scholarly journals Rhizobium alvei sp. nov., isolated from a freshwater river

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 472-478 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Hsing-Wei Huang ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Encoding ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach ◽  
Freshwater River

A bacterial strain designated TNR-22T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TNR-22T were facultatively anaerobic, Gram-stain-negative, rod-shaped, motile by a single polar flagellum and formed cream-coloured colonies. Growth occurred at 4–45 °C (optimum, 25–30 °C), with 0–1.0 % (w/v) NaCl (optimum, 0.5 %) and at pH 7.0–8.0 (optimum, pH 7.0). Strain TNR-22T did not form nodules on Macroptilium atropurpureum. The nifH gene encoding denitrogenase reductase was not detected by PCR. The major fatty acids (>10 %) of strain TNR-22T were C18 : 1ω7c and C16 : 0. The DNA G+C content was 60.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an uncharacterized aminoglycolipid and an uncharacterized phospholipid. Comparative analysis of 16S rRNA gene sequences showed that strain TNR-22T constituted a distinct branch within the genus Rhizobium , showing the highest level of sequence similarity with Rhizobium rosettiformans W3T (96.3 %). Phenotypic characteristics of the novel strain also differed from those of the most closely related species of the genus Rhizobium . On the basis of the genotypic, chemotaxonomic and phenotypic data, strain TNR-22T represents a novel species in the genus Rhizobium , for which the name Rhizobium alvei sp. nov. is proposed. The type strain is TNR-22T ( = BCRC 80408T = LMG 26895T = KCTC 23919T).

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).

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).

Vogesella fluminis sp. nov., isolated from a freshwater river, and emended description of the genus Vogesella

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3043-3049 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Jhen-Ci Chen ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Freshwater River

A bacterial strain designated Npb-07T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Strain Npb-07T was Gram-negative, aerobic, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 10–37 °C (optimum, 20–30 °C), at pH 6.0–9.0 (optimum, pH 6.0–7.0) and with 0–1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-07T belonged to the genus Vogesella and its most closely related neighbour was Vogesella indigofera ATCC 19706T with sequence similarity of 98.4 %. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 44.4 %) and C16 : 0 (31.9 %). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 65.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two uncharacterized aminophospholipids and an uncharacterized phospholipid. The DNA–DNA relatedness of strain Npb-07T with respect to V. indigofera ATCC 19706T was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Npb-07T represents a novel species in the genus Vogesella , for which the name Vogesella fluminis sp. nov. is proposed. The type strain is Npb-07T ( = LMG 26669T = BCRC 80377T = KCTC 23713T).

Pseudorhodoferax aquiterrae sp. nov., isolated from groundwater

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 169-174 ◽  
Author(s):  
Wen-Ming Chen ◽  
Yang-Shun Lin ◽  
Chiu-Chung Young ◽  
Shih-Yi Sheu
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Taxonomic Approach

A Gram-negative, rod-shaped, motile, non-spore-forming and poly-β-hydroxybutyrate-containing bacterial strain, designated NAFc-7T, was isolated from groundwater in Taiwan and was characterized using a polyphasic taxonomic approach. Growth occurred at 15–40 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 6.0–7.0) and with 0–3 % NaCl (optimum, 0–1 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain NAFc-7T, together with Pseudorhodoferax soli TBEA3T (98.2 % sequence similarity) and Pseudorhodoferax caeni SB1T (98.0 %), formed a deep line within the family Comamonadaceae . Strain NAFc-7T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C17 : 0 cyclo as the predominant fatty acids. The major 3-hydroxy fatty acid was C10 : 0 3-OH. The major isoprenoid quinone was Q-8 and the DNA G+C content was 67.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and an uncharacterized phospholipid. The DNA–DNA relatedness of strain NAFc-7T with respect to recognized species of the genus Pseudorhodoferax was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain NAFc-7T represents a novel member of the genus Pseudorhodoferax , for which the name Pseudorhodoferax aquiterrae sp. nov. is proposed. The type strain is NAFc-7T ( = BCRC 80210T = LMG 26333T = KCTC 23314T).

