Identification of Saccharomonospora Strains by the Use of Genomic DNA Fragments and rRNA Gene Probes

Yoon, Jung‐Hoon; Kim, Hongik; Kim, Sam-Bong; Kim, Hong-Joong; Kim, Won Yong; Lee, Sung Taik; Goodfellow, Michael; Park, Yong-Ha

doi:10.1099/00207713-46-2-502

International Journal of Systematic Bacteriology

1996

DOI: 10.1099/00207713-46-2-502

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Identification of Saccharomonospora Strains by the Use of Genomic DNA Fragments and rRNA Gene Probes

Jung‐Hoon Yoon

Hongik Kim

Sam-Bong Kim

et al.

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Cited by 479 publications

(387 citation statements)

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“…Cell biomass of F. agariphila KCTC 12365 T , F. algae KCTC 12364 T and F. spongicola KCTC 22662 T for DNA extraction and for polar lipid analysis was obtained from cultures grown for 2 days at 25 uC in MB. Chromosomal DNA was isolated and purified according to the method described by Yoon et al (1996), with the exception that RNase T1 was used in combination with RNase A to minimize the contamination of RNA. The 16S rRNA gene was amplified by PCR as described previously (Yoon et al, 1998) using two universal primers, 9F (59-GAGTTTGA-TCCTGGCTCAG-39) and 1512R (59-ACGGTTACCTT-GTTACGACTT-39), and the PCR products were purified by using a QIAquick PCR purification kit (Qiagen).…”

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confidence: 99%

Formosa undariae sp. nov., isolated from a reservoir containing the brown algae Undaria pinnatifida

Park

Lee

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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A strain of Gram-staining-negative, aerobic, non-flagellated, non-gliding and rod-shaped bacteria, designated WS-MY3 T , was isolated from a brown algae reservoir in South Korea. Strain WS-MY3 T grew optimally at 25 6C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain WS-MY3 T fell within the cluster comprising the type strains of species of the genus Formosa, clustering coherently with the type strains of Formosa agariphila and Formosa algae. It exhibited 16S rRNA gene sequence similarity values of 98.7, 97.9 and 96.8 % to the type strains of F. agariphila, F. algae and Formosa spongicola, respectively. Strain WS-MY3 T contained MK-6 as the predominant menaquinone and iso-C 15 : 0 , iso-C 16 : 0 3-OH, iso-C 15 : 1 G and summed feature 3 (C 16 : 1 v7c and/or C 16 : 1 v6c) as the major fatty acids. The major polar lipids of strain WS-MY3 T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain WS-MY3 T was 37.3 mol% and its DNA-DNA relatedness values with F. agariphila KCTC 12365 T and F. algae KCTC 12364 T were 23 % and 17 %, respectively. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WS-MY3 T is separate from the three recognized species of the genus Formosa. On the basis of the data presented, strain WS-MY3 T is considered to represent a novel species of the genus Formosa, for which the name Formosa undariae sp. nov. is proposed. The type strain is WS-MY3 T (5KCTC 32328 T 5CECT 8286 T ).

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Formosa undariae sp. nov., isolated from a reservoir containing the brown algae Undaria pinnatifida

Park

Lee

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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“…Cell mass of G. marinus KCTC 23046 T and G. lutimaris D1-y4 T for DNA extraction was obtained from cultures grown for 3 days at 30 8C in MB. Chromosomal DNA was isolated and purified according to the method described by Yoon et al (1996), with the exception that RNase T1 was used in combination with RNase A to minimize contamination with RNA. The 16S rRNA gene was amplified by PCR using two universal primers (59-GAGTTTGATCC-TGGCTCAG-39 and 59-AGAAAGGAGGTGATCCAGCC-39) as described previously (Yoon et al, 1998), and the PCR products were purified by using a QIAquick PCR purification kit (Qiagen).…”

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Gaetbulibacter aquiaggeris sp. nov., a member of the Flavobacteriaceae isolated from seawater

Jung

Lee

Yoon

2016

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated KEM-8 T , was isolated from seawater in the Korean peninsula. Strain KEM-8 T was found to grow optimally at pH 7.0-8.0, at 30 8C and in the presence of 2-3 % (w/v) NaCl. A neighbourjoining phylogenetic tree based on 16S rRNA gene sequences showed that strain KEM-8 T falls within the clade comprising species of the genus Gaetbulibacter, clustering with the type strains of Gaetbulibacter marinus and Gaetbulibacter lutimaris with which it exhibits 98.4 and 97.2 % 16S rRNA gene sequence similarity, respectively. Sequence similarities to Gaetbulibacter saemankumensis SMK-12 T and Gaetbulibacter aestuarii KCTC 23303 T were 95.4 and 95.2 %, respectively. Strain KEM-8 T was found to contain MK-6 as the predominant menaquinone and iso-C 15 : 0 , iso-C 17 : 0 3-OH, iso-C 16 : 0 3-OH and iso-C 15 : 1 G as the major fatty acids. The major polar lipids were identified as phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain KEM-8 T was 36.0 mol% and mean DNA-DNA relatedness values with G. marinus KCTC 23046 T and G. lutimaris D1-y4 T were 27.6¡0.9 and 10.3¡1.4 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain KEM-8 T is distinguishable from species of the genus Gaetbulibacter with validly published names. On the basis of the data presented, strain KEM-8 T represents a novel species of the genus Gaetbulibacter, for which the name Gaetbulibacter aquiaggeris sp. nov. is proposed. The type strain is KEM-8 T (5KCTC 42198 T 5NBRC 110553 T ).The genus Gaetbulibacter, a member of the family Flavobacteriaceae (phylum Bacteroidetes), was established by Jung et al. (2005) with the description of Gaetbulibacter saemankumensis, isolated from seawater of the Yellow Sea in South Korea. Subsequently, three further species of the genus, Gaetbulibacter marinus, Gaetbulibacter aestuarii and Gaetbulibacter lutimaris, were described from marine environments in Korea (Yang & Cho, 2008;Park et al., 2012;Yoon et al., 2013).The standard dilution plating technique was used for isolation of bacterial strains from seawater from Geumgang Estuary Bank (368 009 48.960 N 1268 449 23.9990 E) in South Korea. Strain KEM-8 T was isolated on marine agar 2216 (MA; Becton Dickinson) at 25 8C and cultivated routinely on MA at 30 8C. Strain KEM-8 T was maintained on MA at 4 8C for short-term preservation and as a glycerol suspension (20 %, w/v in distilled water) at 280 8C for long-term preservation. G. marinus KCTC 23046 T and G. lutimaris D1-y4 T were used as reference strains for DNA-DNA hybridization, phenotypic characterization (except for some characters) and fatty acid analysis. G. saemankumensis (type species of the genus Gaetbulibacter) SMK-12 T and G. aestuarii KCTC 23303 T were used as reference strains for phenotypic characterization (except for some characters) and fatty acid analysis. G. saemankumensis SMK-12 T and G. lutimaris D1-y4 T were obta...

