Biodegradation of 2-bromonitrobenzene by Pseudomonas stutzeri ZWLR2-1

Evolution of pollutant biodegradation

Pollutant-derived risks to human and environmental health are exacerbated by slow natural attenuation rates, often driven by pollutant toxicity to microorganisms that can degrade them or limitations to the ability of microorganisms to metabolise them. This review explores mechanisms employed by bacteria to protect themselves from pollutant toxicity in the context of the evolution of pollutant-degrading abilities. The role of promiscuous enzymes in pollutant transformation is subsequently reviewed, highlighting the emergence of novel metabolic pathways and their transcriptional regulation in response to pollutant exposure, followed by the gene transcription regulation to optimise the cellular component synthesis for adaptation on the novel substrate. Additionally, we discuss epistatic interactions among mutations vital for this process both at macromolecular and at cellular levels. Finally, evolutionary constraints towards enhanced fitness in the context of pollutant degradation are considered, the constraints imposed by the epistasis from mutations on both enzyme level and cellular level, concluding with challenges and emerging opportunities to develop sustainable contaminated site remediation technologies. KEY POINTS: •Pollutants can exert toxicity on cellular membrane, enzyme and gene transcription. •Bacteria can patch promiscuous enzymes into novel pathway to degrade pollutants. •The evolution trajectory is constrained by epistasis from mutations on enzyme and cellular level.

In vivo detection of endogenous toxic phenolic compounds of intestine

Phenol and p-cresol are two common toxic small molecules related to various diseases. Existing reports confirmed that high L-tyrosine in the daily diet can increase the concentration of phenolic compounds in blood and urine. L-tyrosine is a common component of protein-rich foods. Some anaerobic bacteria in the gut can convert non-toxic l-tyrosine into these two toxic phenolic compounds, phenol and p-cresol. Existing methods have been constructed for measuring the concentration of phenolic compound in feces. However, there is still a lack of direct visual evidence to measure the phenolic compounds in the intestine. In this study, we aimed to construct a whole-cell biosensor for phenolic compounds detection based on the dmpR, the regulator from the phenol metabolism cluster. The commensal bacterium Citrobacter amalonaticus PS01 was selected and used as the chassis. Compared with the biosensor based on ECN1917, the biosensor PS01[dmpR] could better implant into the mouse gut through gavage and showed a higher sensitive to phenolic compound. And the concentration of phenolic compounds in the intestines could be observed with the help of in vivo imaging system using PS01[dmpR]. This paper demonstrated endogenous phenol synthesis in the gut and the strategy of using commensal bacteria to construct whole-cell biosensors for detecting small molecule compounds in the intestines.

Microbial degradation of virgin polyethylene by bacteria isolated from a landfill site

Abstract

In this study we evaluate the extent of degradation of high-density polyethylene by bacterial isolates obtained from landfill. The microorganisms are isolated from plastic wastes deposited in the landfill for 2–3 years and 17 years. Experiments are conducted under laboratory conditions to degrade virgin high-density polyethylene used in the manufacture of packaging materials. Gravimetric and GC–MS analyses are performed to describe polyethylene decomposition. Of all the bacterial isolates tested, the degradation of polyethylene by Bacillus cereus is the highest, 1.78%, based on weight loss. On the other hand, degradation by Pseudomonas tuomurensis is 0.3%. Degradation products are detected, confirming the progressive degradation of the plastic. The hydrocarbons with single and double bonds are observed most frequently. Our study provides insight into the microbial biodegradation of polyethylene in the environment and contributes to the understanding of the biodegradation processes that may occur in landfills and their progress.

Article Highlights

Characterization of petroleum degrading bacteria and its optimization conditions on effective utilization of petroleum hydrocarbons

