scholarly journals Modestobacter marinus sp. nov., a psychrotolerant actinobacterium from deep-sea sediment, and emended description of the genus Modestobacter

2011 ◽  
Vol 61 (7) ◽  
pp. 1710-1714 ◽  
Author(s):  
Jing Xiao ◽  
Yingxue Luo ◽  
Jing Xu ◽  
Shujie Xie ◽  
Jun Xu
Keyword(s):  
Deep Sea ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Deep Sea Sediment ◽  
Distinct Branch ◽  
Type Strains ◽  
The 16S Rrna Gene

The taxonomic status of an actinobacterium that changed colour during growth, strain 42H12-1T, isolated from deep-sea sediment collected from the Atlantic Ocean, was established using a combination of genotypic and phenotypic data. Strain 42H12-1T formed a distinct branch in the 16S rRNA gene phylogenetic tree together with the type strains in the genus Modestobacter. The highest sequence similarity by blast analysis was to Modestobacter versicolor CP153-2T (98.5 %) and the second-highest sequence similarity was to Modestobacter multiseptatus AA-826T (97.5 %). DNA–DNA relatedness of only 12 % (sd 1.82 %) between strain 42H12-1T and M. versicolor DSM 16678T differentiated them as members of separate genomic species. Colonies of strain 42H12-1T were black on oligotrophic medium, but orange to red, turning black, on copiotrophic medium. The peptidoglycan contained meso-diaminopimelic acid. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and an unknown aminophospholipid. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 and C17 : 1ω8c. The DNA G+C content was 72.3±1 mol%. Strain 42H12-1T ( = DSM 45201T  = CGMCC 4.5581T) is assigned as the type strain of a novel species of the genus Modestobacter, for which the name Modestobacter marinus sp. nov. is proposed.

Streptomyces indicus sp. nov., an actinomycete isolated from deep-sea sediment

2011 ◽  
Vol 61 (11) ◽  
pp. 2712-2716 ◽  
Author(s):  
Yingxue Luo ◽  
Jing Xiao ◽  
Yin Wang ◽  
Jing Xu ◽  
Shujie Xie ◽  
...  
Keyword(s):  
Deep Sea ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Deep Sea Sediment ◽  
Diamino Acid ◽  
The Indian Ocean ◽  
Genotypic Characteristics ◽  
Type Strains

The taxonomic position of an actinomycete isolated from deep-sea sediment from the Indian Ocean was determined by using a polyphasic approach. The presence of iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0 as the major cellular fatty acids, ll-diaminopimelic acid as the characteristic diamino acid, and MK-9(H4, H6 and H8) as the major menaquinones supported the affiliation of strain IH32-1T to the genus Streptomyces. Comparison of 16S rRNA gene sequences showed that strain IH32-1T exhibited highest similarities to the type strains of Streptomyces globosus (97.6 %) and Streptomyces toxytricini (97.6 %). However, DNA–DNA relatedness values between strain IH32-1T and the type strains of S. globosus and S. toxytricini were determined as 55.2±4.7 and 38.3±2.5 %, respectively. Based on its chemotaxonomic, phenotypic and genotypic characteristics, strain IH32-1T is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces indicus sp. nov. is proposed. The type strain is IH32-1T ( = DSM 42001T = CGMCC 4.5727T).

scholarly journals Streptomyces fenghuangensis sp. nov., isolated from seawater

2011 ◽  
Vol 61 (12) ◽  
pp. 2811-2815 ◽  
Author(s):  
Honghui Zhu ◽  
Shumei Jiang ◽  
Qing Yao ◽  
Yonghong Wang ◽  
Meibiao Chen ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Substrate Mycelium ◽  
Physiological And Biochemical Characteristics ◽  
Type Strains ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

