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Phylogenetic Analysis of Pectobacterium Species Using the 16S-23S rRNA Intergenic Spacer Regions
Kwon, Soon-Wo,Cheun, Meung-Sook,Kim, Sang-Hee,Lim, Chun-Keun The Korean Society of Plant Pathology 2000 Plant Pathology Journal Vol.16 No.2
For the taxonomic evaluaition, 15 strains of the genus Pectobacterium and Erwinia were analyzed for 16S-23S rDNA intergenic spacer regions (ISRs). These species contained two types of ISRs, large and small ISRs. Large ISRs were on the range of 474-569 bp size, and coding transfer $\textrm{RNA}^{11e}$($\textrm{tRNA}^{11e}$) and $\textrm{tRNA}^{Ala}$. Small ISRs were 354-459 bp in length and coding $\textrm{tRNA}^{Glu}$. The sequence variations of two ISRs among species and strains were very high as compared with 16S rRNA gene sequences. By phylogenetic trees on the basis of two ISRs, Pectobacterium ere differentiated into P. carotovorum-P. cactiaidum group and P. chrysanthemi group. However, the taxonomic position of E. cypripedii and E. rhapontici, which were not clear on taxonomic delineation between Pectobacterium and Erwinia, were not clearly resolved on the basis of ISRs.
Kwon, Soon-Wo,Myung, In-Sik,Go, Seung-Joo The Korean Society of Plant Pathology 2000 Plant Pathology Journal Vol.16 No.5
The 16S-23S rRNA intergenic spacer regions (ISRs) were sequenced and analyzed to design specific primer for identification of Pectobacterium chrysanthemi. Two types ISRs, large and small ISRs, were identified from three strains (ATCC 11663, KACC 10163 and KACC 10165) of P. chrysanthemi and Pectobacterium carotovorum subsp. carotovorum ATCC 15713.Large ISRs contained transfer RNA-Ile(tRNA$^{Ile}$)and tRNA$^{Ala}$, and small ISRs contained tRNA$^{Glu}$. Size of the small ISRs of P. chrysanthemi ranged on 354-356 bp, while it was 451 bp in small ISR of P. carotovorum subsp. carotovorum ATCC 15713. From hypervariable region of small ISRs, species-specific primer for P. chrysanthemi with 20 bp length (CHPG) was designed from hypervariable region of small ISRs, which was used as forward promer to detect P. chrysanthemi strains with R23-1R produced PCR product of about 260bp size (CHSF) only from P. chrysanthemi strains, not from other Pectobacterium spp. and Erwinia spp. Direct PCR from bacterial cell without extracting DNA successfully amplified a specific fragment, CHSF, from P. chrysanthemi ATCC 11663. The limit of PCR detection was 1${\pm}10^2$ cfu/ml.
Sporosarcina koreensis sp. nov. and Sporosarcina soli sp. nov., isolated from soil in Korea
Kwon, Soon-Wo,Kim, Byung-Yong,Song, Jaekyeong,Weon, Hang-Yeon,Schumann, Peter,Tindall, Brian J.,Stackebrandt, Erko,Fritze, Dagmar Microbiology Society 2007 International journal of systematic and evolutiona Vol.57 No.8
Paludibacterium yongneupense gen. nov., sp. nov., isolated from a wetland, Yongneup, in Korea.
Kwon, Soon-Wo,Kim, Byung-Yong,Kim, Wan-Gyu,Yoo, Kwan-Hee,Yoo, Seung-Hee,Son, Jung-A,Weon, Hang-Yeon Society for General Microbiology 2008 International journal of systematic and evolutiona Vol.58 No.1
<P>A cream-coloured bacterial strain, 5YN8-15(T), was isolated from a wetland, Yongneup, in the Inje region of the Republic of Korea. The bacterium was facultatively anaerobic, Gram-negative, motile with a single polar flagellum and curved-rod-shaped. Based on 16S rRNA gene sequence analysis, strain 5YN8-15(T) is a member of the Betaproteobacteria. Closely related taxa were Gulbenkiania mobilis E4FC31(T) (94.9% sequence similarity), Chromobacterium species (94.1-94.4%), Aquitalea magnusonii TRO-001DR8(T) (93.2%) and Aquaspirillum serpens IAM 13944(T) (92.5%). All other species with validly published names analysed showed sequence similarities of below 92%. Strain 5YN8-15(T) had ubiquinone 8 as the major isoprenoid quinone. The major fatty acids were summed feature 3 (C(16:1)omega7c and/or iso-C(15:0) 2-OH), C(16:0) and C(18:1)omega7c. The DNA G+C content was 63.0 mol%. Based on the data from the polyphasic study, strain 5YN8-15(T) represents a novel genus and species of the family Neisseriaceae, for which the name Paludibacterium yongneupense gen. nov., sp. nov. is proposed. The type strain is 5YN8-15(T) (=KACC 11601(T)=DSM 18731(T)).</P>