• Journal of Microbiology
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• v.43 no.6
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• pp.572-576
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• 2005

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.

• Microbiology and Biotechnology Letters
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• v.33 no.3
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• pp.169-177
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• 2005

This study focuses on investigating roles of microorganisms in decontamination of reed rhizosphere in Sunchon Bay, Korea, which is considered one of the marsh and mud environment severely affected by human activities such as agriculture and fisheries. In general, the bay is known to play the role of the buffering zone to reduce the sudden impact or change by environmental stresses. In our initial efforts to elucidate the microbial functions in decontamination process in reed rhizosphere, pure bacteria capable of degrading aromatic hydrocarbons were isolated from reed (Phragmites communis) rhizosphere of Sunchon bay by enrichment culture using either benzene, toluene, ethylbenzene, or xylene (BTEX) as a sole source of carbon and energy. Measurement of the rates of BTEX degradation and cell growth during the incubation in BTEX media under several temperature conditions demonstrated maximized degradation of BTEX at $37^{\circ}C$ in both strains. Both strains were also resistant to all the heavy metals and antibiotics tested in this study, as well as they grew well at $42^{\circ}C$. Identification of the isolates based on 16S rRNA gene sequences, and a variety of phenotypic and morphologic properties revealed that the two strains capable of BTEX catabolism were among Microbacterium sp., and Rhodococcus sp. with over $95{\%}$ confidence, designated Microbacterium sp. EMB-1 and Rhodococcus sp. EMB-2, respectively This result suggested that in the rhizosphere of reed, one of major salt marsh plants they might play an important roles in decontamination process of reed rhizosphere contaminated with petroleum such as BTEX.

• Proceedings of the Microbiological Society of Korea Conference
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• 2005.05a
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• pp.201.1-201
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• 2005

• Korean Journal of Microbiology
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• v.41 no.3
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• pp.208-215
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• 2005

This study was accomplished in order to collect fundamental data on microbial roles in recycling process of reed rhizosphere. Sunchon bay, which is considered as one of the marsh and mud environments severely affected by human activities such agriculture and fisheries, was selected as a model place. In our initial efforts, two bacterial consortia were obtained by enrichment culture using PAH mixtures containing anthracene, naphthalene, phenanthrene and pyrene as the sources of carbon and energy, and four pure bacteria capable of rapid degradation of PAH were isolated from them. Four strains designated as SCB1, SCB2, SCB6, and SCB7 revealed by morphological, physiological and molecular analyses were identified as Burkholderia anthina, Alcaligenes sp., Achromobacter xylosoxidans., and Pseudomonas putida, respectively with over $99{\%}$ confidence. Notably, Burkholderia anthina SCB1 and Alcaligenes sp. SCB2 were found to utilize anthracene and pyrene more quickly than naphthalene and phenanthrene, whereas Achromobacter xylosoxidans SCB6 and Pseudomonas putida SCB7 exhibited similar growth and degradation patterns except for pyrene. These facts suggest that the rhizosphere microorganisms capable of PAH degradation might be used to clean up the contamination sites with polycyclic aromatic hydrocarbons.

• Microbiology and Biotechnology Letters
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• v.48 no.4
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• pp.480-490
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• 2020

A novel lipase gene, Lip-1420, was isolated from a metagenomic library constructed from reed marsh from Mt. Jumbong in Korea, comprising 112,500 members of recombinant plasmids. The DNA sequence of Lip-1420-subclone (5,513 bp) was found to contain at least 11 ORFs according to the GenBank database. The ORF-3 gene was inserted into the pET21a plasmid containing the C-terminal 6-His tag and transformed into E. coli BL21(DE3) to express the recombinant lipase protein. Lip-1420 was purified using a fast protein liquid chromatography system. The gene was registered in GenBank (MH628529). The values of Km and Vmax were determined as 0.268 mM and 1.821 units, respectively, at 40℃ and pH 8.0, using p-nitrophenyl palmitate as the substrate. This lipase belongs to family IV taxonomically because it has conserved HGGG and GDSAG motifs in the constitutive amino acid sequence. According to the predicted structural model, the binding sites are represented by residues H78, G81, D150, S151, A152, V181, and D236. Finally, Lip-1420 showed triolein selectivity for methanolysis between triolein (18:1) and tristearin (18:0) substrates. Further study of the selective mechanism and structure-function relationship of this new lipase could be useful for more practical applications.

• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.753-760
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• 2007

The diversity of Paenibacillus species was assessed in the rhizospheres of four cultivars of sorghum sown in Cerrado soil amended with two levels of nitrogen fertilizer(12 and 120 kg/ha). Two cultivars(IS 5322-C and IS 6320) demanded the higher amount of nitrogen to grow, whereas the other two(FBS 8701-9 and IPA 1011) did not. Using the DNA extracted from the rhizospheres, a Paenibacillus-specific PCR system based on the RNA polymerase gene(rpoB) was chosen for the molecular analyses. The resulting PCR products were separated into community fingerprints by DGGE and the results showed a clear distinction between cultivars. In addition, clone libraries were generated from the rpoB fragments of two cultivars(IPA 1011 and IS 5322-C) using both fertilization conditions, and 318 selected clones were sequenced. Analyzed sequences were grouped into 14 Paenibacillus species. A greater diversity of Paenibacillus species was observed in cultivar IPA 1011 compared with cultivar IS 5322-C. Moreover, statistical analyses of the sequences showed that the bacterial diversity was more influenced by cultivar type than nitrogen fertilization, corroborating the DGGE results. Thus, the sorghum cultivar type was the overriding determinative factor that influenced the community structures of the Paenibacillus communities in the habitats investigated.