Biodegradation of 2-nitrotoluene by Micrococcus sp. strain SMN-1

Decolorization of various dyes by microorganisms and green-synthesized nanoparticles: current and future perspective

Various types of colored pigments have been recovered naturally from biological sources including shells, flowers, insects, and so on in the past. At present, such natural colored substances (dyes) are replaced by manmade dyes. On the other hand, due to their continuous usage in various purpose, these artificial dyes or colored substances persist in the environmental surroundings. For example, industrial wastewater contains diverse pollutant substances including dyes. Several of these (artificial dyes) were found to be toxic to living organisms. In recent times, microbial-based removal of dye(s) has gained more attention. These methods were relatively inexpensive for eliminating such contaminants in the environmental system. Hence, various researchers were isolated microbes from environmental samples having the capability of decolorizing synthetic dyes from industrial wastewater. Furthermore, the microorganisms which are genetically engineered found higher degradative/decolorize capacity to target compounds in the natural environs. Very few reviews are available on specific dye treatment either by chemical treatments or by bacteria and/or fungal treatments. Here, we have enlightened literature reports on the removal of different dyes in microbes like bacteria (including anaerobic and aerobic), fungi, GEM, and microbial enzymes and also green-synthesized nanoparticles. This up-to-date literature survey will help environmental managements to co-up such contaminates in nature and will help in the decolorization of dyes.

A Bph-Like Nitroarene Dioxygenase Catalyzes the Conversion of 3-Nitrotoluene to 3-Methylcatechol by Rhodococcus sp. Strain ZWL3NT

All nitroarene dioxygenases reported so far originated from Nag-like naphthalene dioxygenase of Gram-negative strains, belonging to group III of aromatic ring-hydroxylating oxygenases (RHOs). Gram-positive Rhodococcus sp. strain ZWL3NT utilizes 3-nitrotoluene (3NT) as the sole source of carbon, nitrogen, and energy for growth. It was also reported that 3NT degradation was constitutive and the intermediate was 3-methylcatechol. In this study, a gene cluster (bndA1A2A3A4) encoding a multicomponent dioxygenase, belonging to group IV of RHOs, was identified. Recombinant Rhodococcus imtechensis RKJ300 carrying bndA1A2A3A4 exhibited 3NT dioxygenase activity, converting 3NT into 3-methylcatechol exclusively, with nitrite release. The identity of the product 3-methylcatechol was confirmed using liquid chromatography-mass spectrometry. A time course of biotransformation showed that the 3NT consumption was almost equal to the 3-methylcatechol accumulation, indicating a stoichiometry conversion of 3NT to 3-methylcatechol. Unlike reported Nag-like dioxygenases transforming 3NT into 4-methylcatechol or both 4-methylcatechol and 3-methylcatechol, this Bph-like dioxygenase (dioxygenases homologous to the biphenyl dioxygenase from Rhodococcus sp. strain RHA1) converts 3NT to 3-methylcatechol without forming 4-methylcatechol. Furthermore, whole-cell biotransformation of strain RKJ300 with bndA1A2A3A4 and strain ZWL3NT exhibited the extended and same substrate specificity against a number of nitrobenzene or substituted nitrobenzenes, suggesting that BndA1A2A3A4 is likely the native form of 3NT dioxygenase in strain ZWL3NT.IMPORTANCE Nitroarenes are synthetic molecules widely used in the chemical industry. Microbial degradation of nitroarenes has attracted extensive attention, not only because this class of xenobiotic compounds is recalcitrant in the environment but also because the microbiologists working in this field are curious about the evolutionary origin and process of the nitroarene dioxygenases catalyzing the initial reaction in the catabolism. In contrast to previously reported nitroarene dioxygenases from Gram-negative strains, which originated from a Nag-like naphthalene dioxygenase, the 3-nitrotoluene (3NT) dioxygenase in this study is from a Gram-positive strain and is an example of a Bph-like nitroarene dioxygenase. The preference of hydroxylation of this enzyme at the 2,3 positions of the benzene ring to produce 3-methylcatechol exclusively from 3NT is also a unique property among the studied nitroarene dioxygenases. These findings will enrich our understanding of the diversity and origin of nitroarene dioxygenase in microorganisms.

