Plasmid-encoded degradation of p-nitrophenol and 4-nitrocatechol by Arthrobacter protophormiae

Chemotactic response of p-nitrophenol degrading Pseudomonas asiatica strain PNPG3 through phenotypic and genome sequence-based in silico studies

The Pseudomonas asiatica strain PNPG3 was documented to possess chemotactic potential toward p-nitrophenol (PNP), and other nitroaromatic compounds. Initial screening with drop plate and swarm plate assays demonstrated significant movement of the strain toward the test compounds. A quantitative capillary assay revealed the highest chemotactic potential of the strain toward 4-Aminophenol (4AP), (CI: 12.33); followed by p-benzoquinone (PBQ), (CI: 6.8); and PNP, (CI: 5.33). Gene annotation revealed the presence of chemotactic genes (Che), (Methyl-accepting Proteins) MCPs, rotary motor proteins, and flagellar proteins within the genome of strain PNPG3. The chemotactic machinery of the strain PNPG3 comprised of thirteen Che genes, twenty-two MCPs, eight rotary motors, and thirty-four flagellar proteins that are involved in sensing chemoattractant. Two chemotactic gene clusters were recorded in the genome, of which the major cluster consisted of two copies of CheW, one copy of CheA, CheY, CheZ, one MotD gene, and several Fli genes. Various conserved regions and motifs were documented in them using a standard bioinformatics tool. Genes involved in the chemotaxis of strain PNPG3 were compared with three closely related strains and one distantly related strain belonging to Burkholderia sp. Considering these phenotypic and genotypic data, it can be speculated that it is metabolism-dependent chemotaxis; and that test compound activated the Che. This study indicated that strain PNPG3 could be used as a model organism for the study of the molecular mechanism of chemotaxis and bioremediation of PNP.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03809-3.

Biodegradation of p-nitrophenol by a member of the genus Brachybacterium, isolated from the river Ganges

A p-nitrophenol (PNP) degrading halotolerant, Gram-variable bacterial strain designated as DNPG3, was isolated from a water sample collected from the river Ganges in Hooghly, West Bengal (WB), India, by enrichment culture technique. Based on 16S rRNA gene sequence analysis (carried out at EzTaxon server and Ribosomal data base project site), the strain DNPG3 was identified as Brachybacterium sp., with B. zhongshanense strain JBT (97.08% identity) as it is nearest phylogenetic relative. The strain could tolerate up to 3 mM of PNP, while the optimal growth for the strain was recorded as 0.25 mM. The strain could carry out biodegradation of PNP with concomitant release of nitrite and p-benzoquinone (PBQ) was detected as a hydrolysis product. Under the catabolic condition, it could carry out 36% biodegradation of PNP within 144 h, while, under co-metabolic condition (with glucose), 100% biodegradation was achieved within 48 h at 30 °C. Calcium alginate bead-based cell immobilization studies (of the strain DNPG3) indicated complete biodegradation of PNP (under catabolic condition) within 26 h. This is the first report of PNP biodegradation by any representative strain of the genus Brachybacterium. The study definitely indicated that Brachybacterium sp. strain DNPG3 has biotechnological potential and the strain may be a suitable candidate for developing clean, green, eco-friendly, cost-effective bioremediation processes towards effective removal of PNP from the contaminated sites.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03263-7.

Biodegradation of persistent environmental pollutants by Arthrobacter sp

Persistent environmental pollutants are a growing problem around the world. The effective control of the pollutants is of great significance for human health. Some microbes, especially Arthrobacter, can degrade pollutants into nontoxic substances in various ways. Here, we review the biological properties of Arthrobacter adapting to a variety of environmental stresses, including starvation, hypertonic and hypotonic condition, oxidative stress, heavy metal stress, and low-temperature stress. Furthermore, we categorized the Arthrobacter species that can degrade triazines, organophosphorus, alkaloids, benzene, and its derivatives. Metabolic pathways behind the various biodegradation processes are further discussed. This review will be a helpful reference for comprehensive utilization of Arthrobacter species to tackle environmental pollutants.

Simultaneous p-nitrophenol and nitrogen removal in PNP wastewater treatment: Comparison of two integrated membrane-aerated bioreactor systems

The chemical p-nitrophenol (PNP) is a priority pollutant, and PNP wastewater is highly toxic and resistant to biodegradation. The traditional physical and chemical methods (adsorption, extraction, and oxidation) for treating PNP wastewater have the disadvantages of complicated processes, high costs and secondary pollution generation. In this study, two integrated membrane-aerated bioreactor systems (RA and RB) with anoxic and aerated zones were constructed to enhance PNP biodegradation. The results showed that a helical silicone rubber membrane module displayed a high oxygen supply rate under a low membrane aeration pressure, and the hydraulic flow state of the reactor approached ideal mixing. At an influent PNP concentration of 500 mg/L, the average removal rates of PNP, chemical oxygen demand (COD) and total nitrogen (TN) reached 95.86%, 89.77%, and 94.81%, respectively, for RA and 89.48%, 74.26% and 64.78%, respectively, for RB, indicating efficient simultaneous PNP and nitrogen removal. Compared with that of RB, the pre-anoxic zone in RA not only performed detoxification pretreatment but also enhanced PNP degradation and denitrification effects, which relieved the biological treatment burden of the subsequent aerated zone. Based on these comprehensive analyses of reactor performance, the hydroquinone pathway might be the main route in the aerobic degradation of PNP.

Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1

Rhodococcus sp.strain BUPNP1 can utilize the priority environmental pollutant 4-nitrophenol (4-NP) as its sole source of carbon and energy. In this study, genome and transcriptome sequencing were used to gain mechanistic insights into 4-NP degradation. The draft BUPNP1 genome is 5.56 Mbp and encodes 4,963 proteins, which are significantly enriched in hypothetical proteins compared to other Rhodococcus sp. A novel 4-NP catabolic 43 gene cluster “nph” was identified that encodes all the genes required for the conversion of 4-NP into acetyl-CoA and succinate, via 4-nitrocatechol. The cluster also encodes pathways for the catabolism of other diverse aromatic compounds. Comparisons between BUPN1 growing on either 4-NP or glucose resulted in significant changes in the expression of many nph cluster genes, and, during 4-NP growth, a loss of lipid inclusions. Moreover, fatty acid degradation/synthesis genes were found within the nph cluster, suggesting fatty acids may be concurrently catabolised with 4-NP. A holistic model for the action of the nph gene cluster is proposed which incorporates genetic architecture, uptake and metabolism of aromatic compounds, enzymatic activities and transcriptional regulation. The model provides testable hypotheses for further biochemical investigations into the genes of the nph cluster, for potential exploitation in bioremediation.

Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1

The genus Arthrobacter is ubiquitously distributed in different natural environments. Many xenobiotic-degrading Arthrobacter strains have been isolated and described; however, few have been systematically characterized with regard to multiple interrelated metabolic pathways and the genes that encode them. In this study, the biodegradability of seven aromatic compounds by Arthrobacter sp. YC-RL1 was investigated. Strain YC-RL1 could efficiently degrade p-xylene (PX), naphthalene, phenanthrene, biphenyl, p-nitrophenol (PNP), and bisphenol A (BPA) under both separated and mixed conditions. Based on the detected metabolic intermediates, metabolic pathways of naphthalene, biphenyl, PNP, and BPA were proposed, which indicated that strain YC-RL1 harbors systematic metabolic pathways toward aromatic compounds. Further, genomic analysis uncovered part of genes involved in the proposed pathways. Both intradiol and extradiol ring-cleavage dioxygenase genes were identified in the genome of strain YC-RL1. Meanwhile, gene clusters predicted to encode the degradation of biphenyl (bph), para-substituted phenols (npd) and protocatechuate (pca) were identified, and bphA1A2BCD was proposed to be a novel biphenyl-degrading gene cluster. The complete metabolic pathway of biphenyl was deduced via intermediates and functional gene analysis (bph and pca gene clusters). One of the these genes encoding ring-cleavage dioxygenase in bph gene cluster, a predicted 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) gene, was cloned and its activity was confirmed by heterologous expression. This work systematically illuminated the metabolic versatility of aromatic compounds in strain YC-RL1 via the combination of metabolites identification, genomics analysis and laboratory experiments. These results suggested that strain YC-RL1 might be a promising candidate for the bioremediation of aromatic compounds pollution sites.

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem

A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called "rare biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species.IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants.

Optimization study of 2-hydroxyquinoxaline (2-HQ) biodegradation by Ochrobactrum sp. HQ1

A novel aerobic gram-negative bacterial strain capable of utilizing 2-hydroxyquinoxaline (2-HQ) as sole source of carbon and energy was isolated from Indian agricultural soil and named as HQ1. Strain HQ1 was identified as Ochrobactrum sp. on the basis of morphology, physico-biochemical characteristics and 16S rRNA sequence analysis. The generation time of Ochrobactrum sp. HQ1 on 2-HQ at log phase is 0.71 h or 42.6 min. The degradation of 2-HQ by HQ1 under various physico-chemical parameters was analysed by HPLC and observed to be optimum with a high inoculum density (1.0 OD) at pH 7–8, temperatures 37–40°C and a high concentration of 2-HQ (500 ppm). Degradation of 2-HQ was also improved when additional nitrogen sources were used and this was attributed to the enhanced growth of the bacterium on the readily available nitrogen sources. Analysis of 2-HQ degradation by GC–MS resulted in elucidation of the degradation pathway for HQ1, a novel observation for aerobic Gram-negative bacteria. These findings are a possible indication of the application of HQ1 in the bioremediation of pesticide/metabolite contamination.

Selection and identification of a bacterial community able to degrade and detoxify m-nitrophenol in continuous biofilm reactors

Nitroaromatics are widely used for industrial purposes and constitute a group of compounds of environmental concern because of their persistence and toxic properties. Biological processes used for decontamination of nitroaromatic-polluted sources have then attracted worldwide attention. In the present investigation m-nitrophenol (MNP) biodegradation was studied in batch and continuous reactors. A bacterial community able to degrade the compound was first selected from a polluted freshwater stream and the isolates were identified by the analysis of the 16S rRNA gene sequence. The bacterial community was then used in biodegradation assays. Batch experiments were conducted in a 2L aerobic microfermentor at 28 °C and with agitation (200 rpm). The influence of abiotic factors in the biodegradation process in batch reactors, such as initial concentration of the compound and initial pH of the medium, was also studied. Continuous degradation of MNP was performed in an aerobic up-flow fixed-bed biofilm reactor. The biodegradation process was evaluated by determining MNP and ammonium concentrations and chemical oxygen demand (COD). Detoxification was assessed by Vibrio fischeri and Pseudokirchneriella subcapitata toxicity tests. Under batch conditions the bacterial community was able to degrade 0.72 mM of MNP in 32 h, with efficiencies higher than 99.9% and 89.0% of MNP and COD removals respectively and with concomitant release of ammonium. When the initial MNP concentration increased to 1.08 and 1.44 mM MNP the biodegradation process was accomplished in 40 and 44 h, respectively. No biodegradation of the compound was observed at higher concentrations. The community was also able to degrade 0.72 mM of the compound at pH 5, 7 and 9. In the continuous process biodegradation efficiency reached 99.5% and 96.8% of MNP and COD removal respectively. The maximum MNP removal rate was 37.9 gm(-3) day(-1). Toxicity was not detected after the biodegradation process.

Biodegradation of Benzo[a]Pyrene through the use of algae

In this work for disposal of the biologically hard decomposed pollutant Benzo[a]Pyrene (BaP) photooxidation Chlorella kessleri was used. The simulation model system under the different experimental conditions (varying biomass and light intensity) was evaluated. For quantitative analysis of the decrease in BaP, GC/MS technique was used. The highest degradation efficiency was achieved in the case of biomass from the culture of live algae (29%) and light intensity at level of 13.5 W m−2. When the dry biomass was used, degradation under the same conditions was lower because of lack of enzymatic activity in the system.

Biodegradation of 2-hydroxyquinoxaline (2-HQ) by Bacillus sp

An aerobic Gram +ve bacterial strain capable of utilizing 2-Hydroxyquinoxaline (2-HQ) as sole source of carbon and energy was isolated from Chrysanthemum indicum Indian agricultural soil and named as HQ2. On the basis of morphology, physico-biochemical characteristics and 16S rRNA sequence analysis, strain HQ2 was identified as Bacillus sp. The generation time of Bacillus sp. in log phase during growth on 2-HQ is 0.79 h or 47.4 min. The optimal conditions for 2-HQ degradation by Bacillus sp. were inoculum density of 1.0 OD, pH of 6-8, temperature of 37-45 °C and 2-HQ concentration of 500 ppm. Among the additional carbon and nitrogen sources, carbon sources did not influence the degradation rate of 2-HQ, but nitrogen sources-yeast extract marginally enhanced the rate of degradation of 2-HQ. GC-MS analysis of the culture Bacillus sp. grown on 2-HQ indicated the formation of dimers from 2 molecules of 2-hydroxyquinoxaline. The formation of dimer for degradation of 2-HQ by the culture appears to be the first report to our scientific knowledge.

Bioremediation of p-Nitrophenol by Pseudomonas putida 1274 strain

BACKGROUND

p-Nitrophenol (PNP) occurs as contaminants of industrial effluents and it is the most important environmental pollutant and causes significant health and environmental risks, because it is toxic to many living organisms. Nevertheless, the information regarding PNP degradation pathways and their enzymes remain limited.

OBJECTIVE

To evaluate the efficacy of the Pseudomonas Putida 1274 for removal of PNP.

METHODS

P. putida MTCC 1274 was obtained from MTCC Chandigarh, India and cultured in the minimal medium in the presence of PNP. PNP degradation efficiency was compared under different pH and temperature ranges. The degraded product was isolated and analyzed with different chromatographic and spectroscopic techniques.

RESULTS

P. putida 1274 shows good growth and PNP degradation at 37°C in neutral pH. Acidic and alkali pH retarded the growth of P. putida as well as the PNP degradation. On the basis of specialized techniques, hydroquinone was identified as major degraded product. The pathway was identified for the biodegradation of PNP. It involved initial removal of the nitrate group and formation of hydroquinone as one of the intermediates.

