In-Cheol Park

The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice

The nucleotide sequence was determined for the genome of Xanthomonas oryzae pathovar oryzae (Xoo) KACC10331, a bacterium that causes bacterial blight in rice (Oryza sativa L.). The genome is comprised of a single, 4 941 439 bp, circular chromosome that is G + C rich (63.7%). The genome includes 4637 open reading frames (ORFs) of which 3340 (72.0%) could be assigned putative function. Orthologs for 80% of the predicted Xoo genes were found in the previously reported X.axonopodis pv. citri (Xac) and X.campestris pv. campestris (Xcc) genomes, but 245 genes apparently specific to Xoo were identified. Xoo genes likely to be associated with pathogenesis include eight with similarity to Xanthomonas avirulence (avr) genes, a set of hypersensitive reaction and pathogenicity (hrp) genes, genes for exopolysaccharide production, and genes encoding extracellular plant cell wall-degrading enzymes. The presence of these genes provides insights into the interactions of this pathogen with its gramineous host.

Analyses of bacterial communities in meju, a Korean traditional fermented soybean bricks, by cultivation-based and pyrosequencing methods

Despite the importance of meju as a raw material used to make Korean soy sauce (ganjang) and soybean paste (doenjang), little is known about the bacterial diversity of Korean meju. In this study, the bacterial communities in meju were examined using both culture-dependent and independent methods in order to evaluate the diversity of the bacterial population. Analyses of the 16S rRNA gene sequences of the bacterial strains isolated from meju samples showed that the dominant species were related to members of the genera Bacillus, Enterococcus, and Pediococcus. The community DNAs extracted from nine different meju samples were analyzed by barcoded pyrosequencing method targeting of the V1 to V3 hypervariable regions of the 16S rRNA gene. In total, 132,374 sequences, with an average read length of 468 bp, were assigned to several phyla, with Firmicutes (93.6%) representing the predominant phylum, followed by Proteobacteria (4.5%) and Bacteroidetes (0.8%). Other phyla accounted for less than 1% of the total bacterial sequences. Most of the Firmicutes were Bacillus and lactic acid bacteria, mainly represented by members of the genera Enterococcus, Lactococcus, and Leuconostoc, whose ratio varied among different samples. In conclusion, this study indicated that the bacterial communities in meju were very diverse and a complex microbial consortium containing various microorganisms got involved in meju fermentation than we expected before.

Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris)

Two bacterial strains, 01-96(T) and 15-51(T), isolated from rhizosphere soil of Chinese cabbage (Brassica campestris) were characterized by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 01-96(T) was phylogenetically related most closely to Pedobacter suwonensis 15-52(T) and Pedobacter roseus CL-GP80(T) (96.7 and 96.7% similarity, respectively), and strain 15-51(T) to Pedobacter borealis G-1(T) and P. suwonensis 15-52(T) (97.2 and 97.1%, respectively). However, levels of DNA-DNA relatedness between strain 15-51(T) and P. borealis KACC 14287(T) and P. suwonensis KACC 11317(T) were low (<50%). The G+C content of the genomic DNA was 37.8 mol% for strain 01-96(T) and 38.6 mol% for strain 15-51(T). The major fatty acids of the two strains were iso-C(17:0) 3-OH, iso-C(15:0) and summed feature 3 (iso-C(15:0) 2-OH and/or C(16:1)ω7c). The results of DNA-DNA hybridization and phenotypic data showed that strains 01-96(T) and 15-51(T) could be distinguished from their closest phylogenetic relatives, and that these strains represented two novel species of the genus Pedobacter, for which the names Pedobacter rhizosphaerae sp. nov. (type strain 01-96(T) =KACC 14938(T) =NBRC 107690(T)) and Pedobacter soli sp. nov. (type strain 15-51(T) =KACC 14939(T) =NBRC 107691(T)) are proposed.

Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost

A Gram-positive, aerobic, non-motile, short rod, designated SMC46(T), was isolated from a spent mushroom compost sample collected in the Suwon region, South Korea. 16S rRNA gene sequence analysis revealed that strain SMC46(T) was a member of the family Microbacteriaceae; however, the isolate formed a branch separate from other genera within the family. Sequence similarity between strain SMC46(T) and other members of the family Microbacteriaceae was ≤97 %, the highest sequence similarity being with Frigoribacterium faeni 801(T) and Frondihabitans australicus E1HC-02(T) (both 97.0 %). Some chemotaxonomic properties of strain SMC46(T) were consistent with those of the family Microbacteriaceae: MK-11 and MK-12 as the predominant menaquinones, anteiso-C(15 : 0), iso-C(16 : 0) and anteiso-C(17 : 0) as the major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid as the polar lipids. However, strain SMC46(T) contained a B-type peptidoglycan not previously found in the family Microbacteriaceae. The DNA G+C content was 68 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain SMC46(T) was considered to represent a novel genus and species in the family Microbacteriaceae, for which the name Compostimonas suwonensis gen. nov., sp. nov. is proposed. The type strain of the type species is SMC46(T) ( = KACC 13354(T)  = NBRC 106304(T)).

