Isolation of Alcaligenes sp. strain L6 at low oxygen concentrations and degradation of 3-chlorobenzoate via a pathway not involving (chloro)catechols

Isolation and Genomic Analysis of 3-Chlorobenzoate-Degrading Bacteria from Soil

The compound 3-chlorobenzoate (3-CBA) is a hazardous industrial waste product that can harm human health and the environment. This study investigates the physiological and genetic potential for 3-chlorobenzoate (3-CBA) degradation. Six 3-CBA Gram-negative degraders with different degradation properties belonging to the genera Caballeronia, Paraburkholderia and Cupriavidus were isolated from the soil. The representative strains Caballeronia 19CS4-2 and Paraburkholderia 19CS9-1 showed higher maximum specific growth rates (µmax, h^-1) than Cupriavidus 19C6 and degraded 5 mM 3-CBA within 20-28 h. Two degradation products, chloro-cis,cis-muconate and maleylacetate, were detected in all isolates using high-performance liquid chromatography and mass spectrometry. Genomic analyses revealed the presence of cbe and tfd gene clusters in strains 19CS4-2 and 19CS9-1, indicating that they probably metabolized the 3-CBA via the chlorocatechol ortho-cleavage pathway. Strain 19C6 possessed cbe genes, but not tfd genes, suggesting it might have a different chlorocatechol degradation pathway. Putative genes for the metabolism of 3-hydroxybenzoate via gentisate were found only in 19C6, which utilized the compound as a sole carbon source. 19C6 exhibited distinct characteristics from strains 19CS4-2 and 19CS9-1. The results confirm that bacteria can degrade 3-CBA and improve our understanding of how they contribute to environmental 3-CBA biodegradation.

Aerobic degradation of 2,4,6-trinitrophenol by Proteus sp. strain OSES2 obtained from an explosive contaminated tropical soil

A 2,4,6-trinitrophenol (TNP) degrading bacterial strain isolated from a site polluted with explosives was identified as Proteus sp. strain OSES2 via 16S rRNA gene sequencing. Metabolic investigation showed that the organism grew exponentially on 100 mg l^-1 of TNP as a source of carbon, nitrogen, and energy. In addition, the growth of the organism was sustainable on 3-nitrotoluene, 2,4-dinitrotoluene, 2,4,6-trinitrotoluene, 4-nitrophenol, methyl-3-nitrobenzoate, 4-nitroaniline, aniline and nitrobenzene. Strain OSES2 was able to utilize TNP within a concentration range of 100 mg l^-1 to 500 mg l^-1. The specific growth rate and degradation rates on TNP were 0.01043 h^-1 and 0.01766 mg l^-1 h^-1 respectively. Effective degradation of TNP in a chemically defined medium was evident with a gradual reduction in the concentration of TNP concomitant with an increase in cell density as well as the substantial release of ammonium (NH₄⁺), nitrite (NO₂^-), and nitrate (NO₃^-) as metabolites in 96 h. Degradation competence of the organism was enhanced in the presence of starch and acetate. On starch-supplemented TNP, the highest specific growth rate and degradation rates were 0.02634 h^-1 and 0.04458 mg l^-1 h^-1, respectively, while the corresponding values on acetate were 0.02341 h^-1 and 0.02811 mg l^-1 h^-1. However, amendment with nitrogen sources yielded no substantial improvement in degradation. TNP was utilized optimally at pH 7 to 9 and within the temperature range of 30 °C to 37 °C. The enzyme hydride transferase II [HTII], encoded by the npdI gene which is the first step involved in the TNP degradation pathway, was readily expressed by the isolate thus suggesting that substrate was utilized through the classical metabolic pathway.

The Discovery of Vitreoscilla Hemoglobin and Early Studies on Its Biochemical Functions, the Control of Its Expression, and Its Use in Practical Applications

In 1986, the surprising identification of a hemoglobin (VHb) in the bacterium Vitreoscilla greatly extended the range of taxa in which this oxygen binding protein functions. Elucidation of many of its biochemical properties and relation to overall cell physiology, as well as the sequence of the gene encoding it and aspects of control of its expression were determined in the following years. In addition, during the early years following its discovery, strategies were developed to use its expression in heterologous microbial hosts to enhance processes of practical usefulness. The VHb discovery also served as the foundation for what has become the fascinatingly rich field of bacterial hemoglobins. VHb's position as the first known bacterial hemoglobin and its extensive use in biotechnological applications, which continue today, make a review of the early studies of its properties and uses an appropriate and interesting topic thirty-five years after its discovery.

Biochemical Barriers on the Path to Ocean Anoxia?

The kinetics of microbial respiration suggests that, if excess organic matter is present, oxygen should fall to nanomolar levels in the range of the Michaelis-Menten constants (K_m). Yet even in many biologically productive coastal regions, lowest observed O₂ concentrations often remain several orders of magnitude higher than respiratory K_m values. We propose the hypoxic barrier hypothesis (HBH) to explain this apparent discrepancy. The HBH postulates that oxidative enzymes involved in organic matter catabolism are kinetically limited by O₂ at concentrations far higher than the thresholds for respiration. We found support for the HBH in a meta-analysis of 1,137 O₂ K_m values reported in the literature: the median value for terminal respiratory oxidases was 350 nM, but for other oxidase types, the median value was 67 μM. The HBH directs our attention to the kinetic properties of an important class of oxygen-dependent reactions that could help explain the trajectories of ocean ecosystems experiencing O₂ stress. IMPORTANCE Declining ocean oxygen associated with global warming and climate change is impacting marine ecosystems across scales from microscopic planktonic communities to global fisheries. We report a fundamental dichotomy in the affinities of enzymes for oxygen-the terminal proteins catalyzing respiration are active at much lower oxygen concentrations than oxygenase enzymes involved in organic matter catabolism. We hypothesize that this dichotomy in oxygen affinities will cause some types of organic matter to accumulate in hypoxic ecosystems and will slow rates of oxygen decline. This proposed biochemical barrier may explain why many ocean ecosystems rarely reach anoxia. Competition between intracellular enzymes for oxygen may also have impacted microbial strategies of adaptation to low oxygen, requiring cells to regulate oxygen respiration so that it does not compete with other cellular processes that also require oxygen.

