Carbazole biodegradation in gas oil/water biphasic media by a new isolated bacterium Burkholderia sp. strain IMP5GC

Characterization of lipopeptide biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis: The role of biosurfactant in carbazole solubilisation

AIM

Characterization of biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis and proteomic analysis of intracellular proteins of bacterium while growing on glucose and carbazole medium.

METHODS AND RESULTS

The bacterium R. cervicalis was isolated from a soil sample contaminated with crude petroleum oil. PCR amplification ascertained the existence of some hydrocarbon-degrading catabolic genes (alkB and PAH-RHDα, C12O, and C23O) in the bacterial genome. GC-MS and RP-HPLC analyses demonstrated 62% and 60% carbazole degradation, respectively, by R. cervicalis 144 h post-incubation at 37℃ and pH 6.5. Due to the paucity of protein databases, expressions of only 29 and 14 intracellular proteins were explicitly recognized and quantitated by mass spectrometry analysis when R. cervicalis was grown in carbazole and glucose medium, respectively. FTIR, NMR and HR-MS/MS analyses demonstrated the lipopeptide nature of the purified biosurfactant produced by R. cervicalis. The biosurfactant is also presumed to assist in the solubilization of carbazole.

CONCLUSION

The isolated R. cervicalis strain is a potential candidate for the bioremediation of carbazole in petroleum-oil-contaminated sites.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of the promising R. cervicalis strain proficient in carbazole biodegradation.

Post-reclamation microbial diversity and functions in hexachlorocyclohexane (HCH) contaminated soil in relation to spontaneous HCH tolerant vegetation

The toxicity, volatility and persistence of the obsolete organochlorine pesticide hexachlorocyclohexane (HCH), makes reclamation of contaminated areas a priority for the health and welfare of neighboring human communities. Microbial diversity and functions and their relation to spontaneous vegetation in post-excavation situations, are essential indicators to consider in bioaugmentation or microbe-assisted phytoremediation strategies at field scale. Our study aimed to evaluate the effects of long-term HCH contamination on soil and plant-associated microbial communities, and whether contaminated soil has the potential to act as a bacterial inoculum in post-excavation bioremediation strategies. To scrutinize the role of vegetation, the potential nitrogen fixation of free-living and symbiotic diazotrophs of the legume Lotus tenuis was assessed as a measure of nutrient cycling functions in soil under HCH contamination. Potential nitrogen fixation was generally not affected by HCH, with the exception of lower nifH gene counts in excavated contaminated rhizospheres, most probably a short-term HCH effect on early bacterial succession in this compartment. HCH shaped microbial communities in long-term contaminated bulk soil, where we identified possible HCH tolerants such as Sphingomonas and Altererythrobacter. In L. tenuis rhizosphere, microbial community composition was additionally influenced by plant growth stage. Sphingobium and Massilia were the bacterial genera characteristic for HCH contaminated rhizospheres. Long-term HCH contamination negatively affected L. tenuis growth and development. However, root-associated bacterial community composition was driven solely by plant age, with negligible HCH effect. Results showed that L. tenuis acquired possible HCH tolerant bacteria such as the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade, Sphingomonas, Massilia or Pantoea which could simultaneously offer plant growth promoting (PGP) benefits for the host. Finally, we identified an inoculum with possibly HCH tolerant, PGP bacteria transferred from the contaminated bulk soil to L. tenuis roots through the rhizosphere compartment, consisting of Mesorhizobium loti, Neorhizobium galegae, Novosphingobium lindaniclasticum, Pantoea agglomerans and Lysobacter bugurensis.

Effects of co-contamination of heavy metals and total petroleum hydrocarbons on soil bacterial community and function network reconstitution

Due to the accumulation of heavy metals in soil ecosystems, the response of soil microorganisms to the disturbance of heavy metals were widely studied. However, little was known about the interactions among microorganisms in heavy metals and total petroleum hydrocarbons (TPH) co-contaminated soils. In the present study, the microbiota shifts of 2 different contamination types of heavy metal-TPH polluted soils were investigated. NGS sequencing approach was adopted to illustrate the microbial community structure and to predict community function. Networks were established to reveal the interactions between microbes and environmental pollutants. Results showed that the alpha diversity and OTUs number of soil microbiota were reduced under heavy metals and TPH pollutants. TPH was the major pollutant in HT1 group, in which Proteobacteria phylum increased significantly, including Arenimonas genus, Sphingomonadaceae family and Burkholderiaceae family. Moreover, the function structures based on the KEGG database of HT1 group was enriched in the benzene matter metabolism and bacterial motoricity in microbiota. In contrast, severe Cr-Pb-TPH co-pollutants in HT2 increased the abundance of Firmicutes. In details, the relative abundance of Streptococcus genus and Bacilli class raised sharply. The DNA replication functions in microbiota were enriched under severely contaminated soil as a result of high concentrations of heavy metals and TPH pollutants' damage to bacteria. Furthermore, according to the correlation analysis between microbes and the pollutants, Streptococcus, Neisseria, Aeromonas, Porphyromonas and Acinetobacter were suggested as the bioremediation bacteria for Cr and Pb polluted soils, while Syntrophaceae spp. and Immundisolibacter were suggested as the bioremediation bacteria for TPH polluted soil. The study took a survey on the microbiota shifts of the heavy metals and TPH polluted soils, and the microbe's biomarkers provided new insights for the candidate strains of biodegradation, while further researches are required to verify the biodegradation mechanism of these biomarkers.

