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A Gram-negative, short rod-shaped bacterium, strain GA2-M15 T , was isolated from a sea-sand sample at Homi Cape, Pohang city, Republic of Korea. 16S rRNA gene sequence analysis demonstrated that this isolate was unique, showing 95.9 % sequence similarity to the type strain of Thalassobacter stenotrophicus and similarities of 94.0-95.2 % to the type strains of species of the genera Octadecabacter (94.4-95.2 %), Jannaschia (94.0-94.4 %) and Thalassobius (94.0-94.7 %). Chemotaxonomic characteristics (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as the major polar lipids and C 18 : 1 v7c as the predominant fatty acid) and DNA G+C content (56 mol%) were also similar to those of Thalassobacter stenotrophicus. 16S rRNA gene sequence similarity, physiological properties and some fatty acid components showed that strain GA2-M15T could be differentiated fromThalassobacter stenotrophicus. On the basis of these results, strain GA2-M15 T is considered to represent a novel species of the genus Thalassobacter, for which the name Thalassobacter arenae sp. nov. is proposed. The type strain is GA2-M15 T (5KACC 12675The genus Thalassobacter was described to accommodate a single bacterial strain isolated from Mediterranean seawater (Macián et al., 2005). A subsequent polyphasic taxonomic approach revealed that the type strains of Jannaschia cystaugens (Adachi et al., 2004) and Thalassobacter stenotrophicus (Macián et al., 2005) were highly similar and should be considered to be members of the same species. Pujalte et al. (2005) thus proposed the unification of the two species as Thalassobacter stenotrophicus and provided an emended description of the genus Thalassobacter. Phylogenetically, this genus is a member of the Alphaproteobacteria, and is closely related to the genera Jannaschia, Octadecabacter and Thalassobius. Thalassobacter was characterized as comprising Gramnegative, strictly aerobic, chemo-organotrophic, slightly halophilic bacteria, with C 18 : 1 v7c as the major fatty acid and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine as the major polar lipids.Strain GA2-M15 T was isolated from a sea-sand sample collected from the coast of Homi Cape, Pohang city, Republic of Korea. Isolation of the strain was performed by using the standard dilution-plating method on marine agar 2216 (MA; Difco) kept at 30 u C for 10 days. The culture was maintained routinely on MA at 30 uC and was preserved as glycerol suspensions (15 %, v/v) at 280 u C. Strain GA2-M15 T grew weakly on nutrient agar (NA), but did not grow on R2A, trypticase soy agar (TSA) or MacConkey agar (all from Difco). Thalassobacter stenotrophicus DSM 16310 T was obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ), Braunschweig, Germany, and was used as a reference strain.The methods described by Smibert & Krieg (1994) were used for Gram staining and to detect accumulation of polyhydroxybutyrate, the presence of catalase and oxidase, and hydrolysis of casein, DNA and sta...

Abstract:The temperate and herbaceous genus Vicia L. is a member of the legume tribe Fabeae of the subfamily Papilionoideae. The genus Vicia comprises 166 annual or perennial species distributed mainly in Europe, Asia, and North America, but also extending to the temperate regions of South America and tropical Africa. The use of simple sequence repeat (SSR) markers for Vicia species has not been investigated as extensively as for other crop species. In this study, we assessed the potential for cross-species amplification of cDNA microsatellite markers developed from common vetch (Vicia sativa subsp. sativa). For cross-species amplification of the SSRs, amplification was carried out with genomic DNA isolated from two to eight accessions of 22 different Vicia species. For individual species or subspecies, the transferability rates ranged from 33% for V. ervilia to 82% for V. sativa subsp. nigra with an average rate of 52.0%. Because the rate of successful SSR marker amplification generally correlates with genetic distance, these SSR markers are potentially useful for analyzing genetic relationships between or within Vicia species.

Two aerobic, Gram-positive, rod-shaped bacterial strains, 5YN10-14T and GR21-5T, were isolated from the Yongneup wetland and ginseng soil in Korea, respectively. The two strains formed ellipsoidal or oval spores positioned centrally or paracentrally in swollen sporangia. On the basis of 16S rRNA gene sequence analysis, these strains were related to members of the genus Cohnella. 16S rRNA gene sequence similarity between strains 5YN10-14T and GR21-5T was 95.9 %. Strains 5YN10-14T and GR21-5T showed, respectively, 94.3 and 95.2 % 16S rRNA gene sequence similarity to Cohnella thermotolerans CCUG 47242T, 94.6 and 94.4 % to Cohnella hongkongensis HKU3T, 94.7 and 94.7 % to Cohnella laeviribosi RI-39T, and 95.4 and 94.8 % to Cohnella phaseoli GSPC1T. The major fatty acids of strain 5YN10-14T were anteiso-C15 : 0 (51.1 %), iso-C16 : 0 (18.5 %) and C16 : 0 (13.2 %), and the major fatty acids of strain GR21-5T were anteiso-C15 : 0 (48.9 %), iso-C16 : 0 (15.0 %) and iso-C15 : 0 (12.2 %). The two strains contained menaquinone with seven isoprene units (MK-7) as the predominant quinone, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids; however, strain 5YN10-14T also contained lysylphosphatidylglycerol as a major polar lipid, whereas strain GR21-5T had an unknown aminophospholipid as another major polar lipid. The DNA G+C contents of strains 5YN10-14T and GR21-5T were 58.8 and 61.3 mol%, respectively. Based on the results of the phylogenetic and phenotypic data presented, it was concluded that the two strains represent two novel species of the genus Cohnella, for which the names Cohnella yongneupensis sp. nov. (type strain 5YN10-14T=KACC 11768T=DSM 18998T) and Cohnella ginsengisoli sp. nov. (type strain GR21-5T=KACC 11771T=DSM 18997T) are proposed.