Environmental persistence, hazard, and mitigation challenges of nitroaromatic compounds

Nitroaromatic compounds (NACs) are extensively used in different industries and are synthesized in large quantity due to their heavy demand worldwide. The broad use of NACs poses a serious pollution threat. The treatment processes used for the removal of NACs are not effective and sustainable, leading to their release into the environment. The nitro group attached to benzene ring makes the compounds recalcitrant due to which they persist in the environment. Being hazardous to human as well as other living organisms, NACs are listed in the USEPA's priority pollutant group. This review provides updated information on the sources of NACs, prevalence in different environmental matrices, and recent developments in methods of their detection, with emphasis on current trends as well as future prospects. The harmful effects of NACs due to exposure through different routes are also highlighted. Further, the technologies reported for the treatment of NACs, including physico-chemical and biological methods, and the challenges faced for their effective implementation are discussed. Thus, the review discusses relevant issues in detail making suitable recommendations, which can be helpful in guiding further research in this subject.

Aerobic degradation of fenvalerate by a Gram-positive bacterium, Bacillus flexus strain XJU-4

Synthetic pyrethroid-fenvalerate-is one of the most widespread toxic pollutants and has adverse effect on living systems. However, little is known about its biotransformation mechanism in different microorganisms. To elucidate the pathway that might be involved in the catabolism of fenvalerate, we used Bacillus flexus strain XJU-4 (3-nitrobenzoate degrading organism) as an ideal fenvalerate degrading bacterium. Thin layer chromatography, high performance liquid chromatography and gas chromatography-mass spectrometry analysis results revealed that 3-phenoxybenzoate, protocatechuate, and catechol are the three main by-products of fenvalerate metabolism. Additionally, the bacterial cell-free enzymes showed the activities of fenvalerate hydrolyzing esterase, 3-phenoxybenzaldehyde dehydrogenase, 3-phenoxybenzoate dioxygenase, phenol hydroxylase, protocatechuate 2,3-dioxygenase and catechol-2,3-dioxygenase. Thus, in strain XJU-4, protocatechuate and catechol were further metabolized through meta-cleavage pathway. Moreover, laboratory-scale soil experiments results suggest that B. flexus strain XJU-4 is a suitable contender for bioremediation of pyrethroid fenvalerate-contaminated sites.

Evaluation of p-cresol degradation with polyphenol oxidase (PPO) immobilized in various matrices

p-Cresol is an environmental pollutant due to its vast use, toxicity and persistence, nevertheless, its degradation in an enzyme is unclear. In this study, we used Pleurotus sp. isolate VLECK02 polyphenol oxidase (PPO) for the determination of p-cresol degradation. On the basis of UV, FT-IR and chromatographic (HPLC and GC-MS) analysis, 4-methylcatechol was identified as the main metabolite of p-cresol catabolism. In addition, batch and semi-continuous degradation of p-cresol (10 and 20 mM) were studied and compared by free and immobilized PPO in different matrices like sodium alginate (SA), sodium alginate-polyvinyl alcohol (SA-PVA) and sodium alginate-polyvinyl alcohol-silver nanoparticles (SA-PVA-AgNPs). The experimental data showed that an enzyme (PPO) immobilized in SA-PVA-AgNPs was completely degraded p-cresol at initial concentrations of 10 and 20 mM within 30 h. These results suggest that the enzyme immobilized in SA-PVA-AgNPs has achieved higher degradation rates at a given time than free PPO and PPO immobilized in SA-PVA and SA. The SA-PVA-AgNPs and SA-PVA immobilized enzyme could be reused for more than 12 and 8 cycles, respectively, without losing any degradation capacity. Moreover, the immobilized PPO showed higher tolerance to various temperatures and pH than free PPO. Hence, immobilized PPO could be useful for the bioremediation of environment contaminated with phenolic compounds like p-cresol.

