scholarly journals Dyella japonica gen. nov., sp. nov., a γ-proteobacterium isolated from soil

2005 ◽  
Vol 55 (2) ◽  
pp. 753-756 ◽  
Author(s):  
Cheng-Hui Xie ◽  
Akira Yokota
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Fatty Acid Profile ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Ph Values ◽  
The Family

Three strains isolated from the soil of a garden in Tokyo, Japan, were characterized physiologically, biochemically and in terms of fatty acid profile, DNA–DNA relatedness and 16S rRNA gene sequence. The isolates were Gram-negative, aerobic, rod-shaped cells with polar flagellation. According to DNA–DNA similarity, the strains belonged to the same species. The bacteria grew at temperatures from 10 to 37 °C, with an optimum around 25–30 °C. Growth was observed at pH values from 5·6 to 8·0. The DNA G+C content ranged from 63·4 to 64·0 mol%. Phylogenetic analyses of 16S rRNA gene sequences revealed a clear affiliation with members of the family ‘Xanthomonadaceae’. The closest relationship was seen with Fulvimonas soli and Frateuria aurantia, but, in terms of physiology and fatty acid profile, the bacteria described were rather distant from Fulvimonas and Frateuria. On the basis of phenotypic and phylogenetic distinctness, it is proposed that the isolates represent a novel species in a novel genus, namely Dyella japonica gen. nov., sp. nov. The type strain is XD53T (=IAM 15069T=DSM 16301T=ATCC BAA-939T).

scholarly journals Description of Olleya aquimaris sp. nov., isolated from seawater, and emended description of the genus Olleya Mancuso Nichols et al. 2005

2010 ◽  
Vol 60 (4) ◽  
pp. 887-891 ◽  
Author(s):  
Soo-Young Lee ◽  
Sooyeon Park ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The Family ◽  
Emended Description

A Gram-stain-negative, non-flagellated, motile (by gliding), yellow-pigmented, rod-shaped bacterial strain, designated L-4T, was isolated from seawater of Baekdo harbour in the East Sea, Korea. Strain L-4T grew optimally at 37 °C, at pH 6.5–7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain L-4T clustered with Olleya marilimosa CAM030T, a member of the family Flavobacteriaceae. Strain L-4T exhibited 16S rRNA gene sequence similarity values of 97.2 % to O. marilimosa CAM030T and less than 95.8 % to other members of the family Flavobacteriaceae. Strain L-4T and O. marilimosa CIP 108537T contained MK-6 as the predominant menaquinone. The fatty acid and polar lipid profiles of strain L-4T were similar to those of O. marilimosa CIP 108537T. The DNA G+C content of strain L-4T was 35 mol% and DNA–DNA relatedness between strain L-4T and O. marilimosa CIP 108537T was 7 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, enable strain L-4T to be distinguished from O. marilimosa. On the basis of these data, strain L-4T is considered to represent a novel species of the genus Olleya for which the name Olleya aquimaris sp. nov. is proposed; the type strain is L-4T (=KCTC 22661T =CCUG 58074T). An emended description of the genus Olleya is also provided.

scholarly journals Paracoccus fistulariae sp. nov., a lipolytic bacterium isolated from bluespotted cornetfish, Fistularia commersonii

2010 ◽  
Vol 60 (12) ◽  
pp. 2908-2912 ◽  
Author(s):  
Young-Ok Kim ◽  
Hee Jeong Kong ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Kyung-Kil Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Type Strains

A Gram-stain-negative, non-motile, non-spore-forming and short rod- or rod-shaped bacterial strain, designated 22-5T, was isolated from a bluespotted cornetfish, Fistularia commersonii, and subjected to taxonomic study. Strain 22-5T grew optimally at 30 °C and in the presence of 2–5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 22-5T belonged to the genus Paracoccus and joined the cluster comprising Paracoccus homiensis DD-R11T and Paracoccus zeaxanthinifaciens ATCC 21588T, with which strain 22-5T exhibited 97.4 and 96.9 % 16S rRNA gene sequence similarity, respectively. Strain 22-5T exhibited 94.0–96.6 % 16S rRNA gene sequence similarity with the other type strains of species of the genus Paracoccus. Strain 22-5T contained Q-10 as the predominant menaquinone and C18 : 1 ω7c as the predominant fatty acid. In this study, P. zeaxanthinifaciens KCTC 22688T also contained Q-10 as the predominant isoprenoid quinone. The DNA G+C content of strain 22-5T was 63.6 mol%. Strain 22-5T exhibited 44 and 32 % DNA–DNA relatedness to P. homiensis KACC 11518T and P. zeaxanthinifaciens KCTC 22688T, respectively. On the basis of phenotypic, phylogenetic and genetic data, strain 22-5T is considered to represent a novel species of the genus Paracoccus, for which the name Paracoccus fistulariae sp. nov. is proposed. The type strain is 22-5T (=KCTC 22803T =CCUG 58401T).

