Degradation of carbazole and its derivatives by a Pseudomonas sp

Different Roles of Dioxin-Catabolic Plasmids in Growth, Biofilm Formation, and Metabolism of Rhodococcus sp. Strain p52

Microorganisms harbor catabolic plasmids to tackle refractory organic pollutants, which is crucial for bioremediation and ecosystem health. Understanding the impacts of plasmids on hosts provides insights into the behavior and adaptation of degrading bacteria in the environment. Here, we examined alterations in the physiological properties and gene expression profiles of Rhodococcus sp. strain p52 after losing two conjugative dioxin-catabolic megaplasmids (pDF01 and pDF02). The growth of strain p52 accelerated after pDF01 loss, while it decelerated after pDF02 loss. During dibenzofuran degradation, the expression levels of dibenzofuran catabolic genes on pDF01 were higher compared to those on pDF02; accordingly, pDF01 loss markedly slowed dibenzofuran degradation. It was suggested that pDF01 is more beneficial to strain p52 under dibenzofuran exposure. Moreover, plasmid loss decreased biofilm formation, especially after pDF02 loss. Transcriptome profiling revealed different pathways enriched in upregulated and downregulated genes after pDF01 and pDF02 loss, indicating different adaptation mechanisms. Based on the transcriptional activity variation, pDF01 played roles in transcription and anabolic processes, while pDF02 profoundly influenced energy production and cellular defense. This study enhances our knowledge of the impacts of degradative plasmids on native hosts and the adaptation mechanisms of hosts, contributing to the application of plasmid-mediated bioremediation in contaminated environments.

Biotreatment of oily sludge by a bacterial consortium: Effect of bioprocess conditions on biodegradation efficiency and bacterial community structure

We studied the biodegradation of oily sludge generated by a petroleum plant in Bahrain by a bacterial consortium (termed as AK6) under different bioprocess conditions. Biodegradation of petroleum hydrocarbons in oily sludge (C₁₁-C₂₉) increased from 24% after two days to 99% after 9 days of incubation in cultures containing 5% (w/v) of oily sludge at 40°C. When the nitrogen source was excluded from the batch cultures, hydrocarbon biodegradation dropped to 45% within 7 days. The hydrocarbon biodegradation decreased also by increasing the salinity to 3% and the temperature above 40°C. AK6 tolerated up to 50% (w/v) oily sludge and degraded 60% of the dichloromethane-extractable oil fraction. Illumina-MiSeq analyses revealed that the AK6 consortium was mainly composed of Gammaproteobacteria (ca. 98% of total sequences), with most sequences belonging to Klebsiella (77.6% of total sequences), Enterobacter (16.7%) and Salmonella (5%). Prominent shifts in the bacterial composition of the consortium were observed when the temperature and initial sludge concentration increased, and the nitrogen source was excluded, favoring sequences belonging to Pseudomonas and Stenotrophomonas. The AK6 consortium is endowed with a strong oily sludge tolerance and biodegradation capability under different bioprocess conditions, where Pseudomonas spp. appear to be crucial for hydrocarbon biodegradation.

Unveiling degradation mechanism of PAHs by a Sphingobium strain from a microbial consortium

Polycyclic aromatic hydrocarbons (PAHs) are a class of persistent pollutants with adverse biological effects and pose a serious threat to ecological environments and human health. The previously isolated phenanthrene-degrading bacterial consortium (PDMC) consists of the genera Sphingobium and Pseudomonas and can degrade a wide range of PAHs. To identify the degradation mechanism of PAHs in the consortium PDMC, metagenomic binning was conducted and a Sphingomonadales assembly genome with 100% completeness was obtained. Additionally, Sphingobium sp. SHPJ-2, an efficient degrader of PAHs, was successfully isolated from the consortium PDMC. Strain SHPJ-2 has powerful degrading abilities and various degradation pathways of high-molecular-weight PAHs, including fluoranthene, pyrene, benzo[a]anthracene, and chrysene. Two ring-hydroxylating dioxygenases, five cytochrome P450s, and a pair of electron transfer chains associated with PAH degradation in strain SHPJ-2, which share 83.0%-99.0% similarity with their corresponding homologous proteins, were identified by a combination of Sphingomonadales assembly genome annotation, reverse-transcription quantitative polymerase chain reaction and heterologous expression. Furthermore, when coexpressed in Escherichia coli BL21(DE3) with the appropriate electron transfer chain, PhnA1B1 could effectively degrade chrysene and benzo[a]anthracene, while PhnA2B2 degrade fluoranthene. Altogether, these results provide a comprehensive assessment of strain SHPJ-2 and contribute to a better understanding of the molecular mechanism responsible for the PAH degradation.

