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Rup Lal - One of the best experts on this subject based on the ideXlab platform.
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comparative genomic analysis of nine sphingobium strains insights into their evolution and hexachlorocyclohexane hch Degradation pathways
BMC Genomics, 2014Co-Authors: Helianthous Verma, Naseer Sangwan, Roshan Kumar, Jitendra P Khurana, Jack A Gilbert, Phoebe Oldach, Rup LalAbstract:Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the Degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6). Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many Xenobiotic Degradation pathways other than HCH, despite the absence of these Xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity. The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on Degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.
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enzymes and operons mediating Xenobiotic Degradation in bacteria
Critical Reviews in Microbiology, 2001Co-Authors: Vachaspati Mishra, Rup LalAbstract:Aromatic hydrocarbons constitute a major group of environmental pollutants. Bioremediation appears to be the only viable alternative for large-scale decontamination. A number of bacteria have been identified that can degrade a variety of Xenobiotics. Extensive studies of the enzymes and genes involved in Degradation of aromatic hydrocarbons have revealed that the degradative enzymes could be broadly grouped into two major categories, peripheral and ring-cleavage enzymes. The peripheral enzymes are the ones that catabolize the pollutants initially to a metabolite that is further degraded. A majority of peripheral enzymes are oxygenases that hydroxylate the aromatic compounds, rendering them susceptible to the enzymes of ring-cleavage pathway. The genes of ring-cleavage enzymes have been shown to be highly conserved between different bacterial species. Presently, a number of constraints limit the use of available strains for efficient bioremediation. This review describes the enzymes and genes involved in Xenobiotic Degradation and underscores the importance of understanding the expression and regulation of genes encoding peripheral enzymes and their intelligent manipulation using recombinant DNA technology for efficient Degradation of aromatic compounds.
Nyukmin Chong - One of the best experts on this subject based on the ideXlab platform.
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conditions for supplemental biogenic substrates to enhance activated sludge Degradation of Xenobiotic
Applied Microbiology and Biotechnology, 2015Co-Authors: Lan Huong Nguyen, Nyukmin ChongAbstract:The effects of biogenic presence on the Degradation of Xenobiotic organics by natural microbial populations have been reported as either advantageous or disadvantageous. The inconsistency of the reports implies there could be a turning point from disadvantageous to advantageous outcomes so that conditions may exist that could bring an optimum advantage. This study tested the supplementations of varying concentrations of sucrose and peptone, separately and combined, to acclimated activated sludge Degradation of Xenobiotic 2,4-D, while other operational and microbiological conditions were held constant. Our test results showed that biogenic may indeed enhance or slow down Xenobiotic Degradation rates. The highest enhancements exist at concentrations of 50 and 80 mg/L, respectively, for sucrose and peptone when supplemented separately, and 20 mg/L sucrose and 40 mg/L peptone combined. Conditions for advantageous biogenic supplementation were identified for activated sludge Degradation of a Xenobiotic; specifically, the highest Degradation rate enhancements occurred when biogenic supplementation was approximately 0.5 to 0.7 the concentration of 2,4-D base on chemical oxygen demand (COD), which brought a biomass yield of approximately double that yielded by 2,4-D. Kinetics analyses provided clues for the possible causes of advantageous and disadvantageous effects due to biogenic supplementation.
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the biomass yielding process of Xenobiotic Degradation
Bioresource Technology, 2010Co-Authors: Nyukmin Chong, Shiuching TsaiAbstract:Yields of activated sludge and an Arthrobacter sp. biomass on organic Xenobiotic 2,4-dichlorophenoxyacetic acid (2,4-D) and on the intermediates of selected 2,4-D metabolism pathways were measured. Activated sludge yield on 2,4-D was lower by approximately 24-45% compared to the combined yields produced separately by the lower intermediates. For activated sludge, cell synthesis only consumed 33% of the electrons generated from 2,4-D oxidation, while the other 67% were used for energy. The high energy consumption, which was the primary cause of low activated sludge yield from 2,4-D Degradation, occurred mainly in the catabolism of 2,4-D. The degrader sludge supplied this catabolism energy demand with the ATP contained in the biomass. As a result, the sludge's ATP contents suffered a deficit that was not fully remunerated after 2,4-D was degraded. Metabolism of the lower intermediates provided materials for further biomass growth and refilled part of the energy initially consumed.