Gibberella fujikuroi species complex (GFSC) was isolated from rice (Oryza sativa L.) seed samples from ten Asian countries and investigated for incidence of GFSC, molecular characteristics, and pathogenicity. Regardless of geographic origin, GFSC was detected with incidences ranging from 3% to 80%. Four species, Fusarium fujikuroi, F. concentricum, F. proliferatum, and F. verticillioides, were found to show an association with rice seeds, with F. fujikuroi being the predominant species. In phylogenetic analyses of DNA sequences, no relationship was found between species, isolates, and geographic sources of samples. Unidentified fragments of the β-tubulin gene were observed in ten isolates of F. fujikuroi and F. verticillioides. With the exception of three isolates of F. fujikuroi, F. fujikuroi, F. proliferatum, and F. verticillioides were found to have FUM1 (the fumonisin biosynthetic gene); however, FUM1 was not found in isolates of F. concentricum. Results of pathogenicity testing showed that all isolates caused reduced germination of rice seed. In addition, F. fujikuroi and F. concentricum caused typical symptoms of bakanae, leaf elongation and chlorosis, whereas F. proliferatum and F. verticillioides only caused stunting of seedlings. These findings provide insight into the characteristics of GFSC associated with rice seeds and might be helpful in development of strategies for management of bakanae.

Two bacterial isolates from ginseng fields in Korea, strains GR17-7 T and GP18-1 T , were characterized using a polyphasic approach. Phylogenetic analysis of their 16S rRNA gene sequences revealed a clear affiliation with the Gammaproteobacteria, and showed that the closest phylogenetic relationships were with members of the genus Rhodanobacter. The 16S rRNA gene sequence similarity between strains GR17-7 T and GP18-1 T was 97.2 %. Both strains showed 16S rRNA gene sequence similarities of 95.2-96.9 % to type strains of recognized Rhodanobacter species. The G+C contents of the DNA of strains GR17-7 T and GP18-1 T were 61.0 and 62.5 mol%, respectively. According to the DNA-DNA hydridization tests, the hybridization value between strains GR17-7 T and GP18-1 T was 34 %. Strains GR17-7 T and GP18-1 T showed less than 32 % DNA-DNA relatedness with Rhodanobacter fulvus KCTC 12098 T and Rhodanobacter spathiphylli LMG 23181 T . Strains GR17-7 T and GP18-1 T were aerobic, Gram-negative, rod-shaped, and catalase-and oxidase-positive. Major fatty acids of both strains were iso-C 17 : 1 v9c and iso-C 16 : 0 . Based on the data presented, two novel Rhodanobacter species are proposed, with the names Rhodanobacter ginsengisoli sp. nov. (type strain GR17-7 T 5KACC 11762 T 5DSM 18993 T ) and Rhodanobacter terrae sp. nov. (type strain GP18-1 T 5KACC 11761 T 5DSM 19241 T ).The genus Rhodanobacter was proposed for Gram-negative, aerobic, yellow-coloured bacteria isolated from soil. The major fatty acids are iso-C 17 : 1 v9c, iso-C 15 : 0 and iso-C 17 : 0 , and the DNA G+C contents are in the range 63-67.8 mol%. Phylogenetically, these micro-organisms are related to the genera Dyella, Frateuria and Fulvimonas within the family Xanthomonadaceae. In the course of a study of bacterial diversity in fields cultivated with Korean ginseng (Panax ginseng C. A. Meyer), two bacterial strains, GR17-7 T and GP18-1 T , were isolated in Yeongju and Ansung provinces, respectively, South Korea. Soil samples were suspended in sterilized water and diluted solutions were spread on R2A agar (Difco) and incubated at 28 u C. Purified colonies were obtained from subcultures.The isolates were tested for a number of key characteristics, such as Gram staining, catalase, oxidase and hydrolysis of casein, DNA, gelatin, starch and Tween 80, by using standard procedures (Smibert & Krieg, 1994). Growth was assessed at 5, 10, 20, 25, 30, 35 and 40 u C, at pH 4, 5, 6, 7, 8, 9 and 10, and at 0, 1, 3, 5 and 7 % (w/v) NaCl. Hydrolysis of carboxymethylcellulose (0.1 %, w/v; Sigma), chitin from crab shells (1 %, w/v), pectin (0.5 %, w/v) and tyrosine (0.5 %, w/v) was also determined. Cell morphology and motility were observed using light microscopy (AXIO; Zeiss) and transmission electron microscopy (model 912AB; LEO). In addition, the strains were characterized by using the whole test-spectrum of the API 20NE, API ID 32GN and API ZYM systems (bioMérieux), according to the manufacturer's instructions. The API ZYM test strip was read after 4 h incubation at 37 u C and the...

The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3%) type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%). The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry). These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.

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