scholarly journals Williamsia limnetica sp. nov., isolated from a limnetic lake sediment

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1414-1418 ◽  
Author(s):  
Anil Sazak ◽  
Nevzat Sahin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Lake Sediment ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Distinct Lineage ◽  
Actinomycete Strain

An actinomycete, strain L1505T, was isolated from a limnetic lake sediment and found to have morphological, biochemical, physiological and chemotaxonomic properties consistent with its classification in the genus Williamsia . Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain L1505T formed a distinct lineage within the genus Williamsia . The isolate belonged to a cluster containing W. muralis MA140/96T, W. marianensis MT8T and W. faeni N1350T, with which the isolate shared 99.0–98.2 % 16S rRNA gene sequence similarity. Genotypic and phenotypic data also indicated that the isolate was different from known members of the genus Williamsia . On the basis of these data, strain 1505T is considered to represent a novel species of the genus Williamsia , for which the name Williamsia limnetica sp. nov. is proposed (type strain L1505T = DSM 45521T = NRRL B-24829T = KCTC 19981T).

scholarly journals Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1786-1793 ◽  
Author(s):  
Wallace Rafael Souza ◽  
Rafael Eduardo Silva ◽  
Michael Goodfellow ◽  
Kanungnid Busarakam ◽  
Fernanda Sales Figueiro ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Gene Tree ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus Amycolatopsis and formed a branch in the Amycolatopsis 16S rRNA gene tree together with Amycolatopsis bullii NRRL B-24847T, Amycolatopsis plumensis NRRL B-24324T, Amycolatopsis tolypomycina DSM 44544T and Amycolatopsis vancoresmycina NRRL B-24208T. It was related most closely to A. bullii NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus Amycolatopsis as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).

Sphingobium sufflavum sp. nov., isolated from a freshwater lake

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3444-3450 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yu-Wen Shiau ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Distinct Branch ◽  
The 16S Rrna Gene

A Gram-stain negative, rod-shaped, non-motile, non-spore-forming and aerobic bacterial strain, designated HL-25T, was isolated and characterized in a taxonomic study using a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences showed that the isolate constituted a distinct branch within the genus Sphingobium , showing the highest level of 16S rRNA gene sequence similarity to Sphingobium vulgare HU1-GD12T (96.6 %). The major fatty acids (>10 %) of strain HL-25T were C18 : 1ω7c, C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C18 : 0. The major cellular hydroxy fatty acid was C14 : 0 2-OH. The major isoprenoid quinone was Q-10 and the DNA G+C content was 63.8 mol%. The polar lipid profile consisted of a mixture of sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, an uncharacterized glycolipid, an uncharacterized aminophospholipid and four uncharacterized phospholipids. The polyamine pattern of strain HL-25T contained spermidine and putrescine. On the basis of these genotypic, chemotaxonomic and phenotypic data, strain HL-25T represents a novel species in the genus Sphingobium , for which the name Sphingobium sufflavum sp. nov. is proposed. The type strain is HL-25T ( = BCRC 80413T = KCTC 23953T).

Marininema halotolerans sp. nov., a novel thermoactinomycete isolated from a sediment sample, and emended description of the genus Marininema Li et al. 2012

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4562-4567 ◽  
Author(s):  
Xiao-Mei Zhang ◽  
Jie He ◽  
Dao-Feng Zhang ◽  
Wei Chen ◽  
Zhao Jiang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sediment Sample ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A novel Gram-stain-positive bacterium, designated strain YIM M11385T, was isolated from a marine sediment sample collected from the South Bay, Little Andaman Island, India with a salinity of 35 p.p.m., pH 8.5. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M11385T belongs to the genus Marininema , supported by a bootstrap value of 100 %. The taxonomic position of this organism was further established by using a polyphasic approach. Strain YIM M11385T grew optimally at 28 °C, pH 7.0 and in the presence of 0–5 % (w/v) NaCl. The 16S rRNA gene sequence similarity between strain YIM M11385T and Marininema mesophilum SCSIO 10219T was 98.3 %. Strain YIM M11385T exhibited a quinone system with only MK-7, the polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major components, and the major fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The level of DNA–DNA relatedness between strain YIM M11385T and M. mesophilum SCSIO 10219T was 59.36 %. On the basis of genotypic and phenotypic data, it is apparent that strain YIM M11385T represents a novel species of the genus Marininema , for which the name Marininema halotolerans sp. nov. is proposed. The type strain is YIM M11385T ( = CCTCC AB 2012052T = DSM 45789T). In addition, we propose that the description of the genus Marininema should be further emended based on the results of the present study.

