See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/26306888 Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil Article in International Journal of Systematic and Evolutionary Microbiology · July 2009 DOI: 10.1099/ijs.0.004838-0 · Source: PubMed CITATIONS READS 27 148 6 authors, including: Hang-Yeon Weon Rangasamy Anandham RURAL DEVELOPMENT ADMINISTRATION Tamil Nadu Agricultural University 233 PUBLICATIONS 4,199 CITATIONS 168 PUBLICATIONS 2,042 CITATIONS SEE PROFILE SEE PROFILE Byung-Yong Kim Seung-Beom Hong chunlab RURAL DEVELOPMENT ADMINISTRATION 152 PUBLICATIONS 3,339 CITATIONS 292 PUBLICATIONS 8,892 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Fruit ripening using microbes View project Quinoa View project All content following this page was uploaded by Soon-Wo Kwon on 29 September 2015. 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International Journal of Systematic and Evolutionary Microbiology (2009), 59, 1685–1690 DOI 10.1099/ijs.0.004838-0 Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil Hang-Yeon Weon,1 Rangasamy Anandham,2 Byung-Yong Kim,3 Seung-Beom Hong,3 Young-Ah Jeon3 and Soon-Wo Kwon3 Correspondence 1Applied Microbiology Division, National Institute of Agricultural Science and Technology, Rural Soon-Wo Kwon Development Administration (RDA), Suwon 441-707, Republic of Korea [email protected] 2Organic Farming Division, National Institute of Agricultural Science and Technology, Rural Development Administration (RDA), Suwon 441-707, Republic of Korea 3Korean Agricultural Culture Collection (KACC), Microbial Genetics Division, National Institute of Agricultural Biotechnology, RDA, Suwon 441-707, Republic of Korea Two novel strains isolated from soils, JS12-10T and JS14-6T, were characterized using a polyphasic approach to determine their taxonomic positions. These isolates were found to be aerobic, Gram-negative, motile with one polar flagellum, non-spore-forming and rod-shaped. Phenotypic and fatty acid data supported the affiliation of JS12-10T and JS14-6T to the genus Dyella. However, chemotaxonomic data and DNA–DNA relatedness values allowed differentiation of these strains from other Dyella species with validly published names. Strains JS12-10T and JS14-6T showed the highest 16S rRNA gene sequence similarities with Dyella ginsengisoli Gsoil 3046T (98.4 %) and Dyella japonica XD53T (97.9 %), respectively, and the 16S rRNA gene sequence similarity between them was 97.1 %. DNA–DNA hybridization values between the novel isolates and strains of other recognized Dyella species were 29–38 %. Therefore, strains JS12- 10T and JS14-6T represent two novel species of the genus Dyella, for which the names Dyella soli sp. nov. (type strain JS12-10T 5KACC 12747T 5JCM 15423T) and Dyella terrae sp. nov. (type strain JS14-6T 5KACC 12748T 5JCM 15424T) are proposed. Xie & Yokota (2005) isolated three bacterial strains from the genus Dyella includes five species, namely D. japonica garden soil and assigned them to a novel genus, Dyella, (Xie & Yokota, 2005), D. koreensis (An et al., 2005), D. with Dyella japonica as the type species. Members of the yeojuensis (Kim et al., 2006), D. ginsengisoli (Jung et al., genus Dyella are yellow-coloured rods that are catalase- 2009) and D. marensis (Lee & Lee, 2009). and oxidase-positive and urease-negative. These yellow- During a survey on cultivable bacterial communities, we pigmented strains were shown to be distinguished from T T other genera, as represented by Frateuria aurantia (Swings isolated two yellow-coloured strains, JS12-10 and JS14-6 , et al., 1980), Rhodanobacter lindaniclasticus (Nalin et al., from forest soil and soil cultivated with Citrus species, 1999), Fulvimonas soli (Mergaert et al., 2002) and respectively, taken from Jeju island, Republic of Korea. Luteibacter rhizovicinus (Johansen et al., 2005), based on These two strains were shown to be affiliated with the 16S rRNA gene sequences. In addition, the genus Dyella genus Dyella of the order Xanthomonadales and subjected can be differentiated from Frateuria aurantia by the to further taxonomic characterization. The results from absence of cellular fatty acids C 2-OH, C 3-OH, phenotypic, chemotaxonomic and phylogenetic analyses, 12 : 0 12 : 0 in combination with DNA–DNA hybridization experi- C18 : 0 and C17 : 0 cyclo in Dyella species and from T + ments, showed the distinctiveness of strains JS12-10 and Fulvimonas soli on the basis of G C content (63–67 T compared with 71.7 mol% for Fulvimonas soli). At present, JS14-6 , both from each other and from the type strains of species of Dyella. Abbreviations: DIG, digoxigenin–11-dUTP; ML, maximum-likelihood; Soil samples (1 g) were suspended in 9 ml 0.85 % NaCl (w/ MP, maximum-parsimony; NJ, neighbour-joining. v) solution and mixed in a shaker for 30 min. Aliquots of The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene the serially diluted sample were spread on R2A agar plates sequences of strains JS12-10T and JS14-6T are EU604272 and (Reasoner & Geldreich, 1985) and incubated at 28 uC for T T EU604273, respectively. 