Statistical modeling and optimization of culture conditions by response surface methodology for 2,4- and 2,6-dinitrotoluene biodegradation using Rhodococcus pyridinivorans NT2

To improve biodegradability (% biodegradation) and specific growth rate of Rhodococcus pyridinivorans NT2, culture medium and environmental parameters were screened and optimized using the statistical design techniques of Plackett-Burman and response surface methodology. Of the process variables screened, DNTs (2,4-DNT and 2,6-DNT), MgSO₄·7H₂O, temperature and inoculum size (O.D.) were selected as the most important (P value <0.05) factors. In multiresponse analysis of central composite design, medium formulation consisting of 474/470 mg l^-1 2,4-DNT/2,6-DNT, 0.11 g l^-1 MgSO₄·7H₂O, 37.5 °C temperature and 1.05 OD inoculum size were found to predict maximum % degradation and specific growth rate of 97.55 % and 0.19 h^-1, respectively. The validity of the optimized variables was verified in shake flasks. The optimized media significantly shortened the time required for biodegradation of DNTs while providing a nearly 30 % (for 2,4-DNT) and 70 % (for 2,6-DNT) increased biodegradation along with 5.64-fold increase in specific growth rate for both DNTs.

Selection for growth on 3-nitrotoluene by 2-nitrotoluene-utilizing Acidovorax sp. strain JS42 identifies nitroarene dioxygenases with altered specificities

Acidovorax sp. strain JS42 uses 2-nitrotoluene as a sole source of carbon and energy. The first enzyme of the degradation pathway, 2-nitrotoluene 2,3-dioxygenase, adds both atoms of molecular oxygen to 2-nitrotoluene, forming nitrite and 3-methylcatechol. All three mononitrotoluene isomers serve as substrates for 2-nitrotoluene dioxygenase, but strain JS42 is unable to grow on 3- or 4-nitrotoluene. Using both long- and short-term selections, we obtained spontaneous mutants of strain JS42 that grew on 3-nitrotoluene. All of the strains obtained by short-term selection had mutations in the gene encoding the α subunit of 2-nitrotoluene dioxygenase that changed isoleucine 204 at the active site to valine. Those strains obtained by long-term selections had mutations that changed the same residue to valine, alanine, or threonine or changed the alanine at position 405, which is just outside the active site, to glycine. All of these changes altered the regiospecificity of the enzymes with 3-nitrotoluene such that 4-methylcatechol was the primary product rather than 3-methylcatechol. Kinetic analyses indicated that the evolved enzymes had enhanced affinities for 3-nitrotoluene and were more catalytically efficient with 3-nitrotoluene than the wild-type enzyme. In contrast, the corresponding amino acid substitutions in the closely related enzyme nitrobenzene 1,2-dioxygenase were detrimental to enzyme activity. When cloned genes encoding the evolved dioxygenases were introduced into a JS42 mutant lacking a functional dioxygenase, the strains acquired the ability to grow on 3-nitrotoluene but with significantly longer doubling times than the evolved strains, suggesting that additional beneficial mutations occurred elsewhere in the genome.

