Molecular cloning and characterization of pentachlorophenol-degrading monooxygenase genes of Pseudomonas sp. from the chemostat

Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation

Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.

Bacterial-mediated biodegradation of pentachlorophenol via electron shuttling

Pentachlorophenol (PCP) degradation by soil indigenous bacteria represents a practical and cost-effective solution. In the present study, bacteria isolated from paddy soil was investigated and the role of electron shuttling (ES) in the PCP degradation process was assessed. Two strains demonstrated the highest PCP degradation of 93.5% and 94.88% in the presence of citrate and were identified using 16S rRNA phylogenetic analysis as Pseudomonas chengduensis and Pseudomonas plecoglossicida, respectively. Both strains showed higher PCP degradation in free form as opposed to a reduced activity in immobilized and respiratory impaired form. The addition of pyruvate resulted in about 80% PCP degradation in 5 days for P. chengduensis, on the other hand, P. plecoglossicida showed the same result under anaerobic conditions whether pyruvate was added or not. Phenazine and the outer membrane c-type cytochrome were reported only for P. chengduensis as opposed to P. plecoglossicida. The results indicate that despite following different approaches in PCP degradation, both strains are useful in PCP clean-up under aerobic and anaerobic conditions and in free direct contact. The degradation is enhanced via ES. This is considered both an effective and feasible technology for in situ clean-up of contaminated sites or on-site bioreactors.

Assessment of genetic diversity and bioremediation potential of pseudomonads isolated from pesticide-contaminated artichoke farm soils

A total of 68 dimethoate and pentachlorophenol-tolerant rhizobacteria, isolated from a pesticide-contaminated agricultural soil, have been identified and typed by means of 16S-23S rRNA internal transcribed spacers analysis (ITS-PCR), 16S rRNA gene sequencing and by repetitive extragenic palindromic (BOX-PCR). The majority of bacterial isolates (84.31%) belonged to Proteobacteria (with a predominance of Gammaproteobacteria, 72.54%), while the remaining isolates were affiliated with Firmicutes (9.80%), Bacteroidetes (1.96%) and Actinobacteria (3.92%). The pesticide-tolerant bacterial isolates belonged to 11 genera, namely Pseudomonas, Bacillus, Acinetobacter, Flavobacterium, Comamonas, Achromobacter, Rhodococcus, Ochrobactrum, Aquamicrobium, Bordetella and Microbacterium. Within the well-represented genus Pseudomonas (n = 36), the most common species was Pseudomonas putida (n = 32). The efficacy of the selected strain, Pseudomonas putida S148, was further investigated for biodegradation of pentachlorophenol (PCP) in minimal medium, when used as a sole carbon and energy source. At an initial concentration of 100 mg/L, P. putida S148 degraded 91% of PCP after 7 days. GC-MS analyses revealed the formation of tetrachlorohydroquinone, tri- and di-chlorophenols as biodechlorination products in PCP remediation experiments. The toxicity estimation showed that 50% lethal concentration (LC50) and 50% growth inhibition concentration (IGC50) obtained values for the major identified compounds (2,3,4,6 tetrachlorophenol, 2,3,5,6 tetrachlorophenol and tetrachlorohydroquinone) were higher than those estimated for the PCP indicating that the metabolites are less toxic than the original compound for those specific organisms. S148 strain could be added to pesticide-contaminated agricultural soils as a bacterial inoculant for its potential to improve soil quality.

Characterization of the genome of a Nocardia strain isolated from soils in the Qinghai-Tibetan Plateau that specifically degrades crude oil and of this biodegradation

A strain of Nocardia isolated from crude oil-contaminated soils in the Qinghai-Tibetan Plateau degrades nearly all components of crude oil. This strain was identified as Nocardia soli Y48, and its growth conditions were determined. Complete genome sequencing showed that N. soli Y48 has a 7.3 Mb genome and many genes responsible for hydrocarbon degradation, biosurfactant synthesis, emulsification and other hydrocarbon degradation-related metabolisms. Analysis of the clusters of orthologous groups (COGs) and genomic islands (GIs) revealed that Y48 has undergone significant gene transfer events to adapt to changing environmental conditions (crude oil contamination). The structural features of the genome might provide a competitive edge for the survival of N. soli Y48 in oil-polluted environments and reflect the adaptation of coexisting bacteria to distinct nutritional niches.

