scholarly journals Paracoccus isoporae sp. nov., isolated from the reef-building coral Isopora palifera

2011 ◽  
Vol 61 (5) ◽  
pp. 1138-1143 ◽  
Author(s):  
Ming-Hui Chen ◽  
Shih-Yi Sheu ◽  
Chaolun Allen Chen ◽  
Jih-Terng Wang ◽  
Wen-Ming Chen
Keyword(s):  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Major Respiratory Quinone ◽  
Taxonomic Approach ◽  
Isopora Palifera

A bacterial strain, designated SW-3T, was isolated from the reef-building coral Isopora palifera, from Southern Taiwan, and was characterized by using a polyphasic taxonomic approach. Cells of strain SW-3T were Gram-reaction-negative, aerobic, rod-shaped and motile by means of monopolar flagella and formed cream–white colonies. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-3T belonged to the genus Paracoccus and its most closely related neighbours were P. aestuarii B7T, P. homiensis DD-R11T, P. marinus KKL-A5T, P. denitrificans DSM 413T and P. zeaxanthinifaciens R-1512T, with sequence similarities of 96.8, 96.6, 96.1 , 95.8 and 94.9 %, respectively. Strain SW-3T exhibited optimal growth at 25–30 °C and pH 9–10 and in 3–5 % (w/v) NaCl. The predominant cellular fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 75 %). The major respiratory quinone was Q-10. The polar lipid profile consisted of a mixture of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and several uncharacterized polar lipids. The DNA G+C content of strain SW-3T was 63.7 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from recognized species of the genus Paracoccus. It is evident from the genotypic, phenotypic and chemotaxonomic data that strain SW-3T represents a novel species of the genus Paracoccus, for which the name Paracoccus isoporae sp. nov. is proposed. The type strain is SW-3T ( = LMG 25205T  = BCRC 17967T).

scholarly journals Arcicella aurantiaca sp. nov., isolated from stream water

2010 ◽  
Vol 60 (12) ◽  
pp. 2979-2983 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Cho-Song Yang ◽  
Ming-Hui Chen ◽  
A. B. Arun ◽  
Chiu-Chung Young ◽  
...  
Keyword(s):  
Stream Water ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Major Respiratory Quinone ◽  
Southern Taiwan ◽  
Taxonomic Approach

A bacterial strain designated TNR-18T was isolated from stream water in southern Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TNR-18T were Gram-stain-negative, strictly aerobic, non-motile and vibrioid, and the strain formed orange colonies. Growth occurred at 10–30 °C, with 0–0.2 % NaCl and at pH 6.0–10.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TNR-18T belonged to the genus Arcicella; its closest neighbours were Arcicella rosea TW5T and Arcicella aquatica NO-502T, with respective sequence similarities of 97.9 and 97.8 %. Predominant cellular fatty acids (>10 %) were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 37.7 %), C16 : 1 ω5c (13.0 %) and iso-C15 : 0 (11.1 %). The major respiratory quinone was MK-7. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized polar lipids. The DNA G+C content was 39.9 mol%. On the basis of the phylogenetic and phenotypic data, strain TNR-18T should be classified as representing a novel species, for which the name Arcicella aurantiaca sp. nov. is proposed. The type strain is TNR-18T (=LMG 25207T =BCRC 17969T).

scholarly journals Arcicella rigui sp. nov., isolated from water of a wetland, and emended descriptions of the genus Arcicella , Arcicella aquatica , Arcicella rosea and Arcicella aurantiaca

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 134-140 ◽  
Author(s):  
Wen-Ming Chen ◽  
Shwu-Harn Yang ◽  
Chiu-Chung Young ◽  
Shih-Yi Sheu
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach

A bacterial strain, designated NSW-5T, was isolated from a water sample taken from Niao-Song Wetland Park in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain NSW-5T were strictly aerobic, Gram-stain-negative, non-motile and polymorphic, being straight, vibrioid, curved and spiral-shaped rods surrounded by a thick capsule and forming light pink-coloured colonies. Some rings consisting of several cells were present. Growth occurred at 10–40 °C (optimum, 25 °C), with 0–3.0 % NaCl (optimum, 0 %) and at pH 6.0–8.0 (optimum, pH 7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain NSW-5T belonged to the genus Arcicella with sequence similarities of 98.6, 98.0 and 97.3 % with Arcicella aquatica NO-502T, Arcicella rosea TW5T and Arcicella aurantiaca TNR-18T, respectively. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 20.8 %), C16 : 0 (14.6 %), iso-C15 : 0 (13.8 %), C16 : 1ω5c (12.5 %) and C18 : 0 (11.4 %), and the only respiratory quinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized glycolipids, aminolipids, phospholipids and aminophospholipids. The DNA G+C content of strain NSW-5T was 44.1 mol%. The DNA–DNA relatedness of strain NSW-5T with respect to recognized species of the genus Arcicella was less than 70 %. On the basis of phylogenetic inference and phenotypic data, strain NSW-5T should be classified as a representative of a novel species, for which the name Arcicella rigui sp. nov. is proposed. The type strain is NSW-5T ( = KCTC 23307T = BCRC 80260T). Emended descriptions of the genus Arcicella and of Arcicella aquatica , Arcicella rosea and Arcicella aurantiaca are also proposed.