Roles of the Gentisate 1,2-Dioxygenases DsmD and GtdA in the Catabolism of the Herbicide Dicamba in Rhizorhabdus dicambivorans Ndbn-20

3-Chlorogentisate is a key intermediate in the catabolism of the herbicide dicamba in R. dicambivorans Ndbn-20. In this study, we identified two gentisate 1,2-dioxygenases (GDOs), DsmD and GtdA, from Ndbn-20. The amino acid sequence similarity between DsmD and GtdA is 51%. Both of them are dimers and showed activities to gentisate and 3-chlorogentisate but not 3,6-dichlorogentisate (3,6-DCGA) or 6-chlorogentisate in vitro. The k_cat/K_m of DsmD for 3-chlorogentisate was 28.7 times higher than that of GtdA, whereas the k_cat/K_m of DsmD for gentisate was only one-fourth of that of GtdA. Transcription of dsmD was dramatically induced by 3-chlorogentisate but not gentisate, whereas gtdA was not induced. Disruption of dsmD resulted in a significant decline in the degradation rates of 3-chlorogentisate and dicamba but had no effect on the degradation of gentisate, whereas the result of disruption of gtdA was converse; the disruption of both dsmD and gtdA led to the inability to degrade 3-chlorogentisate and gentisate. This study revealed that 3-chlorogentisate but not gentisate or 3,6-DCGA is the ring-cleavage substrate in the dicamba degradation pathway in R. dicambivorans Ndbn-20; DsmD is specifically responsible for cleavage of 3-chlorogentisate, whereas GtdA is a general GDO involved in the catabolism of various natural aromatic compounds.

Aminobacter sp. MSH1 Mineralizes the Groundwater Micropollutant 2,6-Dichlorobenzamide through a Unique Chlorobenzoate Catabolic Pathway

2,6-Dichlorobenzamide (BAM) is a major groundwater micropollutant posing problems for drinking water treatment plants (DWTPs) that depend on groundwater intake. Aminobacter sp. MSH1 uses BAM as the sole source of carbon, nitrogen, and energy and is considered a prime biocatalyst for groundwater bioremediation in DWTPs. Its use in bioremediation requires knowledge of its BAM-catabolic pathway, which is currently restricted to the amidase BbdA converting BAM into 2,6-dichlorobenzoic acid (2,6-DCBA) and the monooxygenase BbdD transforming 2,6-DCBA into 2,6-dichloro-3-hydroxybenzoic acid. Here, we show that the 2,6-DCBA catabolic pathway is unique and differs substantially from catabolism of other chlorobenzoates. BbdD catalyzes a second hydroxylation, forming 2,6-dichloro-3,5-dihydroxybenzoic acid. Subsequently, glutathione-dependent dehalogenases (BbdI and BbdE) catalyze the thiolytic removal of the first chlorine. The remaining chlorine is then removed hydrolytically by a dehalogenase of the α/β hydrolase superfamily (BbdC). BbdC is the first enzyme in that superfamily associated with dehalogenation of chlorinated aromatics and appears to represent a new subtype within the α/β hydrolase dehalogenases. The activity of BbdC yields a unique trihydroxylated aromatic intermediate for ring cleavage that is performed by an extradiol dioxygenase (BbdF) producing 2,4,6-trioxoheptanedioic acid, which is likely converted to Krebs cycle intermediates by BbdG.

Enhanced heme protein expression by ammonia-oxidizing communities acclimated to low dissolved oxygen conditions

This study has investigated the acclimation of ammonia-oxidizing communities (AOC) to low dissolved oxygen (DO) concentrations. Under controlled laboratory conditions, two sequencing batch reactors seeded with activated sludge from the same source were operated at high DO (near saturation) and low DO (0.1 mg O₂/L) concentrations for a period of 220 days. The results demonstrated stable and complete nitrification at low DO conditions after an acclimation period of approximately 140 days. Acclimation brought about increased specific oxygen uptake rates and enhanced expression of a particular heme protein in the soluble fraction of the cells in the low DO reactor as compared to the high DO reactor. The induced protein was determined not to be any of the enzymes or electron carriers present in the conventional account of ammonia oxidation in ammonia-oxidizing bacteria (AOB). Further research is required to determine the specific nature of the heme protein detected; a preliminary assessment suggests either a type of hemoglobin protein or a lesser-known component of the energy-transducing pathways of AOB. The effect of DO on AOC dynamics was evaluated using the 16S rRNA gene as the basis for phylogenetic comparisons and organism quantification. Ammonium consumption by ammonia-oxidizing archaea and anaerobic ammonia-oxidizing bacteria was ruled out by fluorescent in situ hybridization in both reactors. Even though Nitrosomonas europaea was the dominant AOB lineage in both high and low DO sequencing batch reactors at the end of operation, this enrichment could not be linked in the low DO reactor to acclimation to oxygen-limited conditions.