Fungal Unspecific Peroxygenases Oxidize the Majority of Organic EPA Priority Pollutants

Unspecific peroxygenases (UPOs) are secreted fungal enzymes with promiscuity for oxygen transfer and oxidation reactions. Functionally, they represent hybrids of P450 monooxygenases and heme peroxidases; phylogenetically they belong to the family of heme-thiolate peroxidases. Two UPOs from the basidiomycetous fungi Agrocybe aegerita (AaeUPO) and Marasmius rotula (MroUPO) converted 35 out of 40 compounds listed as EPA priority pollutants, including chlorinated benzenes and their derivatives, halogenated biphenyl ethers, nitroaromatic compounds, polycyclic aromatic hydrocarbons (PAHs) and phthalic acid derivatives. These oxygenations and oxidations resulted in diverse products and—if at all—were limited for three reasons: (i) steric hindrance caused by multiple substitutions or bulkiness of the compound as such (e.g., hexachlorobenzene or large PAHs), (ii) strong inactivation of aromatic rings (e.g., nitrobenzene), and (iii) low water solubility (e.g., complex arenes). The general outcome of our study is that UPOs can be considered as extracellular counterparts of intracellular monooxygenases, both with respect to catalyzed reactions and catalytic versatility. Therefore, they should be taken into consideration as a relevant biocatalytic detoxification and biodegradation tool used by fungi when confronted with toxins, xenobiotics and pollutants in their natural environments.

Antioxidant enzymes are induced by phenol in the marine microalga Lingulodinium polyedrum

Knowing the impacts of different anthropogenic activities on ecosystems promotes preservation of aquatic organisms. Aiming to facilitate the identification of polluted or contaminated areas, the study of microalga Lingulodinium polyedrum in phenol-containing medium comprises the determination of toxic and metabolic phenol effects, featuring a possible use of this microorganism as bioindicator for this pollutant. Marine microalga L. polyedrum exposure to phenol increases superoxide dismutase (SOD) and catalase (CAT) activities. The 20% and 50% inhibitory concentrations (IC20 and IC50) of cells exposed to phenol were 40 μmol L(-1) and 120 μmol L(-1), respectively. Phenol biodegradation by L. polyedrum was 0.02 μmol h(-1)cell(-1), and its biotransformation was catalyzed by glutathione S-transferase (GST), phenol hydroxylase and catechol 2,3-dihydroxygenase metabolic pathways. Phenol exposure produced the metabolites 2-hydroxymuconic semialdehyde acid, 1,2-dihydroxybenzene (catechol), and 2-oxo-4-pentenoic acid; also, it induced the activity of key antioxidant biomarker enzymes SOD and CAT by three folds compared to that in the controls. Further, phenol decreased the glutathione/oxidized glutathione ratio (GSH/GSSG), highlighting the effective glutathione oxidation in L. polyedrum. Overall, our results suggest that phenol alters microalga growth conditions and microalgae are sensitive bioindicators to pollution by phenol in marine environments.

Enhanced removal of a pesticides mixture by single cultures and consortia of free and immobilized Streptomyces strains

Pesticides are normally used to control specific pests and to increase the productivity in crops; as a result, soils are contaminated with mixtures of pesticides. In this work, the ability of Streptomyces strains (either as pure or mixed cultures) to remove pentachlorophenol and chlorpyrifos was studied. The antagonism among the strains and their tolerance to the toxic mixture was evaluated. Results revealed that the strains did not have any antagonistic effects and showed tolerance against the pesticides mixture. In fact, the growth of mixed cultures was significantly higher than in pure cultures. Moreover, a pure culture (Streptomyces sp. A5) and a quadruple culture had the highest pentachlorophenol removal percentages (10.6% and 10.1%, resp.), while Streptomyces sp. M7 presented the best chlorpyrifos removal (99.2%). Mixed culture of all Streptomyces spp. when assayed either as free or immobilized cells showed chlorpyrifos removal percentages of 40.17% and 71.05%, respectively, and for pentachlorophenol 5.24% and 14.72%, respectively, suggesting better removal of both pesticides by using immobilized cells. These results reveal that environments contaminated with mixtures of xenobiotics could be successfully cleaned up by using either free or immobilized cultures of Streptomyces, through in situ or ex situ remediation techniques.

