilevel sampling well with high spatial resolution served as key constraints for the parametrization of the model simulations. The results of the numerical simulations illustrate particularly well the evolution of the isotope signature of toluene, which is the most rapidly degrading compound and the most important reductant at the site. The resulting depth profiles at the observation well show distinct differences between the small isotopic enrichment in the contaminant plume core and the much stronger enrichment of up to 3.3 per thousand at the plume fringes.

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.

Quantification of biodegradation for o-xylene and naphthalene using first order decay models, Michaelis-Menten kinetics and stable carbon isotopes

At a former wood preservation plant severely contaminated with coal tar oil, in situ bulk attenuation and biodegradation rate constants for several monoaromatic (BTEX) and polyaromatic hydrocarbons (PAH) were determined using (1) classical first order decay models, (2) Michaelis-Menten degradation kinetics (MM), and (3) stable carbon isotopes, for o-xylene and naphthalene. The first order bulk attenuation rate constant for o-xylene was calculated to be 0.0025 d(-1) and a novel stable isotope-based first order model, which also accounted for the respective redox conditions, resulted in a slightly smaller biodegradation rate constant of 0.0019 d(-1). Based on MM-kinetics, the o-xylene concentration decreased with a maximum rate of k(max)=0.1 microg/L/d. The bulk attenuation rate constant of naphthalene retrieved from the classical first order decay model was 0.0038 d(-1). The stable isotope-based biodegradation rate constant of 0.0027 d(-1) was smaller in the reduced zone, while residual naphthalene in the oxic part of the plume further downgradient was degraded at a higher rate of 0.0038 d(-1). With MM-kinetics a maximum degradation rate of k(max)=12 microg/L/d was determined. Although best fits were obtained by MM-kinetics, we consider the carbon stable isotope-based approach more appropriate as it is specific for biodegradation (not overall attenuation) and at the same time accounts for the dominant electron-accepting process. For o-xylene a field based isotope enrichment factor epsilon(field) of -1.4 could be determined using the Rayleigh model, which closely matched values from laboratory studies of o-xylene degradation under sulfate-reducing conditions.

Effect of molecule size on carbon isotope fractionation during biodegradation of chlorinated alkanes by Xanthobacter autotrophicus GJ10

The effect of the number of carbon and chlorine atoms on carbon isotope fractionation during dechlorination of chlorinated alkanes by Xanthobacter autotrophicus GJ10 was studied using pure culture and cell-free extract experiments. The magnitude of carbon isotope fractionation decreased with increasing carbon number. The decrease can be explained by an increasing probability that the heavy isotope is located at a non-reacting position for increasing molecule size. The isotope data were corrected for the number of carbons as well as the number of reactive sites to obtain reacting-site-specific values denoted as apparent kinetic isotope effect (AKIE). Even after the correction, the obtained AKIE values varied (on average 1.0608, 1.0477, 1.0616, and 1.0555 for 1,2-dichloroethane, chloropentane, 1,3-dichloropentane and chlorobutane, respectively). Cell-free extract experiments were carried out to evaluate the effect of transport across the cell membrane on the observed variability in the AKIE values, which revealed that variability still persisted. The study demonstrates that even after differences related to the carbon number and structure of the molecule are taken into account, there still remain differences in AKIE values even for compounds that are degraded by the same pure culture and an identical reaction mechanism.

Anaerobic catabolism of aromatic compounds: a genetic and genomic view

Aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. Since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. The mineralization of aromatic compounds by facultative or obligate anaerobic bacteria can be coupled to anaerobic respiration with a variety of electron acceptors as well as to fermentation and anoxygenic photosynthesis. Since the redox potential of the electron-accepting system dictates the degradative strategy, there is wide biochemical diversity among anaerobic aromatic degraders. However, the genetic determinants of all these processes and the mechanisms involved in their regulation are much less studied. This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies (e.g., genome sequencing, transcriptomics, proteomics, and metagenomics) have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways. These studies revealed that the anaerobic catabolism of aromatic compounds is more diverse and widespread than previously thought, and the complex metabolic and stress programs associated with the use of aromatic compounds under anaerobic conditions are starting to be unraveled. Anaerobic biotransformation processes based on unprecedented enzymes and pathways with novel metabolic capabilities, as well as the design of novel regulatory circuits and catabolic networks of great biotechnological potential in synthetic biology, are now feasible to approach.

