Degradation of toluene and m-xylene and transformation of o-xylene by denitrifying enrichment cultures

Identifying anaerobic amino acids degraders through the comparison of short-term and long-term enrichments

Degradation of amino acids is an important process in methanogenic environments. Early studies in the 1980s focused on isolated clostridia species to study the degradation behaviours. However, it is now well-recognized that isolated species may not represent those with important roles in situ. This study conducted a continuous enrichment experiment with focus on the comparison of the microbial communities after short-term enrichment (SE) and long-term enrichment (LE). Individual amino acids were used as the substrate, and two different anaerobic digester sludge were used as the inoculum. Based on 16S rRNA and 16S rRNA gene, a clear community shift was observed during a time course of 18 months. The SE communities were dominated by microbial populations such as an uncultured Bacteroidales that was different from known fermenters. In the LE communities, known amino acids fermenters were consistently observed with high abundance, including Peptoclostridium acidaminophilum, Acidaminobacter hydrogenoformans and Propionivibrio pelophilus. The community structures could be classified into four types depending on the diversity of fermenters and syntrophs. A culturability index was developed to compare the SE and LE community and revealed that long-term enrichment tended to select microbial populations closely related to species that has been cultivated whereas larger fractions of the inoculum and SE communities remained uncultured.

Bioremediation Strategies Aimed at Stimulating Chlorinated Solvent Dehalogenation Can Lead to Microbially-Mediated Toluene Biogenesis

In situ bioremediation practices that include subsurface addition of fermentable electron donors to stimulate reductive dechlorination by anaerobic bacteria have become widely employed to combat chlorinated solvent contamination in groundwater. At a contaminated site located near Baton Rouge, Louisiana (USA), toluene was transiently observed in groundwater at concentrations that sometimes far exceeded the US drinking water maximum contaminant level (MCL) of 1 mg/L after a fermentable substrate (agricultural feed grade cane molasses) was injected into the subsurface with the intent of providing electron donors for reductive dechlorination. Here, we present data that demonstrate that indigenous microorganisms can biologically produce toluene by converting phenylacetic acid, phenylalanine, phenyllactate, and phenylpyruvate to toluene. When grown in defined medium with phenylacetic acid at concentrations ≤350 mg/L, the molar ratio between toluene accumulated and phenylacetic acid supplied was highly correlated ( R² ≥ 0.96) with a toluene yield exceeding 0.9:1. Experiments conducted using ¹³C labeled compounds (phenylacetic acid-2-¹³C and l-phenylalanine-3-¹³C) resulted in production of toluene-α-¹³C, confirming that toluene was synthesized from these precursors by two independently developed enrichment cultures. Results presented here suggest that monitoring of aromatic hydrocarbons is warranted during enhanced bioremediation activities where electron donors are introduced to stimulate anaerobic biotransformation of chlorinated solvents.

Pharmaceutical biodegradation under three anaerobic redox conditions evaluated by chemical and toxicological analyses

Biodegradation of pharmaceutically active compounds (PhACs) in the subsurface layer of constructed wetlands (CWs) under various anaerobic redox conditions is rarely studied. In this study, CW sediment microbial populations were enriched for PhAC biodegrading organisms. Biodegradation effectivity of a mixture of six PhACs (caffeine, CAF; naproxen, NAP; metoprolol, MET; propranolol, PRO; ibuprofen, IBP; carbamazepine, CBZ) and single compounds (CAF, NAP) was investigated under nitrate reducing, sulfate reducing, and methanogenic conditions using chemical and toxicological analyses. Biodegradation efficiencies varied strongly among the six PhACs and three redox conditions chosen. CAF and NAP were completely biodegraded under sulfate reducing and methanogenic conditions whereas biodegradation efficiencies of the other PhACs were much less (MET, PRO <20%; IBP, CBZ, negligible). CAF and NAP showed significantly lower biodegradation under nitrate reducing conditions than under the other two redox conditions. No difference was found in biodegradation efficiencies of CAF and NAP when present as single compound, or as a mixture with other PhACs. Different intermediates were observed, indicating different biodegradation pathways under different redox conditions and when the PhACs were present as single compound or in a mixture. From toxicological perspective, toxicity of PhACs and/or their intermediates to Vibrio fischeri was attenuated during the biodegradation process. Chemical and toxicological data showed positive correlations in principle component analysis, by which potentially toxic PhACs and intermediates are indicated for further ecotoxicological hazard assessment.

Who Is the Rock Miner and Who Is the Hunter? The Use of Heavy-Oxygen Labeled Phosphate (P18O4) to Differentiate between C and P Fluxes in a Benzene-Degrading Consortium

Phosphorus availability and cycling in microbial communities is a key determinant of bacterial activity. However, identifying organisms critical to P cycling in complex biodegrading consortia has proven elusive. Here we assess a new DNA stable isotope probing (SIP) technique using heavy oxygen-labeled phosphate (P¹⁸O₄) and its effectiveness in pure cultures and a nitrate-reducing benzene-degrading consortium. First, we successfully labeled pure cultures of Gram-positive Micrococcus luteus and Gram-negative Bradyrhizobium elkanii and separated isotopically light and heavy DNA in pure cultures using centrifugal analyses. Second, using high-throughput amplicon sequencing of 16S rRNA genes to characterize active bacterial taxa (¹³C-labeled), we found taxa like Betaproteobacteria were key in denitrifying benzene degradation and that other degrading (nonhydrocarbon) inactive taxa (P¹⁸O₄-labeled) like Staphylococcus and Corynebacterium may promote degradation through production of secondary metabolites (i.e., "helper" or "rock miner" bacteria). Overall, we successfully separated active and inactive taxa in contaminated soils, demonstrating the utility of P¹⁸O₄-DNA SIP for identifying actively growing bacterial taxa. We also identified potential "miner" bacteria that choreograph hydrocarbon degradation by other microbes (i.e., the "hunters") without directly degrading contaminants themselves. Thus, while several taxa degrade benzene under denitrifying conditions, microbial benzene degradation may be enhanced by both direct degraders and miner bacteria.