Microbial dechlorination of chloroorganics and simultaneous decolorization of pulp-paper mill effluent by Pseudomonas putida MTCC 10510 augmentation

The physicochemical analyses of pulp-paper mill effluent revealed that it was dark brown with 1761 ± 2.3 color PtCo units having slightly alkaline pH, high biological oxygen demand and chemical oxygen demand values, and contained large quantities of organic and inorganic constituents, well above the prescribed standards. The bacterial growth, color reduction, and dechlorination were evident in all the four sets of experiments with different possible combinations of nutrient supplementation and Pseudomonas putida augmentation. A high degree of decolorization at 29.7% and 27.4% was observed by the effluent native microflora during 48 and 24 h, in unaugmented effluent supplemented with glucose + yeast extract and glucose + peptone, respectively. The extent of decolorization in glucose + yeast extract unaugmented effluent also corresponded with high degree of dechlorination (59.3%) during 60-h incubation (SET III). An appreciable level of growth, decolorization, and dechlorination was evident in nutrient unsupplemented P. putida augmented effluent as well as in the control natural effluent. However, a maximum level of growth response (OD 1.641-1.902) during 36-48 h, removal of color (39.72-48.2%) during 24-36 h, and chloride ions (80.1-83.5%) during 36 h was achieved in P. putida augmented effluent supplemented with glucose + yeast extract or peptone. Therefore, supplementation of effluent with glucose and yeast extract or peptone and concomitant augmentation with P. putida is required for efficient effluent decolorization and detoxification.

Isolation and Growth Characteristics of Chromium(VI) and Pentachlorophenol Tolerant Bacterial Isolate from Treated Tannery Effluent for its Possible Use in Simultaneous Bioremediation

The bacterial strains resistant to pentachlorophenol (PCP) and hexavalent chromium [Cr(VI)] were isolated from treated tannery effluent of a common effluent treatment plant. Most of the physico-chemical parameters analyzed were above permissible limits. Thirty-eight and four bacterial isolates, respectively were found resistant to >50 μg/ml concentration of [Cr(VI)] and the same level of PCP. Out of the above 42 isolates, only one was found simultaneously tolerant to higher levels of both PCP (500 μg/ml) and Cr(VI) (200 μg/ml), and hence was selected for further studies. To the best of our knowledge, this is the first report in which a native bacterial isolate simultaneously tolerant to such a high concentrations of Cr(VI) and PCP has been reported. The culture growth was best at 0.4% (w/v) glucose as an additional carbon source and 0.2% (w/v) ammonium chloride as a nitrogen source. The growth results with cow urine as a nitrogen source were comparable with the best nitrogen source ammonium chloride. The isolate exhibited resistance to multiple heavy metals (Pb, As, Hg, Zn, Co & Ni) and to antibiotics nalidixic acid and polymixin-B. The efficacy of bacterial isolate for growth, PCP degradation (56.5%) and Cr(VI) bioremediation (74.5%) was best at 48 h incubation. The isolate was identified as Bacillus sp. by morphological and biochemical tests. The 16S rDNA sequence analysis revealed 98% homology with Bacillus cereus. However, further molecular analysis is underway to ascertain its likelyhood of a novel species.