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.

Polyhalogenated Carbazoles in Surface Sediment from Sanmen Bay, East China Sea: Spatial Distribution and Congener Profile

Polyhalogenated carbazoles (PHCZs) have recently emerged as a group of halogenated pollutants with broad occurrences and bioaccumulation potential in aquatic systems. However, investigations on their occurrences in coastal waters remain very limited. In the present study we investigated PHCZs in surface sediment collected from 29 sites in Sanmen Bay, East China Sea. The results demonstrated a universal presence of PHCZs in sediment, with concentrations of ∑PHCZs (including all congeners) ranging from 7.7 to 17.5 ng/g dry weight (median: 11.3 ng/g dw). The PHCZ congener composition profile revealed a dominance of 3,6-dichlorocarbazole (36-CCZ) with comparable concentration with that of carbazole. Given that PHCZs are widely distributed in Sanmen Bay sediment and their concentrations rivaled other well-known persistent organic pollutants in the same area, this group of halogenated pollutants merits additional investigations of their potential risks to the studied aquatic system, as well as other important watersheds.

Carbazole hydroxylation by the filamentous fungi of the Cunninghamella species

Nitrogen heterocyclic compounds, especially carbazole, quinolone, and pyridine are common types of environmental pollutants. Carbazole has a toxic influence on living organisms, and the knowledge of its persistence and bioconversion in ecosystems is still not complete. There is an increasing interest in detoxification of hazardous xenobiotics by microorganisms. In this study, the ability of three filamentous fungi of the Cunninghamella species to eliminate carbazole was evaluated. The Cunninghamella elegans IM 1785/21Gp and Cunninghamella echinulata IM 2611 strains efficiently removed carbazole. The IM 1785/21Gp and IM 2611 strains converted 93 and 82 % of the initial concentration of the xenobiotic (200 mg L(-1)) after 120 h incubation. 2-Hydroxycarbazole was for the first time identified as a carbazole metabolite formed by the filamentous fungi of the Cunninghamella species. There was no increase in the toxicity of the postculture extracts toward Artemia franciscana. Moreover, we showed an influence of carbazole on the phospholipid composition of the cells of the tested filamentous fungi, which indicated its harmful effect on the fungal cell membrane. The most significant modification of phospholipid levels after the cultivation of filamentous fungi with the addition of carbazole was showed for IM 1785/21Gp strain.

Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance

Increased exploration and exploitation of resources in the Arctic is leading to a higher risk of petroleum contamination. A number of Arctic microorganisms can use petroleum for growth-supporting carbon and energy, but traditional approaches for stimulating these microorganisms (for example, nutrient addition) have varied in effectiveness between sites. Consistent environmental controls on microbial community response to disturbance from petroleum contaminants and nutrient amendments across Arctic soils have not been identified, nor is it known whether specific taxa are universally associated with efficient bioremediation. In this study, we contaminated 18 Arctic soils with diesel and treated subsamples of each with monoammonium phosphate (MAP), which has successfully stimulated degradation in some contaminated Arctic soils. Bacterial community composition of uncontaminated, diesel-contaminated and diesel+MAP soils was assessed through multiplexed 16S (ribosomal RNA) rRNA gene sequencing on an Ion Torrent Personal Genome Machine, while hydrocarbon degradation was measured by gas chromatography analysis. Diversity of 16S rRNA gene sequences was reduced by diesel, and more so by the combination of diesel and MAP. Actinobacteria dominated uncontaminated soils with <10% organic matter, while Proteobacteria dominated higher-organic matter soils, and this pattern was exaggerated following disturbance. Degradation with and without MAP was predictable by initial bacterial diversity and the abundance of specific assemblages of Betaproteobacteria, respectively. High Betaproteobacteria abundance was positively correlated with high diesel degradation in MAP-treated soils, suggesting this may be an important group to stimulate. The predictability with which bacterial communities respond to these disturbances suggests that costly and time-consuming contaminated site assessments may not be necessary in the future.

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.

Isolation and description of a stable carbazole-degrading microbial consortium consisting of Chryseobacterium sp. NCY and Achromobacter sp. NCW

A stable microbial consortium, separated from a refinery wastewater sample, was able to utilize carbazole as the sole source of carbon, nitrogen, and energy, and liberated ammonia from excess nitrogen. Two bacterial strains (NCY and NCW) were isolated from the microbial consortium using a nutrient agar plate. Based on the 16S rDNA sequence analysis, the two bacteria were identified as Chryseobacterium sp. NCY and Achromobacter sp. NCW, respectively. No intermediates of carbazole degradation were detected by high-performance liquid chromatography. The substrate specificity assay showed that the consortium could utilize compounds similar to carbazole, such as phenanthrene, naphthalene, and imidazole. Neither the pure strain NCY nor NCW could degrade carbazole after domestication for several times. It was suggested that the two bacteria formed a microbial consortium capable of metabolizing carbazole.