CONCLUSION

Our results suggested that P. putida 1274 strain would be a suitable aspirant for bioremediation of nitro-aromatic compounds contaminated sites in the environment.

Evidence for vital role of endo-β-N-acetylglucosaminidase in the resistance of Arthrobacter protophormiae RKJ100 towards elevated concentrations of o-nitrobenzoate

Arthrobacter protophormiae RKJ100 was previously characterized for its ability to tolerate extremely high concentrations of o-nitrobenzoate (ONB), a toxic xenobiotic environmental pollutant. The physiological responses of strain RKJ100 to ≥30 mM ONB indicated towards a resistance mechanism manifested via alteration of cell morphology and cell wall structure. In this study, we aim to characterize gene(s) involved in the resistance of strain RKJ100 towards extreme concentrations (i.e. 150 mM) of ONB. Transposon mutagenesis was carried out to generate a mutant library of strain RKJ100, which was then screened for ONB-sensitive mutants. A sensitive mutant was defined and selected as one that could not tolerate ≥30 mM ONB. Molecular and biochemical characterization of this mutant showed that the disruption of endo-β-N-acetylglucosaminidase (ENGase) gene caused the sensitivity. ENGase is an important enzyme for oligosaccharide processing and cell wall recycling in bacteria, fungi, plants and animals. Previous reports have already indicated several possible roles of this enzyme in cellular homeostasis. Results presented here provide the first evidence for its involvement in bacterial resistance towards extreme concentrations of a toxic xenobiotic compound and also suggest that strain RKJ100 employs ENGase as an important component in osmotic shock response for resisting extreme concentrations of ONB.

Bacterial degradation of nitrophenols and their derivatives

This review intends to provide an overview of bacterial degradation of nitrophenols (NPs) and their derivatives. The main scientific focus is on biochemical and genetic characterization of bacterial degradation of NPs. Other aspects such as bioremediation and chemotaxis correlated with biodegradation of NPs are also discussed. This review will increase our current understanding of bacterial degradation of NPs and their derivatives.

Genes involved in degradation of para-nitrophenol are differentially arranged in form of non-contiguous gene clusters in Burkholderia sp. strain SJ98

Biodegradation of para-Nitrophenol (PNP) proceeds via two distinct pathways, having 1,2,3-benzenetriol (BT) and hydroquinone (HQ) as their respective terminal aromatic intermediates. Genes involved in these pathways have already been studied in different PNP degrading bacteria. Burkholderia sp. strain SJ98 degrades PNP via both the pathways. Earlier, we have sequenced and analyzed a ~41 kb fragment from the genomic library of strain SJ98. This DNA fragment was found to harbor all the lower pathway genes; however, genes responsible for the initial transformation of PNP could not be identified within this fragment. Now, we have sequenced and annotated the whole genome of strain SJ98 and found two ORFs (viz., pnpA and pnpB) showing maximum identity at amino acid level with p-nitrophenol 4-monooxygenase (PnpM) and p-benzoquinone reductase (BqR). Unlike the other PNP gene clusters reported earlier in different bacteria, these two ORFs in SJ98 genome are physically separated from the other genes of PNP degradation pathway. In order to ascertain the identity of ORFs pnpA and pnpB, we have performed in-vitro assays using recombinant proteins heterologously expressed and purified to homogeneity. Purified PnpA was found to be a functional PnpM and transformed PNP into benzoquinone (BQ), while PnpB was found to be a functional BqR which catalyzed the transformation of BQ into hydroquinone (HQ). Noticeably, PnpM from strain SJ98 could also transform a number of PNP analogues. Based on the above observations, we propose that the genes for PNP degradation in strain SJ98 are arranged differentially in form of non-contiguous gene clusters. This is the first report for such arrangement for gene clusters involved in PNP degradation. Therefore, we propose that PNP degradation in strain SJ98 could be an important model system for further studies on differential evolution of PNP degradation functions.

Arthrobacter nitrophenolicus sp. nov. a new 2-chloro-4-nitrophenol degrading bacterium isolated from contaminated soil

Strain SJCon^T, a 2-chloro-4-nitrophenol (2C4NP) degrading bacterium, was isolated from soil collected from a pesticide-contaminated site in Punjab, India. The strain, which stained Gram positive, displayed a rod-coccus life cycle, and possessed a type A3_α peptidoglycan (l-Lys–l-Ala₃), MK-9(H2) as the major menaquinone, anteiso-C15 and iso-C15:0 as the major cellular fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and a glycolipid as the major polar lipids, showed morphological and chemotaxonomic properties consistent with those reported for members of the genus Arthrobacter. Phylogenetic analysis of the 16S rRNA gene sequence of strain SJCon^T confirmed that it was a member of this genus with Arthrobacter globiformis DSM 20124^T being the closest relative (sequence similarity of 97 %). The DNA G + C content of strain SJCon^T was 69 ± 1 mol% and DNA homology with A. globiformis DSM 20124^T was 45 %, suggesting that strain SJCon^T represented a novel species of the genus Arthrobacter, which we have named Arthrobacter nitrophenolicus sp. nov The type strain is SJCon^T (=MTCC 10104^T =DSM 23165^T).

Branching of the p-nitrophenol (PNP) degradation pathway in burkholderia sp. Strain SJ98: Evidences from genetic characterization of PNP gene cluster

Aerobic microbial degradation of p-nitrophenol (PNP) has been classically shown to proceed via ‘Hydroquinone (HQ) pathway’ in Gram-negative bacteria, whereas in Gram-positive PNP degraders it proceed via ‘Benzenetriol (BT) pathway’. These pathways are characterized by the ring cleavage of HQ and BT as terminal aromatic intermediates respectively. Earlier reports on PNP degradation have indicated these pathways to be mutually exclusive. We report involvement of both ‘HQ’ and ‘BT’ ring cleavage pathways in PNP degradation by Burkholderia sp. strain SJ98. Genetic characterization of an ~41 Kb DNA fragment harboring PNP degradation gene cluster cloned and sequenced from strain SJ98 showed presence of multiple orfs including pnpC and pnpD which corresponded to previously characterized ‘benzenetriol-dioxygenase (BtD)’ and ‘maleylacetate reductase (MaR)’ respectively. This gene cluster also showed presence of pnpE1 and pnpE2, which shared strong sequence identity to cognate sub-units of ‘hydroquinone dioxygenase’ (HqD). Heterologous expression and biochemical characterization ascertained the identity of PnpE1 and PnpE2. In in vitro assay reconstituted heterotetrameric complex of PnpE1 and PnpE2 catalyzed transformation of hydroquinone (HQ) into corresponding hydroxymuconic semialdehyde (HMS) in a substrate specific manner. Together, these results clearly establish branching of PNP degradation in strain SJ98. We propose that strain SJ98 presents a useful model system for future studies on evolution of microbial degradation of PNP.