Sorption and biodegradation of six pharmaceutically active compounds under four different redox conditions

This study explored the removal of six pharmaceutically active compounds (PhACs) in lab-scale experiments with sediments under four redox conditions, namely aerobic, nitrate reducing, sulfate reducing, and methanogenic conditions using batch and column set-ups. Redox conditions were found to influence PhAC removal by sorption and biodegradation. The most optimal PhAC removal was observed at the outer ranges of the redox spectrum, i.e. either aerobic or deep anaerobic (sulfate reducing and methanogenic conditions), whereas nitrate reducing conditions were found least effective for PhACs biodegradation and sorption. For instance, sorption coefficient K_d values for metoprolol in column experiments were 90, 65, 42 and 11 L/kg for sulfate reducing, methanogenic, aerobic and nitrate reducing conditions, respectively. For the same conditions K_d values for propranolol were 101, 94, 55 and 55 L/kg, respectively. As expected, biodegradation efficiencies were highest under aerobic conditions, showing >99% removal of caffeine and naproxen, but no removal for propranolol and carbamazepine. The adaptive capacity of sediment was demonstrated by pre-exposure to PhACs leading to improved PhAC biodegradation. The results of this study indicate the necessity to combine diverse redox conditions, including aerobic conditions, for maximizing PhAC removal by sorption and biodegradation. Furthermore, our findings stress the need for additional treatment measures as recalcitrant PhACs are not effectively removed under any redox condition.

Correlation of thermostability and conformational changes of catechol 2, 3-dioxygenases from two disparate micro-organisms

We have investigated the structure of recombinant catechol 2, 3-dioxygenase (C23O) purified from two species in which the enzyme has evolved to function at different temperature. The two species are mesophilic bacterium Pseudomonas putida strain mt-2 and thermophilic archaea Sulfolobus acidocaldariusDSM639. Using the primary sequence analysis, we show that both C23Os have only 30% identity and 48% similarity but contain conserved amino acid residues forming an active site area around the iron ion. The corresponding differences in homology, but structural similarity in active area residues, appear to provide completely different responses to heating the two enzymes. We confirm this by small angle X-ray scattering and demonstrate that the overall structure of C23O from P. putida is slightly different from its crystalline form whereas the solution scattering of C23O from S. acidocaldarius at temperatures between 4 and 85°C ideally fits the calculated scattering from the single crystal structure. The thermostability of C23O from S. acidocaldarius correlates well with conformation in solution during thermal treatment. The similarity of the two enzymes in primary and tertiary structure may be taken as a confirmation that two enzymes have evolved from a common ancestor.

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.

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.

Degradation of 4-n-nonylphenol under nitrate reducing conditions

Nonylphenol (NP) is an endocrine disruptor present as a pollutant in river sediment. Biodegradation of NP can reduce its toxicological risk. As sediments are mainly anaerobic, degradation of linear (4-n-NP) and branched nonylphenol (tNP) was studied under methanogenic, sulphate reducing and denitrifying conditions in NP polluted river sediment. Anaerobic bioconversion was observed only for linear NP under denitrifying conditions. The microbial population involved herein was further studied by enrichment and molecular characterization. The largest change in diversity was observed between the enrichments of the third and fourth generation, and further enrichment did not affect the diversity. This implies that different microorganisms are involved in the degradation of 4-n-NP in the sediment. The major degrading bacteria were most closely related to denitrifying hexadecane degraders and linear alkyl benzene sulphonate (LAS) degraders. The molecular structures of alkanes and LAS are similar to the linear chain of 4-n-NP, this might indicate that the biodegradation of linear NP under denitrifying conditions starts at the nonyl chain. Initiation of anaerobic NP degradation was further tested using phenol as a structure analogue. Phenol was chosen instead of an aliphatic analogue, because phenol is the common structure present in all NP isomers while the structure of the aliphatic chain differs per isomer. Phenol was degraded in all cases, but did not affect the linear NP degradation under denitrifying conditions and did not initiate the degradation of tNP and linear NP under the other tested conditions.

Degradation of Trimethylbenzene Isomers by an Enrichment Culture under N(inf2)O-Reducing Conditions

A microbial culture enriched from a diesel fuel-contaminated aquifer was able to grow on 1,3,5-trimethylbenzene (1,3,5-TMB) and 1,2,4-TMB under N(inf2)O-reducing conditions, but it did not degrade 1,2,3-TMB. The oxidation of 1,3,5-TMB to CO(inf2) was coupled to the production of biomass and the reduction of N(inf2)O. N(inf2)O was used to avoid toxic effects caused by NO(inf2)(sup-) accumulation during growth with NO(inf3)(sup-) as the electron acceptor. In addition to 1,3,5-TMB and 1,2,4-TMB, the culture degraded toluene, m-xylene, p-xylene, 3-ethyltoluene, and 4-ethyltoluene.