Hydrocarbon contamination is continuing to be a serious environmental problem because of their toxicity. Hydrocarbon components have been known to be carcinogens and neurotoxic organic pollutants. The physical and chemical methods of petroleum removal have become ineffective and also are very costly. Therefore, bioremediation is considered the promising technology for the treatment of these contaminated sites since it is cost-effective and will lead to complete mineralization.The current study also concentrates on bioremediation of petroleum products by bacterium isolated from petroleum hydrocarbon contaminated soil. The current work shows that bacterial strains obtained from a petroleum hydrocarbon contaminated environment may degrade petroleum compounds. Two strains Bacillus licheniformis ARMP2 and Pseudomonas aeruginosa ARMP8 were identified as petroleum-degrading bacteria of the isolated bacterial colonies. The best growth conditions for the ARMP2 strain were determined to be pH 9, temperature 29 °C with sodium nitrate as its nitrogen source, whereas for the ARMP8 strain the optimal growth was found at pH 7, temperature 39 °C, and ammonium chloride as the nitrogen source. Both strains were shown to be effective at degrading petroleum chemicals confirmed by GCMS. Overall petroleum product degradation efficiency of the strains ARMP2 and ARMP8 was about 88 % and 73 % respectively in 48 h.The strains Bacillus licheniformis ARMP2 and Pseudomonas aeruginosa ARMP8 were shown to be effective at degrading petroleum compounds in the current study. Even greater results might be obtained if the organisms were utilised in consortia or the degradation time period was extended.

Biodegradation of 3-Chloronitrobenzene and 3-Bromonitrobenzene by Diaphorobacter sp. Strain JS3051

Halonitrobenzenes are toxic chemical intermediates used widely for industrial synthesis of dyes and pesticides. Bacteria able to degrade 2- and 4-chloronitrobenzene have been isolated and characterized; in contrast, no natural isolate has been reported to degrade meta-halonitrobenzenes. In this study, Diaphorobacter sp. strain JS3051, previously reported to degrade 2,3-dichloronitrobenzene, grew readily on 3-chloronitrobenzene and 3-bromonitrobenzene, but not on 3-fluoronitrobenzene, as sole sources of carbon, nitrogen, and energy. A Rieske nonheme iron dioxygenase (DcbAaAbAcAd) catalyzed the dihydroxylation of 3-chloronitrobenzene and 3-bromonitrobenzene, resulting in the regiospecific production of ring-cleavage intermediates 4-chlorocatechol and 4-bromocatechol. The lower activity and relaxed regiospecificity of DcbAaAbAcAd toward 3-fluoronitrobenzene is likely due to the higher electronegativity of the fluorine atom, which hinders it from interacting with E204 residue at the active site. DccA, a chlorocatechol 1,2-dioxygenase, converts 4-chlorocatechol and 4-bromocatechol into the corresponding halomuconic acids with high catalytic efficiency, but with much lower K_cat/K_m values for fluorocatechol analogues. The results indicate that the Dcb and Dcc enzymes of Diaphorobacter sp. strain JS3051 can catalyze the degradation of 3-chloro- and 3-bromonitrobenzene in addition to 2,3-dichloronitrobenzene. The ability to utilize multiple substrates would provide a strong selective advantage in a habitat contaminated with mixtures of chloronitrobenzenes. IMPORTANCE Halonitroaromatic compounds are persistent environmental contaminants, and some of them have been demonstrated to be degraded by bacteria. Natural isolates that degrade 3-chloronitrobenzene and 3-bromonitrobenzene have not been reported. In this study, we report that Diaphorobacter sp. strain JS3051 can degrade 2,3-dichloronitrobenzene, 3-chloronitrobenzene, and 3-bromonitrobenzene using the same catabolic pathway, whereas it is unable to grow on 3-fluoronitrobenzene. Based on biochemical analyses, it can be concluded that the initial dioxygenase and lower pathway enzymes are inefficient for 3-fluoronitrobenzene and even misroute the intermediates, which is likely responsible for the failure to grow. These results advance our understanding of how the broad substrate specificities of catabolic enzymes allow bacteria to adapt to habitats with mixtures of xenobiotic contaminants.

A Nag-like dioxygenase initiates 3,4-dichloronitrobenzene degradation via 4,5-dichlorocatechol in Diaphorobacter sp. strain JS3050