Microbial diversity, community composition and metabolic potential in hydrocarbon contaminated oily sludge: prospects for in situ bioremediation

Microbial community composition and metabolic potential have been explored in petroleum-hydrocarbon-contaminated sludge of an oil storage facility. Culture-independent clone library-based 16S rRNA gene analyses revealed that the bacterial community within the sludge was dominated by the members of β-Proteobacteria (35%), followed by Firmicutes (13%), δ-Proteobacteria (11%), Bacteroidetes (10%), Acidobacteria (6%), α-Proteobacteria (3%), Lentisphaerae (2%), Spirochaetes (2%), and unclassified bacteria (5%), whereas the archaeal community was composed of Thermoprotei (54%), Methanocellales (33%), Methanosarcinales/Methanosaeta (8%) and Methanoculleus (1%) members. Methyl coenzyme M reductase A (mcrA) gene (a functional biomarker) analyses also revealed predominance of hydrogenotrophic, methanogenic Archaea (Methanocellales, Methanobacteriales and Methanoculleus members) over acetoclastic methanogens (Methanosarcinales members). In order to explore the cultivable bacterial population, a total of 28 resident strains were identified and characterized in terms of their physiological and metabolic capabilities. Most of these could be taxonomically affiliated to the members of the genera Bacillus, Paenibacillus, Micrococcus, Brachybacterium, Aerococcus, and Zimmermannella, while two strains were identified as Pseudomonas and Pseudoxanthomonas. Metabolic profiling exhibited that majority of these isolates were capable of growing in presence of a variety of petroleum hydrocarbons as sole source of carbon, tolerating different heavy metals at higher concentrations (≥1 mM) and producing biosurfactant during growth. Many strains could grow under a wide range of pH, temperature, or salinity as well as under anaerobic conditions in the presence of different electron acceptors and donors in the growth medium. Correlation between the isolates and their metabolic properties was estimated by the unweighted pair group method with arithmetic mean (UPGMA) analysis. Overall observation indicated the presence of diverse groups of microorganisms including hydrocarbonoclastic, nitrate reducing, sulphate reducing, fermentative, syntrophic, methanogenic and methane-oxidizing bacteria and Archaea within the sludge community, which can be exploited for in situ bioremediation of the oily sludge.

Expression, purification and substrate specificities of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2

3-Nitotoluene dioxygenase (3-NTDO) is the first enzyme in the degradation pathway of 3-nitrotoluene (3-NT) by Diaphorobacter sp. strain DS2. The complete gene sequences of 3-NTDO were PCR amplified from genomic DNA of Diaphorobacter sp., cloned, sequenced and expressed. The 3-NTDO gene revealed a multi component structure having a reductase, a ferredoxin and two oxygenase subunits. Clones expressing the different subunits were constructed in pET21a expression vector system and overexpressed in E. coli BL21(DE3) host. Each subunit was individually purified separately to homogeneity. The active recombinant enzyme was reconstituted in vitro by mixing all three purified subunits. The reconstituted recombinant enzyme could catalyse biotransformations on a variety of organic aromatics.

3-Nitrotoluene dioxygenase from Diaphorobacter sp. strains: cloning, sequencing and evolutionary studies

The first step in the degradation of 3-nitrotoluene by Diaphorobacter sp. strain DS2 is the dihydroxylation of the benzene ring with the concomitant removal of nitro group. This is catalyzed by a dioxygenase enzyme system. We report here the cloning and sequencing of the complete dioxygenase gene with its putative regulatory sequence from the genomic DNA of Diaphorobacter sp. strains DS1, DS2 and DS3. Analysis of the 5 kb DNA stretch that was cloned, revealed five complete open reading frames (ORFs) encoding for a reductase, a ferredoxin and two dioxygenase subunits with predicted molecular weights (MW) of 35, 12, 50 and 23 kDa respectively. A regulatory protein was also divergently transcribed from the reductase subunit and has a predicated MW of 34 kDa. Presence of parts of two functional ORFs in between the reductase and the ferredoxin subunits reveals an evolutionary route from a naphthalene dioxygenase like system of Ralstonia sp. strain U2. Further a 100 % identity of its ferredoxin subunit reveals its evolution via dinitrotoluene dioxygenase like system present in Burkholderia cepacia strain R34. A modeled structure of oxygenase3NT from strain DS2 was generated using nitrobenzene dioxygenase as a template. The modeled structure only showed minor changes at its active site. Comparison of growth patterns of strains DS1, DS2 and DS3 revealed that Diaphorobacter sp. strain DS1 has been evolved to degrade 4-nitrotoluene better by an oxidative route amongst all three strains.