Isolation of effective 3-chlorobenzoate-degraders in soil using community analyses by PCR-DGGE

The screening of pollutant degraders by relying solely on cultivation techniques such as liquid enrichment often fails to isolate the actual degraders in the environment. Community analyses by PCR-denaturing gradient gel electrophoresis (DGGE) were performed to isolate bacteria that can degrade 3-chlorobenzoate (3CB) effectively in soil. A forest soil sample was repeatedly dosed with 3CB (500 mg kg(-1)) to enrich it with indigenous 3CB-degraders, and changes in the bacterial community were monitored by PCR-DGGE of the 16S rRNA gene and benzoate 1,2-dioxygenase alpha subunit gene (benA). Initially, it required about 3 weeks to degrade 3CB in the soil, whereas it took only 3 days after the third dose. With this accelerated degradation, several intensified bands appeared in the DGGE profiles of both 16S rRNA gene and benA. We succeeded in isolating five 3CB-degrading Burkholderia strains corresponding to these bands by direct plating, while most of them were eliminated by liquid enrichment. Inoculation of the strains into the soil demonstrated that the five strains could degrade 3CB effectively in the soil. This study clearly shows significant bias during the liquid enrichment process and the advantage of using PCR-DGGE in screening effective degraders under environmental conditions.

Characterization of multiple chlorobenzoic acid-degrading organisms from pristine and contaminated systems: mineralization of 2,4-dichlorobenzoic acid

Multiple bacterial strains with CBA metabolic properties were isolated using a simple selective strategy. Phylogenetic analysis of the 16S rRNA gene sequences grouped them into two main clusters consisting of four bacterial phyla and belonging to 17 genera. Whereas growth was more frequent with 2-CBA (∼68%), 50% grew on 4-CBA and ∼7% utilized 3-CBA. One third of the strains exhibited 2,4-dichlorobenzoic acid (2,4-diCBA) catabolic function and were mainly representatives of α-, β- and γ-Proteobacteria. In batch experiments, growth was concomitant with substrate disappearance and near-stoichiometric release of chloride. Doubling times for 2,4-diCBA degradation doubled those determined for mono-substituted CBAs. Out of the six 2,4-diCBA degraders submitted for enzyme assays, significant induction of catechol 1,2-dioxygenase types I and II activities in cell-free extracts were found in four while protocatechuate 3,4-dioxygenase activity was detected in the remaining two. Activities in CBA-grown cells were 20 orders-of-magnitude higher than those grown on benzoic acid.

Aerobic nonylphenol degradation and nitro-nonylphenol formation by microbial cultures from sediments

Nonylphenol (NP) is an estrogenic pollutant which is widely present in the aquatic environment. Biodegradation of NP can reduce the toxicological risk. In this study, aerobic biodegradation of NP in river sediment was investigated. The sediment used for the microcosm experiments was aged polluted with NP. The biodegradation of NP in the sediment occurred within 8 days with a lag phase of 2 days at 30°C. During the biodegradation, nitro-nonylphenol metabolites were formed, which were further degraded to unknown compounds. The attached nitro-group originated from the ammonium in the medium. Five subsequent transfers were performed from original sediment and yielded a final stable population. In this NP-degrading culture, the microorganisms possibly involved in the biotransformation of NP to nitro-nonylphenol were related to ammonium-oxidizing bacteria. Besides the degradation of NP via nitro-nonylphenol, bacteria related to phenol-degrading species, which degrade phenol via ring cleavage, are abundantly present.

The use of oxygen uptake rate to monitor discovery of microbial and enzymatic biocatalysts

Arising from the requirement for discovery of novel biocatalysts with unusual properties, a process was developed which uniquely combines aspects of continuous culture with the measurement of oxygen uptake. This adaptation of the chemostat can be used to facilitate the isolation of a number of microorganisms with desirable properties, particularly those with useful metabolic capabilities and/or enzymes. The technique was also used to provide feedback on the metabolic status of a microbial population and increase the feed flow rate (i.e., dilution rate) thereby enabling the isolation of microorganisms with enhanced 1,3-propanediol dehydrogenase activity. The use of oxygen uptake as an indicator of cellular activity enables indirect measurement of substrate utilization and provides a real-time online assessment of the status of microbial enrichment or evolutionary processes and provides an opportunity, through the use of feedback systems, to control these processes. To demonstrate the utility of the technique, oxygen uptake rate (OUR) was compared with a range of conventional analytical techniques that are typically used to monitor enrichment/evolutionary processes and showed good correlation. Further validation was demonstrated by monitoring a characterizable microbial population shift using OUR. The population change was confirmed using off-line analytical techniques that are traditionally used to determine microbial activity. OUR was then used to monitor the enrichment of microorganisms capable of using a solvent (1-methyl-2-pyrrolidinone) as the sole source of carbon for energy and biomass formation from a heterogeneous microbial population. After purification the microorganisms taken from the enrichment process were able to completely utilize 1 g L(-1) 1-methyl-2-pyrrolidinone within 24 h demonstrating that the technique had correctly indicated the enriched population was capable of growth on 1-methyl-2-pyrrolidinone. The technique improves on conventional microbial enrichment that utilizes continuous culture by providing a real-time assessment of the enrichment process and the opportunity to use the OUR output for automated control and variation of one or more growth parameters.

Use of Genetically Engineered Microorganisms (GEMs) for the Bioremediation of Contaminants

This paper presents a critical review of the literature on the application of genetically engineered microorganisms (GEMs) in bioremediation. The important aspects of using GEMs in bioremediation, such as development of novel strains with desirable properties through pathway construction and the modification of enzyme specificity and affinity, are discussed in detail. Particular attention is given to the genetic engineering of bacteria using bacterial hemoglobin (VHb) for the treatment of aromatic organic compounds under hypoxic conditions. The application of VHb technology may advance treatment of contaminated sites, where oxygen availability limits the growth of aerobic bioremediating bacteria, as well as the functioning of oxygenases required for mineralization of many organic pollutants. Despite the many advantages of GEMs, there are still concerns that their introduction into polluted sites to enhance bioremediation may have adverse environmental effects, such as gene transfer. The extent of horizontal gene transfer from GEMs in the environment, compared to that of native organisms including benefits regarding bacterial bioremediation that may occur as a result of such transfer, is discussed. Recent advances in tracking methods and containment strategies for GEMs, including several biological systems that have been developed to detect the fate of GEMs in the environment, are also summarized in this review. Critical research questions pertaining to the development and implementation of GEMs for enhanced bioremediation have been identified and posed for possible future research.