The chemical synthesis intermediate 3,4-dichloronitrobenzene (3,4-DCNB) is an environmental pollutant. Diaphorobacter sp. strain JS3050 utilizes 3,4-DCNB as a sole source of carbon, nitrogen and energy. However, the molecular determinants of its catabolism are poorly understood. Here, the complete genome of strain JS3050 was sequenced and key genes were expressed heterologously to establish the details of its degradation pathway. A chromosome-encoded three-component nitroarene dioxygenase (DcnAaAbAcAd) converted 3,4-DCNB stoichiometrically to 4,5-dichlorocatechol, which was transformed to 3,4-dichloromuconate by a plasmid-borne ring-cleavage chlorocatechol 1,2-dioxygenase (DcnC). On the chromosome, there are also genes encoding enzymes (DcnDEF) responsible for the subsequent transformation of 3,4-dichloromuconate to β-ketoadipic acid. The fact that the genes responsible for the catabolic pathway are separately located on plasmid and chromosome indicates that recent assembly and ongoing evolution of the genes encoding the pathway is likely. The regiospecificity of 4,5-dichlorocatechol formation from 3,4-DCNB by DcnAaAbAcAd represents a sophisticated evolution of the nitroarene dioxygenase that avoids misrouting of toxic intermediates. The findings enhance the understanding of microbial catabolic diversity during adaptive evolution in response to xenobiotics released into the environment.

Heterologous expression of azoreductase-encoding gene azrS of Bacillus sp. MR-1/2 for enhanced azo dye decolorization and wastewater treatment

In Pakistan, 55% of textile exports are contributed by textile-units of Faisalabad. The effluents of these textile units, being discharged without any treatment, contain the contamination of a huge amount of synthetic azo dyes. The objective of the current research was to evaluate the contribution of an azoreductase-encoding gene (azrS) from a pre-characterized azo dye decolorizing bacterial strain Bacillus sp. MR-1/2 in a high copy number host system (pUC19-T7-Top-T) of Escherichia coli strain DH5α followed by in-silico prediction of azoreductase enzyme (AzrS) function. The recombinant cells that contained azrS had a significantly higher rate of color removal in congo red and reactive black-5 dyes when compared to wild-type MR-1/2 and E. coli DH5α after 72 h of incubation. Moreover, we were able to show that the recombinant strain significantly reduced the values of all tested parameters (pH, EC, turbidity, TSS, and COD) in actual wastewater. In support of our results, it was also predicted through bioinformatics analysis that the deduced azoreductase protein of strain MR-1/2 is linked with the dye decolorization ability of the strain through NAD(P)H-ubiquinone: oxidoreductase activity. Furthermore, we also found that the deduced protein resembled closely related proteins of protein databank in many features, yet some unique features were predicted in the enzyme activity of strain MR-1/2. It was concluded that the recombinant strain could be examined in pilot-scale experiments for textile wastewater treatment.

Microbial degradation kinetics and molecular mechanism of 2,6-dichloro-4-nitrophenol by a Cupriavidus strain

2,6-Dichloro-4-nitrophenol (2,6-DCNP) is an emerging chlorinated nitroaromatic pollutant, and its fate in the environment is an important question. However, microorganisms with the ability to utilize 2,6-DCNP have not been reported. In this study, Cupriavidus sp. CNP-8 having been previously reported to degrade various halogenated nitrophenols, was verified to be also capable of degrading 2,6-DCNP. Biodegradation kinetics assay showed that it degraded 2,6-DCNP with the specific growth rate of 0.124 h^-1, half saturation constant of 0.038 mM and inhibition constant of 0.42 mM. Real-time quantitative PCR analyses indicated that the hnp gene cluster was involved in the catabolism of 2,6-DCNP. The hnpA and hnpB gene products were purified to homogeneity by Ni-NTA chromatography. Enzymatic assays showed that HnpAB, a FAD-dependent two-component monooxygenase, converted 2,6-DCNP to 6-chlorohydroxyquinol with a K_m of 3.9 ± 1.4 μM and a k_cat/K_m of 0.12 ± 0.04 μΜ^-1 min^-1. As the oxygenase component encoding gene, hnpA is necessary for CNP-8 to grow on 2,6-DCNP by gene knockout and complementation. The phylogenetic analysis showed that the hnp cluster originated from the cluster involved in the catabolism of chlorophenols rather than nitrophenols. To our knowledge, CNP-8 is the first bacterium with the ability to utilize 2,6-DCNP, and this study fills a gap in the microbial degradation mechanism of this pollutant at the molecular, biochemical and genetic levels. Moreover, strain CNP-8 could degrade three chlorinated nitrophenols rapidly from the synthetic wastewater, indicating its potential in the bioremediation of chlorinated nitrophenols polluted environments.

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.