Jeongeupia chitinilytica sp. nov., a chitinolytic bacterium isolated from soil

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 934-938 ◽  
Author(s):  
Wen-Ming Chen ◽  
Rey-Chang Chang ◽  
Chih-Yu Cheng ◽  
Yu-Wen Shiau ◽  
Shih-Yi Sheu
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium

A novel bacterium, designated strain JchiT, was isolated from soil in Taiwan and characterized using a polyphasic approach. Cells of strain JchiT were aerobic, Gram-stain-negative, motile and rod-shaped. They contained poly-β-hydroxybutyrate granules and formed dark-yellow colonies. Growth occurred at 20–37 °C (optimum between 25 and 30 °C), at pH 6.0–8.0 (optimum between pH 7.0 and pH 8.0) and with 0–2 % NaCl (optimum between 0 and 1 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain JchiT belonged to the genus Jeongeupia and that its closest neighbour was Jeongeupia naejangsanensis BIO-TAS4-2T (98.0 % sequence similarity). The major fatty acids (>10 %) of strain JchiT were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C12 : 0 3-OH. The isoprenoid quinone was Q-8 and the genomic DNA G+C content was 66.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and two unidentified phospholipids. The DNA–DNA relatedness value between strain JchiT and J. naejangsanensis BIO-TAS4-2T was about 41.0 %. On the basis of the genotypic and phenotypic data, strain JchiT represents a novel species in the genus Jeongeupia , for which the name Jeongeupia chitinilytica sp. nov. is proposed. The type strain is JchiT ( = BCRC 80367T  = KCTC 23701T).

Streptomyces ziwulingensis sp. nov., isolated from grassland soil

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1545-1549 ◽  
Author(s):  
Yan Bing Lin ◽  
Xin Ye Wang ◽  
Ting Ting Wang ◽  
Shao Shan An ◽  
Peng Shi ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Grassland Soil ◽  
Content Type ◽  
Link Type ◽  
Hybridization Data ◽  
Antibacterial And Antifungal

A novel actinobacterium, designated strain F22T, was isolated from grassland soil collected from the Ziwuling area on the Loess Plateau, China. The novel strain was found to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces . Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain F22T belonged to the genus Streptomyces , being most closely related to Streptomyces resistomycificus NBRC 12814T (98.28 % sequence similarity), Streptomyces ciscaucasicus NBRC 12872T (98.14 %), Streptomyces chartreusis NBRC 12753T (98.14 %) and Streptomyces canus NRRL B-1989T (98.14 %). In DNA–DNA hybridizations and comparisons of morphological and phenotypic data, strain F22T could be distinguished from all of its closest phylogenetic relatives. Strain F22T exhibited antibacterial and antifungal activity, especially against Staphylococcus aureus , Bacillus subtilis and Cylindrocarpon destructans. Based on the DNA–DNA hybridization data and morphological, phenotypic and phylogenetic evidence, strain F22T represents a novel species of the genus Streptomyces , for which the name Streptomyces ziwulingensis sp. nov. is proposed. The type strain is F22T ( = CCNWFX 0001T = JCM 18081T = ACCC41875T).

Pedobacter ginsenosidimutans sp. nov., with ginsenoside-converting activity

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4396-4401 ◽  
Author(s):  
Jung-Eun Yang ◽  
Heung-Min Son ◽  
Jung Min Lee ◽  
Heon-Sub Shin ◽  
Sang-Yong Park ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Biochemical Tests ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
The Republic