Degradation of chlorinated nitroaromatic compounds

Chlorinated nitroaromatic compounds (CNAs) are persistent environmental pollutants that have been introduced into the environment due to the anthropogenic activities. Bacteria that utilize CNAs as the sole sources of carbon and energy have been isolated from different contaminated and non-contaminated sites. Microbial metabolism of CNAs has been studied, and several metabolic pathways for degradation of CNAs have been proposed. Detoxification and biotransformation of CNAs have also been studied in various fungi, actinomycetes and bacteria. Several physicochemical methods have been used for treatment of wastewater containing CNAs; however, these methods are not suitable for in situ bioremediation. This review describes the current scenario of the degradation of CNAs.

Chemotaxis of Burkholderia sp. strain SJ98 towards chloronitroaromatic compounds that it can metabolise

Background

Burkholderia sp. strain SJ98 is known for its chemotaxis towards nitroaromatic compounds (NACs) that are either utilized as sole sources of carbon and energy or co-metabolized in the presence of alternative carbon sources. Here we test for the chemotaxis of this strain towards six chloro-nitroaromatic compounds (CNACs), namely 2-chloro-4-nitrophenol (2C4NP), 2-chloro-3-nitrophenol (2C3NP), 4-chloro-2-nitrophenol (4C2NP), 2-chloro-4-nitrobenzoate (2C4NB), 4-chloro-2-nitrobenzoate (4C2NB) and 5-chloro-2-nitrobenzoate (5C2NB), and examine its relationship to the degradation of such compounds.

Results

Strain SJ98 could mineralize 2C4NP, 4C2NB and 5C2NB, and co-metabolically transform 2C3NP and 2C4NB in the presence of an alternative carbon source, but was unable to transform 4C2NP under these conditions. Positive chemotaxis was only observed towards the five metabolically transformed CNACs. Moreover, the chemotaxis was induced by growth in the presence of the metabolisable CNAC. It was also competitively inhibited by the presence of nitroaromatic compounds (NACs) that it could metabolise but not by succinate or aspartate.

Conclusions

Burkholderia sp. strain SJ98 exhibits metabolic transformation of, and inducible chemotaxis towards CNACs. Its chemotactic responses towards these compounds are related to its previously demonstrated chemotaxis towards NACs that it can metabolise, but it is independently inducible from its chemotaxis towards succinate or aspartate.

Identification and characterization of another 4-nitrophenol degradation gene cluster, nps, in Rhodococcus sp. strain PN1

4-Nitrophenol (4-NP) is a toxic compound formed in soil by the hydrolysis of organophosphorous pesticides, such as parathion. We previously reported the presence of the 4-NP degradation gene cluster (nphRA1A2) in Rhodococcus sp. strain PN1, which encodes a two-component 4-NP hydroxylase system that oxidizes 4-NP into 4-nitrocatechol. In the current study, another gene cluster (npsC and npsRA2A1B) encoding a similar 4-NP hydroxylase system was cloned from strain PN1. The enzymes from this 4-NP hydroxylase system (NpsA1 and NpsA2) were purified as histidine-tagged (His-) proteins and then characterized. His-NpsA2 showed NADH/FAD oxidoreductase activity, and His-NpsA1 showed 4-NP oxidizing activity in the presence of His-NpsA2. In the 4-NP oxidation using the reconstituted enzyme system (His-NpsA1 and His-NpsA2), hydroquinone (35% of 4-NP disappeared) and hydroxyquinol (59% of 4-NP disappeared) were detected in the presence of ascorbic acid as a reducing reagent, suggesting that, without the reducing reagent, 4-NP was converted into their oxidized forms, 1,4-benzoquinone and 2-hydroxy-1,4-benzoquinone. In addition, in the cell extract of recombinant Escherichia coli expressing npsB, a typical spectral change showing conversion of hydroxyquinol into maleylacetate was observed. These results indicate that this nps gene cluster, in addition to the nph gene cluster, is also involved in 4-NP degradation in strain PN1.

Nitroaromatic compounds, from synthesis to biodegradation

Nitroaromatic compounds are relatively rare in nature and have been introduced into the environment mainly by human activities. This important class of industrial chemicals is widely used in the synthesis of many diverse products, including dyes, polymers, pesticides, and explosives. Unfortunately, their extensive use has led to environmental contamination of soil and groundwater. The nitro group, which provides chemical and functional diversity in these molecules, also contributes to the recalcitrance of these compounds to biodegradation. The electron-withdrawing nature of the nitro group, in concert with the stability of the benzene ring, makes nitroaromatic compounds resistant to oxidative degradation. Recalcitrance is further compounded by their acute toxicity, mutagenicity, and easy reduction into carcinogenic aromatic amines. Nitroaromatic compounds are hazardous to human health and are registered on the U.S. Environmental Protection Agency's list of priority pollutants for environmental remediation. Although the majority of these compounds are synthetic in nature, microorganisms in contaminated environments have rapidly adapted to their presence by evolving new biodegradation pathways that take advantage of them as sources of carbon, nitrogen, and energy. This review provides an overview of the synthesis of both man-made and biogenic nitroaromatic compounds, the bacteria that have been identified to grow on and completely mineralize nitroaromatic compounds, and the pathways that are present in these strains. The possible evolutionary origins of the newly evolved pathways are also discussed.

p-Nitrophenol degradation via 4-nitrocatechol in Burkholderia sp. SJ98 and cloning of some of the lower pathway genes

Microbial degradation studies have pointed toward the occurrence of two distinct PNP catabolic pathways in Gram positive and Gram negative bacteria. The former involves 4-nitrocatechol (4-NC), 1,2,4-benzenetriol (BT), and maleylacetate (MA) as major degradation intermediates, whereas the later proceeds via formation of 1,4-benzoquinone (BQ) and hydroquinone (HQ). In the present study we identified a Gram negative organism viz. Burkholderia sp. strain SJ98 that degrades PNP via 4NC, BT, and MA. A 6.89 Kb genomic DNA fragment of strain SJ98 that encompasses seven putatively identified ORFs (orfA, pnpD, pnpC, orfB, orfC, orfD, and orfE) was cloned. PnpC is benzenetriol dioxygenase belonging to the intradiol dioxygenase superfamily, whereas PnpD is identified as maleylacetate reductase, a member of the Fe-ADH superfamily showing NADH dependent reductase activity. The in vitro activity assays carried out with purified pnpC and pnpD (btd and mar) gene products transformed BT to MA and MA to beta-ketoadipate, respectively. The cloning, sequencing, and characterization of these genes along with the functional PNP degradation studies ascertained the involvement of 4-NC, BT, and MA as degradation intermediates of PNP pathway in this strain. This is one of the first conclusive reports for 4-NC and BT mediated degradation of PNP in a Gram negative organism.