Isolation and identification of 1,3,6,8-tetrabromocarbazole - degrading bacteria

Halogenated carbazoles are a new class of persistent organic pollutants with dioxin-like toxicity, and this study focused on the microbial degradation of 1,3,6,8-tetrabromocarbazole. In this study, a novel 1,3,6,8-tetrabromocarbazole (1,3,6,8-TBCZ) degrading strain TB-1 was isolated from contaminated soil and identified as Achromobacter sp. based on its 16S rRNA gene sequence analysis, morphological, physiological, and biochemical characteristics. The soil sample was collected from a pharmaceutical factory in Suzhou, China. The strain was able to effectively degrade 1 mg L^-1 1,3,6,8-TBCZ in 7 d at pH 7.0 and 30 °C with 80% degradation rate. During the process, the intermediate metabolites were identified as Tribromocarbazole, dibromocarbazole and bromocarbazole via gas chromatography mass spectrometry (GC-MS). The results indicated that strain TB-1 may contribute to the bioremediation of polyhalogenated carbazoles (PHCs) in contaminated environment.

Microbial degradation of multiple PAHs by a microbial consortium and its application on contaminated wastewater

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in the environment and pose a serious threat to human health. Due to their unfavorable biological effects and persistent properties, it is extremely urgent to effectively degrade PAHs that are present in the environment, especially in wastewater. In this study, we obtained an efficient bacterial consortium (PDMC), consisting of the genera Sphingobium (58.57-72.40%) and Pseudomonas (25.93-39.75%), which is able to efficiently utilize phenanthrene or dibenzothiophene as the sole carbon source. The phenanthrene-cultivated consortium could also degrade naphthalene, acenaphthene, fluorene, anthracene, fluoranthene, benzo[a]anthracene, dibenzofuran, carbazole and indole, respectively. Furthermore, we identified the multiple key intermediates of aforementioned 11 substrates and discussed proposed pathways involved. Notably, a novel intermediate 1,2-dihydroxy-4a,9a-dihydroanthracene-9,10-dione of anthracene degradation was detected, which is extremely rare compared to previous reports. The PDMC consortium removed 100% of PAHs within 5 days in the small-scale wastewater bioremediation added with PAHs mixture, with a sludge settling velocity of 5% after 10 days of incubation. Experiments on the stability reveal the PDMC consortium always has excellent degrading ability for totaling 24 days. Combined with the microbial diversity analysis, the results suggest the PDMC consortium is a promising candidate to facilitate the bioremediation of PAHs-contaminated environments.

Genetic mapping of highly versatile and solvent-tolerant Pseudomonas putida B6-2 (ATCC BAA-2545) as a 'superstar' for mineralization of PAHs and dioxin-like compounds

Polycyclic aromatic hydrocarbons (PAHs) and dioxin-like compounds, including sulfur, nitrogen and oxygen heterocycles, are widespread and toxic environmental pollutants. A wide variety of microorganisms capable of growing with aromatic polycyclic compounds are essential for bioremediation of the contaminated sites and the Earth's carbon cycle. Here, cells of Pseudomonas putida B6-2 (ATCC BAA-2545) grown in the presence of biphenyl (BP) are able to simultaneously degrade PAHs and their derivatives, even when they are present as mixtures, and tolerate high concentrations of extremely toxic solvents. Genetic analysis of the 6.37 Mb genome of strain B6-2 reveals coexistence of gene clusters responsible for central catabolic systems of aromatic compounds and for solvent tolerance. We used functional transcriptomics and proteomics to identify the candidate genes associated with catabolism of BP and a mixture of BP, dibenzofuran, dibenzothiophene and carbazole. Moreover, we observed dynamic changes in transcriptional levels with BP, including in metabolic pathways of aromatic compounds, chemotaxis, efflux pumps and transporters potentially involved in adaptation to PAHs. This study on the highly versatile activities of strain B6-2 suggests it to be a potentially useful model for bioremediation of polluted sites and for investigation of biochemical, genetic and evolutionary aspects of Pseudomonas.