Microbial Diversity and Community Analysis in Lettuce or Cucumber Cultivated Greenhouse Soil in Korea

The soil chemical properties, microbial community structures and biochemical properties of lettuce or cucumber-cultivated greenhouse soil samples were analyzed to assess soil health and characterize microbial distribution in 8 locations in Korea. Although most of chemical properties were within the soil management guidelines, the available phosphate, and the contents of exchangeable potassium and calcium were higher than those of recommended levels. In the culture-dependent analysis, 841 bacterial strains were isolated from the greenhouse soils and were identified at the genus level by 16S rRNA gene sequences analysis. The dominant bacterial genera were Bacillus (35.7%), Microbacterium (9.3%), Arthrobacter (5.7%) and Lysobacter (5.1%). The abundance of pseudomonads was highly variable depending on the soil samples. In the culture-independent analysis, soil microbial community was investigated by using phospholipid fatty acid (PLFA) method. Principal component analysis (PCA) showed that a specific grouping for microbial community structure in the greenhouse soils was not observed based on cultivated crops and investigated sites. The results revealed that the greenhouses soils examined are relatively sound managed in terms of soil chemical contents and microbial properties.

Nevskia terrae sp. nov., isolated from soil.

A Gram-negative bacterium, designated KIS13-15(T), was isolated from soil in Korea. Cells were strictly aerobic rods and were motile with 1-3 subpolar flagella. 16S rRNA gene sequence analysis revealed that strain KIS13-15(T) belonged to the order Xanthomonadales of the class Gammaproteobacteria and was closely related to Nevskia soli GR15-1(T) (97.9 % 16S rRNA gene sequence similarity) and Nevskia ramosa Soe1(T) (96.8 %). Strain KIS13-15(T) exhibited 38 and 29 % DNA-DNA relatedness with N. soli KACC 11703(T) and N. ramosa DSM 11499(T), respectively. The major fatty acids (>10 % of the total) were C(18 : 1)ω7c (40.6 %) and C(16 : 0) (12.4 %). The major isoprenoid quinone was ubiquinone 8. DNA G+C content was 67.3 mol%. The phenotypic characterization combined with 16S rRNA gene sequence analysis and DNA-DNA hybridization clearly classified strain KIS13-15(T) in a novel species of the genus Nevskia, for which the name Nevskia terrae sp. nov. is proposed. The type strain is KIS13-15(T) ( = KACC 12736(T)  = JCM 15425(T)).

Kaistia terrae sp. nov., isolated from a wetland in Korea

An ivory-coloured bacterium, designated strain 5YN7-3(T), was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3(T) belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8(T) (97.8 %), Kaistia granuli Ko04(T) (97.6 %) and Kaistia adipata Chj404(T) (97.4 %). Strain 5YN7-3(T) showed DNA-DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04(T), K. soli 5YN9-8(T) and K. adipata Chj404(T), respectively. The major fatty acids were C(18 : 1)omega7c (51.2 %), C(19 : 0) cyclo omega8c (25.0 %), C(18 : 0) (12.9 %) and C(16 : 0) (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA-DNA hybridization data clearly define strain 5YN7-3(T) as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3(T) (=KACC 12910(T) =DSM 21341(T)).

New species of agaricales.

Clitocybe alboinfundibulliforme sp. nov. is widely distributed in Korea. Volvariella koreana sp. nov. is rarely distributed in Korea. These taxa were occasionally found together at the same place. Both of these species seem to be associated with each other. These two species are fully described and illustrated in this paper.

Notes on Some Unrecorded Species in Korean Hypholoma

Department of Biology, Sang-ji University, Wonju 220-702, Korea(Received 19, November 2012., Revised 1, December 2012., Accepted 14, December 2012)ABSTRACT: Different mushroom species have collected from various areas and their taxonomic identification wascarried out for species diversity. Among them, Hypholoma elongatum (Pers.) Ricken that was collected from Yong-moon mountain of Gyonggi in Korea was confirmed as new collection in Korea and registered here with descrip-tions and Korean common name. All collections cited here are deposited in the Herbarium Conservation Centerof National Academy of Agricultural Sciences.KEYWORDS : Basidiomycota, Hypholoma elongatum, Unrecorded species

Tectella patellaris from Korea.

One rare and interesting species collected from Gyeryong-san, Chungnam Province is described and illustrated in detail. The species “Tectella patellaris (Fr.) Murr.” and genus “Tectella Earle” is a first record for Korean fungal flora. Specimens cited here have been deposited in the Herbarium Conservation Center of National Academy of Agricultural Sciences.