Kinetics of toluene degradation by a nitrate-reducing bacterium isolated from a groundwater aquifer

Groundwater from a xylene-contaminated acquifer was enriched in the laboratory in the presence of toluene, xylenes, ethylbenzene, and benzene. A pure culture that degrades toluene and m-xylene under nitrate-reducing conditions was isolated. Fatty acid analysis, 16S rRNA sequencing, and morphological traits indicate that the isolate was a strain of Azoarcus tolulyticus. The kinetics of toluene degradation under nitrate-reducing conditions by this isolate was determined. Nitrate reduction does not proceed beyond nitrite. Nitrate and toluene are substrate limiting at low concentrations, whereas toluene, nitrate, and nitrite are inhibitory at high concentrations. Several inhibition models were compared to experimental data to represent inhibition by these substrates. A kinetic model for toluene and nitrate degradation as well as for cell growth and nitrite production was developed and compared to experimental data. The results of this work may find important application in the remediation of groundwater aquifers contaminated with aromatic hydrocarbons.

A novel arsenate respiring isolate that can utilize aromatic substrates

A novel anaerobic bacterium was isolated from the sediment of Onondaga Lake (Syracuse, NY), which can use arsenate [As(V)] as a respiratory electron acceptor. The isolate, designated strain Y5 is a spore-forming, motile rod, with lateral flagella. It is Gram-negative though it phylogenetically falls within the low G + C Gram-positive organisms. In addition to the more usual electron donors such as lactate and succinate, strain Y5 also can use H(2)+ CO(2) chemoautotrophically and metabolize aromatic compounds such as syringic acid, ferulic acid, phenol, benzoate and toluene, coupled to arsenate reduction. Aside from As(V), nitrate, sulfate, thiosulfate and Fe(III) can also serve as electron acceptors. Based on 16S rDNA phylogeny and its physiological characteristics, strain Y5 was identified as most closely related to the genus Desulfosporosinus. The ability of microorganisms to reduce arsenate for respiration appears to be widely distributed and may be relevant in the biogeochemical cycling of arsenic in environments containing mixed contaminants.

The use of naturally generated volatile fatty acids for herbicide removal via denitrification

This research focuses on the removal of 2, 4-D via denitrification, with a particular emphasis on the effect of adding naturally generated volatile fatty acids (VFAs) as a carbon source. These VFAs had been produced from an acid-phase anaerobic digester (mean VFA concentration of 3153 +/- 801 mg/L [as acetic acid]). The first step involved developing 2, 4-D degrading bacteria in a sequencing batch reactor (SBR) fed with both sewage and 2, 4-D (30-100 mg/L). Subsequent denitrification batch tests demonstrated that the specific denitrification rate increased from 0.0119 +/- 0.0039 to 0.0192 +/- 0.0079 g NO(3)-N/g volatile suspended solids (VSS) per day, when using 2, 4-D alone versus 2, 4-D plus natural VFAs from the digester as a carbon source. Similarly, the specific 2, 4-D consumption rate increased from 0.0016 +/- 0.0009 to 0.0055 +/- 0.0021 g 2,4-D/g VSS per day, when using 2, 4-D alone as compared to using 2, 4-D plus natural VFAs. Finally, a parallel increase in the percent 2, 4-D removal was observed, rising from 28.33 +/- 11.88 using 2, 4-D alone to 54.17 +/- 21.89 using 2, 4-D plus natural VFAs.

Competitive, microbially-mediated reduction of nitrate with sulfide and aromatic oil components in a low-temperature, western Canadian oil reservoir

Fields from which oil is produced by injection of sulfate-bearing water often exhibit an increase in sulfide concentration with time (souring). Nitrate added to the injection water lowers the sulfide concentration by the action of sulfide-oxidizing, nitrate-reducing bacteria (SO-NRB). However, the injected nitrate can also be reduced with oil organics by heterotrophic NRB (hNRB). Aqueous volatile fatty acids (VFAs; a mixture of acetate, propionate, and butyrate) are considered important electron donors in this regard. Injection and produced waters from a western Canadian oil field with a low in situ reservoir temperature (30 degrees C) had only 0.1-0.2 mM VFAs. Amendment of these waters with nitrate gave therefore only partial reduction. More nitrate was reduced when 2% (v/v) oil was added, with light oil giving more reduction than heavy oil. GC-MS analysis of in vitro degraded oils and electron balance considerations indicated that toluene served as the primary electron donor for nitrate reduction. The differences in the extent of nitrate reduction were thus related to the toluene content of the light and heavy oil (30 and 5 mM, respectively). Reduction of nitrate with sulfide by SO-NRB always preceded that with oil organics by hNRB, even though microbially catalyzed kinetics with either electron donor were similar. Inhibition of hNRB by sulfide is responsible for this phenomenon. Injected nitrate will thus initially be reduced with sulfide through the action of SO-NRB. However, once sulfide has been eliminated from the near-injection wellbore region, oil organics will be targeted by the action of hNRB. Hence, despite the kinetic advantage of SO-NRB, the nitrate dose required to eliminate sulfide from a reservoir depends on the concentration of hNRB-degradable oil organics, with toluene being the most important in the field under study. Because the toluene concentration is lower in heavy oilthan in light oil, nitrate injection into a heavy-oil-producing field of low temperature is more likely to succeed in containing souring.