Strategies for decolorization and detoxification of pulp and paper mill effluent

The potential hazards associated with industrial effluents, coupled with increasing awareness of environment problems, have prompted many countries to limit the indiscriminate discharge of untreated wastewaters. The pulp and paper industry has been among the most significant of industrial polluters of the waterways, and therefore has been one of the industries of concern. The pulp and paper industry produces large quantities of brown/black effluent that primarily result from pulping, bleaching, and paper-making production stages. The dark color and toxicity of pulp-paper mill effluent comes primarily from lignin and its chlorinated derivatives (e.g., lignosulphonic acid, resins, phenols, and hydrocarbons) that are released during various processing steps of lignocellulosic materials. The color originates from pulping and pulp bleaching stages, while adsorbable organic halides (AOX) originates exclusively from chlorine bleaching. Discharge of untreated effluent results in increased BOD/COD, slime growth, thermal problems, scum formation, discoloration, loss of aesthetic quality and toxicity to the aquatic life, in the receiving waterbodies. The dark brow color of pulp-paper effluent is not only responsible for aesthetic unacceptability, but also prevents the passage of sunlight through colored waterbodies. This reduces the photosynthetic activity of aquatic flora, ultimately causing depletion of dissolved oxygen. The pulp-paper organic waste, coupled with the presence of chlorine, results in the generation of highly chlorinated organic compounds. These toxic constituents of wastewater pose a human health risk through long term exposure. via drinking water and\or through consumption of fish that can bioaccumulate certain pollutants from the food chain. Therefore, considerable attention has been focused by many countries on decolorization of paper mill effluents , along with reduction in the contaminants that pose human health or other environmental hazards. Various physicochemical remediation treatments in the pulp-paper industry are now used, or have been suggested, but often are not implemented, because of the high cost involved. More recently, the paper and pulp industry has been investigating the use of biological remediation steps to replace or augment current treatment strategies. Certain biological treatments offer opportunities to reduce cost (both capital and operating), reduce energy consumption, and minimize environmental impact. Two primary approaches may be effective to curtail release of toxic effluents: first, development of pulping and bleaching processes that emphasize improved oxygen delignification or biopulping, plus partial or complete replacement of chlorine treatment with hydrogen peroxide or with biobleaching; second, implementation of biological processing that involves sequential two-step anaerobic-aerobic or three-step aerobic-anaerobic treatment technologies at end of pipe. The selection of the specific process will depend upon the type of pollutants/toxicants/mutagens present in the effluent. The use of environmental-friendly technologies in the pulp and paper industry is becoming more popular, partly because of increasing regulation, and partly because of the availability of new techniques that can be used to economically deal with pollutants in the effluents. Moreover, biotechnology research methods are offering promise for even greater improvements in the future. The obvious ultimate goal of the industry and the regulators should be zero emission through recycling of industrial wastewater, or discharge of the bare minimum amount of toxicants or color.

Isolation and characterization of alkalotolerant Pseudomonas sp. strain ISTDF1 for degradation of dibenzofuran

An alkalotolerant Pseudomonas strain was enriched and isolated from effluent of the pulp and paper industry. This strain was able to degrade dibenzofuran and utilize it as a sole source of energy and carbon. The GC-MS based detection of various intermediary metabolites of biodegradation suggested the involvement of angular as well as lateral pathway of dibenzofuran biodegradation. The GC-MS based detection of various intermediary metabolites of biodegradation suggested the involvement of angular as well as lateral pathway of dibenzofuran biodegradation. This diverse dioxygenation property of the strain allowed it to utilize various recalcitrant chlorinated xenobiotics and PAHs compounds. This strain showed optimum utilization (~85%) of dibenzofuran (200 mg l⁻¹) within 36 h at pH 10 at 40 °C. The growth of the strain was supported by a wide range of environmental conditions such as temperature, pH, and concentration of dibenzofuran, suggesting that it can be used for in situ bioremediation of dioxin-like compound.

Reduction of pollutants in pulp paper mill effluent treated by PCP-degrading bacterial strains

Two PCP-degrading bacterial strains, Bacillus cereus (ITRC-S6) and Serratia marcescens (ITRC-S7) were used for the treatment of pulp and paper mill effluent at conditions; 1.0% glucose and 0.5% peptone at 30 +/- 1 degrees C at 120 rpm for 168 h of incubation. These two bacterial strains effectively reduced colour (45-52%), lignin (30-42%), BOD (40-70%), COD (50-60%), total phenol (32-40%) and PCP (85-90%) within 168 h of incubation. However, the highest reduction in colour (62%), lignin (54%), BOD (70%), COD (90%), total phenol (90%) and PCP (100%) was recorded by mixed culture treatment. The bacterial mechanism for the degradation of pulp and paper mill effluent may be explained by an increase in the cells biomass using added co-substrates resulting liberation of significant amount of chloride due to bacterial dechlorination of chlorolignins and chlorophenols this showed reduction in colour, lignin and toxicity in the effluent. Further, GC-MS analysis of ethyl acetate-extractable compounds from treated pulp paper mill effluent reinforces the bacterium capability for the degradation of lignin and pentachlorophenol, as many aromatic compounds such as 2-chlorophenol, 2, 4, 6-trichlorophenol and tetrachlorohydroquinone, 6-chlorohydroxyquinol and tetrachlorohydroquinone detected which were not present in the untreated effluent.