Biodegradation of textile azo dye by Shewanella decolorationis S12 under microaerophilic conditions

The complete biodegradation of azo dye, Fast Acid Red GR, was observed under microaerophilic conditions by Shewanella decolorationis S12. Although the highest decolorizing rate was measured under anaerobic condition and the highest biomass was obtained under aerobic condition, a further biodegradation of decolorizing products can only be achieved under microaerophilic conditions. Under microaerophilic conditions, S. decolorationis S12 could use a range of carbon sources for azo dye decolorization, including lactate, formate, glucose and sucrose, with lactate being the optimal carbon source. Sulfonated aromatic amines were not detected during the biotransformation of Fast Acid Red GR, while H(2)S formed. The decolorizing products, aniline, 1,4-diaminobenzene and 1-amino-2-naphthol, were followed by complete biodegradation through catechol and 4-aminobenzoic acid based on the analysis results of GC-MS and HPLC.

Kinetic gas-water transfer and gas accumulation in porous media during pulsed oxygen sparging

Gas-water mass transfer and the transport of dissolved gases in variably saturated porous media are key processes for in-situ remediation by pulsed gas sparging. In this context, gas dissolution tests were conducted during pulsed oxygen gas injection into sand columns. The columns were recharged with anoxic water, effluents were analyzed for dissolved O2, and tracer tests were performed to detect accumulation of trapped gas. In a second series oxygen gas was blended with sulfur hexafluoride (SF6), and O2 and SF6 breakthrough curves were recorded. To interpret experimental results, a numerical model was applied that simulates multi-species kinetic mass transfer during gas dissolution. The model predicted breakthrough curves of dissolved gas species and delivered spatially resolved values for gas phase accumulation and composition, which are not directly accessible experimentally. It was shown how dissolved nitrogen accumulates increasingly in trapped gas phase and inhibits its complete dissolution, in case the pulsed gas injections were operated based on O2 breakthrough only. Accumulation of nitrogen also retarded dissolved oxygen transport and thus oxygen breakthrough. Experiments plus modeling demonstrated that SF6 measurements are highly sensitive to the gas dissolution processes, and provide a more sensitive criterion for determining gas injection frequencies during pulsed biosparging.

Aerobic MTBE biodegradation in the presence of BTEX by two consortia under batch and semi-batch conditions

This study explores the effect of microbial consortium composition and reactor configuration on methyl tert-butyl ether (MTBE) biodegradation in the presence of benzene, toluene, ethylbenzene and p-xylenes(BTEX). MTBE biodegradation was monitored in the presence and absence of BTEX in duplicate batch reactors inoculated with distinct enrichment cultures: MTBE only (MO-originally enriched on MTBE) and/or MTBE BTEX (MB-originally enriched on MTBE and BTEX). The MO culture was also applied in a semi-batch reactor which received both MTBE and BTEX periodically in fresh medium after allowing cells to settle. The composition of the microbial consortia was explored using a combination of 16S rRNA gene cloning and quantitative polymerase chain reaction targeting the known MTBE-degrading strain PM1T. MTBE biodegradation was completely inhibited by BTEX in the batch reactors inoculated with the MB culture, and severely retarded in those inoculated with the MO culture (0.18+/-0.04 mg/L-day). In the semi-batch reactor, however, the MTBE biodegradation rate in the presence of BTEX was almost three times as high as in the batch reactors (0.48+/-0.2 mg/L-day), but still slower than MTBE biodegradation in the absence of BTEX in the MO-inoculated batch reactors (1.47+/-0.47 mg/L-day). A long lag phase in MTBE biodegradation was observed in batch reactors inoculated with the MB culture (20 days), but the ultimate rate was comparable to the MO culture (0.95+/-0.44 mg/L-day). Analysis of the cultures revealed that strain PM1T concentrations were lower in cultures that successfully biodegraded MTBE in the presence of BTEX. Also, other MTBE degraders, such as Leptothrix sp. and Hydrogenophaga sp. were found in these cultures. These results demonstrate that MTBE bioremediation in the presence of BTEX is feasible, and that culture composition and reactor configuration are key factors.

Comparison of 2-chlorobenzoic acid biodegradation in a membrane bioreactor by B. cepacia and B. cepacia bearing the bacterial hemoglobin gene

Degradation of 2-chlorobenzoic acid (2-CBA), a model recalcitrant chlorinated organic compound, by pure cultures of Burkholderia cepacia strain DNT with (transformed B. cepacia) and without (untransformed B. cepacia) the bacterial hemoglobin (Vitreoscilla hemoglobin, VHb) gene, vgb, was investigated in parallel membrane bioreactors (MBRs). This was done aseptically to prevent contamination during the operation of the MBRs. The objective was to determine whether the degradation of 2-CBA by cometabolism, using acetate as a primary carbon source, under hypoxic conditions might be enhanced for vgb-bearing cells in MBRs. The 2-CBA removal efficiency of transformed B. cepacia (97-99%) was slightly higher than that of untransformed B. cepacia (95-99%) at all stages. The average amount of chloride released from 2-CBA by transformed cells was also higher than for untransformed cells, 92-96% compared to 64-84% of the maximum theoretical amount, the exact value depending on the operating conditions. These results indicate that 2-CBA degradation/transformation is not accompanied by the stoichiometric release of chloride for the untransformed strain. The difference between percentages of 2-CBA removal and chloride release by untransformed cells was attributed to persistence, under hypoxic conditions, of the 2-CBA chlorine atom in 2-CBA metabolites. Growth of transformed cells was also significantly enhanced under hypoxic conditions compared to untransformed cells. For varying media compositions, the transformed cells reached higher cell densities (3.2-5.4 g/L) relative to untransformed cells (2.8-4.7 g/L) at food to microorganism ratios ranging from 0.44-0.59 to 0.38-0.49 g COD/g biomass-d The observed yields thus ranged from 0.16-0.20 and 0.15-0.18 g TSS/g COD for untransformed and transformed cells, respectively. The value of the yield depended on medium composition. The MBR system using vgb-containing B. cepacia maintained a high biomass concentration without oxygen limitations and provided cell-free effluent. Hence, it may be useful for treating high volumes of water contaminated with low levels of recalcitrant organics.