Degradation of recalcitrant aliphatic and aromatic hydrocarbons by a dioxin-degrader Rhodococcus sp. strain p52

This study investigates the ability of Rhodococcus sp. strain p52, a dioxin degrader, to biodegrade petroleum hydrocarbons. Strain p52 can use linear alkanes (tetradecane, tetracosane, and dotriacontane), branched alkane (pristane), and aromatic hydrocarbons (naphthalene and phenanthrene) as sole carbon and energy sources. Specifically, the strain removes 85.7 % of tetradecane within 48 h at a degradation rate of 3.8 mg h(-1) g(-1) dry cells, and 79.4 % of tetracosane, 66.4 % of dotriacontane, and 63.9 % of pristane within 9-11 days at degradation rates of 20.5, 14.7, and 20.3 mg day(-1) g(-1) dry cells, respectively. Moreover, strain p52 consumes 100 % naphthalene and 55.3 % phenanthrene within 9-11 days at respective degradation rates of 16 and 12.9 mg day(-1) g(-1) dry cells. Metabolites of the petroleum hydrocarbons by strain p52 were analyzed. Genes encoding alkane-hydroxylating enzymes, including cytochrome P450 (CYP450) enzyme (CYP185) and two alkane-1-monooxygenases, were amplified by polymerase chain reaction. The transcriptional activities of these genes in the presence of petroleum hydrocarbons were detected by reverse transcription-polymerase chain reaction. The results revealed potential of strain p52 to degrade petroleum hydrocarbons.

Carbazole angular dioxygenation and mineralization by bacteria isolated from hydrocarbon-contaminated tropical African soil

Four bacterial strains isolated from hydrocarbon-contaminated soils in Lagos, Nigeria, displayed extensive degradation abilities on carbazole, an N-heterocyclic aromatic hydrocarbon. Physicochemical analyses of the sampling sites (ACPP, MWO, NESU) indicate gross pollution of the soils with a high hydrocarbon content (157,067.9 mg/kg) and presence of heavy metals. Phylogenetic analysis of the four strains indicated that they were identified as Achromobacter sp. strain SL1, Pseudomonas sp. strain SL4, Microbacterium esteraromaticum strain SL6, and Stenotrophomonas maltophilia strain BA. The rates of degradation of carbazole by the four isolates during 30 days of incubation were 0.057, 0.062, 0.036, and 0.050 mg L(-1) h(-1) for strains SL1, SL4, SL6, and BA. Gas chromatographic (GC) analyses of residual carbazole after 30 days of incubation revealed that 81.3, 85, 64.4, and 76 % of 50 mg l(-1) carbazole were degraded by strains SL1, SL4, SL6, and BA, respectively. GC-mass spectrometry and high-performance liquid chromatographic analyses of the extracts from the growing and resting cells of strains SL1, SL4, and SL6 cultured on carbazole showed detection of anthranilic acid and catechol while these metabolites were not detected in strain BA under the same conditions. This study has established for the first time carbazole angular dioxygenation and mineralization by isolates from African environment.

Genome sequences of Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R, two efficient carbazole-degrading strains

Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R are two efficient carbazole-degrading pseudomonad strains. Here we present 4.63- and 4.70-Mb assemblies of their genomes. Their annotated key genes for carbazole catabolism are similar, which may provide further insights into the molecular mechanism of carbazole degradation in Pseudomonas.

Isolation and characterization of Pseudomonas sp. STM 997 from soil sample having potentiality to degrade 3,6-dimethyl-1-keto-1,2,3,4-tetrahydrocarbazole: a novel approach

A pure colony of a bacterium from contaminated soil was isolated by exploiting 3,6-dimethyl-1-keto-1,2,3,4-tetrahydrocarbazole, a novel carbazole derivative, having indole moiety as well as 3-methyl functionality both in aromatic and hydro-aromatic moiety, as a sole source of carbon and energy. Taxonomical studies, biochemical analysis, and 16S rDNA sequence analysis indicated that the isolated strain has close similarity with Pseudomonas sp. Thin-layer chromatography followed by HPLC and mass spectroscopic study indicates that the isolated Pseudomonas sp. STM 997 degrades 3,6-dimethyl-1-keto-1,2,3,4-tetrahydrocarbazole, and this strain may be useful in the bioremediation of environments contaminated by the compounds containing carbazole moiety with methyl substituents at various reactive sites. This study also provides an evidence in favor of the suggested biodegradation of 3-methylcarbazole to carbazole in plants.