Carbon and chlorine isotope fractionation during aerobic oxidation and reductive dechlorination of vinyl chloride and cis-1,2-dichloroethene

The study investigated carbon and chlorine isotope fractionation during aerobic oxidation and reductive dechlorination of vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE). The experimental data followed a Rayleigh trend. For aerobic oxidation, the average carbon isotope enrichment factors were -7.2 per thousand and -8.5% for VC and cDCE, respectively, while average chlorine isotope enrichment factors were only -0.3 per thousand for both compounds. These values are consistent with an initial transformation by epoxidation for which a significant primary carbon isotope effect and only a small secondary chlorine isotope effect is expected. For reductive dechlorination, larger carbon isotope enrichment factors of -25.2 per thousand for VC and -18.5 per thousand for cDCE were observed consistent with previous studies. Although the average chlorine isotope enrichmentfactors were larger than those of aerobic oxidation (-1.8 per thousand for VC, -1.5 per thousand for cDCE), they were not as large as typically expected for a primary chlorine isotope effect suggesting that no cleavage of C-Cl bonds takes place during the initial rate-limiting step. The ratio of isotope enrichment factors for chlorine and carbon were substantially different for the two reaction mechanisms suggesting that the reaction mechanisms can be differentiated at the field scale using a dual isotope approach.

Isotopic evidence suggests different initial reaction mechanisms for anaerobic benzene biodegradation

The initial metabolic reactions for anaerobic benzene biodegradation remain uncharacterized. Isotopic data for carbon and hydrogen fractionation from nitrate-reducing, sulfate-reducing, and methanogenic benzene-degrading enrichment cultures and phylogenic information were used to investigate the initial reaction step in anaerobic benzene biodegradation. Dual parameter plots of carbon and hydrogen isotopic data (deltadelta2H/ deltadelta13C) from each culture were linear, suggesting a consistent reaction mechanism as degradation proceeded. Methanogenic and sulfate-reducing cultures showed consistently higher slopes (m = 29 +/- 2) compared to nitrate-reducing cultures (m = 13 +/- 2) providing evidence for different initial reaction mechanisms. Phylogenetic analyses confirmed that culture conditions were strictly anaerobic, precluding any involvement of molecular oxygen in the observed differences. Using published kinetic data, we explored the possibility of attributing such slopes to reaction mechanisms. The higher slopes found under methanogenic and sulfate-reducing conditions suggest against an alkylation mechanism for these cultures. Observed differences between the methanogenic and nitrate-reducing cultures may not represent distinct reactions of different bonds, but rather subtle differences in relative reaction kinetics. Additional mechanistic conclusions could not be made because kinetic isotope effect data for carboxylation and other putative mechanisms are not available.

Compound-specific isotope analysis of RDX and stable isotope fractionation during aerobic and anaerobic biodegradation

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a common contaminant at explosives production sites. Here, we report on the use of compound-specific isotope analysis of RDX to obtain delta(15)N and delta(18)O enrichment factors during biodegradation in batch cultures. A new preparation method has been developed based on RDX purification using thin-layer chromatography. RDX is then subjected to an elemental analyzer coupled with an isotope-ratio mass spectrometer (EA-IRMS). The precision of the method shows standard deviations of 0.13% per hundred and 1.18% per hundred for delta(15)N and delta(18)O, respectively, whereas the accuracy of the method has been checked routinely, adhering to external standards. The method was applied to RDX samples subjected to biodegradation under aerobic or anaerobic conditions. Enrichment factors under aerobic conditions were -2.1% per hundred and -1.7% per hundred for delta(15)N and delta(18)O, respectively, and under anaerobic conditions, -5.0% per hundred and -5.3% per hundred for delta(15)N and delta(18)O, respectively. The results of this study provide a tool for monitoring natural attenuation of RDX in a contaminated environment.

Precise and accurate compound specific carbon and nitrogen isotope analysis of atrazine: critical role of combustion oven conditions