Arsenic transformation and mobilization from minerals by the arsenite oxidizing strain WAO

Analysis of arsenic concentrations in New Jersey well water from the Newark Basin showed up to 15% of the wells exceed 10 microg L(-1), with a maximum of 215 microg L(-1). In some geologic settings in the basin, this mobile arsenic could be from the weathering of pyrite (FeS2) found in black shale that contains up to 4% arsenic by weight. We hypothesized that under oxic conditions at circumneutral pH, the microbially mediated oxidation of sulfide in the pyrite lattice would lead to the release of pyrite-bound arsenic. Moreover, the oxidation of aqueous As(III) to As(V) by aerobic microorganisms could further enhance arsenic mobilization from the solid phase. Enrichment cultures under aerobic, As(III)-oxidizing conditions were established under circumneutral pH with weathered black shale from the Newark Basin as the inoculum source. Strain WAO, an autotrophic inorganic-sulfur and As(III)-oxidizer, was isolated and phylogenetically and physiologically characterized. Arsenic mobilization studies from arsenopyrite (FeAsS) mineral, conducted with strain WAO at circumneutral pH, showed microbially enhanced mobilization of arsenic and complete oxidation of released arsenic and sulfur to stoichiometric amounts of arsenate and sulfate. In addition, WAO preferentially colonized pyrite on the surface of arsenic-bearing, black shale thick sections. These findings support the hypothesis that microorganisms can directly mobilize and transform arsenic bound in mineral form at circumneutral pH and suggest that the microbial mobilization of arsenic into groundwater may be important in other arsenic-impacted aquifers.

Redox pathways in a petroleum contaminated shallow sandy aquifer: Iron and sulfate reductions

A comprehensive hydro-geochemical characterization was carried out in a petroleum-contaminated shallow sandy aquifer in South Africa. The results indicate the presence of a BTEX (benzene, toluene, ethylbenzene, and xylene) plume that has moved, although only slightly, along the regional hydraulic gradient from the spill site. Associated with the contaminant plume, spatial distribution pattern of terminal electron acceptors and metabolites indicates simultaneous occurrence of nitrate, manganese, iron and sulfate reductions resulting in overlapping redox zones within the aquifer. From the measured concentration of metabolic by-products, sulfate and iron reductions seem to be the dominant metabolic pathways, though. Incubation experiments conducted with hydrocarbon contaminated aquifer sediments and inherent microbial assemblages provide a sulfate reduction rate of 4272 nmol cm(-3) day(-1) and 96 nmol cm(-3) day(-1) for winter and summer, respectively. As oppose to this, iron reduction dominates in summer with measured respiration rate of 1414 nmol cm(-3) day(-1). In winter iron reduction was measured to be only 24 nmol cm(-3) day(-1). Based on the dissimilatory iron and sulfate reduction rate measurements, we predict that at the aquifer site, intrinsic BTEX oxidation is primarily occurring in winter and is coupled to sulfate reduction. Although widespread in the aquifer, the contribution of iron reduction for the removal of aromatic monocyclic hydrocarbons is relatively minor.

Site-directed mutagenesis of the Thauera aromatica strain T1 tutE tutFDGH gene cluster

Benzylsuccinate synthase, encoded by the tutF, tutD, and tutG genes of Thauera aromatica strain T1, is responsible for the first step of anaerobic toluene metabolism. Previous work has shown that these genes are part of the tutE tutFDGH gene cluster and strains carrying a mutation in the tutE, tutF, tutD, or tutG genes are unable to metabolize toluene. In this study, we performed site-directed mutagenesis of the tutE, tutF, and tutG genes and determined that the cysteines at position 72 and 79 of TutE are likely to be critical for the radical activation of benzylsuccinate synthase, while the cysteine alanine at positions 9 and 10 of TutF, and the cysteine at position 29 of TutG are also essential for toluene metabolism. Additionally, we report that the tutH gene is necessary for toluene metabolism and the glycine lysine serine (part of the putative ATP/GTP binding domain) at positions 52-54 of the TutH protein is essential for toluene metabolism.

Anaerobic arsenite oxidation by novel denitrifying isolates

Autotrophic microorganisms have been isolated that are able to derive energy from the oxidation of arsenite [As(III)] to arsenate [As(V)] under aerobic conditions. Based on chemical energetics, microbial oxidation of As(III) can occur in the absence of oxygen, and may be relevant in some environments. Enrichment cultures were established from an arsenic contaminated industrial soil amended with As(III) as the electron donor, inorganic C as the carbon source and nitrate as the electron acceptor. In the active enrichment cultures, oxidation of As(III) was stoichiometrically coupled to the reduction of NO(3) (-). Two autotrophic As(III)-oxidizing strains were isolated that completely oxidized 5 mM As(III) within 7 days under denitrifying conditions. Based on 16S rRNA gene sequencing results, strain DAO1 was 99% related to Azoarcus and strain DAO10 was most closely related to a Sinorhizobium. The nitrous oxide reductase (nosZ) and the RuBisCO Type II (cbbM) genes were successfully amplified from both isolates underscoring their ability to denitrify and fix CO(2) while coupled to As(III) oxidation. Although limited work has been done to examine the diversity of anaerobic autotrophic oxidizers of As(III), this process may be an important component in the biological cycling of arsenic within the environment.