2-Chlorobenzoate biodegradation by recombinant Burkholderia cepacia under hypoxic conditions in a membrane bioreactor

The feasibility of applying bacterial hemoglobin technology to degrade 2-chlorobenzoate (2-CBA) through co-metabolism under hypoxic conditions in a membrane bioreactor (MBR) process has been studied in the laboratory. 2-chlorobenzoate removal and chloride release rates in the MBR system varied from 99 to 78% and 98 to 73%, respectively, depending on the operation conditions. Chemical oxygen demand (COD) removal efficiencies were more than 90% at food-to-microorganism ratios ranging from 0.32 to 0.62 g/g/d, and the observed yield was 0.13 to 0.20 g biomass/g COD. The bacterial cell-floc size-distribution analysis showed that there is a significant change in bacterial floc size due to high shear stress during operation of the MBR. To characterize growth kinetics of Burkholderia cepacia strain dinitrotoluene, a mathematical model that describes co-metabolic oxidation of 2-CBA in an MBR has been developed.

Aerobic degradation of polychlorinated biphenyls

The microbial degradation of polychlorinated biphenyls (PCBs) has been extensively studied in recent years. The genetic organization of biphenyl catabolic genes has been elucidated in various groups of microorganisms, their structures have been analyzed with respect to their evolutionary relationships, and new information on mobile elements has become available. Key enzymes, specifically biphenyl 2,3-dioxygenases, have been intensively characterized, structure/sequence relationships have been determined and enzymes optimized for PCB transformation. However, due to the complex metabolic network responsible for PCB degradation, optimizing degradation by single bacterial species is necessarily limited. As PCBs are usually not mineralized by biphenyl-degrading organisms, and cometabolism can result in the formation of toxic metabolites, the degradation of chlorobenzoates has received special attention. A broad set of bacterial strategies to degrade chlorobenzoates has recently been elucidated, including new pathways for the degradation of chlorocatechols as central intermediates of various chloroaromatic catabolic pathways. To optimize PCB degradation in the environment beyond these metabolic limitations, enhancing degradation in the rhizosphere has been suggested, in addition to the application of surfactants to overcome bioavailability barriers. However, further research is necessary to understand the complex interactions between soil/sediment, pollutant, surfactant and microorganisms in different environments.

Effects of oxygen on biodegradation of benzoate and 3-chlorobenzoate in a denitrifying chemostat

A mixed microbial culture degraded a mixture of benzoate (863 mg/L), 3-chlorobenzoate (3-CB) (69.7 mg/L), and pyruvate (244 mg/L) under denitrifying conditions in a chemostat. Biodegradation under denitrifying conditions was stable, complete (effluent concentrations below detection limits), and proceeded without the production of toxic intermediates like chlorocatechols. The addition of oxygen at mass input rates of 6.2%, 15.5%, and 43.9% of the mass input rate of chemical oxygen demand (COD) (337 mg COD/h) did not induce the synthesis of aerobic biodegradation pathways and thus did not disrupt biodegradation. Rather, the oxygen was used as a terminal electron acceptor, displacing a stoichiometric amount of nitrate, leading to microaerobic conditions (dissolved oxygen concentration <0.050 mg/L) in which oxygen utilization and denitrification occurred simultaneously. The reduction of nitrate occurred fully to N(2) gas with no accumulation of nitrite, nitrous oxide, or nitric oxide, although the ability of the culture to transfer electrons to the nitrogen oxides decreased as the oxygen input was increased. The anoxic benzoate uptake capability was unaffected by the increase in oxygen addition, but the anoxic 3-CB uptake capability increased, as did the level of benzoyl-CoA reductase in the cells.

Enhanced kinetics of genetically engineeredBurkholderia cepacia: the role ofvgb in the hypoxic metabolism of 2-CBA

Application of Vitreoscilla hemoglobin (VHb) technology to 2-CBA degradation by Burkholderia cepacia strain DNT under hypoxic conditions was studied in continuous culture chemostats. Dechlorination abilities of both recombinant (VHb gene (vgb) containing) and untransformed cells were investigated at various dilution rates to ensure complete degradation of 2-CBA. As the dilution rate increased from 0.025 to 0.25 h(-1), the ratios of chloride release to degraded 2-CBA concentration decreased from 0.95 to 0.72 and from 0.89 to 0.39 for recombinant and untransformed cells, respectively. A nonstoichiometric relationship between chloride release and 2-CBA degradation was more pronounced for untransformed cells. Recombinant cell densities were 0.1-0.2. g L(-1) greater than untransformed cell densities for a range of dilution rates. As the dilution rate increased, the oxygen uptake rate (OUR) and the substrate utilization rate (SUR) decreased for both strains. The OUR/SUR ratio increased as the dilution rate increased for both strains but was much higher for the recombinant strain compared to untransformed cells. The specific 2-CBA degradation rate of recombinant cells was greater than that of untransformed cells (1.17 vs. 0.46 mg CBA (mg) day(-1), and half-saturation constants for recombinant cells were lower than those of untransformed cells (0.18 and 0.32 mg CBA L(-1), respectively). The pseudo-first-order degradation constants, k(1CBA) and k(1ACE), were higher for recombinant cells (6.5 L (mg cells)(-1) day(-1) and 95.6 L (mg cells)(-1) day(-1), respectively) than those of untransformed cells (1.44 L (mg cells)(-1) day(-1) and 73.7 L (mg cells)(-1) day(-1), respectively).