scholarly journals Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth

2004 ◽  
Vol 54 (3) ◽  
pp. 955-959 ◽  
Author(s):  
Yasuhiro Tanaka ◽  
Satoshi Hanada ◽  
Akira Manome ◽  
Takayasu Tsuchida ◽  
Ryuichiro Kurane ◽  
...  
Keyword(s):  
Optimal Growth ◽  
Cellular Fatty Acid ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Respiratory Quinone ◽  
Vigorous Growth ◽  
Major Respiratory Quinone ◽  
Ubiquinone 10 ◽  
Phototrophic Growth

A bacterial strain, designated AST4T, was isolated from activated sludge. The bacterium did not show significant growth on nutrient broth, but growth was clearly stimulated by addition of supernatant from other bacterial cultures. Culture filtrate of a strain related to the genus Sphingomonas in particular increased the cell yield and growth rate of strain AST4T. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AST4T is located within the ‘Rhodobacter group’ in the α-3 subclass of Proteobacteria, but is clearly distant from related genera in this group such as Paracoccus, Rhodobacter and Rhodovulum. Strain AST4T is a Gram-negative, non-motile, rod-shaped (0·6–0·8×1·3–2·0 μm) and aerobic bacterium. It was not able to reduce nitrate to nitrite or N2. No phototrophic growth was observed. Optimal growth occurred at 30 °C and pH 6·5–7·5. The dominant cellular fatty acid in the isolate was C18 : 1 cis11. Ubiquinone-10 was the major respiratory quinone. The G+C content was 64·5 mol% (by HPLC). Based on the phylogenetic and phenotypic traits, the name Catellibacterium nectariphilum gen. nov., sp. nov. is proposed for this isolate; the type strain is AST4T (=NBRC 100046T=JCM 11959T=DSM 15620T).

Rheinheimera tilapiae sp. nov., isolated from a freshwater culture pond

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1457-1463 ◽  
Author(s):  
Wen-Ming Chen ◽  
Shwu-Harn Yang ◽  
Chiu-Chung Young ◽  
Shih-Yi Sheu
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Cichlid Fish ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach

A bacterial strain designated Ruye-90T was isolated from a freshwater tilapiine cichlid fish culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Strain Ruye-90T was Gram-negative, aerobic, yellow-coloured, rod-shaped, and motile by means of a single polar flagellum. Growth occurred at 4–30 °C (optimum, 20–30 °C), at pH 7.0–9.0 (optimum, pH 8.0–9.0) and with 0–2 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Ruye-90T belonged to the genus Rheinheimera and its most closely related neighbour was Rheinheimera tangshanensis JA3-B52T with sequence similarity of 97.5 %. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 41.3 %), C16 : 0 (19.3 %), C18 : 1ω7c (8.4 %) and C12 : 0 3-OH (7.0 %). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 49.0 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, aminolipid and two uncharacterized phospholipids. The DNA–DNA relatedness of strain Ruye-90T with respect to recognized members of the genus Rheinheimera was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Ruye-90T represents a novel species in the genus Rheinheimera , for which the name Rheinheimera tilapiae sp. nov. is proposed. The type strain is Ruye-90T ( = LMG 26339T = BCRC 80263T = KCTC 23315T).