Anaerobic degradation of benzene, toluene, ethylbenzene, and xylene compounds by Dechloromonas strain RCB

Dechloromonas strain RCB has been shown to be capable of anaerobic degradation of benzene coupled to nitrate reduction. As a continuation of these studies, the metabolic versatility and hydrocarbon biodegradative capability of this organism were investigated. The results of these revealed that in addition to nitrate, strain RCB could alternatively degrade benzene both aerobically and anaerobically with perchlorate or chlorate [(per)chlorate] as a suitable electron acceptor. Furthermore, with nitrate as the electron acceptor, strain RCB could also utilize toluene, ethylbenzene, and all three isomers of xylene (ortho-, meta-, and para-) as electron donors. While toluene and ethylbenzene were completely mineralized to CO2, strain RCB did not completely mineralize para-xylene but rather transformed it to some as-yet-unidentified metabolite. Interestingly, with nitrate as the electron acceptor, strain RCB degraded benzene and toluene concurrently when the hydrocarbons were added as a mixture and almost 92 microM total hydrocarbons were oxidized within 15 days. The results of these studies emphasize the unique metabolic versatility of this organism, highlighting its potential applicability to bioremediative technologies.

Metabolic biomarkers for monitoring in situ anaerobic hydrocarbon degradation

During the past 15 years researchers have made great strides in understanding the metabolism of hydrocarbons by anaerobic bacteria. Organisms capable of utilizing benzene, toluene, ethylbenzene, xylenes, alkanes, and polycyclic aromatic hydrocarbons have been isolated and described. In addition, the mechanisms of degradation for these compounds have been elucidated. This basic research has led to the development of methods for detecting in situ biodegradation of petroleum-related pollutants in anoxic groundwater. Knowledge of the metabolic pathways used by anaerobic bacteria to break down hydrocarbons has allowed us to identify unique intermediate compounds that can be used as biomarkers for in situ activity. One of these unique intermediates is 2-methylbenzylsuccinate, the product of fumarate addition to o-xylene by the enzyme responsible for toluene utilization. We have carried out laboratory studies to show that this compound can be used as a reliable indicator of anaerobic toluene degradation. Field studies confirmed that the biomarker is detectable in field samples and its distribution corresponds to areas where active biodegradation is predicted. For naphthalene, three biomarkers were identified [2-naphthoic acid (2-NA), tetrahydro-2-NA, and hexahydro-2-NA] that can be used in the field to identify areas of active in situ degradation.

Denitrification in presence of benzene, toluene, and m-xylene

Denitrification of the electron donors toluene-C (15-100 mg/L), m-xylene-C (15-70 mg/L), benzene-C (5-25 mg/L), and acetate-C as experimental reference (50-140 mg/L) was carried out in batch culture. An initial concentration of 1.1 +/- 0.15 g of volatile suspended solids/L of denitrifying sludge without previous exposure to aromatic compounds was used as inoculum. The results showed toluene and nitrate consumption efficiency (ET and EN, respectively) of 100%. Toluene was completely mineralized (oxidized) to CO2. In all cases, the N2 (YN2) and HCO3-yields (YHCO3) were 0.97 +/- 0.01 and 0.8 +/- 0.05, respectively. The consumption efficiency (EX) of m-xylene (53 +/- 5.7%) was partial. The YN2 and YHCO3 were 0.96 +/- 0.01 and 0.86 +/- 0.02, respectively. Benzene was not consumed under denitrifying conditions. The specific consumption rates of toluene (qT) and m-xylene (qX) were lower than that of acetate (qA). The differences in specific consumption rates were probably owing to the negative effect of benzene, toluene, and isomers of xylene on the cell membrane.

Role of benzylsuccinate in the induction of the tutE tutFDGH gene complex of T. aromatica strain T1

Expression of the tutE tutFDGH gene cluster of Thauera aromatica strain T1 was examined by Northern and Western analysis in a wild-type strain and chromosomally deleted strains with or without in-frame deletion plasmids. While expression was observed when the wild-type strain was induced with toluene, various chromosomally deleted strains exhibited little or no expression of the tut genes. In contrast, both wild-type and chromosomally deleted strains expressed the tut genes when induced with benzylsuccinate. We conclude that benzylsuccinate is required for the full induction of the tutE tutFDGH gene cluster of T. aromatica strain T1.

Construction and characterization of insertion/deletion mutations of the tutF, tutD, and tutG genes of Thauera aromatica strain T1

Thauera aromatica T1 was isolated for its ability to use toluene as a sole carbon source under denitrifying conditions. A genetic approach was used to examine the roles of the tutF, tutD, and tutG gene products (part of a single operon) in the metabolism of toluene. The genes were individually deleted from the chromosome and each resulting mutant strain was unable to metabolize toluene. Plasmids carrying individual in-frame gene deletions failed to complement the corresponding chromosomal deletions but did complement chromosomal deletions downstream of the in-frame deletion. Hence, the tutF, tutD, and tutG genes are each essential for toluene metabolism in T. aromatica T1.