Kinetics of benzene biotransformation under microaerophilic and oxygen-limited conditions

A special microbial consortium adapted to degrade petroleum hydrocarbons at limited availability of oxygen, transformed benzene, a highly toxic and carcinogenic contaminant of groundwater and soil, at low initial dissolved oxygen (DO) concentrations of 0.05-2 mg/L. The employed initial concentrations of dissolved oxygen were considerably lower than the previously reported values. Under these conditions, the overall transformation of benzene ranged from 34% +/- 1.7% to 100%, considerably higher than the theoretical predictions for complete mineralization of benzene based on the requirement of 3.08 mg oxygen/mg benzene. Unlike biotransformation that proceeded at the lowest examined DO concentration of 0.05 mg/L, the mineralization of benzene, defined by its conversion to CO(2) and water, required a minimum DO concentration of 0.2 mg/L. The mineralization of benzene under microaerophilic conditions (DO < 2 mg/L), ranged from 0.83% +/- 0.06% to 89% +/- 1.3%, which was less than the theoretical predictions at any given initial DO concentration. The regulatory effects of dissolved oxygen concentration or its partial pressure on the activities of enzymes catalyzing the biotransformation of aromatic hydrocarbons was postulated to account for the reduced mineralization of benzene. The ratio between the transformed benzene and the consumed oxygen increased with the decrease of initial DO concentration, reaching a value of 2.8, considerably higher than the theoretical value of 0.33 obtained for a complete aerobic oxidation of benzene. Phenol was the major and the most stable intermediate metabolite during the biotransformation of benzene at low concentrations of DO. While benzene transformation stopped after the depletion of oxygen in the experimental system, phenol continued to accumulate under strictly anaerobic conditions, indicating its formation from an alternative carbon source, possibly biomass.

Biodegradation of dimethylphenols by bacteria with different ring-cleavage pathways of phenolic compounds

The biodegradation of 3,4, 2,4, 2,3, 2,6 and 3,5-dimethylphenol in combination with phenol and p-cresol by axenic and mixed cultures of bacteria was investigated. The strains, which degrade phenol and p-cresol through different catabolic pathways, were isolated from river water continuously polluted with phenolic compounds of leachate of oil shale semicoke ash heaps. The proper research of degradation of 2,4 and 3,4-dimethylphenol in multinutrient environments was performed. The degradation of phenolic compounds from mixtures indicated a flux of substrates into different catabolic pathways. Catechol 2,3-dioxygenase activity was induced by dimethylphenols in Pseudomonas mendocina PC1, where meta cleavage pathway was functional during the degradation of p-cresol. In the case of strains PC18 and PC24 of P. fluorescens, the degradation of p-cresol occurred via the protocatechuate ortho pathway and the key enzyme of this pathway, p-cresol methylhydroxylase, was also induced by dimethylphenols. 2,4 and 3,4-dimethylphenols were converted into the dead-end products 4-hydroxy-3-methylbenzoic acid and 4-hydroxy-2-methylbenzoic acid. In the degradation of 3,4-dimethylphenol, the transient accumulation of 4-hydroxy-2-methylbenzaldehyde repressed the consumption of phenol from substrate mixtures. A mixed culture of strains with different catabolic types made it possible to overcome the incompatibilities at degradation of studied substrate mixtures.

Identification and functional characterization of CbaR, a MarR-like modulator of the cbaABC-encoded chlorobenzoate catabolism pathway

In Comamonas testosteroni BR60 (formerly Alcaligenes sp. strain BR60), catabolism of the pollutant 3-chlorobenzoate (3CBA) is initiated by enzymes encoded by cbaABC, an operon found on composite transposon Tn5271 of plasmid pBRC60. The cbaABC gene product CbaABC converts 3CBA to protocatechuate (PCA) and 5-Cl-PCA, which are then metabolized by the chromosomal PCA meta (extradiol) ring fission pathway. In this study, cbaA was found to possess a sigma(70) type promoter. O(2) uptake experiments with whole cells and expression studies with cbaA-lacZ constructs showed that cbaABC was induced by 3CBA. Benzoate, which is not a substrate of the 3CBA pathway, was a gratuitous inducer, and CbaR, a MarR family repressor coded for by a divergently transcribed gene upstream of cbaABC, could modulate induction mediated by benzoate. Purified CbaR bound specifically to two regions of the cbaA promoter (P(cbaA)); site I, a high-affinity site, is between the transcriptional start point (position +1) and the start codon of cbaA, while site II, a lower-affinity site, overlaps position +1. 3CBA at concentrations as low as 40 microM interfered with binding to P(cbaA). PCA also interfered with binding, while benzoate only weakly disrupted binding. Unexpectedly, benzoate with a hydroxyl or carboxyl at position 3 improved CbaR binding. Data are also presented that suggest that an unidentified regulator is encoded on the chromosome that induces cbaABC in response to benzoate and 3CBA.

