Kyung-Sook Whang

Oligotrophic bacteria from rendzina forest soil

Oligotrophic bacteria were shown to exist abundantly in all layers of a rendzina forest soil throughout the year. Two-hundred-three oligotrophic bacteria were isolated from forest soil (Aoba, Sendai) at different layers (L, F, H and A layers) throughout the year, and their morphological and physiological characteristics were examined. A high proportion (95%) of the isolated oligotrophs were Gram-negative, non-spore forming bacteria. Based on the cell shape, the isolates were divided into four groups: regular rods, curved/spiral bacteria, irregular rods, and buddin and/or prosthecate bacteria. Each group of bacteria is discussed in relation to the physiological characteristics. Notably oligotrophic bacteria of different cell types showed a marked zonal distribution in respect to profile depth.

Terrimonas rhizosphaerae sp. nov., isolated from ginseng rhizosphere soil

The novel isolate belonging to the genus Terrimonas, designated CR94T, was isolated from rhizosphere soil of a ginseng field in Geumsan, Korea. Cells of strain CR94T were strictly aerobic, Gram-stain-negative, non-motile, non-filamentous single rods. Growth was observed at 10-37 °C (optimum 28 °C) and at pH 4.0-10.0 (optimum pH 6.0). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CR94T belonged to the genus Terrimonas, showing highest sequence similarity to Terrimonas lutea DYT (97.3 %), Terrimonas pekingensis QHT (97.1 %), Terrimonas aquatica RIB1-6T (95.6 %), Terrimonas rubra M-8T (94.7 %) and Terrimonas ferruginea ATCC 13524T (93.8 %). DNA-DNA relatedness values between strain CR94T and T. lutea KACC 13047T, T. pekingensis KACC 18795T, T. ferruginea KACC 11310T and T. aquatica LMG 24825T were 30.5, 28.9, 17.8 and 13.5 %, respectively. The DNA G+C content was 46.5 mol% and the major respiratory quinone was menaquinone-7 (MK-7). The major cellular fatty acids of strain CR94T were iso-C15:1 G and iso-C15 : 0. On the basis of the polyphasic analysis, strain CR94T represents a novel species of the genus Terrimonas, for which the name Terrimonas rhizosphaerae sp. nov. is proposed. The type strain is CR94T (=KACC 17564T=NCAIM B 025317T).

Molecular Identification of Meloidogyne spp. in Soils from Fruit and Vegetable Greenhouses in Korea

ABSTRACT: In this study, we analyzed the phylogenetic characterization of root-knot nematodes ( Meloidogyne spp.) in soils from fruitsand vegetables greenhouses in Korea. Soil samples were collected from 12 greenhouse fields in which tomato, cucumber, watermelo n, and Oriental melon were being cultivated. Meloidogyne spp. were detected in all the soil samples at an average number of 72±6nematodes/300 g of soil to 2,898±468 nematodes/300 g of soil. Phylogenetic analysis using polymerase chain reaction-restriction fragment length polymorphism was attempted for the second-stage juveniles (J2) of Meloidogyne spp. collected from the greenhouse soils.Twelve Meloidogyne spp. from the greenhouse soils were classified into two groups by using HinfI digestion of mitochondrial DNA, resulting in 900, 410, 290, and 170 bp fragments (group A) and 900, 700, and 170 bp fragments (group B). Phylogenetic analysis basedon mitochondrial DNA sequences (1,483 –1,521 bp) showed that nine group A isolates were identified as Meloidogyne incognita (99.73–99.93%) and three group B isolates showed 99.54–99.73% similarity to Meloidogyne arenaria.Key words: Greenhouse soil, Root-knot nematode, PCR-RFLP, Meloidogyne incognita초 록: 국내 과채류 시설재배지 토양 내 분포하는 뿌리혹선충의 계통학적 특성을 조사하였다 . 토마토, 오이, 수박, 참외를 재배하는 12개 과채류 시설재배지 토양 내 뿌리혹선충의 밀도를 조사한 결과, 모든 시설재배지 토양에 광범위하게 분포하였으며 토양 300 g 당 평균 72±6~2,898±468마리로 검출되었다. 시설재배지 토양에서 수집한 뿌리혹선충 2령 유충을 대상으로 PCR-RFLP 계통분석을 수행하였다. 시설재배지 토양에서 분리한 12개 뿌리혹선충의 mtDNA PCR 증폭산물을 대상으로 제한효소 HinfI을 처리한 결과 900, 410, 290 및 170 bp의 DNA 절편 양상을 나타내는 Group A와 900, 700 및 170 bp의 DNA 절편 양상을 나타내는 Group B로 분류되었다. 각 그룹에 속하는 뿌리혹선충의 mtDNA 유전자 염기서열(1,483~1,521 bp)을 결정하여 계통분석한 결과, Group A에 속하는 9개의 뿌리혹선충은 고구마뿌리혹선충(Meloidogyne incognita)과 99.73~99.93%의 상동성을 나타내었고 그리고 Group B에 속하는 3개의 뿌리혹선충은 땅콩뿌리혹선충(Meloidogyne arenaria)과 99.54~ 99.73%의 상동성을 나타내어 유사한 종으로 확인되었다.검색어: 시설재배지 토양, 뿌리혹선충, 유전자 다형성 연구기법, 고구마뿌리혹선충*Corresponding author: kswhang@mokwon.ac.krReceived July 30 2013; Revised September 16 2013Accepted October 7 2013식물기생선충 중 피해가 가장 심각한 것으로 알려진 뿌리혹선충(Meloidogyne spp.)은 1850년대 영국의 온실에서 재배중인 오이 뿌리혹에서 최초로 발견되어진 이래 현재 전 세계적으로 90종 이상이 보고되었다(Perry et al., 2009). 뿌리혹선충은 온도에 대한 적응력이 높아 분포가 매우 광범위하나 주로 한대지방보다는 온도가 높은 아열대지방에서 피해가 심한 것으로 보고되고 있다(Kim et al., 1998). 뿌리혹선충은 토양에 서식하면서 식물 뿌리에 침입하여 뿌리 내부에 기생하며 영양분을 흡