Enhanced degradation of 2-nitrotoluene by immobilized cells of Micrococcus sp. strain SMN-1

Nitrotoluenes are the toxic pollutants of the environment because of their large scale use in the production of explosives. Biodegradation of such chemicals by microorganisms may provide an effective method for their detoxification. We have studied the degradation of 2-nitrotoluene by cells of Micrococcus sp. strain SMN-1 immobilized in various matrices such as polyurethane foam (PUF), sodium alginate (SA), sodium alginate-polyvinyl alcohol (SA-PVA), agar and polyacrylamide. The rate of degradation of 15 and 30 mM 2-nitrotoluene by freely suspended cells and immobilized cells in batches and fed-batch with shaken cultures were compared. The PUF-immobilized cells achieved higher degradation of 15 and 30 mM 2-nitrotoluene than freely suspended cells and the cells immobilized in SA-PVA, polyacrylamide, SA and agar. The PUF-immobilized cells could be reused more than 24 cycles without loosing their degradation capacity and showed more tolerance to pH and temperature changes than freely suspended cells. These results revealed the enhanced rate of degradation of 2-nitrotoluene by PUF-immobilized cells of Micrococcus sp. strain SMN-1.

Biodegradation of 3-nitrotoluene by Rhodococcus sp. strain ZWL3NT

A pure bacterial culture was isolated by its ability to utilize 3-nitrotoluene (3NT) as the sole source of carbon, nitrogen, and energy for growth. Analysis of its 16S rRNA gene showed that the organism (strain ZWL3NT) belongs to the genus Rhodococcus. A rapid disappearance of 3NT with concomitant release of nitrite was observed when strain ZWL3NT was grown on 3NT. The isolate also grew on 2-nitrotoluene, 3-methylcatechol and catechol. Two metabolites, 3-methylcatechol and 2-methyl-cis,cis-muconate, in the reaction mixture were detected after incubation of cells of strain ZWL3NT with 3NT. Enzyme assays showed the presence of both catechol 1,2-dioxygenase and catechol 2,3-dioxygenase in strain ZWL3NT. In addition, a catechol degradation gene cluster (catRABC cluster) for catechol ortho-cleavage pathway was cloned from this strain and cell extracts of Escherichia coli expressing CatA and CatB exhibited catechol 1,2-dioxygenase activity and cis,cis-muconate cycloisomerase activity, respectively. These experimental evidences suggest a novel pathway for 3NT degradation with 3-methylcatechol as a key metabolite by Rhodococcus sp. strain ZWL3NT.

Extrachromosomal genetic elements in Micrococcus

Micrococci are Gram-positive G + C-rich, nonmotile, nonspore-forming actinomycetous bacteria. Micrococcus comprises ten members, with Micrococcus luteus being the type species. Representatives of the genus play important roles in the biodegradation of xenobiotics, bioremediation processes, production of biotechnologically important enzymes or bioactive compounds, as test strains in biological assays for lysozyme and antibiotics, and as infective agents in immunocompromised humans. The first description of plasmids dates back approximately 28 years, when several extrachromosomal elements ranging in size from 1.5 to 30.2 kb were found in Micrococcus luteus. Up to the present, a number of circular plasmids conferring antibiotic resistance, the ability to degrade aromatic compounds, and osmotolerance are known, as well as cryptic elements with unidentified functions. Here, we review the Micrococcus extrachromosomal traits reported thus far including phages and the only quite recently described large linear extrachromosomal genetic elements, termed linear plasmids, which range in size from 75 kb (pJD12) to 110 kb (pLMA1) and which confer putative advantageous capabilities, such as antibiotic or heavy metal resistances (inferred from sequence analyses and curing experiments). The role of the extrachromosomal elements for the frequently proven ecological and biotechnological versatility of the genus will be addressed as well as their potential for the development and use as genetic tools.