Bacterial community changes and enrichment of Burkholderia-like bacteria induced by chlorinated benzoates in a peat-forest soil-microcosm

Bacterial community shifts in a peat-forest soil spiked with 3-chlorobenzoate (3CBA) or 2,5-dichlorobenzoate (2,5DCB) were monitored by PCR-amplification of the V6 to V8 regions of the 16S rRNA and rDNA, followed by separation of the amplicons by temperature gradient gel electrophoresis. 3CBA disappeared to non-detectable levels after 15 days by a biologically mediated process, while 2,5DCB remained at the initial concentration values. The experiments were conducted under microcosms systems. Addition of the chlorinated benzoates to the soil resulted in a rapid decrease of the microbial diversity, as judged by a time-dependent reduction in the number of amplicons detected by temperature gradient gel electrophoresis. Few amplicons specifically enriched in the spiked soils were cloned and characterised by sequence analysis. The identity of the cloned DNA and the corresponding soil amplicons was confirmed by hybridisation with a radioactively labelled V6-probe. Analysis of the 16S rDNA sequences indicated that Burkholderia-related bacteria dominated the enriched soil populations under 3CBA stress. In addition, enrichment cultures growing on 3CBA as sole C-source were obtained from the respective spiked soil, which were found to contain bacteria with identical 16S rDNA sequences as those induced by 3CBA stress in soil.

A novel ortho-dehalogenation reaction of 2-chlorocinnamic acid catalyzed by the pink yeast Rhodotorula rubra Y-1529

In the present study, a resting cells suspension of Rhodotorula rubra Y-1529 was shown to have the capacity to perform an ortho-dehalogenation reaction on 2-chlorocinnamic acid. The results from the biodegradation of U-[14C]benzoic acid, cinnamic acid, 3-chlorocinnamic acid and 4-chlorocinnamic acid suggest that the first step of the ortho-dehalogenation reaction occurred during the oxidation of the unsaturated C3 side chain of 2-chlorocinnamic acid to 2-chlorobenzoic acid. None of the 2-chlorobenzoic acid was found in the biodegradation system, suggesting that this step was a highly regulated step. After the side-chain oxidation reaction, the hydroxylation of the benzene ring was determined to be at the para-position first, followed by the meta-position. The occurrence of 3:4-position ring fission reactions and the production of the final product, CO2, was proven by the biodegradation of U-[14C] benzoic acid. This oxidative dehalogenation reaction catalyzed by R. rubra was found to be regiospecific for 2-chlorocinnamic acid; the chloride ion was probably removed after the ring fission reaction. A pathway of the ortho-dehalogenation reaction of 2-chlorocinnamic acid catalyzed by R. rubra was proposed based on these data.

Characterization of 3-chlorobenzoate degrading aerobic bacteria isolated under various environmental conditions

The rates of bacterial growth in nature are often restricted by low concentrations of oxygen or carbon substrates. In the present study the metabolic properties of 24 isolates that had been isolated using various concentrations of 3-chlorobenzoate, benzoate and oxygen as well as using continuous culture at high and low growth rates were determined to investigate the effects of these parameters on the metabolism of monoaromatic compounds. Bacteria were enriched from different sampling sites and subsequently isolated. In batch culture this was done both under low oxygen (2% O(2)) and air-saturated concentrations. Chemostat enrichments were performed under either oxygen or 3-chlorobenzoate limiting conditions. Bacteria metabolizing aromatics with gentisate or protocatechuate as intermediates (gp bacteria) as well as bacteria metabolizing aromatic compounds via catechols (cat bacteria) were isolated from batch cultures when either benzoate or 3CBA were used as C sources, regardless of the enrichment conditions applied. In contrast, enrichments performed in chemostats at low dilution rates resulted in gp-type organisms only, whereas at high dilution rates cat-type organisms were enriched, irrespective of the oxygen and 3-chlorobenzoate concentration used during enrichment. It is noteworthy that the gp-type of bacteria possessed relatively low µ(max) values on 3CBA and benzoate along with relatively high substrate and oxygen affinities for these compounds. This is in contrast with cat-type of bacteria, which seemed to be characterized by high maximum specific growth rates on the aromatic substrates and relatively high apparent half saturation constants. In contrast, bacteria degrading chlorobenzoate via gentisate or protocatechuate may possibly be better adapted to conditions leading to growth at reduced rates such as low oxygen and low substrate concentrations.

Three types of phenol and p-cresol catabolism in phenol- and p-cresol-degrading bacteria isolated from river water continuously polluted with phenolic compounds

A total of 39 phenol- and p-cresol-degraders isolated from the river water continuously polluted with phenolic compounds of oil shale leachate were studied. Species identification by BIOLOG GN analysis revealed 21 strains of Pseudomonas fluorescens (4, 8 and 9 of biotypes A, C and G, respectively), 12 of Pseudomonas mendocina, four of Pseudomonas putida biotype A1, one of Pseudomonas corrugata and one of Acinetobacter genospecies 15. Computer-assisted analysis of rep-PCR fingerprints clustered the strains into groups with good concordance with the BIOLOG GN data. Three main catabolic types of degradation of phenol and p-cresol were revealed. Type I, or meta-meta type (15 strains), was characterized by meta cleavage of catechol by catechol 2,3-dioxygenase (C23O) during the growth on phenol and p-cresol. These strains carried C23O genes which gave PCR products with specific xylE-gene primers. Type II, or ortho-ortho type (13 strains), was characterized by the degradation of phenol through ortho fission of catechol by catechol 1,2-dioxygenase (C12O) and p-cresol via ortho cleavage of protocatechuic acid by protocatechuate 3,4-dioxygenase (PC34O). These strains carried phenol monooxygenase gene which gave PCR products with pheA-gene primers. Type III, or meta-ortho type (11 strains), was characterized by the degradation of phenol by C23O and p-cresol via the protocatechuate ortho pathway by the induction of PC34O and this carried C23O genes which gave PCR products with C23O-gene primers, but not with specific xylE-gene primers. In type III strains phenol also induced the p-cresol protocatechuate pathway, as revealed by the induction of p-cresol methylhydroxylase. These results demonstrate multiplicity of catabolic types of degradation of phenol and p-cresol and the existence of characteristic assemblages of species and specific genotypes among the strains isolated from the polluted river water.