5 days. Strains JS12-10 and JS14-6 , which could be Maximum-likelihood and maximum-parsimony trees based on 16S rRNA distinguished by their yellow-coloured colonies, were gene sequences are available with the online version of this paper. cultured and maintained on R2A agar at 28 uC and were Downloaded from www.sgmjournals.org by 004838 G 2009 IUMS Printed in Great Britain 1685 IP: 1.179.143.178 On: Thu, 27 Aug 2015 02:14:27 H.-Y. Weon and others subjected to taxonomic investigation. D. japonica DSM ditions for the DIG-labelled probes were as described for 16301T, D. koreensis KCTC 12359T, D. yeojuensis KACC the DIG High Prime DNA Labeling and Detection Starter 11405T, Frateuria aurantia DSM 6220T and L. rhizovicinus kit II. After hybridization, the blots were subjected to KACC 12830T were used as reference strains in biochem- stringent washing steps, after which the chemiluminescence ical, chemotaxonomic and DNA–DNA hybridization detection kit, based on CSPD, was used. Levels of experiments. To investigate basic morphological, physio- relatedness were determined by scanning the X-ray logical and biochemical characteristics, the methods membranes and slot intensities were determined by using described by Smibert & Krieg (1994) were used for Gram the 1D Image Analysis Software version 3.0 (Kodak Digital staining, oxidase and catalase reactions and to test for Science). Self-hybridization values were considered to hydrolysis of CM-cellulose, casein, chitin, DNA, pectin, represent 100 % of the maximal achievable signal and starch, tyrosine, Tween 80 and xanthine. R2A medium was values obtained with the other strains were compared with used to determine growth at various temperatures this standard. The experiments were carried out in (5–45 uC at intervals of 5 uC) and requirement for NaCl triplicate for each sample. G+C contents were determined (0–5 %, w/v). The pH range for growth (pH 4–10 at by HPLC analysis of deoxyribonucleosides as described by intervals of 1 pH unit) was determined in R2A broth Mesbah et al. (1989), using a reversed-phase column adjusted with citrate-phosphate buffer or Tris/HCl buffer (Supelcosil LC-18 S; Supelco). (Breznak & Costilow, 1994). Cell morphology was Strains JS12-10T and JS14-6T were Gram-negative, aerobic, observed by transmission electron microscopy (model rod-shaped and motile with one flagellum. Both grew well 912AB; LEO) and phase-contrast microscopy (Axio; on R2A agar, nutrient agar and tryptic soy agar (Difco). Zeiss). For observation of cell morphology by TEM, cells Strain JS14-6T grew on MacConkey agar (Difco) but strain were grown on R2A agar and suspended in physiological JS12-10T did not. The strains could be differentiated from saline solution. A small drop of the suspension was placed each other on the basis of DNA hydrolysis, nitrate on a carbon-coated copper grid and the cells were reduction, arginine hydrolysis, assimilation of carbon negatively stained with 0.5 % uranyl acetate. For other compounds and enzyme activities. Also, the two strains phenotypic tests, API 20 NE, ID 32 GN and API ZYM test could be separated from other members of genus Dyella, kits (bioMe´rieux) were used according to the manufac- Frateuria aurantia and L. rhizovicinus on the basis of turer’s recommendations. The API ZYM tests were read phenotypic properties (Table 1). after 4 h incubation at 37 uC, the other API tests after 5 days at 28 uC. Whole-cell fatty acids were analysed For the 16S rRNA gene sequence analysis, continuous according to the standard protocol of the MIDI/Hewlett stretches of 1420 bp (strain JS12-10T) and 1423 bp (JS14- Packard Microbial Identification System (Sasser, 1990) 6T) were obtained and analysed. Strain JS12-10T showed after cultivation on R2A agar for 2 days at 28 uC. the highest sequence similarities to D. ginsengisoli Gsoil 3046T (98.4 %) and D. koreensis BB4T (98.1 %), followed by Genomic DNA was isolated and purified following the D. japonica XD53T (97.9 %), Frateuria aurantia DSM method described by Ausubel et al. (1987). The 16S rRNA 6220T (97.5 %), D. marensis CS5-B2T (97.2 %), strain JS14- gene sequence was amplified by using the universal primers 6T (97.1 %) and D. yeojuensis R2A16-10T (96.1 %). Strain fD1 and rP2 (Weisburg et al., 1991) and sequenced as JS14-6T showed high sequence similarities to D. japonica described by Weon et al. (2005) with an automatic DNA XD53T (97.9 %), D. ginsengisoli Gsoil 3046T (97.3 %), D. sequencer (ABI 3100; Applied Biosystems). The 16S rRNA marensis CS5-B2T (97.2 %), strain JS12-10T (97.1 %), D. gene sequences were aligned with the CLUSTAL W program koreensis BB4T (96.8 %), D. yeojuensis R2A16-10T (96.7 %) (Thompson et al., 1994).