scholarly journals Salinicoccus jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood

2007 ◽  
Vol 57 (3) ◽  
pp. 633-638 ◽  
Author(s):  
Zubair Aslam ◽  
Ju Hyoung Lim ◽  
Wan-Taek Im ◽  
Muhammad Yasir ◽  
Young Ryun Chung ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
Gene Sequence Analysis ◽  
The Family

A novel, moderately halophilic, Gram-positive coccus, designated strain S2R53-5T, was isolated from jeotgal, a traditional Korean fermented seafood. The organism was strictly aerobic, non-motile, non-sporulating and catalase- and oxidase-positive. Strain S2R53-5T grew in the presence of 0.5–15 % (w/v) NaCl and at pH 6.5–11.0, with optimum growth at 5 % (w/v) NaCl and pH 7.0. The temperature range for growth was 20.0–30.0 °C, with an optimum temperature of 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2R53-5T belongs to the family Staphylococcaceae and was most closely related to Salinicoccus roseus DSM 5351T (96.8 % gene sequence similarity), Salinicoccus hispanicus DSM 5352T (96.1 %), Salinicoccus alkaliphilus T8T (95.2 %) and Jeotgalicoccus halotolerans YKJ-101T (95.1 %). The genomic DNA G+C content was 47.0 mol%, which is in the range of 46–51 mol% that is characteristic for the genus Salinicoccus. Levels of DNA–DNA relatedness between strain S2R53-5T and S. roseus DSM 5351T, S. hispanicus DSM 5352T and S. alkaliphilus KCTC 13928T were 32.2, 15.4 and 4.6 %, respectively. Chemotaxonomic data (major menaquinone, MK-6; major fatty acids, iso-C15 : 0 and anteiso-C15 : 0; cell-wall murein type, Lys and Gly) and 16S rRNA gene sequence analysis supported the affiliation of strain S2R53-5T with the genus Salinicoccus. The combined evidence from the low DNA–DNA relatedness, physiological, biochemical and other genotypic data indicate that strain S2R53-5T clearly represents a novel species of the genus Salinicoccus, for which the name Salinicoccus jeotgali sp. nov. is proposed. The type strain is S2R53-5T (=KCTC 13030T=LMG 23640T).

scholarly journals Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3878-3884 ◽  
Author(s):  
Akira Nakamura
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Physiological Data ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
Type Strains ◽  
The 16S Rrna Gene

Strain 43PT was isolated as an l-glucose-utilizing bacterium from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic and non-motile cocci. The 16S rRNA gene sequence of the strain showed high similarity to that of Paracoccus limosus (98.5 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that this strain belongs to the genus Paracoccus. Strain 43PT contained Q-10 as the sole isoprenoid quinone. The major cellular fatty acids were C18 : 1ω7c or C18 : 1ω6c and C16 : 0, and C18 : 0, C18 : 1ω9c, C10 : 0 3-OH and summed feature 2 were detected as minor components. The DNA G+C content of strain 43PT was 64.1 mol%. Strain 43PT contained the major polar lipids phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and two unknown glycolipids. The DNA–DNA relatedness between strain 43PT and the six related type strains of the genus Paracoccus, including P. limosus, was below 23 %. Based on the chemotaxonomic and physiological data and the values of DNA–DNA relatedness, especially the ability to assimilate l-glucose, this strain should be classified as a representative of a novel species of the genus Paracoccus, for which the name Paracoccus laeviglucosivorans sp. nov. (type strain 43PT = JCM 30587T = DSM 100094T) is proposed.

scholarly journals Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the Cytophaga–Flavobacterium–Bacteroides group isolated from surface water of the central Baltic Sea

2004 ◽  
Vol 54 (6) ◽  
pp. 2335-2341 ◽  
Author(s):  
Ingrid Brettar ◽  
Richard Christen ◽  
Manfred G. Höfle
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Baltic Sea ◽  
New Genus ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Family