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“…For the determination of the DNA G+C content and genomic DNA-DNA hybridization (DDH), the chromosomal DNA of strain BUT-3 T and R. appendicifer 120-1 T was extracted and purified according to the method described by Yoon et al (1996), except that RNaseT1 was used in combination with RNaseA to minimize contamination with RNA. The DNA G+C content of strain BUT-3 T , determined according to the thermal denaturation method of Marmur & Doty (1962), was 67.7 mol%; higher than that of R. appendicifer 120-1 T (61.1 mol%) (Fukuda et al, 2012).…”

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Rhodoligotrophos jinshengii sp. nov., isolated from activated sludge

Deng

Chen

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, non-spore-forming, non-motile, ovoid, aerobic bacterial strain, designated BUT-3 T , was isolated from activated sludge from the wastewater treatment facility of a herbicidemanufacturing plant in Kunshan city, Jiangsu province, PR China. Strain BUT-3 T grew between 15 and 40 6C, with optimum growth at 30 6C. The pH range for growth was between 5.0 and 10.0 (optimum pH 7.0). The range of NaCl concentrations for growth of strain BUT-3 T was 0-7.0 % (w/v), with an optimum of 1.5-3.0 % (w/v). A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain BUT-3 T clustered closely with Rhodoligotrophos appendicifer 120-1 T (98.32 % similarity), with a bootstrap confidence level of 100 %. The major fatty acids (.5 % of total fatty acids) were C 19 : 0 cyclo v8c, C 18 : 1 v7c, C 16 : 0 , anteiso-C 15 : 0 and iso-C 15 : 0 . Strain BUT-3 T contained ubiquinone Q-10 as the predominant respiratory quinone. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, three unidentified aminolipids (AL1-3), two unknown phospholipids (PL1, 5), four unidentified glycolipids (GL1-4) and two unknown lipids (L1, 2). The G+C content of the genomic DNA was 67.7 mol%. The DNA-DNA relatedness between BUT-3 T and R. appendicifer 120-1 T was 44.1±0.6 %. Based on the polyphasic taxonomic data, strain BUT-3 T should be classified as a representative of a novel species of the genus Rhodoligotrophos, for which the name Rhodoligotrophos jinshengii sp. nov. is proposed. The type strain is BUT-3 T (5CCTCC AB2013083 T 5KACC 17220 T ).The genus Rhodoligotrophos, established recently by Fukuda et al. (2012), belongs to the class Alphaproteobacteria, order Rhizobiales, family Rhodobiaceae. The type strain, Rhodoligotrophos appendicifer 120-1 T , was isolated from samples of freshwater from the bottom of a freshwater lake in the Antarctica. It is an oligotroph partly due to the relatively low levels of nutrients in its ecological niche. In this study, we reported a Rhodoligotrophos-like bacterial strain, designated BUT-3 T , which was isolated from activated sludge. Taxonomic analyses demonstrated that the isolate should be placed into a novel species within the genus Rhodoligotrophos.R. appendicifer 120-1 T was used as a reference strain and was purchased from the Japan Collection of Micro-organisms. Unless indicated otherwise, experiments on morphological, physiological, molecular and chemotaxonomic characteristics were performed on cells grown on 0.256LB medium (l 21 :10.0 g tryptone, 5.0 g yeast extract and 5.0 g NaCl) under aerobic conditions at 30 u C.Strain BUT-3 T was isolated from a soil sample collected from Kunshan city, Jiangsu province, PR China, using the standard dilution plating technique at 30 uC on 0.256LB medium. Unlike R. appendicifer 120-1 T , strain BUT-3 T is a copiotroph, and can grow in LB medium, TSB medium (l 21 :15.0 g tryptone, 5.0 g soy peptone and 5.0 g NaCl), R2A medium (l 21 :0.5 g tryptone, 0.5 g yeast extrac...

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Identification of Saccharomonospora Strains by the Use of Genomic DNA Fragments and rRNA Gene Probes

Cited by 479 publications

References 21 publications

Formosa undariae sp. nov., isolated from a reservoir containing the brown algae Undaria pinnatifida

Formosa undariae sp. nov., isolated from a reservoir containing the brown algae Undaria pinnatifida

Gaetbulibacter aquiaggeris sp. nov., a member of the Flavobacteriaceae isolated from seawater

Rhodoligotrophos jinshengii sp. nov., isolated from activated sludge

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