Marinobacter halotolerans sp. nov., a halophilic bacterium isolated from a saltern crystallizing pond

A Gram-stain-negative, moderately halophilic, motile bacterium, designated strain CP12T, was isolated from a crystallizing pond of a saltern of the Yellow Sea in Korea. Cells of strain CP12T were non-spore-forming rods and produced whitish-yellow colonies. Growth was observed at 10-37 °C (optimum 37 °C), at pH 6.0-9.0 (optimum pH 7.0), and in the presence of 0.5-20 % (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CP12T was closely related to Marinobacter flavimaris SW-145T (98.4 % 16S rRNA gene sequence similarity), Marinobacter algicola DG893T (98.2 %), Marinobacter adhaerens HP15T (98.2 %), Marinobacter salsuginis SD-14BT (97.9 %), Marinobacter salarius R9SW1T (97.6 %) and Marinobacter lipolyticus SM19T (97.1 %). DNA-DNA hybridization studies showed values lower than 18.6 % between strain CP12T and any of these species. The predominant respiratory isoprenoid quinone was ubiquinone-9 and the major cellular fatty acids of strain CP12T were C16 : 0, C12 : 0 3-OH, C12 : 0, Summed feature 3, C16 : 0 10-methyl and C18 : 1ω9c. On the basis of phenotypic properties, and phylogenetic and chemotaxonomic data, it is evident that strain CP12T represents a novel species of the genus Marinobacter, for which the name Marinobacter halotolerans sp. nov. is proposed. The type strain is CP12T (=KACC 18381T=NBRC 110910T).

Streptomyces fuscigenes sp. nov., isolated from bamboo (Sasa borealis) litter

Three actinomycetes strains, designated JBL-5, JBL-14 and JBL-20T, were isolated from bamboo (Sasa borealis) litter in Damyang, Republic of Korea. Morphological, chemotaxonomic and phylogenetic analyses demonstrated that the three strains belong to the genus Streptomyces. Microscopic observation revealed that the three strains produced Spirales spore chains with smooth surfaces. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that these strains showed the highest sequence similarity to Streptomyces gelaticus NRRL B-2928T (97.8 %), Streptomyces pulveraceus LMG 20322T (97.7 %), Streptomyces intermedius NBRC 13049T (97.7 %), Streptomyces althioticus NRRL B-3981T (97.7 %) and Streptomyces matensis NBRC 12889T (97.7 %). The DNA-DNA hybridization values between strains JBL-5, JBL-14 and JBL-20T were 91.2-92.4 %, and the values between the three strains and their close phylogenetic relatives were also below 70 %. The predominant menaquinones were MK-9 (H4) and MK-9 (H6). The cell wall contained ll-diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositolmannoside, two unidentified aminolipids, three unidentified aminophospholipids, one unidentified glycolipid and one unidentified lipid. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0, C18 : 1ω7c and iso-C16 : 0. The DNA G+C contents were 71.8-72.4 mol%. On the basis of phylogenetic analyses and physiological and biochemical characterization, strains JBL-5, JBL-14 and JBL-20T are considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces fuscigenes sp. nov. is proposed. The type strain is JBL-20T (=KACC 18269T=NBRC 110629T).