Compound-specific stable isotope analysis by gas chromatography-isotope ratio mass spectrometry (GC-IRMS) is increasingly used to assess origin and fate of organic substances in the environment. Although analysis without isotopic discrimination is essential, it cannot be taken for granted for new target compounds. We developed and validated carbon isotope analysis of atrazine, a herbicide widely used in agriculture. Combustion was tested with reactors containing (i) CuO/NiO/Pt operating at 940 degrees C; (ii) CuO operating at 800 degrees C; (iii) Ni/NiO operating at 1150 degrees C and being reoxidized for 2 min during each gas chromatographic run. Accurate and precise carbon isotope measurements were only obtained with Ni/NiO reactors giving a mean deviation delta delta(13)C from dual inlet measurements of -0.1-0.2% per hundred and a standard deviation (SD) of +/- 0.4% per hundred. CuO at 800 degrees C gave precise, but inaccurate values (delta delta(13)C = -1.3% per hundred, SD +/- 0.4% per hundred), whereas CuO/NiO/Pt reactors at 940 degrees C gave inaccurate and imprecise data. Accurate (delta delta(15)N = 0.2% per hundred) and precise (SD +/- 0.3% per hundred) nitrogen isotope analysis was accomplished with a Ni/NiO-reactor previously used for carbon isotope analysis. The applicability of the method was demonstrated for alkaline hydrolysis of atrazine at 20 degrees C and pH 12 (nucleophilic aromatic substitution) giving epsilon(carbon) = -5.6% per hundred +/- 0.1% per hundred (SD) and epsilon(nitrogen) = -1.2% per hundred +/- 0.1% per hundred (SD).

Evaluation of toluene degradation pathways by two-dimensional stable isotope fractionation

Toluene degradation by several pure and mixed microbial cultures was investigated bytwo-dimensional compound specific isotope analysis (2D-CSIA). For most of the cultures, the respective toluene degradation pathway and toluene attacking enzymatic step was known. The slope of the linear regression for hydrogen (delta delta(2)H) vs. carbon (delta delta(13)C) discrimination (lamda = delta delta(2)H/ delta delta(13)C approximately epsilonH(bulk)/epsilonC(bulk)) was determined in order to characterize aerobic and anaerobic toluene degradation pathways. The highest lamda value was estimated for the monohydroxylation of the methyl group by Pseudomonas putida (lamda = 53 +/- 5). The lowest value was observed for Rhodococcus opacus (lamda = 2 +/- 2) due to its insignificant hydrogen fractionation, which indicates that a ring dioxygenase was responsible for the initial attack of toluene. The fungus Cladosprium sphaerospermum containing a cytochrome P450-dependent methyl monooxygenase grouped within these extreme values (lamda = 16 +/- 6). Lamda values for organisms attacking toluene under anoxic conditions by benzylsuccinate synthase were significantly different and ranged from lamda = 4 +/- 3 (Blastochloris sulfoviridis) to 31 +/- 11 (strain TRM1). Values were in the same range for organisms using nitrate (lamda = 11-14) or sulfate (lamda = 28-31) as electron acceptor, indicating that it might be possible to distinguish toluene degradation under different electron acceptor conditions by 2D-CSIA.

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.

Does the Rayleigh equation apply to evaluate field isotope data in contaminant hydrogeology?

Stable isotope data have been increasingly used to assess in situ biodegradation of organic contaminants in groundwater. The data are usually evaluated using the Rayleigh equation to evaluate whether isotope data follow a Rayleigh trend, to calculate the extent of contaminant biodegradation, or to estimate first-order rate constants. However, the Rayleigh equation was developed for homogeneous systems while in the subsurface, contaminants can migrate at different velocities due to physical heterogeneity. This paper presents a method to quantify the systematic effect that is introduced by applying the Rayleigh equation to field isotope data. For this purpose, the travel time distribution between source and sampling point is characterized by an analytical solution to the advection-dispersion equation. The systematic effect was evaluated as a function of the magnitude of physical heterogeneity, geometry of the contaminant plume, and degree of biodegradation. Results revealed that the systematic effect always leads to an underestimation of the actual values of isotope enrichment factors, the extent of biodegradation, or first-order rate constants, especially in the dispersion-dominant region representing a higher degree of physical heterogeneity. A substantial systematic effect occurs especially for the quantification of first-order rate constants (up to 50% underestimation of actual rate) while it is relatively small for quantification of the extent of biodegradation (< 5% underestimation of actual degree of biodegradation). The magnitude of the systematic effect is in the same range as the uncertainty due to uncertainty of the analytical data, of the isotope enrichment factor, and the average travel time.