Combined ultrasound/ozone degradation of carbazole in APG1214 surfactant solution

We examined the effects of power and treatment time on the ultrasonically enhanced ozonation of carbazole dissolved in APG(1214) surfactant solutions, including an analysis of the mechanism of OH radical formation, the zeta potential of the colloidal suspension, the influence of ultrasound on micellar morphology, and the degradation kinetics for carbazole and APG(1214). A 30min ultrasound treatment at 28kHz and 20W improved the degradation of carbazole by 5-10%, while power levels of 40W and 80W provided improvements only during the first 5min and resulted in reduced degradation after 15min. The OH concentration was inversely proportional to ultrasound power, and directly proportional to the irradiation time. The absolute value of the APG(1214) micelle zeta potential was inversely proportional to power and decreased with increasing irradiation time. The relationships of OH radical concentration in APG(1214) micelles, the zeta potential, and the micellar dynamic radius (R(h)) to ultrasonic power and time are the key factors affecting carbazole degradation in this system.

Substrate-baited nanoparticles: a catch and release strategy for enzyme recognition and harvesting

The isolation of a single type of protein from a complex mixture is vital for the characterization of the function, structure, and interactions of the protein of interest and is typically the most laborious aspect of the protein purification process. In this work, a model system is utilized to show the efficacy of synthesizing a "baited" nanoparticle to capture and recycle enzymes (proteins that catalyze chemical reactions) from crude cell lysate. Enzyme trapping and recycling is illustrated with the carbazole 1,9a-dioxygenase (CARDO) system, an enzyme important in bioremediation and natural product synthesis. The enzymes are baited with azide-modified carbazolyl moieties attached to poly(propargyl acrylate) nanoparticles through a click transformation. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis indicates the single-step procedure to immobilize the enzymes on the particles is capable of significantly concentrating the protein from raw lysate and sequestering all required components of the protein to maintain bioactivity. These results establish a universal model applicable to concentrating and extracting known substrate-protein pairs, but it can be an invaluable tool in recognizing unknown protein-ligand affinities.

The genes coding for the conversion of carbazole to catechol are flanked by IS6100 elements in Sphingomonas sp. strain XLDN2-5

Background

Carbazole is a recalcitrant compound with a dioxin-like structure and possesses mutagenic and toxic activities. Bacteria respond to a xenobiotic by recruiting exogenous genes to establish a pathway to degrade the xenobiotic, which is necessary for their adaptation and survival. Usually, this process is mediated by mobile genetic elements such as plasmids, transposons, and insertion sequences.

Findings

The genes encoding the enzymes responsible for the degradation of carbazole to catechol via anthranilate were cloned, sequenced, and characterized from a carbazole-degrading Sphingomonas sp. strain XLDN2-5. The car gene cluster (carRAaBaBbCAc) and fdr gene were accompanied on both sides by two copies of IS6100 elements, and organized as IS6100::ISSsp1-ORF1-carRAaBaBbCAc-ORF8-IS6100-fdr-IS6100. Carbazole was converted by carbazole 1,9a-dioxygenase (CARDO, CarAaAcFdr), meta-cleavage enzyme (CarBaBb), and hydrolase (CarC) to anthranilate and 2-hydroxypenta-2,4-dienoate. The fdr gene encoded a novel ferredoxin reductase whose absence resulted in lower transformation activity of carbazole by CarAa and CarAc. The ant gene cluster (antRAcAdAbAa) which was involved in the conversion of anthranilate to catechol was also sandwiched between two IS6100 elements as IS6100-antRAcAdAbAa-IS6100. Anthranilate 1,2-dioxygenase (ANTDO) was composed of a reductase (AntAa), a ferredoxin (AntAb), and a two-subunit terminal oxygenase (AntAcAd). Reverse transcription-PCR results suggested that carAaBaBbCAc gene cluster, fdr, and antRAcAdAbAa gene cluster were induced when strain XLDN2-5 was exposed to carbazole. Expression of both CARDO and ANTDO in Escherichia coli required the presence of the natural reductases for full enzymatic activity.

Conclusions/Significance

We predict that IS6100 might play an important role in the establishment of carbazole-degrading pathway, which endows the host to adapt to novel compounds in the environment. The organization of the car and ant genes in strain XLDN2-5 was unique, which showed strong evolutionary trail of gene recruitment mediated by IS6100 and presented a remarkable example of rearrangements and pathway establishments.