An actinomycete, designated strain GIMN4.003T, was isolated from seawater collected in Sanya, China. It produced white aerial mycelium and yellow substrate mycelium on Gause’s synthetic agar medium no. 1. The substrate mycelium colour was not sensitive to pH. Scanning electron microscopy observations revealed that GIMN4.003T produced straight to flexuous spore chains of rough to warty spores. ll-Diaminopimelic acid was present in the cell-wall hydrolysate. Based on chemotaxonomy and morphological features, strain GIMN4.003T was identified as a member of the genus Streptomyces. Melanin was not produced. No antimicrobial activity was detected against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Penicillium citrinum or Candida albicans. Analysis of the 16S rRNA gene sequence revealed that the highest sequence similarity was to Streptomyces radiopugnans R97T (99.0 %). However, DNA relatedness between GIMN4.003T and S. radiopugnans DSM 41901T was low (41.24±1.47 %). Furthermore, the morphological, physiological and biochemical characteristics of strain GIMN4.003T were different from those of S. radiopugnans DSM 41901T and the type strains of other closely related Streptomyces species. On the basis of its physiological and molecular properties, it is evident that strain GIMN4.003T ( = CCTCCM 208215T  = NRRL B-24801T) represents the type strain of a novel species within the genus Streptomyces, for which the name Streptomyces fenghuangensis sp. nov. is proposed.

scholarly journals Citreicella marina sp. nov., isolated from deep-sea sediment

2011 ◽  
Vol 61 (4) ◽  
pp. 728-731 ◽  
Author(s):  
Qiliang Lai ◽  
Yuanyuan Fu ◽  
Jianning Wang ◽  
Shuangxi Chen ◽  
Huanzi Zhong ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Deep Sea ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Phenotypic Data ◽  
Deep Sea Sediment ◽  
South West Indian Ocean ◽  
West Indian Ocean ◽  
Ocean Ridge

A taxonomic study was carried out on a novel strain, designated CK-I3-6T, which was isolated from deep-sea sediment of the south-west Indian Ocean Ridge. Cells were Gram-reaction-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at 4–38 °C and in 1–12 % (w/v) NaCl. Cells were able to degrade gelatin and oxidize thiosulfate but did not reduce nitrate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CK-I3-6T belonged to the genus Citreicella with a sequence similarity of 97.3 % to Citreicella thiooxidans CHLG 1T, while similarities with other taxa were <95.7 %. DNA–DNA hybridization showed that strain CK-I3-6T and C. thiooxidans CHLG 1T showed a low DNA–DNA relatedness (48±3 %). The principal fatty acids were C16 : 0 (7.8 %), C18 : 1ω7c (66.6 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 6.3 %) and C19 : 0ω8c cyclo (10.0 %). The chromosomal DNA G+C content was 67.5 mol%. On the basis of the combined genotypic and phenotypic data, strain CK-I3-6T represents a novel species of the genus Citreicella, for which the name Citreicella marina sp. nov. is proposed. The type strain is CK-I3-6T ( = CCTCC AB 209064T  = LMG 25230T  = MCCC 1A03060T).

scholarly journals Aestuariivita atlantica sp. nov., isolated from deep-sea sediment

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3281-3285 ◽  
Author(s):  
Guizhen Li ◽  
Qiliang Lai ◽  
Yaping Du ◽  
Xiupian Liu ◽  
Fengqin Sun ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Deep Sea ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Deep Sea Sediment ◽  
Gram Staining

A novel strain, 22II-S11-z3T, was isolated from the deep-sea sediment of the Atlantic Ocean. The bacterium was aerobic, Gram-staining-negative, oxidase-positive and catalase-negative, oval- to rod-shaped, and non-motile. Growth was observed at salinities of 1–9 % NaCl and temperatures of 10–45 °C. The isolate could hydrolyse aesculin and Tweens 20, 40 and 80, but not gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II-S11-z3T belonged to the genus Aestuariivita, with highest sequence similarity to Aestuariivita boseongensis KCTC 42052T (97.5 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain 22II-S11-z3T and A. boseongensis KCTC 42052T were 71.5 % and 20.0 ± 2.3 %, respectively. The G+C content of the chromosomal DNA was 65.5 mol%. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c/ω6c) (35.2 %), C19 : 0 cyclo ω8c (20.9 %), C16 : 0 (11.8 %), 11-methyl C18 : 1ω7c (11.4 %) and C12 : 1 3-OH (9.4 %). The respiratory quinone was determined to be Q-10. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, nine unidentified phospholipids, one unidentified aminolipid and two unidentified lipids were present. The combined genotypic and phenotypic data show that strain 22II-S11-z3T represents a novel species of the genus Aestuariivita, for which the name Aestuariivita atlantica sp. nov. is proposed, with the type strain 22II-S11-z3T ( = KCTC 42276T = MCCC 1A09432T).

