Biodegradation of carbazole by Ralstonia sp. RJGII.123 isolated from a hydrocarbon contaminated soil

Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole

Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ-degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi-omic approach combined with DNA-stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial interactions governing consortium functioning. SIP and amplicon sequencing analysis of the heavy and light DNA fraction of cultures grown on ¹³ C-labelled versus ¹² C-TBZ showed that 66% of the ¹³ C-labelled TBZ was assimilated by Sphingomonas. Metagenomic analysis retrieved 18 metagenome-assembled genomes with the dominant belonging to Sphingomonas, Sinobacteriaceae, Bradyrhizobium, Filimonas and Hydrogenophaga. Meta-transcriptomics/-proteomics and non-target mass spectrometry suggested TBZ transformation by Sphingomonas via initial cleavage by a carbazole dioxygenase (car) to thiazole-4-carboxamidine (terminal compound) and catechol or a cleaved benzyl ring derivative, further transformed through an ortho-cleavage (cat) pathway. Microbial co-occurrence and gene expression networks suggested strong interactions between Sphingomonas and a Hydrogenophaga. The latter activated its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway to satisfy its B12 auxotrophy. Our findings indicate microbial interactions aligning with the 'black queen hypothesis' where Sphingomonas (detoxifier, B12 recipient) and Hydrogenophaga (B12 producer, enjoying detoxification) act as both helpers and beneficiaries.

Environmental contamination by heterocyclic Polynuclear aromatic hydrocarbons and their microbial degradation

Heterocyclic polynuclear aromatic hydrocarbons (PAHs) have been detected in all environmental matrices at few ppb to several ppm concentrations and they are characterized by high polarity. Some heterocyclic PAHs are mutagenic and carcinogenic to humans and various organisms. Despite being potent environmental pollutants, these compounds have received less attention. This paper focuses on the sources and occurrence of these compounds and their microbial degradation using diverse species of bacteria, fungi, and algae. Complete removal of 1.8 to 2614 mg/L of nitrogen heterocyclic PAH (PANH), 0.27 to 184 mg/L of sulfur heterocyclic PAH (PASH), and 0.6 to 120 mg/L of oxygen heterocyclic PAH (PAOH) compounds by various microbial species was observed between 3 h and 18 days, 8 h to 6 days, and 4 h to 250 h, respectively under aerobic condition. Strategies for enhancing the removal of heterocyclic PAHs from aquatic systems are also discussed along with the challenges.

Modeling growth kinetics and carbazole degradation kinetics of a Pseudomonas aeruginosa strain isolated from refinery sludge and uptake considerations during growth on carbazole

Although bacterial degradation of polynuclear aromatic hydrocarbons (PAH) have been studied using various pure cultures, only a few studies have explored the degradation kinetics and uptake mechanism of nitrogen heterocyclic PAHs (PANH) with three or more rings. This work explored growth kinetics of a PAH degrading bacterial strain, Pseudomonas aeruginosa RS1 on carbazole (CBZ) and concomitant degradation kinetics of CBZ over the concentration range 25 to 500 mg/L. For CBZ acclimatized strain, the specific growth rate (μ) and specific CBZ uptake rate (q) varied from 0.96 ± 0.05 to 2 ± 0.15 day^-1 and from 0.002 ± 0.001 to 0.02 ± 0.01 mg CBZ mg VSS^-1 day^-1, respectively. The Moser and Monod model provided best fits to the μ vs CBZ concentration and q vs CBZ concentration profiles, respectively. Biosurfactant activity did not play a role in CBZ uptake. However, elevation in cell surface hydrophobicity as revealed through the water contact angle values on bacterial cell mat indicated the possible role of direct interfacial uptake in facilitating CBZ uptake over and above uptake after dissolution. Elevated catechol 1,2-dioxygenase enzyme activity was observed during CBZ degradation. Interestingly, the specific activity of this enzyme was higher in the culture supernatant than in the cell extract. However, during CBZ degradation, accumulation of some toxic metabolites in the aqueous phase was revealed through increase in TOC of the aqueous phase and Kirby-Bauer disc diffusion study performed using a E. coli strain. Both aqueous phase TOC and toxicity decreased beyond the log growth phase indicating further utilization of the degradation intermediates.