J.-j. Godon - One of the best experts on this subject based on the ideXlab platform.
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Impact of microbial diversity depletion on Xenobiotic Degradation by sewage-activated sludge
Environmental Microbiology Reports, 2013Co-Authors: G. Hernandez-raquet, E. Durand, F. Braun, Cristiana Cravo-laureau, J.-j. GodonAbstract:Microbial diversity is generally considered as having no effect on the major processes of the ecosystem such as respiration or nutrient assimilation. However, information about the impact of diversity on minor functions such as Xenobiotic Degradation is scant. We studied the role of diversity on the capacity of an activated-sludge microbial community to eliminate phenanthrene, a polycyclic aromatic hydrocarbon. We also assessed the impact of diversity erosion on the ability of activated sludge to oxidize a wide range of organic compounds. The diversity of activated sludge was artificially modified by dilution to extinction followed by regrowth stage which led to communities with similar biomass but displaying a diversity gradient. The capacity of activated-sludge community to degrade phenanthrene was greatly modified: at high levels of diversity, the community was able to mineralize phenanthrene whereas at medium levels it first of all partially lost its ability to mineralize this pollutant and at the lowest diversity, the activated sludge completely lost its capacity to transform phenanthrene. Diversity depletion also reduced the metabolic diversity and biomass productivity of sewage-activated sludge. This study demonstrates that diversity erosion can greatly affect major ecosystem services such as pollutant removal.
Charles W. Greer - One of the best experts on this subject based on the ideXlab platform.
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Salix purpurea Stimulates the Expression of Specific Bacterial Xenobiotic Degradation Genes in a Soil Contaminated with Hydrocarbons.
PloS one, 2015Co-Authors: Antoine P. Pagé, Etienne Yergeau, Charles W. GreerAbstract:The objectives of this study were to uncover Salix purpurea-microbe Xenobiotic Degradation systems that could be harnessed in rhizoremediation, and to identify microorganisms that are likely involved in these partnerships. To do so, we tested S. purpurea‘s ability to stimulate the expression of 10 marker microbial oxygenase genes in a soil contaminated with hydrocarbons. In what appeared to be a detoxification rhizosphere effect, transcripts encoding for alkane 1-monooxygenases, cytochrome P450 monooxygenases, laccase/polyphenol oxidases, and biphenyl 2,3-dioxygenase small subunits were significantly more abundant in the vicinity of the plant's roots than in bulk soil. This gene expression induction is consistent with willows' known rhizoremediation capabilities, and suggests the existence of S. purpurea-microbe systems that target many organic contaminants of interest (i.e. C4-C16 alkanes, fluoranthene, anthracene, benzo(a)pyrene, biphenyl, polychlorinated biphenyls). An enhanced expression of the 4 genes was also observed within the bacterial orders Actinomycetales, Rhodospirillales, Burkholderiales, Alteromonadales, Solirubrobacterales, Caulobacterales, and Rhizobiales, which suggest that members of these taxa are active participants in the exposed partnerships. Although the expression of the other 6 marker genes did not appear to be stimulated by the plant at the community level, signs of additional systems that rest on their expression by members of the orders Solirubrobacterales, Sphingomonadales, Actinomycetales, and Sphingobacteriales were observed. Our study presents the first transcriptomics-based identification of microbes whose Xenobiotic Degradation activity in soil appears stimulated by a plant. It paints a portrait that contrasts with the current views on these consortia's composition, and opens the door for the development of laboratory test models geared towards the identification of root exudate characteristics that limit the efficiency of current willow-based rhizoremediation applications.
Gurdeep Rastogi - One of the best experts on this subject based on the ideXlab platform.
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metagenomic analysis reveals genetic insights on biogeochemical cycling Xenobiotic Degradation and stress resistance in mudflat microbiome
Journal of Environmental Management, 2021Co-Authors: Madhusmita Mohapatra, Rakeshkumar Yadav, Vinay Rajput, Mahesh S Dharne, Gurdeep RastogiAbstract:Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and Xenobiotic bioDegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, Xenobiotic bioDegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.