scholarly journals Kangiella profundi sp. nov., isolated from deep-sea sediment

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2315-2319 ◽  
Author(s):  
Fang-di Xu ◽  
Xue-gong Li ◽  
Xiang Xiao ◽  
Jun Xu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Deep Sea Sediment ◽  
South West Indian Ocean ◽  
West Indian Ocean ◽  
Type Strains

A taxonomic study employing a polyphasic approach was carried out on strain FT102T, which was isolated from a deep-sea sediment sample collected in the south-west Indian Ocean at a depth of 2784 m. The strain was Gram-stain-negative, non-motile, rod-shaped and non-spore-forming. It grew optimally at 37–42 °C, pH 6.5–8.5 and in the presence of 1–4 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences confirmed the separation of the novel strain from recognized members of the genus Kangiella that are available in public databases. Strain FT102T exhibited 95.5–98.6 % 16S rRNA gene sequence similarity to the type strains of the eight recognized species of the genus Kangiella. The chemotaxonomically characteristic fatty acid iso-C15:0 and ubiquinone Q-8 were also detected. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content of strain FT102T was 45.0 mol%. The mean DNA–DNA relatedness values between strain FT102T and the type strains of Kangiella aquimarina and Kangiella koreensis were 47.3 % and 13.7 %, respectively. The combined results of phylogenetic, physiological and chemotaxonomic studies indicated that strain FT102T was affiliated with the genus Kangiella but differed from the recognized species of the genus Kangiella. Therefore, strain FT102T represents a novel species of the genus Kangiella, for which the name Kangiella profundi sp. nov. is proposed. The type strain is FT102T ( = CGMCC 1.12959T = KCTC 42297T = JCM 30232T)

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).

scholarly journals Arenibacter echinorum sp. nov., isolated from the sea urchin Strongylocentrotus intermedius

2007 ◽  
Vol 57 (11) ◽  
pp. 2655-2659 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Anatoly M. Lysenko ◽  
Kang Hyun Lee ◽  
Kyung Sook Bae ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Strongylocentrotus Intermedius ◽  
Phenotypic Data ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Distinct Branch ◽  
The 16S Rrna Gene

Two marine, heterotrophic, aerobic, pigmented and gliding bacteria, isolated from the sea urchin Strongylocentrotus intermedius were subjected to a polyphasic taxonomy study. The 16S rRNA gene sequence analysis revealed that strains KMM 6032T and KMM 6047 formed a distinct branch within the genus Arenibacter, a member of the family Flavobacteriaceae. The level of sequence similarity between the novel isolates and members of the genus Arenibacter was 94.5–98.9 %. The DNA G+C content was 39–40 mol%. The dominant fatty acids were iso-C15 : 1, iso-C15 : 0, C15 : 0, C15 : 1 ω6c, iso-C15 : 0 3-OH, iso-C17 : 1 ω9c, iso-C17 : 0 3-OH and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The results of DNA–DNA hybridization experiments supported by phenotypic data indicated that the isolates represent a novel species within the genus Arenibacter, for which the name Arenibacter echinorum sp. nov. is proposed. The type strain is KMM 6032T (=KCTC 22013T=LMG 22574T).

scholarly journals Draconibacterium sediminis sp. nov., isolated from river sediment

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2310-2314 ◽  
Author(s):  
Juan Du ◽  
Qiliang Lai ◽  
Yang Liu ◽  
Chunming Dong ◽  
Yanrong Xie ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A Gram-reaction-negative, facultatively anaerobic and rod-shaped bacterium, designated strain JN14CK-3T, was isolated from surface sediment of the Jiulong River of China and was characterized phenotypically and phylogenetically. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain JN14CK-3T belonged to the genus Draconibacterium, with the highest sequence similarity (98.3 %) to Draconibacterium orientale FH5T. By contrast, strain JN14CK-3T shared low 16S rRNA gene sequence similarities ( < 91.0 %) with other type strains. The sole respiratory quinone was MK-7.The polar lipids were phosphatidylethanolamine and several unidentified phospholipids and lipids. The major fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0, C17:0 2-OH, iso-C16:0 3-OH and iso-C17:0 3-OH. The G+C content of the genomic DNA was 40.9 mol%. The digital DNA–DNA hybridization value and average nucleotide identity (ANI) between strain JN14CK-3T and D. orientale FH5T were 34.2 ± 2.5 % and 87.1 %, respectively. The combined genotypic and phenotypic data showed that strain JN14CK-3T represents a novel species of the genus Draconibacterium, for which the name Draconibacterium sediminis sp. nov. is proposed, with the type strain JN14CK-3T ( = MCCC 1A00734T = KCTC 42152T).