Degradation of 4-nitrophenol, 2-chloro-4-nitrophenol, and 2,4-dinitrophenol by Rhodococcus imtechensis strain RKJ300

A bacterial strain Rhodococcus imtechensis RKJ300 (= MTCC 7085(T) = JCM 13270(T)) was isolated from pesticide-contaminated soil of Punjab by the enrichment technique on minimal medium containing 4-nitrophenol. Strain RKJ300 is capable of utilizing 4-nitrophenol, 2-chloro-4-nitrophenol, and 2,4-dinitrophenol as sole sources of carbon and energy. The strain involved both oxidative and reductive catabolic mechanisms for initial transformation of these compounds. In the case of 2-chloro-4-nitrophenol, colorimetric analysis indicated that nitrite release was followed by stoichiometric elimination of chloride ions. Experiments using whole cells and cell-free extracts showed chlorohydroquinone and hydroquinone as the intermediates of 2-chloro-4-nitrophenol degradation. This is the first report of degradation on 2-chloro-4-nitrophenol by a bacterium under aerobic condition to the best of our knowledge. However, pathways for degradation of 4-nitrophenol and 2,4-dinitrophenol were similar to those reported in other strains of Rhodococcus. Laboratory-scale soil microcosm studies demonstrated that the organism was capable of degrading a mixture of nitrophenols simultaneously, indicating its applicability toward in situ bioremediation of contaminated sites. The fate of the augmented strain as monitored by the plate-counting method and hybridization technique was found to be fairly stable throughout the period of microcosm experiments.

Isolation and characterization of Arthrobacter sp. HY2 capable of degrading a high concentration of p-nitrophenol

A soil bacterium strain, capable of using p-nitrophenol (PNP) as its sole source of carbon and energy, was isolated by enrichment on minimal salt medium (MSM). On the basis of a phylogenetic analysis of 16S rRNA gene sequences the bacterium is a species of Arthrobacter, closely related to Arthrobacter ureafaciens DSM 20126. This strain has an unusually high substrate tolerance for PNP degradation in MSM. Greatest degradation of PNP was observed at 30 degrees C and under slightly alkaline pH (pH 7-9) conditions. Effective degradation rates slowed as the concentration of PNP was increased. Addition of glucose from 0.1% to 0.5% generally enhanced the degradation of PNP at high concentration (400 mg/l) although acidification as a result of glucose metabolism had a negative effect on PNP depletion. Biodegradation of PNP at high concentration was greatly accelerated by beta-cyclodextrin at a concentration of 0.5%, indicating that beta-cyclodextrin could be a promising addictive for effective PNP bioremediation.

Enrichment of a K-strategist microbial population able to biodegrade p-nitrophenol in a sequencing batch reactor

The biological treatment of a high-strength p-nitrophenol (PNP) wastewater in an aerobic Sequencing Batch Reactor (SBR) has been studied. A specific operational strategy was applied with the main aim of developing a K-strategist PNP-degrading activated sludge. The enrichment of a K-strategist microbial population was performed using a non-acclimated biomass coming from a municipal WWTP as inoculum, and following a feeding strategy in which the PNP-degrading biomass was under endogenous conditions during more than 50% of the aerobic reaction phase. Hundred per cent of PNP removal was achieved in the whole operating period with a maximum specific PNP loading rate of 0.26 g PNP g(-1)VSS d(-1). A kinetic characterization of the obtained PNP-degrading population was carried out using respirometry assays in specifically designed batch tests. With the experimental data obtained a kinetic model including substrate inhibition has been used to describe the time-course of the PNP concentration and specific oxygen uptake rate (SOUR), simultaneously. The kinetic parameters obtained through optimization, validated with an additional respirometric test, were k(max)=1.02 mg PNP mg(-1) COD d(-1), K(s)=1.6 mg PNP L(-1) and K(i)=54 mg PNP L(-1). The values obtained for the K(s) and k(max) are lower than those reported in the literature for mixed populations, meaning that the biomass is a K-strategist type, and therefore demonstrating the success of the operational strategy imposed to obtain such a K-strategist population. Moreover, our measured K(i) value is higher than those reported by most of the bibliographic references; therefore the acclimated activated sludge used in this work was evidently more adapted to PNP inhibition than the other reported cultures.

Biodegradation of p-nitrophenol by Rhodococcus sp. CN6 with high cell surface hydrophobicity

Rhodococcus sp. CN6, isolated from a pesticide industry's effluent-sediment, was able to completely degrade and utilize 100mg/L p-nitrophenol (PNP) as the sole carbon, nitrogen and energy sources for growth in the minimal salt media (MSM) within 12h. To study the applicability of the strain for bioremediation of PNP, its degradation potential was examined in the presence of different supplemented carbon and nitrogen sources in MSM with 100mg/L PNP. Dextrin was experienced as the best supplemented carbon source used by the strain CN6 during degrading PNP. Addition of ammonium nitrate could also increase the PNP degradation rate. Preliminary studies on the surface characters of Rhodococcus sp. CN6 were undertaken for the sake of exploring its high efficiency on the degradation of PNP. Microbial adherence to hydrocarbons (MATH) assays illuminated that the strain CN6 was of higher hydrophobicity while grown on higher concentration of PNP. The results suggested that the strain CN6 could be used as a potential and efficient PNP degrader for the bioremediation of contaminated sites.

Kinetics and mechanisms of p-nitrophenol biodegradation by Pseudomonas aeruginosa HS-D38

The kinetics and mechanisms of p-nitrophenol (PNP) biodegradation by Pseudomonas aeruginosa HS-D38 were investigated. PNP could be used by HS-D38 strain as the sole carbon, nitrogen and energy sources, and PNP was mineralized at the maximum concentration of 500 mg/L within 24 h in an mineral salt medium (MSM). The analytical results indicated that the biodegradation of PNP fit the first order kinetics model. The rate constant kPNP is 2.039 x 10(-2)/h in MSM medium, KPNP+N is 3.603 x 10(-2)/h with the addition of ammonium chloride and KPNP+C is 9.74 x 10(-3)/h with additional glucose. The addition of ammonium chloride increased the degradation of PNP. On the contrary, the addition of glucose inhibited and delayed the biodegradation of PNP. Chemical analysis results by thin-layer chromatography (TLC), UV-Vis spectroscopy and gas chromatography (GC) techniques suggested that PNP was converted to hydroquinone (HQ) and further degraded via 1,2,4-benzenetriol (1,2,4-BT) pathway.

Identification and characterization of chlorpyrifos-methyl and 3,5,6-trichloro-2-pyridinol degrading Burkholderia sp. strain KR100

A chlorpyrifos-methyl (CM) degrading bacterium (designated strain KR100) was isolated from a Korean rice paddy soil and was further tested for its sensitivity against eight commercial antibiotics. Based on morphological, biochemical, and molecular characteristics, this bacterium showed greatest similarity to members of the order Burkholderiales and was shown to be most closely related to members of the Burkholderia cepacia group. Strain KR100 hydrolyzed CM to 3,5,6-trichloro-2-pyridinol (TCP) and utilized TCP as the sole source of carbon for its growth. The isolate was also able to degrade chlorpyrifos, dimethoate, fenitrothion, malathion, and monocrotophos at 300 microg/ml but diazinon, dicrotophos, parathion, and parathion-methyl at 100 microg/ml. The ability to degrade CM was found to be encoded on a single plasmid of approximately 50 kb, pKR1. Genes encoding resistance to amphotericin B, polymixin B sulfate, and tetracycline were also located on the plasmid. This bacterium merits further study as a potential biological agent for the remediation of soil, water, or crop contaminated with organophosphorus compounds because of its greater biodegradation activity and its broad specificity against a range of organophosphorus insecticides.