Identification and characterization of integron mediated antibiotic resistance in pentachlorophenol degrading bacterium isolated from the chemostat

A bacterial consortium was developed by continuous enrichment of microbial population isolated from sediment core of pulp and paper mill effluent in mineral salts medium (MSM) supplemented with pentachlorophenol (PCP) as sole source of carbon and energy in the chemostat. The consortia contained three bacterial strains. They were identified as Escherichia coli, Pseudomonas aeruginosa and Acinetobacter sp. by 16S rRNA gene sequence analysis. Acinetobacter sp. readily degraded PCP through the formation of tetrachloro-p-hydroquinone (TecH), 2-chloro-1,4-benzenediol and products of ortho ring cleavage detected by gas chromatograph/mass spectrometer (GC-MS). Out of the three acclimated PCP degrading bacterial strains only one strain, Acinetobacter sp. showed the presence of integron gene cassette as a marker of its stability and antibiotic resistance. The strain possessed a 4.17 kb amplicon with 22 ORF's. The plasmid isolated from the Acinetobacter sp. was subjected to shotgun cloning through restriction digestion by BamHI, HindIII and SalI, ligated to pUC19 vector and transformed into E. coli XLBlue1alpha, and finally selected on MSM containing PCP as sole source of carbon and energy with ampicillin as antibiotic marker. DNA sequence analysis of recombinant clones indicated homology with integron gene cassette and multiple antibiotic resistance genes.

Characterization of pentachlorophenol degrading bacterial consortium from chemostat

A microbial consortium was developed by continuous enrichment of bacterial population isolated from sediment core of pulp and paper mill effluent in mineral salts medium (MSM) supplemented with pentachlorophenol (PCP) as sole source of carbon and energy in the chemostat. The enriched consortium contained three bacterial strains identified as Escherichia coli (PCP1), Pseudomonas aeruginosa (PCP2) and Acinetobacter sp. (PCP3) by morphological and biochemical tests, further confirmation was done using 16S rDNA sequence analysis. The potency of bacterial isolates in degradation of PCP was monitored in terms of growth and utilization of PCP as substrate with spectrophotometer and gas chromatograph-mass spectrometer (GC-MS) analysis. The strains were tested for their utilization of various organic compounds. The strain PCP3, showed higher potency to utilize PCP as sole source of carbon and energy than PCP1 and PCP2. The bacterial strain were able to utilize PCP through an oxidative and reductive route as indicated with the formation of tetrachloro-p-hydroquinone (TeCH), 2-chloro-1,4-benzenediol and 2,3,4,6-tetrachlorophenol, respectively.

Characterization of diverse Acinetobacter isolates for utilization of multiple aromatic compounds

This study demonstrates the multiple catabolic capacities of lab isolates belonging to the genus Acinetobacter. Thirty-one Acinetobacter strains were screened initially for their capacity to utilize ten substrates that includes monocyclic, heterocyclic and polycyclic aromatic compounds. These bacteria were isolated from activated biomass of different effluent treatment plants (ETPs) treating wastewater generated at different industries and selected based on partial sequence data of the 16S rRNA gene. Of these 31 isolates, preliminary plate assay results showed eleven isolates that could utilize multiple substrates. Analytical studies demonstrated multiple degradation of hydrocarbons dibenzothiophene, fluorene, dibenzofuran, benzyl sulfide, and sodium benzoate by two isolates, HPC311 and HPC159.

The recent evolution of pentachlorophenol (PCP)-4-monooxygenase (PcpB) and associated pathways for bacterial degradation of PCP

Man-made polychlorinated phenols such as pentachlorophenol (PCP) have been used extensively since the 1920s as preservatives to prevent fungal attack on wood. During this time, they have become serious environmental contaminants. Despite the recent introduction of PCP in the environment on an evolutionary time scale, PCP-degrading bacteria are present in soils worldwide. The initial enzyme in the PCP catabolic pathway of numerous sphingomonads, PCP-4-monooxygenase (PcpB), catalyzes the para-hydroxylation of PCP to tetrachlorohydroquinone and is encoded by the pcpB gene. This review examines the literature concerning pcpB and supports the suggestion that pcpB/PcpB should be considered a model system for the study of recent evolution of catabolic pathways among bacteria that degrade xenobiotic molecules introduced into the environment during the recent past.