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- Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation
- Dae-Wi Kim , Kihyun Lee , Do-Hoon Lee , Chang-Jun Cha
- J. Microbiol. 2018;56(11):798-804. Published online October 24, 2018
- DOI: https://doi.org/10.1007/s12275-018-8372-0
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- 21 Crossref
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Abstract
- The genome sequences of two pyrene-degrading bacterial strains of Mycobacterium spp. PYR10 and PYR15, isolated from the estuarine wetland of the Han river, South Korea, were determined using the PacBio RS II sequencing platform. The complete genome of strain PYR15 was 6,037,017 bp in length with a GC content of 66.5%, and contained 5,933 protein- coding genes. The genome of strain PYR10 was 5,999,427 bp in length with a GC content of 67.7%, and contained 5,767 protein-coding genes. Based on the average nucleotide identity values, these strains were designated as M. gilvum PYR10 and M. pallens PYR15. A genomic comparison of these pyrene-degrading Mycobacterium strains with pyrene- non-degrading strains revealed that the genomes of pyrene-degrading strains possessed similar repertoires of ringhydroxylating dioxygenases (RHDs), including the pyrenehydroxylating dioxygenases encoded by nidA and nidA3, which could be readily distinguished from those of pyrenenon- degraders. Furthermore, genomic islands, containing catabolic gene clusters, were shared only among the pyrenedegrading Mycobacterium strains and these gene clusters contained RHD genes, including nidAB and nidA3B3. Our genome data should facilitate further studies on the evolution of the polycyclic aromatic hydrocarbon-degradation pathways in the genus Mycobacterium.
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Citations
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- Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically PAH-contaminated soil
Research Support, Non-U.S. Gov'ts
- Molecular Detection of Catabolic Genes for Polycyclic Aromatic Hydrocarbons in the Reed Rhizosphere of Sunchon Bay
- Hyung-Yeel Kahng , Kye-Heon Oh
- J. Microbiol. 2005;43(6):572-576.
- DOI: https://doi.org/2287 [pii]
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Abstract
- This study focused on detecting catabolic genes for polycyclic aromatic hydrocarbons (PAHs) distributed in the reed rhizosphere of Sunchon Bay, Korea. These marsh and mud environments were severely affected by human activities, including agriculture and fisheries. Our previous study on microbial roles in natural decontamination displayed the possibility that PAH-degrading bacteria, such as Achromobacter sp., Alcaligenes sp., Burkholderia sp. and Pseudomonas sp. play an important decontamination role in a reed rhizosphere. In order to gain further fundamental knowledge on the natural decontamination process, catabolic genes for PAH metabolism were investigated through PCR amplification of dioxygenase genes using soil genomic DNA and sequencing. Comparative analysis of predicted amino acid sequences from 50 randomly selected dioxygenase clones capable of hydroxylating inactivated aromatic nuclei indicated that these were divided into three groups, two of which might be originated from PAH-degrading bacteria. Amino acid sequences of each dioxygenase clone were a part of the genes encoding enzymes for initial catabolism of naphthalene, phenanthrene, or pyrene that might be originated from bacteria in the reed rhizosphere of Sunchon Bay.
- Enhancing the Intrinsic Bioremediation of PAH-Contaminated Anoxic Estuarine Sediments with Biostimulating Agents
- Quang-Dung Bach , Sang-Jin Kim , Sung-Chan Choi , Young-Sook Oh
- J. Microbiol. 2005;43(4):319-324.
- DOI: https://doi.org/2259 [pii]
- 45 View
- 0 Download
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Abstract
- Estuarine sediments are frequently polluted with hydrocarbons from fuel spills and industrial wastes. Polycyclic aromatic hydrocarbons (PAHs) are components of these contaminants that tend to accumulate in the sediment due to their low aqueous solubility, low volatility, and high affinity for particulate matter. The toxic, recalcitrant, mutagenic, and carcinogenic nature of these compounds may require aggressive treatment to remediate polluted sites effectively. In petroleum-contaminated sediments near a petrochemical industry in Gwangyang Bay, Korea, in situ PAH concentrations ranged from 10 to 2,900 ug/kg dry sediment. To enhance the biodegradation rate of PAHs under anaerobic conditions, sediment samples were amended with biostimulating agents alone or in combination: nitrogen and phosphorus in the form of slow-release fertilizer (SRF), lactate, yeast extract (YE), and Tween 80. When added to the sediment individually, all tested agents enhanced the degradation of PAHs, including naphthalene, acenaphthene, anthracene, fluorene, phenanthrene, fluoranthene, pyrene, chrysene, and benzo[a]pyrene. Moreover, the combination of SRF, Tween 80, and lactate increased the PAH degradation rate 1.2-8.2 times above that of untreated sediment (0.01-10 ug PAH/kg dry sediment/day). Our results indicated that in situ contaminant PAHs in anoxic sediment, including high molecular weight PAHs, were degraded biologically and that the addition of stimulators increased the biodegradation potential of the intrinsic microbial populations. Our results will contribute to the development of new strategies for in situ treatment of PAH-contaminated anoxic sediments.
- Biodegradation of Phenanthrene by Sphingomonsa sp. Strain KH3-2
- Su-Kyuong Shin , Young-Sook Oh , Sang-Jin Kim
- J. Microbiol. 1999;37(4):185-192.
- 35 View
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Abstract
- A phenanthrene-degrading bacterium was isolated from an oil-spilled intertidal sediment sample and identified as Sphingomonas sp. KH3-2. The strain degraded polycyclic aromatic compounds such naphthalene, fluorene, biphenyl, and dibenzothiophene. When strain KH3-2 was cultured for 28 days at 25C, a total of 500 ppm of phenanthrene was degrated with a concomitant production of biomass and Folin-Ciocalteau reactive aromatic intermediates. Analysis of intermediates during phenanthrene degradation using high-performance liquid chromatography and gas chromatography/mass spectrometry indicated that Sphingomonas sp. KH3-2 primarily degrades phenanthrene to 1-hydroxy-2-naphthoic acid (1H2NA) and further metabolizes 1H2NA through the degradation pathway of naphthalene.
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