A new concept linking observable stable isotope fractionation to transformation pathways of organic pollutants

Measuring stable isotope fractionation of carbon, hydrogen, and other elements by Compound Specific Isotope Analysis (CSIA) is a new, innovative approach to assess organic pollutant degradation in the environment. Central to this concept is the Rayleigh equation which relates degradation-induced decreases in concentrations directly to concomitant changes in bulk (= average over the whole compound) isotope ratios. The extent of in situ transformation may therefore be inferred from measured isotope ratios in field samples, provided that an appropriate enrichment factor (epsilonbulk) is known. This epsilonbulk value, however, is usually only valid for a specific compound and for specific degradation conditions. Therefore, a direct comparison of epsilonbulk values for different compounds and for different types of reactions has in general not been feasible. In addition, it is often uncertain how robust and reproducible epsilonbulk values are and how confidently they can be used to quantify contaminant degradation in the field. To improve this situation and to achieve a more in-depth understanding, this critical review aims to relate fundamental insight about kinetic isotope effects (KIE) found in the physico(bio)chemical literature to apparent kinetic isotope effects (AKIE) derived from epsilonbulk values reported in environmentally oriented studies. Starting from basic rate laws, a quite general derivation of the Rayleigh equation is given, resulting in a novel set of simple equations that take into account the effects of (1) nonreacting positions and (2) intramolecular competition and that lead to position-specific AKIE values rather than bulk enrichment factors. Reevaluation of existing epsilonbulk literature values result in consistent ranges of AKIE values that generally are in good agreement with previously published data in the (bio)-chemical literature and are typical of certain degradation reactions (subscripts C and H indicate values for carbon and hydrogen): AKIEc = 1.01-1.03 and AKIEH = 2-23 for oxidation of C-H bonds; AKIEc = 1.03-1.07 for SN2-reactions; AKIEc = 1.02-1.03 for reductive cleavage of C-Cl bonds; AKIEc = 1.00-1.01 for C=C bond epoxidation; AKIEc = 1.02-1.03 for C=C bond oxidation by permanganate. Hence, the evaluation scheme presented bridges a gap between basic and environmental (bio)chemistry and provides insight into factors that control the magnitude of bulk isotope fractionation factors. It also serves as a basis to identify degradation pathways using isotope data. It is shown how such an analysis may be even possible in complex field situations and/or in cases where AKIE values are smaller than intrinsic KIE values, provided that isotope fractionation is measured for two elements simultaneously ("two-dimensional isotope analysis"). Finally, the procedure is used (1) to point outthe possibility of estimating approximate epsilonbulk values for new compounds and (2) to discuss the moderate, but non-negligible variability that may quite generally be associated with epsilonbulk values. Future research is suggested to better understand and take into account the various factors that may cause such variability.

Stable isotope fractionation of tetrachloroethene during reductive dechlorination by Sulfurospirillum multivorans and Desulfitobacterium sp. strain PCE-S and abiotic reactions with cyanocobalamin

Carbon stable isotope fractionation of tetrachloroethene (PCE) during reductive dechlorination by whole cells and crude extracts of Sulfurospirillum multivorans and Desulfitobacterium sp. strain PCE-S and the abiotic reaction with cyanocobalamin (vitamin B12) was studied. Fractionation was largest during the reaction with cyanocobalamin with alphaC = 1.0132. Stable isotope fractionation was lower but still in a similar order of magnitude for Desulfitobacterium sp. PCE-S (alphaC = 1.0052 to 1.0098). The isotope fractionation of PCE during dehalogenation by S. multivorans was lower by 1 order of magnitude (alphaC = 1.00042 to 1.0017). Additionally, an increase in isotope fractionation was observed with a decrease in cell integrity for both strains. For Desulfitobacterium sp. strain PCE-S, the carbon stable isotope fractionation factors were 1.0052 and 1.0089 for growing cells and crude extracts, respectively. For S. multivorans, alphaC values were 1.00042, 1.00097, and 1.0017 for growing cells, crude extracts, and the purified PCE reductive dehalogenase, respectively. For the field application of stable isotope fractionation, care is needed as fractionation may vary by more than an order of magnitude depending on the bacteria present, responsible for degradation.

Natural attenuation and enhanced bioremediation of organic contaminants in groundwater

An area of intense scientific and practical interest is the biogeochemical and microbial processes determining the success of natural attenuation, biostimulation and/or bioaugmentation treatments for organic contaminants in groundwater. Recent studies in this area have focused on the reductive dechlorination of chlorinated solvents, the degradation of the fuel additive methyl tert-butyl ether, and the removal of long-term hydrocarbon contamination. These studies have been facilitated by the use of stable isotope analysis to demonstrate in situ bioremediation and push-pull tests, in which isotopes are injected into aquifers and then quickly retrieved and analyzed, to measure in situ activity. Molecular tools such as quantitative PCR, the detection of mRNA expression, and numerous DNA fingerprinting methods have also proved valuable, being employed to identify and sometimes quantify environmentally important organisms or changes in communities. Methods to track bacteria and tools to characterize bacterial attachment properties have also offered insight into bacterial transport in situ.

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.