Transport and degradation of toluene and o-xylene in an unsaturated soil with dipping sedimentary layers

A lysimeter trench was established at the Gardermoen delta (50 km north of Oslo, Norway) to study the flow of water and transport and degradation of aromatic jet fuel components (toluene and o-xylene) in the undisturbed unsaturated zone. Site investigations with ground-penetrating radar revealed the presence of dipping sedimentary layers within the foreset unit. This study has shown that the foreset bed of the Gardermoen delta structure provided a preferential flow path for the transport of the solute plumes, but did not have dramatic effects on the degradation potential under the current conditions. The degradation potential for toluene and o-xylene in the unsaturated zone at Gardermoen was very high and almost all of the injected hydrocarbons were biodegraded before reaching the saturated zone. However, the horizontal displacement of the plume showed that knowledge about sedimentary structures in the unsaturated zone is important for a sufficient monitoring of contaminant transport and for remediation purposes. Carbon dioxide and O2 were measured in situ simultaneously with extraction of water samples, and indicated aerobic biodegradation of toluene and o-xylene. Overall, first-order degradation coefficients were calculated to be in the range of 0.19 to 0.21 d(-1) and 0.10 to 0.11 d(-1) for toluene and o-xylene, respectively.

Nitrate-enhanced bioremediation of BTEX-contaminated groundwater: parameter estimation from natural-gradient tracer experiments

Two natural-gradient pulse tracer tests were conducted in a petroleum-contaminated aquifer to evaluate the potential for benzene, toluene, ethylbenzene, and xylenes (BTEX) biodegradation under enhanced nitrate-reducing conditions. Addition of nitrate resulted in loss of toluene, ethylbenzene, and m,p-xylenes (TEX) after an initial lag period of approximately 9 days. Losses of benzene were not observed over the 60-day monitoring period. Tracer breakthrough curves (BTCs) were analyzed to derive transport and biodegradation parameters, including advective velocities, retardation factors, dispersion coefficients, biodegradation rate constants, and nitrate utilization ratios. Using the parameters derived from the BTC analysis, numerical simulations of one of the tracer experiments were conducted using BIONAPL/3D [Molson, J., BIONAPL/3D User Guide, A 3D Coupled Flow and Multi-Component Reactive transport model. University of Waterloo, Waterloo, Ontario, Canada]. Simulations using the BTC-derived transport and biodegradation parameters successfully reproduced benzene, TEX, and nitrate concentrations measured during the tracer experiment. Comparisons of observed and simulated nitrate concentrations indicate that the mass ratio of nitrate-N utilized to TEX degraded increased over time during the experiment, reaching values many times that expected based on stoichiometry of TEX oxidation coupled to nitrate reduction. Excess nitrate loss is likely due to oxidation of other organics in addition to TEX.

Kinetics of inhibition in the biodegradation of monoaromatic hydrocarbons in presence of heavy metals

The toxicity and inhibitory effects of heavy metals such as cadmium, nickel and zinc on alkylbenzene removal were evaluated with a Bacillus strain. The kinetics of alkylbenzene biodegradation with the different heavy metals at various concentrations were modeled using the Andrews equation which yielded a good fit between model and experimental data. Additional experiments undertaken with a Pseudomonas sp. in presence of nickel confirmed a good fit between experimental data and the Andrews model for this strain as well. The heavy metals inhibition constants (Ki) were calculated for different combinations of volatile organic compounds (VOC) and heavy metals. The present approach provides a method for evaluating and quantifying the inhibition effect of heavy metals on the biodegradtion of pollutants by specific microbial strains.

Transcriptional analysis of the tutE tutFDGH gene cluster from Thauera aromatica strain T1

The denitrifying strain T1, identified as Thauera aromatica, is able to grow with toluene serving as its sole carbon source. Previous work identified two genes, tutD and tutE, that are involved in toluene metabolism. Two small open reading frames, tutF and tutG, which may also play a role in toluene metabolism, were also identified. The present work examines the transcriptional organization and regulation of these toluene utilization genes. Northern analysis indicates that the four genes are organized into two operons, tutE and tutFDG, and that both operons are regulated in response to toluene. Primer extension analysis has identified major transcriptional start sites located 177 bp upstream of the tutE translational start and 76 bp upstream of the tutF translational start. Furthermore, a fifth gene, tutH, has been identified immediately downstream of tutG. It is transcribed from the same start site as tutFDG and is predicted to code for a 286-amino-acid protein with a calculated molecular mass of about 31,800 Da. The TutH protein is predicted to have an ATP/GTP binding domain and is similar to the NorQ/NirQ family of proteins.

Effects of cultural conditions on denitrification by pseudomonas stutzeri measured by membrane inlet mass spectrometry

Denitrification is a globally important process leading to loss of fertiliser efficiency and the production of the greenhouse gas nitrous oxide and nitric oxide, an ozone depleter. Membrane inlet mass spectrometry (MIMS) was employed to study the effect of different variables on the process of denitrification by Pseudomonas stutzeri in a defined salts medium. MIMS was used for concomitant measurements of nitrous oxide, nitrogen and oxygen and showed that denitrification occurred in the presence of dissolved oxygen. A nitrate concentration of 15 mmol l-1 and a nitrite concentration of 5 mmol l-1 were found to be optimum for complete denitrification of nitrate or nitrite to nitrogen and varying these concentrations had a marked effect on the ratio of gaseous products released. Denitrification products were also dependant on pH with neutral or alkaline conditions being best for production of gaseous end products. Our results suggest that under nutrient rich conditions the most important factor in the regulation of denitrification by Ps. stutzeri is the amount of nitrite generated at the first enzymatic stage of the process. This appears to cause inhibition of the denitrification pathway above 5 mmol l-1 and at high enough concentrations (15 mmol l-1) restricts growth.

Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria

Various alkylbenzenes were depleted during growth of an anaerobic, sulfate-reducing enrichment culture with crude oil as the only source of organic substrates. From this culture, two new types of mesophilic, rod-shaped sulfate-reducing bacteria, strains oXyS1 and mXyS1, were isolated with o-xylene and m-xylene, respectively, as organic substrates. Sequence analyses of 16S rRNA genes revealed that the isolates affiliated with known completely oxidizing sulfate-reducing bacteria of the delta subclass of the class Proteobacteria. Strain oXyS1 showed the highest similarities to Desulfobacterium cetonicum and Desulfosarcina variabilis (similarity values, 98.4 and 98.7%, respectively). Strain mXyS1 was less closely related to known species, the closest relative being Desulfococcus multivorans (similarity value, 86.9%). Complete mineralization of o-xylene and m-xylene was demonstrated in quantitative growth experiments. Strain oXyS1 was able to utilize toluene, o-ethyltoluene, benzoate, and o-methylbenzoate in addition to o-xylene. Strain mXyS1 oxidized toluene, m-ethyltoluene, m-isoproyltoluene, benzoate, and m-methylbenzoate in addition to m-xylene. Strain oXyS1 did not utilize m-alkyltoluenes, whereas strain mXyS1 did not utilize o-alkyltoluenes. Like the enrichment culture, both isolates grew anaerobically on crude oil with concomitant reduction of sulfate to sulfide.

ATSDR evaluation of health effects of chemicals. V. Xylenes: health effects, toxicokinetics, human exposure, and environmental fate

Xylenes, or dimethylbenzenes, are among the highest-volume chemicals in production. Common uses are for gasoline blending, as a solvent or component in a wide variety of products from paints to printing ink, and in the production of phthalates and polyester. They are often encountered as a mixture of the three dimethyl isomers, together with ethylbenzene. As part of its mandate, the Agency for Toxic Substances and Disease Registry (ATSDR) prepares toxicological profiles on hazardous chemicals found at Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) National Priorities List (NPL) sites that are of greatest concern for public health purposes. These profiles comprehensively summarize toxicological and environmental information. This article constitutes the release of the bulk of this profile (ATSDR, 1995) into the mainstream scientific literature. An extensive listing of known human and animal health effects, organized by route, duration, and end point, is presented. Toxicological information on toxicokinetics, biomarkers, interactions, sensitive subpopulations, reducing toxicity after exposure, and relevance to public health is also included. Environmental information encompasses physical properties, production and use, environmental fate, levels seen in the environment, analytical methods, and a listing of regulations. ATSDR, as mandated by CERCLA (or Superfund), prepares these profiles to inform and assist the public.

Identification and analysis of genes involved in anaerobic toluene metabolism by strain T1: putative role of a glycine free radical

The denitrifying strain T1 is able to grow with toluene serving as its sole carbon source. Two mutants which have defects in this toluene utilization pathway have been characterized. A clone has been isolated, and subclones which contain tutD and tutE, two genes in the T1 toluene metabolic pathway, have been generated. The tutD gene codes for an 864-amino-acid protein with a calculated molecular mass of 97,600 Da. The tutE gene codes for a 375-amino-acid protein with a calculated molecular mass of 41,300 Da. Two additional small open reading frames have been identified, but their role is not known. The TutE protein has homology to pyruvate formate-lyase activating enzymes. The TutD protein has homology to pyruvate formate-lyase enzymes, including a conserved cysteine residue at the active site and a conserved glycine residue that is activated to a free radical in this enzyme. Site-directed mutagenesis of these two conserved amino acids shows that they are also essential for the function of TutD.

Kinetics of BTEX degradation by a nitrate-reducing mixed culture

A culture enriched from a xylene-contamined, groundwater aquifer degraded m- and p-xylene, toluene, and ethylbenzene completedly within 5 days and o-xylene to 55% of its original concentration under nitrate-reducing conditions. The culture did not degrade benzene. The mixed culture had a maximum growth rate of 0.017 h-1 and a yield of 0.66 g dry cell weight/g toluene consumed. Substrate limitation and then inhibition were observed with increasing concentrations of toluene. The Ks and Ki for toluene were found to be 516 microM and 332 microM, respectively, when fitted to the Andrews model for substrate limitation and inhibition and 410 microM and 492 microM, respectively, when fitted to a multiplicative model for substrate limitation and inhibition. A Monod-type dependence of toluene degradation on the nitrate concentration was observed with a Ks for nitrate of 0.21 mM. Nitrate was not inhibitory to growth or to toluene degradation at concentrations up to 10 mM.

Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA

A quantitative molecular technique was developed for rapid analysis of microbial community diversity in various environments. The technique employed PCR in which one of the two primers used was fluorescently labeled at the 5' end and was used to amplify a selected region of bacterial genes encoding 16S rRNA from total community DNA. The PCR product was digested with restriction enzymes, and the fluorescently labeled terminal restriction fragment was precisely measured by using an automated DNA sequencer. Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragment lengths or "ribotypes." Using T-RFLP, we were able to distinguish all bacterial strains in a model bacterial community, and the pattern was consistent with the predicted outcome. Analysis of complex bacterial communities with T-RFLP revealed high species diversity in activated sludge, bioreactor sludge, aquifer sand, and termite guts; as many as 72 unique ribotypes were found in these communities, with 36 ribotypes observed in the termite guts. The community T-RFLP patterns were numerically analyzed and hierarchically clustered. The pattern derived from termite guts was found to be distinctly different from the patterns derived from the other three communities. Overall, our results demonstrated that T-RFLP is a powerful tool for assessing the diversity of complex bacterial communities and for rapidly comparing the community structure and diversity of different ecosystems.