New metabolites in dibenzofuran cometabolic degradation by a biphenyl-cultivated Pseudomonas putida strain B6-2

A biphenyl (BP)-utilizing bacterium, designated B6-2, was isolated from soil and identified as Pseudomonas putida. BP-grown B6-2 cells were capable of transforming dibenzofuran (DBF) via a lateral dioxygenation and meta-cleavage pathway. The ring cleavage product 2-hydroxy-4-(3'-oxo-3'H-benzofuran-2'-yliden)but-2-enoic acid (HOBB) was detected as a major metabolite. B6-2 growing cells could also cometabolically degrade DBF using BP as a primary substrate. A recombinant Escherichia coli strain DH10B (pUC118bphABC) expressing BP dioxygenase, BP-dihydrodiol dehydrogenase, and dihydroxybiphenyl dioxygenase was shown to be capable of transforming DBF to HOBB. Using purified HOBB that was produced by the recombinant as the substrate for B6-2, we newly identified a series of benzofuran derivatives as metabolites. The structures of these metabolites indicate that an unreported HOBB degradation pathway is employed by strain B6-2. In this pathway, HOBB is proposed to be transformed to 2-oxo-4-(3'-oxobenzofuran-2'-yl)butanoic acid and 2-hydroxy-4-(3'-oxobenzofuran-2'-yl)butanoic acid (D4) through two sequential double-bond hydrogenation steps. D4 is suggested to undergo reactions including decarboxylation and oxidation to produce 3-(3'-oxobenzofuran-2'-yl)propanoic acid (D6). 3-Hydroxy-3-(3'-oxobenzofuran-2'-yl)propanoic acid (D7) and 2-(3'-oxobenzofuran-2'-yl)acetic acid (D8) would represent metabolites involved in the processes of beta- and alpha-oxidation of D6, respectively. D7 and D8 are suggested to be transformed to their respective products 3-hydroxy-2,3-dihydrobenzofuran-2-carboxylic acid (D10) and 2-(3'-hydroxy-2',3'-dihydrobenzofuran-2'-yl)acetic acid. D10 is proposed to be transformed to salicylic acid (D14) via 2,3-dihydro-2,3-dihydroxybenzofuran, 2-oxo-2-(2'-hydroxyphenyl)acetic acid and 2-hydroxy-2-(2'-hydroxyphenyl)acetic acid. Further experimental results revealed that B6-2 was capable of growing with D14 as the sole carbon source. Because benzofuran derivatives may have biological, pharmacological, and toxic properties, the elucidation of this new pathway should be significant from both biotechnological and environmental views.

Degradation of carbazole by microbial cells immobilized in magnetic gellan gum gel beads

Polycyclic aromatic heterocycles, such as carbazole, are environmental contaminants suspected of posing human health risks. In this study, we investigated the degradation of carbazole by immobilized Sphingomonas sp. strain XLDN2-5 cells. Four kinds of polymers were evaluated as immobilization supports for Sphingomonas sp. strain XLDN2-5. After comparison with agar, alginate, and kappa-carrageenan, gellan gum was selected as the optimal immobilization support. Furthermore, Fe(3)O(4) nanoparticles were prepared by a coprecipitation method, and the average particle size was about 20 nm with 49.65-electromagnetic-unit (emu) g(-1) saturation magnetization. When the mixture of gellan gel and the Fe(3)O(4) nanoparticles served as an immobilization support, the magnetically immobilized cells were prepared by an ionotropic method. The biodegradation experiments were carried out by employing free cells, nonmagnetically immobilized cells, and magnetically immobilized cells in aqueous phase. The results showed that the magnetically immobilized cells presented higher carbazole biodegradation activity than nonmagnetically immobilized cells and free cells. The highest biodegradation activity was obtained when the concentration of Fe(3)O(4) nanoparticles was 9 mg ml(-1) and the saturation magnetization of magnetically immobilized cells was 11.08 emu g(-1). Additionally, the recycling experiments demonstrated that the degradation activity of magnetically immobilized cells increased gradually during the eight recycles. These results support developing efficient biocatalysts using magnetically immobilized cells and provide a promising technique for improving biocatalysts used in the biodegradation of not only carbazole, but also other hazardous organic compounds.

Cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading Sphingomonas sp. strain

A carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. The isolate, designated Sphingomonas sp. strain XLDN2-5, could utilize carbazole (CA) as the sole source of carbon, nitrogen, and energy. Washed cells of strain XLDN2-5 were shown to be capable of degrading dibenzofuran (DBF) and dibenzothiophene (DBT). Examination of metabolites suggested that XLDN2-5 degraded DBF to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently to salicylic acid through the angular dioxygenation pathway. In contrast to DBF, strain XLDN2-5 could transform DBT through the ring cleavage and sulfoxidation pathways. Sphingomonas sp. strain XLDN2-5 could cometabolically degrade DBF and DBT in the growing system using CA as a substrate. After 40 h of incubation, 90% of DBT was transformed, and CA and DBF were completely removed. These results suggested that strain XLDN2-5 might be useful in the bioremediation of environments contaminated by these compounds.