Microbial Enrichment Culture Responsible for the Complete Oxidative Biodegradation of 3-Amino-1,2,4-triazol-5-one (ATO), the Reduced Daughter Product of the Insensitive Munitions Compound 3-Nitro-1,2,4-triazol-5-one (NTO)

3-Nitro-1,2,4-triazol-5-one (NTO) is one of the main ingredients of many insensitive munitions, which are being used as replacements for conventional explosives. As its use becomes widespread, more research is needed to assess its environmental fate. Previous studies have shown that NTO is biologically reduced to 3-amino-1,2,4-triazol-5-one (ATO). However, the final degradation products of ATO are still unknown. We have studied the aerobic degradation of ATO by enrichment cultures derived from the soil. After multiple transfers, ATO degradation was monitored in closed bottles through measurements of inorganic carbon and nitrogen species. The results indicate that the members of the enrichment culture utilize ATO as the sole source of carbon and nitrogen. As ATO was mineralized to CO₂, N₂, and NH₄⁺, microbial growth was observed in the culture. Co-substrates addition did not increase the ATO degradation rate. Quantitative polymerase chain reaction analysis revealed that the organisms that enriched using ATO as carbon and nitrogen source were Terrimonas spp., Ramlibacter-related spp., Mesorhizobium spp., Hydrogenophaga spp., Ralstonia spp., Pseudomonas spp., Ectothiorhodospiraceae, and Sphingopyxis. This is the first study to report the complete mineralization of ATO by soil microorganisms, expanding our understanding of natural attenuation and bioremediation of the explosive NTO.

Properties, environmental fate and biodegradation of carbazole

The last two decades had witnessed extensive investigation on bacterial degradation of carbazole, an N-heterocyclic aromatic hydrocarbon. Specifically, previous studies have reported the primary importance of angular dioxygenation, a novel type of oxygenation reaction, which facilitates mineralization of carbazole to intermediates of the TCA cycle. Proteobacteria and Actinobacteria are the predominant bacterial phyla implicated in this novel mode of dioxygenation, while anthranilic acid and catechol are the signature metabolites. Several studies have elucidated the degradative genes involved, the diversity of the car gene clusters and the unique organization of the car gene clusters in marine carbazole degraders. However, there is paucity of information regarding the environmental fate as well as industrial and medical importance of carbazole and its derivatives. In this review, attempt is made to harness this information to present a comprehensive outlook that not only focuses on carbazole biodegradation pathways, but also on its environmental fate as well as medical and industrial importance of carbazole and its derivatives.

Characterization of a novel cometabolic degradation carbazole pathway by a phenol-cultivated Arthrobacter sp. W1

Arthrobacter sp. W1 was used to characterize the pathways involved in cometabolic degradation of carbazole (CA) with phenol as the primary substrate. To clarify the upper pathway of cometabolic degradation CA, Escherichia coli strain BL21 expressing phenol hydroxylase from strain W1 (PHIND) was investigated to degrade CA. Firstly, CA was initially monohydroxylated at C-2 and C-4 positions to produce 2- and 4-hydroxycarbazole, followed by successively hydroxylated to the corresponding 1,2- and 3,4-dihydroxycarbazole, of which 3,4-dihydroxycarbazole was unequivocally identified for the first time. To characterize the downstream cometabolic degradation CA pathway, purified 3,4-dihydroxycarbazole was used as the substrate for phenol-grown W1, and a series of novel indole derivatives were identified. These results suggested that a novel pathway of CA catabolism was employed by strain W1 via a successive hydroxylation and meta-cleavage pathway. These findings provide new insights into the cometabolic degradation CA process and have potential applications in biotechnology and bioremediation.

Bioremediation of coking wastewater containing carbazole, dibenzofuran and dibenzothiophene by immobilized naphthalene-cultivated Arthrobacter sp. W1 in magnetic gellan gum

In this study, the cometabolic degradation of carbazole (CA), dibenzofuran (DBF), and dibenzothiophene (DBT) by immobilized Arthrobacter sp. W1 cells pregrown with naphthalene was investigated. Four kinds of polymers were evaluated as immobilization supports for strain W1. After comparison with agar, alginate, and κ-carrageenan, gellan gum was selected as the optimal immobilization support. Furthermore, magnetic Fe₃O₄ nanoparticle was selected as most suitable nanoparticle for immobilization and the optimal concentration was 80 mg/L. The relationship between specific degradation rate and the initial concentration of CA, DBF and DBT was described well by Michaelis-Menten kinetics. The recycling experiments demonstrated that the magnetically immobilized cells coupling with activation zeolite showed highly bioremediation activity on the coking wastewater containing high concentration of phenol, naphthalene, CA, DBF and DBT during seven recycles. Toxicity assessment indicated the treatment of the coking wastewater by magnetically immobilized cells with activation zeolite led to less toxicity than untreated wastewater.

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.