Roseivivax isoporae sp. nov., isolated from a reef-building coral, and emended description of the genus Roseivivax

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1259-1264 ◽  
Author(s):  
Ming-Hui Chen ◽  
Shih-Yi Sheu ◽  
Chaolun Allen Chen ◽  
Jih-Terng Wang ◽  
Wen-Ming Chen
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A bacterial strain, isolated from a sample of reef-building coral (Isopora palifera) collected off the coast of southern Taiwan, was characterized using a polyphasic taxonomic approach. The strain, designated sw-2T, was Gram-staining-negative, aerobic, rod-shaped and motile, with subpolar flagella, and formed greyish pink colonies. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain sw-2T was most closely related to Roseivivax halodurans Och 239T (97.4 % sequence similarity) and Roseivivax halotolerans Och 210T (96.4 %). The novel strain did not require NaCl for growth and exhibited optimal growth at 35–40 °C, at pH 7.5–8.0 and with 3–7 % (w/v) NaCl. It produced bacteriochlorophyll a under aerobic conditions. Summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 63.7 %) predominated in the cellular fatty acid profile. The novel strain’s major respiratory quinone was ubiquinone Q-10 and its genomic DNA G+C content was 68.8 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, sulfo-quinovosyl diacylglycerol and three uncharacterized phospholipids. The level of DNA–DNA relatedness between strain sw-2T and Roseivivax halodurans Och 239T was only 15.0 %. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of the novel strain from all established species of the genus Roseivivax . Based on the genotypic, phenotypic and chemotaxonomic data, strain sw-2T represents a novel species in the genus Roseivivax , for which the name Roseivivax isoporae sp. nov. is proposed. The type strain is sw-2T ( = LMG 25204T = BCRC 17966T).

scholarly journals Paracoccus stylophorae sp. nov., isolated from the reef-building coral Stylophora pistillata

2011 ◽  
Vol 61 (9) ◽  
pp. 2221-2226 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Sing-Rong Jiang ◽  
Chaolun Allen Chen ◽  
Jih-Terng Wang ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Stylophora Pistillata ◽  
Major Respiratory Quinone ◽  
Type Strains

A bacterial strain, designated KTW-16T, was isolated from the reef-building coral Stylophora pistillata, collected from southern Taiwan. Strain KTW-16T was a Gram-negative, facultatively anaerobic, pale-yellow, non-motile short rod. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KTW-16T belonged to the genus Paracoccus in the Alphaproteobacteria and exhibited 93.7–96.9 % 16S rRNA gene sequence similarity with type strains of species of the genus Paracoccus (96.9 % with Paracoccus alcaliphilus JCM 7364T). Strain KTW-16T grew at 15–40 °C (optimum 35 °C), at pH 6.0–10.0 (optimum pH 8.0) and with 0–9 % NaCl (optimum 5 %). The predominant cellular fatty acids were C18 : 1ω7c, C19 : 0 cyclo ω8c and C18 : 0. The major respiratory quinone was Q-10 and the DNA G+C content was 69.1 mol%. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and several unknown polar lipids. The physiological and biochemical tests allowed clear phenotypic differentiation of the isolate from the type strains of already described Paracoccus species. It is evident from the genotypic, phenotypic and chemotaxonomic analysis that strain KTW-16T should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus stylophorae sp. nov. is proposed. The type strain is KTW-16T ( = LMG 25392T  = BCRC 80106T).

Gemmobacter lanyuensis sp. nov., isolated from a freshwater spring

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4039-4045 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yu-Wen Shiau ◽  
Yan-Ting Wei ◽  
Wen-Ming Chen
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Freshwater Spring ◽  
Taxonomic Approach

A bacterial strain designated Orc-4T was isolated from a freshwater spring in Taiwan and characterized using the polyphasic taxonomic approach. Cells of strain Orc-4T were facultatively anaerobic, Gram-reaction-negative, poly-β-hydroxybutyrate-accumulating, non-motile rods surrounded by a thick capsule and forming cream–white colonies. Growth occurred at 15–40 °C (optimum, 25–30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–1 % NaCl (optimum, 0–0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Orc-4T belonged to the genus Gemmobacter within the family Rhodobacteraceae of the class Alphaproteobacteria and its most closely related neighbour was Gemmobacter fontiphilus JS43T with sequence similarity of 97.8 %. Strain Orc-4T contained C18 : 1ω7c as the predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content of the genomic DNA was 63.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one uncharacterized aminolipid and several uncharacterized phospholipids. The DNA–DNA relatedness of strain Orc-4T with respect to recognized species of the genus Gemmobacter was less than 48 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Orc-4T represents a novel species of the genus Gemmobacter , for which the name Gemmobacter lanyuensis sp. nov. is proposed. The type strain is Orc-4T ( = BCRC 80378T = LMG 26667T = KCTC 23714T).

scholarly journals Jannaschia cystaugens sp. nov., an Alexandrium (Dinophyceae) cyst formation-promoting bacterium from Hiroshima Bay, Japan