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain, designated THG-45T, was isolated from soil of a ginseng field of Pocheon province in the Republic of Korea and its taxonomic position was investigated by a polyphasic approach. Growth occurred at 4–30 °C, at pH 5.5–9.0 and with 0–2 % (w/v) NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-45T was shown to belong to the genus Pedobacter and was related to Pedobacter borealis G-1T (98.8 %), P. alluvionis NWER-II11T (97.9 %), P. agri PB92T (97.9 %), P. terrae DS-57T (97.5 %), P. suwonensis 15-52T (97.4 %), P. sandarakinus DS-27T (97.0 %) and P. soli 15-51T (97.0 %), but DNA relatedness between strain THG-45T and these strains was below 36 %. The G+C content of the genomic DNA was 39 mol%. The only isoprenoid quinone detected in strain THG-45T was menaquinone-7 (MK-7). The predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH, and the major polar lipids were phosphatidylethanolamine and an unidentified aminophosphoglycolipid. Phenotypic data and phylogenetic inference supported the affiliation of strain THG-45T to the genus Pedobacter , and a number of biochemical tests differentiated strain THG-45T from the recognized species of the genus Pedobacter . Therefore, the novel isolate represents a novel species, for which the name Pedobacter ginsenosidimutans sp. nov. is proposed, with THG-45T as the type strain ( = KACC 14530T = JCM 16721T).

Fluviimonas pallidilutea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from a freshwater river

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3861-3867 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yu-Siang Chen ◽  
Yu-Wen Shiau ◽  
Wen-Ming Chen
Keyword(s):  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
The Family ◽  
Freshwater River

A bacterial strain designated TQQ6T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain TQQ6T were strictly aerobic, Gram-staining-negative, poly-β-hydroxybutyrate-containing, non-motile, non-spore-forming, long rods surrounded by a thick capsule and forming pale orange colonies. Growth occurred at 20–40 °C (optimum, 25 °C), at pH 7.0–9.0 (optimum, pH 8.0) and with 0–0.5 % NaCl (optimum, 0 %). The predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, C16 : 1ω5c and C16 : 0. The major isoprenoid quinone was MK-7 and the DNA G+C content was 42.2 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, two uncharacterized aminophospholipids and three uncharacterized phospholipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TQQ6T represents a distinct phyletic line that reflects a novel generic status within the family Cytophagaceae with relatively low sequence similarities (less than 90 %) to members of other genera with validly published names. On the basis of the genotypic and phenotypic data, strain TQQ6T represents a new genus and novel species of the family Cytophagaceae , for which the name Fluviimonas pallidilutea gen. nov., sp. nov. is proposed. The type strain is TQQ6T ( = BCRC 80447T = LMG 27056T = KCTC 32035T).

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 Postechiella marina gen. nov., sp. nov., isolated from seawater

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1528-1535 ◽  
Author(s):  
Dong-Heon Lee ◽  
Sun Ja Cho ◽  
Suk Min Kim ◽  
Sun Bok Lee
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-staining-negative, strictly aerobic, non-motile, yellow-pigmented bacterium, designated strain M091T, was isolated from seawater at Damupo beach in Pohang, Republic of Korea, and investigated using a polyphasic taxonomic approach. The novel strain grew optimally at 25 °C, pH 7.0–8.0, and in the presence of 3 % (w/v) NaCl. In a phylogenetic analysis based on 16S rRNA gene sequences, strain M091T formed a lineage within the family Flavobacteriaceae that was distinct from the most closely related genera of Flaviramulus (95.1 % sequence similarity), Algibacter (94.9–93.9 %), Mariniflexile (94.8–94.2 %), Winogradskyella (94.8–93.2 %), Lacinutrix (94.7–93.8 %) and Tamlana (94.7–92.9 %). The polar lipid profile of the novel strain comprised phosphatidylethanolamine, two unidentified aminolipids, one unidentified phospholipid and seven unidentified lipids. The predominant cellular fatty acids were iso-C15 : 0 (20.5 %), iso-C17 : 0 3-OH (15.4 %), iso-C15 : 0 3-OH (12.4 %), C15 : 0 (10.9 %) and iso-C15 : 1 G (9.9 %). The genomic DNA G+C content of strain M091T was 34.4 mol% and the major respiratory quinone was MK-6. Based on phenotypic and genotypic data, strain M091T represents a new genus and novel species in the family Flavobacteriaceae , for which the name Postechiella marina gen. nov., sp. nov. is proposed. The type strain of the type species is M091T ( = KCTC 23537T = JCM 17630T).

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