Survival of prokaryotes in a polluted waste dump during remediation by alkaline hydrolysis

A combination of culture-dependent and culture-independent techniques was used to characterize bacterial and archaeal communities in a highly polluted waste dump and to assess the effect of remediation by alkaline hydrolysis on these communities. This waste dump (Breakwater 42), located in Denmark, contains approximately 100 different toxic compounds including large amounts of organophosphorous pesticides such as parathions. The alkaline hydrolysis (12 months at pH >12) decimated bacterial and archaeal abundances, as estimated by 16S rRNA gene-based qPCR, from 2.1 × 10(4) and 2.9 × 10(3) gene copies per gram wet soil respectively to below the detection limit of the qPCR assay. Clone libraries constructed from PCR-amplified 16S rRNA gene fragments showed a significant reduction in bacterial diversity as a result of the alkaline hydrolysis, with preferential survival of Betaproteobacteria, which increased in relative abundance from 0 to 48 %. Many of the bacterial clone sequences and the 27 isolates were related to known xenobiotic degraders. An archaeal clone library from a non-hydrolyzed sample showed the presence of three main clusters, two representing methanogens and one representing marine aerobic ammonia oxidizers. Isolation of alkalitolerant bacterial pure cultures from the hydrolyzed soil confirmed that although alkaline hydrolysis severely reduces microbial community diversity and size certain bacteria survive a prolonged alkaline hydrolysis process. Some of the isolates from the hydrolyzed soil were capable of growing at high pH (pH 10.0) in synthetic media indicating that they could become active in in situ biodegradation upon hydrolysis.

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.

Urinary metabonomics study of anti-depressive effect of Chaihu-Shu-Gan-San on an experimental model of depression induced by chronic variable stress in rats

Chaihu-Shu-Gan-San (CSGS), a traditional Chinese medicine (TCM) formula, has been effectively used for the treatment of depression in clinic. However, studies of its anti-depressive mechanism are challenging, accounted for the complex pathophysiology of depression, and complexity of CSGS with multiple constituents acting on different metabolic pathways. The variations of endogenous metabolites in rat model of depression after administration of CSGS may offer deeper insights into the anti-depressive effect and mechanism of CSGS. In this study, metabonomics based on ultra performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) was used to profile the metabolic fingerprints of urine obtained from chronic variable stress (CVS)-induced depression model in rats with and without CSGS treatment. Through partial least squares-discriminate analysis, it was observed that metabolic perturbations induced by chronic variable stress were restored in a time-dependent pattern after treatment with CSGS. Metabolites with significant changes induced by CVS, including 3-O-methyldopa (1), pantothenic acid (2), kynurenic acid (3), xanthurenic acid (4), 2,8-dihydroxyquinoline glucuronide (5), 5-hydroxy-6-methoxyindole glucurnoide (8), l-phenylalanyl-l-hydroxyproline (9), indole-3-carboxylic acid (10), proline (11), and the unidentified metabolites (6, 2.11min_m/z 217.0940; 7, 2.11min_m/z 144.0799), were characterized as potential biomarkers involved in the pathogenesis of depression. The derivations of all those biomarkers can be regulated by CSGS treatment except indole-3-carboxylic acid (10), which suggested that the therapeutic effect of CSGS on depression may involve in regulating the dysfunctions of energy metabolism, tryptophan metabolism, bone loss and liver detoxification. This study indicated that the rapid and noninvasive urinary metabonomics approach may be a powerful tool to study the efficacy and mechanism of complex TCM prescriptions.

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.

Degradation of carbazole and its derivatives by a Pseudomonas sp

Carbazole, carbazoles with monomethyl or dimethyls substituted on different positions (C(1)-carbazoles or C(2)-carbazoles), and benzocarbazoles, as toxic and mutagenic components of petroleum and creosote contamination, were biodegradable by an isolated bacterial strain Pseudomonas sp. XLDN4-9. C(1)-carbazoles were degraded in preference to carbazole and C(2)-carbazoles. The biodegradation of C(1)-carbazoles or C(2)-carbazoles was influenced by the positions of methyl substitutions. Among C(1)-carbazole isomers, 1-methyl carbazole was the most susceptible. C(2)-carbazole isomers with substitutions on the same benzo-nucleus were more susceptible at a concentration of less than 3.4 microg g(-1) petroleum, especially when harboring one substitution on position 1. In particular, 1,5-dimethyl carbazole was the most recalcitrant dimethyl isomer.