Amnibacterium soli sp. nov., an actinobacterium isolated from grass soil

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4750-4753 ◽  
Author(s):  
Long Jin ◽  
Hyung-Gwan Lee ◽  
Hee-Sik Kim ◽  
Chi-Yong Ahn ◽  
Hee-Mock Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, aerobic, non-motile, non-spore-forming, short rod-shaped actinobacterium, designated strain PB243T, was isolated from grass soil sampled in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies showed the isolate was clearly affiliated with the class Actinobacteria , and most closely related to Amnibacterium kyonggiense KEMC 51201-037T, showing 98.8 % 16S rRNA gene sequence similarity. Cells of strain PB243T formed yellow colonies on R2A agar, contained MK-11 and MK-12 as the predominant menaquinones, l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, and anteiso-C15 : 0 and iso-C16 : 0 among the major fatty acids. The acyl type of the muramic acid was acetyl. The G+C content of the genomic DNA of strain PB243T was 71.5 mol%. Thus, the combined genotypic and phenotypic data supported the conclusion that strain PB243T represents a novel species of the genus Amnibacterium , for which the name Amnibacterium soli sp. nov. is proposed. The type strain is PB243T ( = KCTC 33147T = JCM 19015T).

Parvularcula dongshanensis sp. nov., isolated from soft coral

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2114-2117 ◽  
Author(s):  
Zhiwei Yu ◽  
Qiliang Lai ◽  
Guizhen Li ◽  
Zongze Shao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Soft Coral ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

A taxonomic study was carried out on strain SH25T, which was isolated from soft coral collected from Dongshan Island, China. The isolate was a heterotrophic organism to the soft coral, and was a Gram-reaction-negative, short rod that was motile by a polar flagellum. Growth was observed at salinities from 0 to 12 % and at temperatures from 10 to 41 °C. It was unable to reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SH25T belonged to the genus Parvularcula , with highest sequence similarity to Parvularcula lutaonensis CC-MMS-1T (96.1 %) and Parvularcula bermudensis HTCC2503T (94.3 %); 16S rRNA gene sequence similarities to other taxa were below 90.0 %. The dominant fatty acids were C16 : 0 and summed feature 8 (C18 : 1ω7c/ω6c,). The G+C content of the chromosomal DNA was 61.8 mol%. The major quinone was Q10. These combined genotypic and phenotypic data show that strain SH25T represents a novel species of the genus Parvularcula , for which the name Parvularcula dongshanensis sp. nov. is proposed. The type strain is SH25T ( = CCTCC AB 2010355T = LMG 26158T = MCCC 1A06534T).

scholarly journals Chitinivorax tropicus gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater lake

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1086-1091 ◽  
Author(s):  
Wen-Ming Chen ◽  
Shwu-Harn Yang ◽  
Wei-Cheng Huang ◽  
Chih-Yu Cheng ◽  
Shih-Yi Sheu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A facultatively anaerobic, chitinolytic bacterium, strain KL-9T, was isolated from a freshwater lake in Taiwan and characterized by using a polyphasic taxonomic approach. Cells of strain KL-9T were Gram-negative, rod-shaped, motile by means of a single polar flagellum and non-spore-forming. Growth occurred at 15–40 °C (optimum, 30–37 °C), at pH 7.0–9.0 (optimum, pH 8.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-8. The DNA G+C content of strain KL-9T was 64.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and several uncharacterized phospholipids and aminolipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KL-9T formed a distinct lineage with respect to closely related genera within the class Betaproteobacteria , being most closely related to members of the genera Leeia , Chitinimonas , Silvimonas and Andreprevotia . Levels of 16S rRNA gene sequence similarity with respect to the type strains of type species of these genera were below 91 %. On the basis of genotypic and phenotypic data, strain KL-9T is thus considered to represent a novel species of a new genus within the class Betaproteobacteria , for which the name Chitinivorax tropicus gen. nov., sp. nov. is proposed. The type strain of Chitinivorax tropicus is KL-9T ( = BCRC 80168T = LMG 25530T).

scholarly journals Paludibacterium paludis sp. nov., isolated from a marsh

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2497-2502 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Zih-Han Chen ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A bacterial strain, designated KBP-21T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain KBP-21T were Gram-stain-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile rods that formed yellow colonies. Growth occurred at 15–40 °C (optimum, 30 °C), at pH 5.0–8.0 (optimum, pH 8.0) and with 0–2 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-21T belonged to the genus Paludibacterium within the family Neisseriaceae of the class Betaproteobacteria and the closest related neighbour was Paludibacterium yongneupense 5YN8-15T with a 16S rRNA gene sequence similarity value of 96.4 %. Strain KBP-21T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the predominant fatty acids. The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 62.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized aminophospholipid and several uncharacterized phospholipids. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain KBP-21T represents a novel species in the genus Paludibacterium , for which the name Paludibacterium paludis sp. nov. is proposed. The type strain is KBP-21T ( = BCRC 80514T = LMG 27230T = KCTC 32182T).