A bacterial isolate from the Baltic Sea, BA160T, was characterized for its physiological and biochemical features, fatty acid profile, G+C content and phylogenetic position based on 16S rRNA gene sequences. The strain was isolated from the surface water of the central Baltic Sea during the decay of a plankton bloom. Phylogenetic analyses of the 16S rRNA gene sequence revealed a clear affiliation with the family ‘Flexibacteraceae’, and showed the closest phylogenetic relationship with the species Belliella baltica and Cyclobacterium marinum. The G+C content of the DNA was 38·4 mol%. The strain was red-coloured due to carotenoids, Gram-negative, rod-shaped, and catalase- and oxidase-positive. Growth was observed at salinities from 0 to 6 %, with an optimum around 1·5 %. Temperature for growth ranged from 4 to 40 °C, with an optimum around 30 °C. The fatty acids were dominated by branched-chain fatty acids (>87 %), with a high abundance of iso-C15 : 0 (23 %) and anteiso-C15 : 0 (19 %). According to its morphology, physiology, fatty acid composition, G+C content and 16S rRNA gene sequence, strain BA160T is considered to represent a new genus of the family ‘Flexibacteraceae’. Due to its aquatic origin, the name Aquiflexum balticum gen. nov, sp. nov. is suggested for the type species (type strain, BA160T=DSM 16537T=LMG 22565T=CIP 108445T) of the new genus.

scholarly journals Yonghaparkia alkaliphila gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an alkaline soil

2006 ◽  
Vol 56 (10) ◽  
pp. 2415-2420 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Peter Schumann ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
The Family

Two Gram-positive, non-motile, non-spore-forming and rod-shaped actinomycete strains, KSL-113T and KSL-133, were isolated from an alkaline soil in Korea, and their taxonomic positions were investigated by using a polyphasic approach. The strains grew optimally at 30 °C and pH 9.0. Phenotypic, phylogenetic and genetic similarities indicated that strains KSL-113T and KSL-133 represent the same species. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains KSL-113T and KSL-133 fell within the family Microbacteriaceae of the suborder Micrococcineae, the highest 16S rRNA gene sequence similarity values (98.2 %) being obtained with respect to Microcella putealis CV-2T. The 16S rRNA gene sequence similarities between strains KSL-113T and KSL-133 and the other members of the family Microbacteriaceae used in the phylogenetic analysis were less than 96.0 %. Strains KSL-113T and KSL-133 could be clearly distinguished from members of the family Microbacteriaceae on the basis of differences in chemotaxonomic properties, including the predominant menaquinone type, the cell-wall peptidoglycan type and the fatty acid profile. Accordingly, on the basis of the combined phenotypic, chemotaxonomic and phylogenetic data, strains KSL-113T and KSL-133 constitute a novel genus and species of the family Microbacteriaceae, for which the name Yonghaparkia alkaliphila gen. nov., sp. nov. is proposed. The type strain of Yonghaparkia alkaliphila is KSL-113T (=KCTC 19126T=CIP 108920T).

scholarly journals Bacillus seohaeanensis sp. nov., a halotolerant bacterium that contains l-lysine in its cell wall

2006 ◽  
Vol 56 (8) ◽  
pp. 1893-1898 ◽  
Author(s):  
Jae-Chan Lee ◽  
Jee-Min Lim ◽  
Dong-Jin Park ◽  
Che Ok Jeon ◽  
Wen-Jun Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Positive Bacterium

A halotolerant, round-endospore-forming, aerobic, Gram-positive bacterium, designated BH724T, was isolated from a solar saltern at Taean in Korea. Cells of this strain were rod-shaped and found to be non-motile. Strain BH724T grew at salinities of 0–10 % (w/v) NaCl with an optimum of 3 % (w/v) NaCl and at temperatures of 15–50 °C with an optimum of 40 °C. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BH724T belonged to the genus Bacillus and that Bacillus aquimaris TF-12T, Bacillus marisflavi TF-11T and Bacillus vietnamensis JCM 11124T were its closest neighbours, sharing 97.3, 97.2 and 97.0 % 16S rRNA gene sequence similarity, respectively. The genomic DNA G+C content was 39 mol% and the predominant menaquinone was MK-7. Its major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The peptidoglycan type was A1α, linked directly through l-lysine. On the basis of morphological, chemotaxonomic, physiological and phylogenetic properties, strain BH724T represents a novel species of the genus Bacillus, for which the name Bacillus seohaeanensis sp. nov. is proposed. The type strain is BH724T (=KCTC 3913T=DSM 16464T).