Microbial degradation of sulfur, nitrogen and oxygen heterocycles

Sulfur (S), nitrogen (N) and oxygen (O) heterocycles are among the most potent environmental pollutants. Microbial degradation of these pollutants is attracting more and more attention because such bioprocesses are environmentally friendly. The biotechnological potential of these processes is being investigated, for example, to achieve better sulfur removal by immobilized biocatalysts with magnetite nanoparticles or by solvent-tolerant bacteria, and to obtain valuable intermediates from these heterocycles. Other recent advances have demonstrated the mechanisms of angular dioxygenation of nitrogen heterocycles by microbes. However, these technologies are not yet available for large-scale applications so future research must investigate proper modifications for industrial applications of these processes. This review focuses on recent progress in understanding how microbes degrade S, N and O heterocycles.

Selective biodegradation of S and N heterocycles by a recombinant Rhodococcus erythropolis strain containing carbazole dioxygenase

The carbazole dioxygenase genes were introduced into a dibenzothiophene degrader. The recombinant Rhodococcus erythropolis SN8 was capable of efficiently degrading dibenzothiophene and carbazole simultaneously. SN8 could also degrade various alkylated derivatives of carbazole and dibenzothiophene in FS4800 crude oil by just a one-step bioprocess.

Degradation of estradiol and ethinyl estradiol by activated sludge and by a defined mixed culture

The aerobic degradation of the natural hormone 17-beta-estradiol (E2) and the synthetic hormone 17-alpha-ethinyl estradiol (EE2) was investigated in batch experiments with activated sludge from a conventional and a membrane sewage treatment plant. E2 was converted to estrone (E1), the well known metabolite, and further completely transformed within 3 days. The turnover rates of E2 did not differ greatly between conventional and membrane activated sludge. EE2 was persistent in both sludges. By several transfers into fresh E2-medium an enrichment culture could be selected that used E2 as growth substrate. Further enrichment and isolation led to a defined mixed culture consisting of two strains, which were identified by a polyphasic approach as Achromobacter xylosoxidans and Ralstonia sp., respectively. The culture used E2 and E1 as growth substrates and transformed estriol (E3) and 16-alpha-hydroxyestrone but not the xenoestrogens bisphenol A, alpha-zearalenol, mestranol or EE2. The turnover rates of E2 were 0.025-0.1 microg h(-1) cfu(-1) and did not depend on the steroid concentration.

Isolation and characterization of Sphingomonas sp. GTIN11 capable of carbazole metabolism in petroleum

A bacterial culture was isolated from a manufactured gas plant (MGP) soil based on its ability to metabolize the nitrogen-containing heterocycle carbazole. The culture was identified as a Sphingomonas sp. and was given the designation GTIN11. A cloned 4.2kb DNA fragment was confirmed to contain genes responsible for carbazole degradation. DNA sequence analysis revealed that the fragment contained five open reading frames (ORFs) with the deduced amino acid sequence showing homology to; carbazole terminal dioxygenase (ORF1), 2,3-dihydroxybiphenyl dioxygenase subunits (ORF2 and ORF3), meta-cleavage compound hydrolases (ORF4), and ferrodoxin component of bacterial multicomponent dioxygenases (ORF5). The percent similarity was 61% of these proteins or less to known proteins. The specific activity of Sphingomonas sp. GTIN11 for the degradation of carbazole at 37 degrees C was determined to be 8.0 micromol carbazole degraded/min/g dry cell. This strain is unique in expressing the carbazole degradation trait constitutively. Resting cells of Sphingomonas sp. GTIN11 removed 95% of carbazole and 50% of C1-carbazoles from petroleum in a 16-h treatment time.

Sphingomonas sp. strain KA1, carrying a carbazole dioxygenase gene homologue, degrades chlorinated dibenzo-p-dioxins in soil

Hybridization analysis showed that a newly isolated carbazole (CAR)-degrading bacterium Sphingomonas sp. strain KA1 did not possess the gene encoding the terminal oxygenase component (carAa) of CAR 1,9a-dioxygenase at high homology (more than 90% identity) to that of another CAR-degrader, Pseudomonas resinovorans strain CA10. However, PCR experiments using the primers for amplifying the internal fragment of the carAa gene (810 bp for strain CA10) showed that a PCR product of unexpected size (1100 bp) was amplified. Sequence analysis revealed that this DNA region contained the portion of two possible ORFs, which showed moderate homology to CarAa and CarBa from strain CA10 (61% and 40% identities at the amino acid level, respectively). Inoculation of strain KA1 into dioxin-contaminated model soil resulted in 96% and 70% degradation of 2-mono- and 2,3-dichlorinated dibenzo-p-dioxin, respectively, after 7-day incubation.