Amycolatopsis magusensis sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1254-1260 ◽  
Author(s):  
Mustafa Camas ◽  
Nevzat Sahin ◽  
Anil Sazak ◽  
Cathrin Spröer ◽  
Hans-Peter Klenk
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

A novel actinomycete, designated strain KT2025T, was isolated from arid soil collected from Magusa, northern Cyprus. The taxonomic position of the novel strain was established by using a polyphasic approach. The organism had chemical and morphological features consistent with its classification in the genus Amycolatopsis . Phylogenetic analyses based on 16S rRNA gene sequences supported the classification of the isolate in the genus Amycolatopsis and showed that the organism formed a cluster with Amycolatopsis nigrescens CSC17-Ta-90T, Amycolatopsis minnesotensis 32U-2T, Amycolatopsis sacchari DSM 44468T and Amycolatopsis dongchuanensis YIM 75904T. 16S rRNA gene sequence similarity analysis indicated that strain KT2025T was most closely related to Amycolatopsis lurida DSM 43134T (97.5 %), Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409T (97.4 %), Amycolatopsis keratiniphila subsp. nogabecina DSM 44586T (97.1 %), Amycolatopsis nigrescens DSM 44992T (97.1 %), Amycolatopsis azurea DSM 43854T (97.1 %) and Amycolatopsis minnesotensis DSM 44988T (96.9 %). The organism was found to have chemical features typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and hydroxy-phosphatidylethanolamine. The major fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0. The G+C content of the genomic DNA was 70.8 mol%. Phenotypic data clearly distinguished the isolate from its closest relatives. The combined genotypic and phenotypic data and low levels of DNA–DNA relatedness with its closest relatives indicated that strain KT2025T represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis magusensis sp. nov. is proposed. The type strain is KT2025T ( = DSM 45510T = KCTC 29056T).

scholarly journals Terrimonas rubra sp. nov., isolated from a polluted farmland soil and emended description of the genus Terrimonas

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2593-2597 ◽  
Author(s):  
Jing Zhang ◽  
Tao Gu ◽  
Yu Zhou ◽  
Jie He ◽  
Liu-Qiang Zheng ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Farmland Soil ◽  
Emended Description

A salmon-red-pigmented bacterial strain, designated M-8T, was isolated from a polluted farmland soil sample in China and was characterized in a taxonomic study using a polyphasic approach. Strain M-8T was Gram-stain-negative, rod-shaped, non-motile and non-spore-forming. Growth occurred at 20–37 °C, at pH 5.0–10.0 and with 0–2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M-8T belonged to the genus Terrimonas .16S rRNA gene sequence similarity values between strain M-8T and the type strains of the three recognized species of the genus Terrimonas , Terrimonas ferruginea KACC 11310T, Terrimonas aquatica LMG 24825T and Terrimonas lutea KACC 13047T, were 97.1, 96.3 and 95.3 %, respectively. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain M-8T was 47.0 mol%. On the basis of genotypic and phenotypic data, strain M-8T is considered to represent a novel species of the genus Terrimonas , for which the name Terrimonas rubra sp. nov. is proposed. The type strain is M-8T ( = CCTCC AB 2010401T = KCTC 23299T). An emended description of the genus Terrimonas is also presented.

scholarly journals Rhodovarius crocodyli sp. nov., isolated from a crocodile pond

2020 ◽  
Vol 70 (9) ◽  
pp. 5141-5148 ◽  
Author(s):  
Wen-Ming Chen ◽  
Yi-Ru Xie ◽  
Der-Shyan Sheu ◽  
Jyh-Ming Tsai ◽  
Shih-Yi Sheu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Freshwater Pond

Bacterial strain CCP-6T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain CCP-6T is affiliated with species in the genus Rhodovarius . Strain CCP-6T was most closely related to Rhodovarius lipocyclicus CCUG 44693T with a 98.9% 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed light pink-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-6T were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, three unidentified aminophospholipids and an unidentified phospholipid. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content of the genomic DNA was 69.3 mol%. Strain CCP-6T showed 85.8% average nucleotide identity and 14.5% digital DNA–DNA hybridization identity with Rhodovarius lipocyclicus CCUG 44693T. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain CCP-6T represents a novel species in the genus Rhodovarius , for which the name Rhodovarius crocodyli sp. nov. is proposed. The type strain is CCP-6T (=BCRC 81095T=LMG 30310T=KCTC 62188T).

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