scholarly journals Citreimonas salinaria gen. nov., sp. nov., a member of the Roseobacter clade isolated from a solar saltern

2006 ◽  
Vol 56 (12) ◽  
pp. 2799-2803 ◽  
Author(s):  
Dong H. Choi ◽  
Byung C. Cho
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Rrna Gene Sequence ◽  
The Family ◽  
The 16S Rrna Gene

A lemon-shaped marine bacterium, strain CL-SP20T, isolated from hypersaline water from a solar saltern in Korea, was characterized in terms of its physiological and biochemical features, its fatty acid profile and its phylogenetic position based on 16S rRNA gene sequences. Analysis of the 16S rRNA gene sequence revealed a clear affiliation with the Roseobacter lineage (91.0–96.3 % similarity) of the family Rhodobacteraceae. However, strain CL-SP20T did not form a robust clade with any species of the Roseobacter clade, forming a distinct subline. Strain CL-SP20T is non-motile and forms beige colonies on marine agar. The strain is able to grow with sea salts at concentrations in the range 1–10 %, with optimal growth between 5 and 6 %. It grows at temperatures in the range 15–40 °C and at pH 6–10. The strain cannot oxidize thiosulfate. The fatty acids are dominated by 18 : 1ω7c (54.3 %) and 19 : 0 cyclo ω8c (20.4 %). The DNA G+C content is 67.3 mol%. According to the physiological data, fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence, strain CL-SP20T represents a novel species in a novel genus of the family Rhodobacteraceae, for which the name Citreimonas salinaria gen. nov., sp. nov. is proposed. The type strain of Citreimonas salinaria is CL-SP20T (=KCCM 42116T=JCM 13036T).

scholarly journals Paucihalobacter ruber gen. nov., sp. nov., isolated from a haloalkaline lake sediment sample

2020 ◽  
Vol 70 (10) ◽  
pp. 5373-5381 ◽  
Author(s):  
Shu-ge Wu ◽  
Jing-jing Wang ◽  
Jia-ning Wang ◽  
Qi Chen ◽  
Zong-jun Du ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacterium, designated CWB-1T, was isolated from a haloalkaline lake sediment sample collected from the bottom of Chaiwopu Lake, Urumchi, Xinjiang Province, PR China. Strain CWB-1T grew at 4–40 °C (optimum, 30–35 °C), pH 6.5–9.0 (optimum, pH 6.5–7.0) and with 0.5–5.5 % (w/v) NaCl (optimum, 2.5–3.0 %). Phylogenetic analyses based on the 16S rRNA gene sequence and the whole genome sequence both revealed that strain CWB-1T belonged to the family Flavobacteriaceae . The strain had the highest similarity of the 16S rRNA gene sequence to Psychroserpens jangbogonensis PAMC 27130T (92.8 %). The genome of strain CWB-1T was 3 548 011 bp long with 36.3 % DNA G+C content. The predominant fatty acids (>10 %) in the CWB-1T cells were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 1 (iso-C15 : 1 H/C13 : 0 3-OH). The major respiratory quinone was menaquinone-6 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. Based on the phylogenetic analyses, as well as the phenotypic characteristics, a novel genus and species of the family Flavobacteriaceae , Paucihalobacter ruber gen. nov., sp. nov., is proposed. The type strain is CWB-1T (=KCTC 72450T=CGMCC 1.17149T).

scholarly journals Pedobacter insulae sp. nov., isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 1999-2003 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Hyun Woo Oh ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Taxonomic Analysis ◽  
The Family ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, rod-shaped bacterium, DS-139T, was isolated from a soil sample collected from Dokdo, Korea, and subjected to a polyphasic taxonomic analysis. Strain DS-139T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–0.5 % (w/v) NaCl. It contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-39T belongs to the genus Pedobacter in the family Sphingobacteriaceae. The similarity values between the 16S rRNA gene sequence of strain DS-139T and those of the type strains of recognized Pedobacter species, except Pedobacter saltans, were in the range 93.9–96.7 %. The differential phenotypic properties, together with the phylogenetic distinctiveness, were sufficient to assign strain DS-139T to a species that is separate from recognized Pedobacter species. On the basis of the phenotypic and phylogenetic data, therefore, strain DS-139T represents a novel species of the genus Pedobacter, for which the name Pedobacter insulae sp. nov. is proposed. The type strain is DS-139T (=KCTC 12820T =DSM 18684T).

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