Identification and sequence analysis of two regulatory genes involved in anaerobic toluene metabolism by strain T1

T1 is a denitrifying bacterium isolated for its ability to grow with toluene serving as the sole carbon source. Mutants of this strain that have defects in the toluene utilization pathway have been isolated and have been separated into classes based on growth phenotypes. A cosmid clone has been isolated by complementing the tutB16 (for toluene utilization) mutation. The complementing gene has been localized to a 3.3-kb DNA fragment. An additional open reading frame upstream of the tutB gene has also been identified and is designated tutC. The nucleotide sequence and the predicted amino acid translation of the 6.4-kb DNA fragment that contains these genes are presented. The tutB and tutC gene products of strain T1 have homology to members of the two-component sensor-regulator family and are proposed to play a role in the regulation of toluene metabolic genes of strain T1. To our knowledge, this is the first published report of the isolation of mutants defective in anaerobic aromatic hydrocarbon degradation. Additionally, we report for the first time the cloning of genes involved in an anaerobic aromatic hydrocarbon degradation pathway.

Assessment of inhibition kinetics of the growth of strain P5 on pentachlorophenol under steady-state conditions in a nutristat

A bacterium degrading pentachlorophenol (PCP) as the only source of carbon and energy was grown in a nutristat , i.e., a continuous culture with on-line measurement and control of the substrate concentration. We improved the PCP nutristat by incorporation of a personal computer with a proportional integral derivative (PID) algorithm for controlling the medium feed pump. The controlled value deviated from the average (set-point) value by 1% maximally. In the PCP nutristat (30 degrees C), the steady-state dilution rate, and hence, specific growth rate, showed a maximum value of 0.142 +/- 0.004 h-1 at set-point PCP concentrations between 37 and 168 microM. At PCP concentrations above 168 microM, the steady-state growth rate decreased because of inhibition. The growth yield coefficient was not seriously affected by the PCP concentration, suggesting that uncoupling was not the inhibitory mechanism. It was concluded that the PCP nutristat is very useful for establishing steady-state conditions that maintain growth-inhibitory PCP concentrations and high cell concentrations, conditions for which the chemostat is not suitable.

Degradation of p-xylene by a denitrifying enrichment culture

Microbial cultures enriched from a diesel fuel-contaminated aquifer were able to grow on p-xylene under denitrifying conditions. The oxidation of p-xylene to CO2 was coupled to the reduction of NO3-. The enrichment cultures also grew on toluene and m-xylene, but they did not degrade benzene, ethylbenzene, and o-xylene.

Transformation of o-xylene to o-methyl benzoic acid by a denitrifying enrichment culture using toluene as the primary substrate

A highly enriched denitrifying mixed culture transformed o-xylene co-metabolically along with toluene by methyl group oxidation. o-Methyl benzaldehyde and o-methyl benzoic acid accumulated transiently as metabolic products of o-xylene transformation. Transformation of o-methyl benzyl alcohol and o-methyl benzaldehyde occurred independently of toluene degradation and resulted in the formation of a compound coeluting with o-methyl benzoic acid on a gas chromatograph. The co-metabolic relationship between toluene and o-xylene could be attributed to a mechanism linked to the initial oxidation of the methyl group.

Stoichiometry and kinetics of microbial toluene degradation under denitrifying conditions

Batch experiments were carried out to investigate the stoichiometry and kinetics of microbial degradation of toluene under denitrifying conditions. The inoculum originated from a mixture of sludges from sewage treatment plants with alternating nitrification and denitrification. The culture was able to degrade toluene under anaerobic conditions in the presence of nitrate, nitrite, nitric oxide, or nitrous oxide. No degradation occurred in the absence of Noxides. The culture was also able to use oxygen, but ferric iron could not be used as an electron acceptor. In experiments with 14C-labeled toluene, 34% +/- 8% of the carbon was incorporated into the biomass, while 53% +/- 10% was recovered as 14CO2, and 6% +/- 2% remained in the medium as nonvolatile water soluble products. The average consumption of nitrate in experiments, where all the reduced nitrate was recovered as nitrite, was 1.3 +/- 0.2 mg of nitrate-N per mg of toluene. This nitrate reduction accounted for 70% of the electrons donated during the oxidation of toluene. When nitrate was reduced to nitrogen gas, the consumption was 0.7 +/- 0.2 mg per mg of toluene, accounting for 97% of the donated electrons. Since the ammonia concentration decreased during degradation, dissimilatory reduction of nitrate to ammonia was not the reductive process. The degradation of toluene was modelled by classical Monod kinetics. The maximum specific rate of degradation, k, was estimated to be 0.71 mg toluene per mg of protein per hour, and the Monod saturation constant, Ks, to be 0.2 mg toluene/l. The maximum specific growth rate, mu max, was estimated to be 0.1 per hour, and the yield coefficient, Y, was 0.14 mg protein per mg toluene.