Evolution of a new bacterial pathway for 4-nitrotoluene degradation

Bacteria that assimilate synthetic nitroarene compounds represent unique evolutionary models, as their metabolic pathways are in the process of adaptation and optimization for the consumption of these toxic chemicals. We used Acidovorax sp. strain JS42, which is capable of growth on nitrobenzene and 2-nitrotoluene, in experiments to examine how a nitroarene degradation pathway evolves when its host strain is challenged with direct selective pressure to assimilate non-native substrates. Although the same enzyme that initiates the degradation of nitrobenzene and 2-nitrotoluene also oxidizes 4-nitrotoluene to 4-methylcatechol, which is a growth substrate for JS42, the strain is incapable of growth on 4-nitrotoluene. Using long-term laboratory evolution experiments, we obtained JS42 mutants that gained the ability to grow on 4-nitrotoluene via a new degradation pathway. The underlying basis for this new activity resulted from the accumulation of specific mutations in the gene encoding the dioxygenase that catalyses the initial oxidation of nitroarene substrates, but at positions distal to the active site and previously unknown to affect activity in this or related enzymes. We constructed additional mutant dioxygenases to identify the order of mutations that led to the improved enzymes. Biochemical analyses revealed a defined, step-wise pathway for the evolution of the improved dioxygenases.

Unusual polar metabolites in the groundwater of a contaminated waste site indicate a new pathway of mononitrotoluene transformation

At a mononitrotoluene-contaminated waste disposal site, the groundwater was screened for polar transformation products of mononitrotoluenes, by means of HPLC-MS, HPLC-NMR and further off-line NMR and MS techniques. Besides expected metabolites such as aminotoluenes (ATs) and nitrobenzoic acids (NBAs), three unknowns (di- and tetrahydro-derivatives of (2-oxo-quinolin-3-yl) acetic acid) could be identified which, in the context of explosives and related compounds, are new metabolites. Evidence could be provided by microcosm experiments with 2-nitrotoluene (2-NT) that these metabolites are microbial transformation products of 2-NT under anaerobic conditions. The NMR and MS data are presented and the possible pathway for the formation of these metabolites after addition of 2-NT to fumarate is discussed.

Highly efficient decolorization of Malachite Green by a novel Micrococcus sp. strain BD15

PURPOSE

Malachite Green (MG) is used for a variety of applications but is also known to be carcinogenic and mutagenic. In this study, a novel Micrococcus sp. (strain BD15) was observed to efficiently decolorize MG. The purposes of this study were to explore the optimal conditions for decolorization and to evaluate the potential use of this strain for MG decolorization.

METHODS

Optical microscope and UV-visible analyses were carried out to determine whether the decolorization was due to biosorption or biodegradation. A Plackett-Burman design was employed to investigate the effect of various parameters on decolorization, and response surface methodology was then used to explore the optimal decolorization conditions. Kinetics analysis and antimicrobial activity tests were also performed.

RESULTS

The results indicated that the decolorization by the strain was mainly due to biodegradation. Concentrations of MG, urea, and yeast extract and inoculum size had significantly positive effects on MG decolorization, while concentrations of CuCl(2) and MgCl(2), and temperature had significantly negative effects. The interaction between different parameters could significantly affect decolorization, and the optimal conditions for decolorization were 1.0 g/L urea, 0.9 g/L yeast extract, 100 mg/L MG, 0.1 g/L inoculums (dry weight), and incubation at 25.2°C. Under the optimal conditions, 96.9% of MG was removed by the strain within 1 h, which represents highly efficient microbial decolorization. Moreover, the kinetic data for decolorization fit a second-order model well, and the strain showed a good MG detoxification capability.

CONCLUSION

Based on the results of this study, we propose Micrococcus sp. strain BD15 as an excellent candidate strain for MG removal from wastewater.