2004 ◽  
Vol 54 (5) ◽  
pp. 1687-1692 ◽  
Author(s):  
Masao Adachi ◽  
Tsukasa Kanno ◽  
Ryo Okamoto ◽  
Azusa Shinozaki ◽  
Kiyomi Fujikawa-Adachi ◽  
...  
Keyword(s):  
Heterotrophic Bacteria ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Cyst Formation ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Optimal Growth Temperature ◽  
Respiratory Quinone

Heterotrophic bacteria isolated from water samples taken from Hiroshima Bay, Japan, and referred to as Alexandrium (Dinophyceae) cyst formation-promoting bacteria, were assigned to the Roseobacter–Sulfitobacter–Silicibacter group within the α-Proteobacteria on the basis of nearly complete 16S rRNA gene sequences. Phylogenetic analyses showed that two strains, CFPB-A9T and CFPB-A5, are closely related to each other and that their closest relative was Jannaschia helgolandensis (95·9 % sequence similarity). These strains were Gram-negative, motile, obligately aerobic rods that required sodium ions and 2–7 % sea salts for growth and did not produce bacteriochlorophyll a. Their optimal growth temperature was 25–30 °C. The strains had Q-10 as the dominant respiratory quinone. Primary cellular fatty acid in both strains was 18 : 1ω7c. The DNA G+C contents of strains CFPB-A9T and CFPB-A5 were 59·1 and 59·2 mol%, respectively. Based on physiological, biological, chemotaxonomic and phylogenetic data, the strains are considered to represent a novel species, Jannaschia cystaugens sp. nov., with type strain CFPB-A9T (=LMG 22015T=NBRC 100362T).

scholarly journals Deinococcus metalli sp. nov., isolated from an abandoned lead-zinc mine

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3457-3461 ◽  
Author(s):  
Guang-Da Feng ◽  
Yong-Hong Wang ◽  
Yan-Xuan Li ◽  
Hong-Hui Zhu
Keyword(s):  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Taxonomic Study ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Gram Staining ◽  
Lead Zinc ◽  
Zinc Mine ◽  
Major Respiratory Quinone ◽  
Deinococcus Ficus

An aerobic, non-motile and Gram-staining-positive bacterial strain (1PNM-19T) was isolated from a lead-zinc ore in an abandoned mine and was investigated in a taxonomic study using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 1PNM-19T was affiliated to the genus Deinococcus and most closely related to Deinococcus aquatilis DSM 23025T and Deinococcus ficus DSM 19119T. The major respiratory quinone was determined to be menaquinone 8 (MK-8) and the major fatty acids contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. A complex polar lipid profile consisted of different unidentified glycolipids and polar lipids, two unidentified aminolipids, an unidentified phosphoglycolipid, phospholipid and aminophospholipid. The genomic DNA G+C content of strain 1PNM-19T was 71.7 ± 0.1 mol%. Based on data from this taxonomic study, strain 1PNM-19T represents a novel species of the genus Deinococcus, for which the name Deinococcus metalli sp. nov. is proposed. The type strain is 1PNM-19T ( = GIMCC 1.654T = CCTCC AB 2014198T = DSM 27521T).

scholarly journals Vogesella amnigena sp. nov., isolated from a freshwater river

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3634-3640 ◽  
Author(s):  
Wen-Ming Chen ◽  
Jhen-Ci Chen ◽  
Chi Wang ◽  
Cheng-Wen Huang ◽  
Shih-Yi Sheu
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Optimum Ph ◽  
Major Respiratory Quinone ◽  
Freshwater River

A bacterial strain, designated Npb-02T, was isolated from a freshwater river in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain Npb-02T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, rod-shaped and non-motile. Growth occurred at 15–40 °C (optimum 25–30 °C), at pH 7.0–8.0 (optimum pH 7.0) and with 0–1 % NaCl (optimum 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-02T belonged to the genus Vogesella and was most closely related to Vogesella perlucida DS-28T with sequence similarity of 98.3 %. Strain Npb-02T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major respiratory quinone was Q-8.The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and an uncharacterized phospholipid. The genomic DNA G+C content of strain Npb-02T was 64.1 mol%. The DNA–DNA hybridization values for strain Npb-02T with Vogesella perlucida DS-28T, Vogesella mureinivorans 389T and Vogesella lacus GR13T were less than 25 %. On the basis of phylogenetic inference and phenotypic data, strain Npb-02T represents a novel species of the genus Vogesella, for which the name Vogesella amnigena sp. nov. is proposed. The type strain is Npb-02T ( = BCRC 80887T = LMG 28419T = KCTC 42195T).

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