Mechanism of 4-nitrophenol oxidation in Rhodococcus sp. Strain PN1: characterization of the two-component 4-nitrophenol hydroxylase and regulation of its expression

4-Nitrophenol (4-NP) is a toxic product of the hydrolysis of organophosphorus pesticides such as parathion in soil. Rhodococcus sp. strain PN1 degrades 4-NP via 4-nitrocatechol (4-NC) for use as the sole carbon, nitrogen, and energy source. A 5-kb EcoRI DNA fragment previously cloned from PN1 contained a gene cluster (nphRA1A2) involved in 4-NP oxidation. From sequence analysis, this gene cluster is expected to encode an AraC/XylS family regulatory protein (NphR) and a two-component 4-NP hydroxylase (NphA1 and NphA2). A transcriptional assay in a Rhodococcus strain revealed that the transcription of nphA1 is induced by only 4-NP (of several phenolic compounds tested) in the presence of nphR, which is constitutively expressed. Disruption of nphR abolished transcriptional activity, suggesting that nphR encodes a positive regulatory protein. The two proteins of the 4-NP hydroxylase, NphA1 and NphA2, were independently expressed in Escherichia coli and purified by ion-exchange chromatography or affinity chromatography. The purified NphA2 reduced flavin adenine dinucleotide (FAD) with the concomitant oxidation of NADH, while the purified NphA1 oxidized 4-NP into 4-NC almost quantitatively in the presence of FAD, NADH, and NphA2. This functional analysis, in addition to the sequence analysis, revealed that this enzyme system belongs to the two-component flavin-diffusible monooxygenase family. The 4-NP hydroxylase showed comparable oxidation activities for phenol and 4-chlorophenol to that for 4-NP and weaker activities for 3-NP and 4-NC.

Diversity of 'benzenetriol dioxygenase' involved in p-nitrophenol degradation in soil bacteria

Ring hydroxylating dioxygenases (RHDOs) are one of the most important classes of enzymes featuring in the microbial metabolism of several xenobiotic aromatic compounds. One such RHDO is benzenetriol dioxygenase (BtD) which constitutes the metabolic machinery of microbial degradation of several mono- phenolic and biphenolic compounds including nitrophenols. Assessment of the natural diversity of benzenetriol dioxygenase (btd) gene sequence is of great significance from basic as well as applied study point of view. In the present study we have evaluated the gene sequence variations amongst the partial btd genes that were retrieved from microorganisms enriched for PNP degradation from pesticide contaminated agriculture soils. The gene sequence analysis was also supplemented with an in silico restriction digestion analysis. Furthermore, a phylogenetic analysis based on the deduced amino acid sequence(s) was performed wherein the evolutionary relatedness of BtD enzyme with similar aromatic dioxygenases was determined. The results obtained in this study indicated that this enzyme has probably undergone evolutionary divergence which largely corroborated with the taxonomic ranks of the host microorganisms.

Hydroquinone dioxygenase from pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases

Hydroquinone 1,2-dioxygenase (HQDO), an enzyme involved in the catabolism of 4-hydroxyacetophenone in Pseudomonas fluorescens ACB, was purified to apparent homogeneity. Ligandation with 4-hydroxybenzoate prevented the enzyme from irreversible inactivation. HQDO was activated by iron(II) ions and catalyzed the ring fission of a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes. HQDO was inactivated by 2,2'-dipyridyl, o-phenanthroline, and hydrogen peroxide and inhibited by phenolic compounds. The inhibition with 4-hydroxybenzoate (K(i) = 14 microM) was competitive with hydroquinone. Online size-exclusion chromatography-mass spectrometry revealed that HQDO is an alpha2beta2 heterotetramer of 112.4 kDa, which is composed of an alpha-subunit of 17.8 kDa and a beta-subunit of 38.3 kDa. Each beta-subunit binds one molecule of 4-hydroxybenzoate and one iron(II) ion. N-terminal sequencing and peptide mapping and sequencing based on matrix-assisted laser desorption ionization--two-stage time of flight analysis established that the HQDO subunits are encoded by neighboring open reading frames (hapC and hapD) of a gene cluster, implicated to be involved in 4-hydroxyacetophenone degradation. HQDO is a novel member of the family of nonheme-iron(II)-dependent dioxygenases. The enzyme shows insignificant sequence identity with known dioxygenases.

Elucidation of the 4-hydroxyacetophenone catabolic pathway in Pseudomonas fluorescens ACB

The catabolism of 4-hydroxyacetophenone in Pseudomonas fluorescens ACB is known to proceed through the intermediate formation of hydroquinone. Here, we provide evidence that hydroquinone is further degraded through 4-hydroxymuconic semialdehyde and maleylacetate to beta-ketoadipate. The P. fluorescens ACB genes involved in 4-hydroxyacetophenone utilization were cloned and characterized. Sequence analysis of a 15-kb DNA fragment showed the presence of 14 open reading frames containing a gene cluster (hapCDEFGHIBA) of which at least four encoded enzymes are involved in 4-hydroxyacetophenone degradation: 4-hydroxyacetophenone monooxygenase (hapA), 4-hydroxyphenyl acetate hydrolase (hapB), 4-hydroxymuconic semialdehyde dehydrogenase (hapE), and maleylacetate reductase (hapF). In between hapF and hapB, three genes encoding a putative intradiol dioxygenase (hapG), a protein of the Yci1 family (hapH), and a [2Fe-2S] ferredoxin (hapI) were found. Downstream of the hap genes, five open reading frames are situated encoding three putative regulatory proteins (orf10, orf12, and orf13) and two proteins possibly involved in a membrane efflux pump (orf11 and orf14). Upstream of hapE, two genes (hapC and hapD) were present that showed weak similarity with several iron(II)-dependent extradiol dioxygenases. Based on these findings and additional biochemical evidence, it is proposed that the hapC and hapD gene products are involved in the ring cleavage of hydroquinone.

Degradation of aromatic compounds and degradative pathway of 4-nitrocatechol by Ochrobactrum sp. B2

The potential capacity of a soil methyl parathion-degrading bacterium strain, Ochrobactrum sp. B2, for degrading various aromatic compounds were investigated. The results showed B2 was capable of degrading diverse aromatic compounds, but amino-substituted benzene compounds, at a concentration up to 100 mg L(-1) in 4 days. B2 could use 4-nitrocatechol (4-NC) as a sole carbon and energy source with release of nitrite ion. The pathway for 4-NC degradation via 1,2,4-benzenetriol (BT) and hydroquinone (HQ) formation in B2 was proposed based on the identification and quantification of intermediates by gas chromatography-mass spectrometry (GC-MS), and high performance liquid chromatography (HPLC). Degradation studies carried out on a plasmid-cured derivative showed that the genes for 4-NC degradative pathway was plasmid-borne in B2, suggesting that B2 degrades both p-nitrophenol and 4-NC by enzymes encoded by genes on the same plasmid.

