Degradation of carbazole, dibenzothiophene and polyaromatic hydrocarbons by recombinant Rhodococcus sp

Kinetic and statistical perspectives on the interactive effects of recalcitrant polyaromatic and sulfur heterocyclic compounds and in-vitro nanobioremediation of oily marine sediment at microcosm level

A halotolerant biosurfactant producer Pseudomonas aeruginosa strain NSH3 (NCBI Gene Bank Accession No. MN149622) was isolated to degrade high concentrations of recalcitrant polyaromatic hydrocarbons (PAHs) and polyaromatic heterocyclic sulfur compounds (PASHs). In biphasic batch bioreactors, the biodegradation and biosurfactant-production activities of NSH3 have been significantly enhanced (p < 0.0001) by its decoration with eco-friendly prepared magnetite nanoparticles (MNPs). On an artificially contaminated sediment microcosm level, regression modeling and statistical analysis based on a 2³ full factorial design of experiments were trendily applied to provide insights into the interactive impacts of such pollutants. MNPs-coated NSH3 were also innovatively applied for nanobioremediation (NBR) of in-vitro diesel oil-polluted sediment microcosms. Gravimetric, chromatographic, and microbial respiratory analyses proved the significantly enhanced biodegradation capabilities of MNPs-coated NSH3 (p < 0.001) and the complete mineralization of various recalcitrant diesel oil components. Kinetic analyses showed that the biodegradation of iso- and n-alkanes was best fitted with a second-order kinetic model equation. Nevertheless, PAHs and PASHs in biphasic batch bioreactors and sediment microcosms followed the first-order kinetic model equation. Sustainable NBR overcome the toxicity of low molecular weight hydrocarbons, mass transfer limitation, and steric hindrance of hydrophobic recalcitrant high molecular weight hydrocarbons and alkylated polyaromatic compounds.

Actinomycetes Rhodococcus ruber CGMCC 17550 degrades neonicotinoid insecticide nitenpyram via a novel hydroxylation pathway and remediates nitenpyram in surface water

Neonicotinoid insecticides are neurotoxicants that cause serious environmental pollution and ecosystem risks. In the present study, a nitenpyram-degrading bacterium, Rhodococcus ruber CGMCC 17550, was isolated from a nitenpyram production sewage treatment tank. Liquid chromatography-mass spectrometry analysis revealed R. ruber degraded nitenpyram via a novel hydroxylation pathway to form three different metabolites, one of which was confirmed to hydroxylate nitenpyram at the C3 site of the 6-chlorpyridine cycle by nuclear magnetic resonance analysis. The nitenpyram degradation rate increased as the biomass of resting R. ruber CGMCC 17550 cells increased, reaching 98.37% at an OD₆₀₀ of 9 in transformation broth containing 100 mg L^-1 nitenpyram after 72 h of incubation. Nitenpyram degradation by R. ruber CGMCC 17550 was insensitive to dissolved oxygen levels. Use of glucose, fructose and pyruvate as co-substrates slightly increased nitenpyram degradation. The cytochrome P450 inhibitor 1-aminobenzotriazole strongly inhibited nitenpyram degradation, indicating that P450 enzymes may mediate nitenpyram hydroxylation. Inoculation of R. ruber CGMCC 17550 enhanced nitenpyram degradation in surface water. Additionally, R. ruber cells immobilized by calcium-alginate remediated 87.11% of 100 mg L^-1 NIT in 8 d. Genome sequencing analysis confirmed that R. ruber CGMCC 17550 has metabolic diversity and abundant KEGG genes involved in xenobiotics biodegradation and metabolism. These findings demonstrate that R. ruber CGMCC 17550 is capable of unique biodegradation of nitenpyram via the hydroxylation pathway and is a promising bacterium for bioremediation of contaminants.

Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8

Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non–destructive sulfur–specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be re-classified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.

Biodegradation of dibenzothiophene by efficient Pseudomonas sp. LKY-5 with the production of a biosurfactant

A potent bacterial strain capable of degrading dibenzothiophene (DBT) was isolated and evaluated for its characteristics. The strain, designated as LKY-5, is rod-shaped, gram-negative, and occurs mainly in clusters. It was identified as belonging to the Pseudomonas genus based on the 16S rDNA sequence and phylogenic analysis. Determination of its DBT depletion efficiency by gas chromatography revealed that the isolate was able to completely degrade up to 100 mg L^-1 DBT within 144 h. The pH values, DBT concentrations, and biomasses in the medium varied significantly in the initial 24 h. A biosurfactant produced by LKY-5 was extracted and identified as a di-rhamnolipid with the formula Rha-Rha-C₈-C_8:1 by HPLC-ESI-MS/MS. There were 26 metabolites in the DBT degradation process. Pseudomonas sp. LKY-5 exhibited unusually high DBT degradation efficiency via multiple metabolic pathways. Compared with the reported 4S and Kodama pathways, two more expanded metabolic pathways for the degradation of DBT are proposed. The polycyclic aromatic sulfur heterocycles (PASHs) in diesel, such as C₁-DBT, C₂-DBT, C₃-DBT, 4,6-DMDBT, and 2,4,6-TMDBT, can also be degraded with 28.2-42.3% efficiency. The results showed that LKY-5 is an excellent bacterial candidate for the bioremediation of PASH-contaminated sites and sediments.

Characteristics of microbial community functional structure of a biological coking wastewater treatment system

Nitrogenous heterocyclic compounds are key pollutants in coking wastewater; however, the functional potential of microbial communities for biodegradation of such contaminants during biological treatment is still elusive. Herein, a high throughput functional gene array (GeoChip 5.0) in combination with Illumina HiSeq2500 sequencing was used to compare and characterize the microbial community functional structure in a long run (500days) bench scale bioreactor treating coking wastewater, with a control system treating synthetic wastewater. Despite the inhibitory toxic pollutants, GeoChip 5.0 detected almost all key functional gene (average 61,940 genes) categories in the coking wastewater sludge. With higher abundance, aromatic ring cleavage dioxygenase genes including multi ring1,2diox; one ring2,3diox; catechol represented significant functional potential for degradation of aromatic pollutants which was further confirmed by Illumina HiSeq2500 analysis results. Response ratio analysis revealed that three nitrogenous compound degrading genes- nbzA (nitro-aromatics), tdnB (aniline), and scnABC (thiocyanate) were unique for coking wastewater treatment, which might be strong cause to increase ammonia level during the aerobic process. Additionally, HiSeq2500 elucidated carbozole and isoquinoline degradation genes in the system. These findings expanded our understanding on functional potential of microbial communities to remove organic nitrogenous pollutants; hence it will be useful in optimization strategies for biological treatment of coking wastewater.