Degradation of 3-chlorobenzoate under low-oxygen conditions in pure and mixed cultures of the anoxygenic photoheterotroph Rhodopseudomonas palustris DCP3 and an aerobic Alcaligenes species

The presence or absence of molecular oxygen has been shown to play a crucial role in the degradability of haloaromatic compounds. In the present study, it was shown that anaerobic phototrophic 3-chlorobenzoate (3CBA) metabolism by Rhodopseudomonas palustris DCP3 is oxygen tolerant up to a concentration of 3 microM O2. Simultaneous oxidation of an additional carbon source permitted light-dependent anaerobic 3CBA degradation at oxygen input levels which, in the absence of such an additional compound, would result in inhibition of light-dependent dehalogenation. Experiments under the same experimental conditions with strain DCP3 in coculture with an aerobic 3CBA-utilizing heterotroph, Alcaligenes sp. strain L6, revealed that light-dependent dehalogenation of 3CBA did not occur. Under both oxygen limitation (O2 < 0.1 microM) and low oxygen concentrations (3 microM O2), all the 3CBA was metabolized by the aerobic heterotroph. These data suggest that biodegradation of (halo)aromatics by photoheterotrophic bacteria such as R. palustris DCP3 may be restricted to anoxic photic environments.

PcaU, a transcriptional activator of genes for protocatechuate utilization in Acinetobacter

The Acinetobacter pcaIJFBDKCHG operon encodes the six enzymes that convert protocatechuate to citric acid cycle intermediates. Directly downstream from the operon are qui and pob genes encoding sets of enzymes that convert quinate and p-hydroxybenzoate, respectively, to protocatechuate. Prior to this investigation, the only known regulatory gene in the pca-qui-pob cluster was pobR, which encodes a transcriptional activator that responds to p-hydroxybenzoate and activates transcription of pobA. The pca and qui genes were known to be expressed in response to protocatechuate, but a protein that mediated this induction had not been identified. This study was initiated by characterization of a spontaneous mutation that mapped upstream from pcaI and prevented expression of the pca genes. Sequencing of wild-type DNA extending from the translational start of pcaI through and beyond the location of the mutation revealed a 282-bp intergenic region and a divergently transcribed open reading frame, designated pcaU. Downstream from pcaU are two open reading frames encoding proteins similar in amino acid sequence to those associated with the oxidation of acyl thioesters. Inactivation of pcaU reduced the induced expression of pca structural genes by about 90% and impeded but did not completely prevent growth of the mutant cells with protocatechuate. PcaU was expressed in Escherichia coli and shown to bind to a portion of the pcaI-pcaU intergenic region containing a sequence identical in 16 of 19 nucleotide residues to a segment of the pob operator. Further similarity of the two regulatory systems is indicated by 54% amino acid sequence identity in the aligned primary structures of PobR and PcaU. The pob and pca systems were shown to differ, however, in the relative orientations of transcriptional starts with respect to the site where the activator binds to DNA, the size of the intergenic region, and the tightness of transcriptional control. The spontaneous mutation blocking pca gene expression was located in the promoter for the pca operon. The 19-nucleotide residue operator sequences were shown to be parts of a consensus associated with transcriptional activation of genes associated with protocatechuate catabolism. Two different binding sites for Pseudomonas putida PcaR differ from the consensus in only a single nucleotide residue, and DNA directly downstream from Acinetobacter pcaU contains a 19-bp segment differing from the consensus in only two residues. PcaU was shown to bind to DNA containing this segment as well as to the DNA in the pcaU-pcaI intergenic region.

The cis-diol dehydrogenase cbaC gene of Tn5271 is required for growth on 3-chlorobenzoate but not 3,4-dichlorobenzoate

The nucleotide sequence of cbaC, the 1-carboxy-3-chloro-4,5-dihydroxycyclohexa-2,6-diene (cis-diol) dehydrogenase gene from the 3-chlorobenzoate (3-Cba) catabolic transposon Tn5271 was determined. The functional significance of the deduced open reading frame was evaluated by deletion of an internal BstEII restriction site in cbaC and by the creation of nested deletions using exonuclease III. Expression studies were carried out with Alcaligenes sp. strain BR6024, a chloramphenicol-resistant, tryptophan auxotroph derived from the wild-type isolate BR60. BR6024 hosts carrying complete cbaAB (3-Cba 3,4-(4,5)-dioxygenase and reductase) genes, with deletions of cbaC, metabolized 3Cba to the cis-4,5-diol metabolite. These mutants failed to grow on 3-Cba; however, they grew on 3,4-dichlorobenzoate, accumulating 5-chloroprotocatechuate transiently. These results indicated the cbaC dehydrogenase was not required for re-aromatization of the unstable 3,4-dCba cis-4,5-diol metabolite. Spontaneous elimination of HCl from this metabolite is proposed to generate 5-chloroprotocatechuate, which is a substrate for the protocatechuate metaring fission pathway in Alcaligenes sp. BR60. The relationship of the deduced amino acid sequence of cbaC with 15 other oxidoreductases and sequences of unknown function from bacteria, plants and animals revealed a conserved N-terminal GxxGxG dinucleotide-binding domain and a conserved region with a H(x11)KHVLxEKPxA consensus flanked by alpha-helical domains. o-Phthalate cis-diol dehydrogenase (Pseudomonas putida), glucose-fructose oxidoreductase (Zymomonas mobilis), myo-inositol-2-dehydrogenase (Bacillus subtilis) and D-galactose-1-dehydrogenase (Pseudomonas fluorescens) are related proteins. These dehydrogenases are unrelated to the Type I, II and III dehydrogenase superfamilies that include the cis-diol dehydrogenases involved in benzoate, toluene, biphenyl and naphthalene catabolism (Type II) and benzene catabolism (Type III).