Induction of somatic embryogenesis in saffron using thidiazuron (TDZ)

In vitro propagation of saffron either through somatic embryogenesis or cormogenesis is considered to be an efficient alternative method for large-scale propagation of pathogen-free corms. In order to develop an efficient protocol for in vitro propagation of saffron, a factorial experiment was carried out based on completely randomized design to investigate the effects of various concentrations of TDZ (0, 0.1, 0.25 and 0.5 mg L(-1)) on somatic embryogenesis induction from 5 different types of corm explants (terminal or axillary buds, upper or lower parts of the corm tissue and terminal buds from pre-treated corms at 4 degrees C for 2 weeks). The results revealed that TDZ concentrations affected the induction of somatic embryogenesis significantly while different types of corm explants showed no significant effect on this process. Among TDZ concentrations used, 0.5 mg L(-1) was the most effective treatment for embryogenesis induction. Embryogenic calli (globular stage) proliferated well when subcultured into MS medium supplemented with 0.25 mg L(-1) TDZ before transferring to hormone-free MS medium containing 6% sucrose for maturation (scutellar or horn-shape stage). Matured embryos were transferred to half strength MS medium without growth regulators for further development, from which microcorms were produced at the basal part after 3 months.

Factors affecting hydrogen production from cassava wastewater by a co-culture of anaerobic sludge and Rhodospirillum rubrum

Series of batch experiments were used to investigate the effects of environmental factors, i.e., total nitrogen and total phosphorus concentrations, initial pH, illumination pattern and stirring conditions on hydrogen production from cassava wastewater by a co-culture of anaerobic sludge and Rhodospirillum rubrum. The maximum of the hydrogen yield of 150.46 and 340.19 mL g-COD(-1) was obtained at the total nitrogen and total phosphorus concentrations of 0.2 and 0.04 M, respectively. An effect of initial pH was investigated at COD:N:P ratio of 100:10:1. Results indicated that an optimum initial pH for hydrogen production was pH 7 with a high hydrogen yield of 158.78 mL g-COD(-1) was obtained. No significantly different (p < 0.05) in the effect of illumination pattern (24 h of light and 12 h dark/light cycle) on hydrogen production were observed under continuous-illumination and periodic-illumination with hydrogen yield of 131.84 and 126.92 mL g-COD(-1), respectively. Therefore, a periodic-illumination was applicable in hydrogen fermentation due to its cost-effective. Hydrogen fermentation with a stirring at 100 rpm provided more effective hydrogen production (164.83 mL g-COD(-1)) than static-fermentation (93.93 mL g-COD(-1)). The major soluble products from hydrogen fermentation were acetic and butyric acids, in the ranges of 28.33-48.30 and 35.23-66.07%, respectively, confirming an ability of a co-culture to produce hydrogen from cassava wastewater.

Microbial remediation of nitro-aromatic compounds: an overview

Nitro-aromatic compounds are produced by incomplete combustion of fossil fuel or nitration reactions and are used as chemical feedstock for synthesis of explosives, pesticides, herbicides, dyes, pharmaceuticals, etc. The indiscriminate use of nitro-aromatics in the past due to wide applications has resulted in inexorable environmental pollution. Hence, nitro-aromatics are recognized as recalcitrant and given Hazardous Rating-3. Although several conventional pump and treat clean up methods are currently in use for the removal of nitro-aromatics, none has proved to be sustainable. Recently, remediation by biological systems has attracted worldwide attention to decontaminate nitro-aromatics polluted sources. The incredible versatility inherited in microbes has rendered these compounds as a part of the biogeochemical cycle. Several microbes catalyze mineralization and/or non-specific transformation of nitro-aromatics either by aerobic or anaerobic processes. Aerobic degradation of nitro-aromatics applies mainly to mono-, dinitro-derivatives and to some extent to poly-nitro-aromatics through oxygenation by: (i) monooxygenase, (ii) dioxygenase catalyzed reactions, (iii) Meisenheimer complex formation, and (iv) partial reduction of aromatic ring. Under anaerobic conditions, nitro-aromatics are reduced to amino-aromatics to facilitate complete mineralization. The nitro-aromatic explosives from contaminated sediments are effectively degraded at field scale using in situ bioremediation strategies, while ex situ techniques using whole cell/enzyme(s) immobilized on a suitable matrix/support are gaining acceptance for decontamination of nitrophenolic pesticides from soils at high chemical loading rates. Presently, the qualitative and quantitative performance of biological approaches of remediation is undergoing improvement due to: (i) knowledge of catabolic pathways of degradation, (ii) optimization of various parameters for accelerated degradation, and (iii) design of microbe(s) through molecular biology tools, capable of detoxifying nitro-aromatic pollutants. Among them, degradative plasmids have provided a major handle in construction of recombinant strains. Although recombinants designed for high performance seem to provide a ray of hope, their true assessment under field conditions is required to address ecological considerations for sustainable bioremediation.

Growth and physiological response of Arthrobacter protophormiae RKJ100 toward higher concentrations of o-nitrobenzoate and p-hydroxybenzoate

Bioremediation of sites that are heavily contaminated with pollutant chemicals is a challenge as most of the microorganisms cannot tolerate higher concentrations of toxic compounds. Only a few strains of the genus Pseudomonas have been studied for their tolerance toward the higher concentrations of aromatic pollutant compounds, a phenomenon that is accompanied by various physiological changes. In the present study we have characterized the growth response and physiological changes (adaptations) of a Gram-positive bacterium, Arthrobacter protophormiae RKJ100, toward the higher concentrations of two aromatic compounds, viz. o-nitrobenzoate (ONB) and p-hydroxybenzoate (PHB). Arthrobacter protophormiae RKJ100 could utilize 30 mM ONB and 50 mM PHB as sole sources of carbon and energy. It was capable of growth on higher concentrations of ONB (up to 200 mM) and PHB (up to 150 mM) when the cells were pre-exposed to lower concentrations of these compounds. The adaptive responses shown by the organism during growth on higher concentrations of these compounds were evident from significant changes in cellular fatty acid profiles. In addition, Bacterial Adhesion To Hydrocarbon (BATH) assay and scanning electron microscopy showed substantial increase in cell surface hydrophobicity and decrease in cell size of A. protophormiae RKJ100 when grown on ONB and PHB as compared to succinate-grown cells.

Variations in T-RFLP profiles with differing chemistries of fluorescent dyes used for labeling the PCR primers

Culture independent molecular methods have emerged as indispensable tools for studying microbial community structure and dynamics in natural habitats, since they allow a closer look at microbial diversity that is not reflected by culturing techniques. Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis is one of the informative and widely used techniques for such studies. However, the method has a few limitations to predict microbial community structure with significant accuracy. One of the major limitations is variation in real Terminal Restriction Fragment (TRF) length and observed TRF length. In the present study we report the generation of TRF length variations using different fluorescent dyes to label the PCR primers. T-RFLP profiles generated from primers labeled with different dyes varied significantly and led to inconsistent microbial species identification. Occurrence of such variations can have serious consequences on interpretation of the T-RFLP profiles from environmental samples representing complex microbial community. Therefore, in a T-RFLP study, the primers and labeling dye system should be carefully evaluated and optimized for an individual community under investigation. Further, it would be recommended to establish a target gene library in parallel with T-RFLP analysis to facilitate the accurate prediction of microbial community structure.