scholarly journals Streptomyces cahuitamycinicus sp. nov., isolated from desert soil and reclassification of Streptomyces galilaeus as a later heterotypic synonym of Streptomyces bobili

2020 ◽  
Vol 70 (4) ◽  
pp. 2750-2759 ◽  
Author(s):  
Hayrettin Saygin ◽  
Hilal Ay ◽  
Kiymet Guven ◽  
Demet Cetin ◽  
Nevzat Sahin
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Sequence Similarity ◽  
Single Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A novel actinobacterial strain, designated 13K301T, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. The taxonomic position of strain 13K301T was revealed by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain 13K301T belongs to the genus Streptomyces and had highest sequence similarity to ‘Streptomyces qaidamensis’ S10T (99.2 %), Streptomyces flavovariabilis NRRL B-16367T (98.9 %) and Streptomyces phaeoluteigriseus DSM 41896T (98.8 %), but the strain formed a distinct clade in the phylogenetic tree. The DNA–DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain 13K301T and closely related type strains were significantly lower than the recommended threshold values. The cell wall contained ll-diaminopimelic acid and the whole-cell hydrolysates were glucose and ribose. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were determined as the predominant polar lipids. The major menaquinones were identified as MK-9(H8) and MK-9(H6). On the basis of these genotypic and phenotypic data, it is proposed that strain 13K301T should be classified as representative of a novel species of the genus Streptomyces , for which the name Streptomyces cahuitamycinicus sp. nov. is proposed. The type strain is 13K301T (=DSM 106873T=KCTC 49110T). In addition, the whole genome-based comparisons as well as the multilocus sequence analysis revealed that the type strains of Streptomyces galilaeus and Streptomyces bobili belong to a single species. It is, therefore, proposed that S. galilaeus be recognised as a heterotypic synonym of S. bobili for which an emended description is given.

scholarly journals Alcanivorax sediminis sp. nov., isolated from deep-sea sediment of the Pacific Ocean

2020 ◽  
Vol 70 (7) ◽  
pp. 4280-4284 ◽  
Author(s):  
Xianzhi Liao ◽  
Qiliang Lai ◽  
Junpeng Yang ◽  
Chunming Dong ◽  
Dengfeng Li ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Deep Sea ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

A taxonomic study was carried out on strain PA15-N-34T, which was isolated from deep-sea sediment of Pacific Ocean. The bacterium was Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Growth was observed at salinity of 0–15.0% NaCl and at temperatures of 10–45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PA15-N-34T belonged to the genus Alcanivorax , with the highest sequence similarity to Alcanivorax profundi MTEO17T (97.7 %), followed by Alcanivorax nanhaiticus 19 m-6T (97.3 %) and 12 other species of the genus Alcanivorax (93.4 %–97.0 %). The average nucleotide identity and DNA–DNA hybridization values between strain PA15-N-34T and type strains of the genus Alcanivorax were 71.46–81.78% and 18.7–25.2 %, respectively. The principal fatty acids (>10 %) were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c; 31.2 %), C16 : 0 (25.0 %) and summed feature 3 (14.6 %). The DNA G+C content was 57.15 mol%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, four unidentified aminolipids and three unidentified lipids. The novel strain can be differentiated from its closest type strain by a negative test for urease and the presence of diphosphatidylglycerol and aminolipid. The combined genotypic and phenotypic data show that strain PA15-N-34T represents a novel species within the genus Alcanivorax , for which the name Alcanivorax sediminis sp. nov. is proposed, with the type strain PA15-N-34T (=MCCC 1A14738T=KCTC 72163T).

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