Isolation and characterization of a bacterial strain of the genus Ochrobactrum with methyl parathion mineralizing activity

AIMS

To isolate and characterize a methyl parathion (MP)-mineralizing bacterium, and to elucidate the degradative pathway of MP and localize the responsible degrading genes.

METHODS AND RESULTS

A bacterial strain, designated B2, capable of mineralizing MP was isolated from the MP-polluted soil. Analysis of the 16S rRNA gene sequence and phenotypic analysis suggested that strain B2 had a close relationship with Ochrobactrum anthropi. B2 could totally degrade MP and four metabolites [p-nitrophenol (PNP), 4-nitrocatechol (4-NC), 1,2,4-benzenetriol (BT) and hydroquinone (HQ)] were identified by HPLC and gas chromatography-mass spectrometry analyses. Plasmid curing of strain B2 resulted in the loss of ability of B2 to degrade PNP, but not the ability to hydrolyse MP.

CONCLUSIONS

Ochrobactrum sp. B2 can mineralize MP rapidly via PNP, 4-NC, BT and HQ pathway. B2 harbours a plasmid encoding the ability to degrade PNP, while MP-hydrolysing activity is encoded on the bacterial chromosome.

SIGNIFICANCE AND IMPACT OF THE STUDY

This new bacterial strain (B2) capable of mineralizing MP will be useful in a pure-culture remediation process of organophosphate pesticides and their metabolites such as nitroaromatics.

Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation

The introduction of culture-independent molecular screening techniques, especially based on 16S rRNA gene sequences, has allowed microbiologists to examine a facet of microbial diversity not necessarily reflected by the results of culturing studies. The bacterial community structure was studied for a pesticide-contaminated site that was subsequently remediated using an efficient degradative strain Arthrobacter protophormiae RKJ100. The efficiency of the bioremediation process was assessed by monitoring the depletion of the pollutant, and the effect of addition of an exogenous strain on the existing soil community structure was determined using molecular techniques. The 16S rRNA gene pool amplified from the soil metagenome was cloned and restriction fragment length polymorphism studies revealed 46 different phylotypes on the basis of similar banding patterns. Sequencing of representative clones of each phylotype showed that the community structure of the pesticide-contaminated soil was mainly constituted by Proteobacteria and Actinomycetes. Terminal restriction fragment length polymorphism analysis showed only nonsignificant changes in community structure during the process of bioremediation. Immobilized cells of strain RKJ100 enhanced pollutant degradation but seemed to have no detectable effects on the existing bacterial community structure.

Microbial degradation of organophosphorus compounds

Synthetic organophosphorus compounds are used as pesticides, plasticizers, air fuel ingredients and chemical warfare agents. Organophosphorus compounds are the most widely used insecticides, accounting for an estimated 34% of world-wide insecticide sales. Contamination of soil from pesticides as a result of their bulk handling at the farmyard or following application in the field or accidental release may lead occasionally to contamination of surface and ground water. Several reports suggest that a wide range of water and terrestrial ecosystems may be contaminated with organophosphorus compounds. These compounds possess high mammalian toxicity and it is therefore essential to remove them from the environments. In addition, about 200,000 metric tons of nerve (chemical warfare) agents have to be destroyed world-wide under Chemical Weapons Convention (1993). Bioremediation can offer an efficient and cheap option for decontamination of polluted ecosystems and destruction of nerve agents. The first micro-organism that could degrade organophosphorus compounds was isolated in 1973 and identified as Flavobacterium sp. Since then several bacterial and a few fungal species have been isolated which can degrade a wide range of organophosphorus compounds in liquid cultures and soil systems. The biochemistry of organophosphorus compound degradation by most of the bacteria seems to be identical, in which a structurally similar enzyme called organophosphate hydrolase or phosphotriesterase catalyzes the first step of the degradation. organophosphate hydrolase encoding gene opd (organophosphate degrading) gene has been isolated from geographically different regions and taxonomically different species. This gene has been sequenced, cloned in different organisms, and altered for better activity and stability. Recently, genes with similar function but different sequences have also been isolated and characterized. Engineered microorganisms have been tested for their ability to degrade different organophosphorus pollutants, including nerve agents. In this article, we review and propose pathways for degradation of some organophosphorus compounds by microorganisms. Isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation are discussed. The major achievements and technological advancements towards bioremediation of organophosphorus compounds, limitations of available technologies and future challenge are also discussed.

The degradation of α-quaternary nonylphenol isomers by Sphingomonas sp. strain TTNP3 involves a type II ipso-substitution mechanism

The degradation of radiolabeled 4(3',5'-dimethyl-3'-heptyl)-phenol [nonylphenol (NP)] was tested with resting cells of Sphingomonas sp. strain TTNP3. Concomitantly to the degradation of NP, a metabolite identified as hydroquinone transiently accumulated and short-chain organic acids were then produced at the expense of hydroquinone. Two other radiolabeled isomers of NP, 4(2',6'-dimethyl-2'-heptyl)-phenol and 4(3',6'-dimethyl-3'-heptyl)-phenol, were synthesized. In parallel experiments, the 4(2',6'-dimethyl-2'-heptyl)-phenol was degraded more slowly than the other isomers of NP by strain TTNP3, possibly because of effects of the side-chain structure on the kinetics of degradation. Alkylbenzenediol and alkoxyphenol derivatives identified as metabolites during previous studies were synthesized and tested as substrates. The derivatives were not degraded, which indicated that the mineralization of NP does not proceed via alkoxyphenol as the principal intermediate. The results obtained led to the elucidation of the degradation pathway of NP isomers with a quaternary alpha-carbon. The proposed mechanism is a type II ipso substitution, leading to hydroquinone and nonanol as the main metabolites and to the dead-end metabolites alkylbenzenediol or alkoxyphenol, depending on the substitution at the alpha-carbon of the carbocationic intermediate formed.

Novel 4-chlorophenol degradation gene cluster and degradation route via hydroxyquinol in Arthrobacter chlorophenolicus A6

Arthrobacter chlorophenolicus A6, a previously described 4-chlorophenol-degrading strain, was found to degrade 4-chlorophenol via hydroxyquinol, which is a novel route for aerobic microbial degradation of this compound. In addition, 10 open reading frames exhibiting sequence similarity to genes encoding enzymes involved in chlorophenol degradation were cloned and designated part of a chlorophenol degradation gene cluster (cph genes). Several of the open reading frames appeared to encode enzymes with similar functions; these open reading frames included two genes, cphA-I and cphA-II, which were shown to encode functional hydroxyquinol 1,2-dioxygenases. Disruption of the cphA-I gene yielded a mutant that exhibited negligible growth on 4-chlorophenol, thereby linking the cph gene cluster to functional catabolism of 4-chlorophenol in A. chlorophenolicus A6. The presence of a resolvase pseudogene in the cph gene cluster together with analyses of the G+C content and codon bias of flanking genes suggested that horizontal gene transfer was involved in assembly of the gene cluster during evolution of the ability of the strain to grow on 4-chlorophenol.