scholarly journals Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China

2019 ◽  
Vol 69 (4) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xiang-yue Zhou ◽  
Zeng-hong Gao ◽  
Mei-hong Chen ◽  
Mei-qi Jian ◽  
Li-hong Qiu
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Broad Leaved Forest ◽  
Gene Sequence Analysis ◽  
Leaved Forest

Cells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11T grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyella flagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyella humi DHG40T and Dyella nitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyella caseinilytica DHOB09T and Dyella mobilis DHON07T, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.

scholarly journals Halioglobus maricola sp. nov., isolated from coastal seawater

2020 ◽  
Vol 70 (3) ◽  
pp. 1868-1875 ◽  
Author(s):  
Shan-Hui Li ◽  
Jaeho Song ◽  
Yeonjung Lim ◽  
Yochan Joung ◽  
Ilnam Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6–97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA–DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-β-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus , for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).

Isolation and description of Selenomonas timonae sp. nov., a novel Selenomonas species detected in a gingivitis patient

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Angéline Antezack ◽  
Manon Boxberger ◽  
Mariem Ben Khedher ◽  
Bernard La Scola ◽  
Virginie Monnet-Corti
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
Optimum Ph

A Gram-stain-negative bacterium, designated strain Marseille-Q3039T, was isolated from subgingival dental plaque of a woman with gingivitis in Marseille, France. Strain Marseille-Q3039T was found to be an anaerobic, motile and spore-forming crescent-shaped bacterium that grew at 25–41.5 °C (optimum, 37 °C), pH 5.5–8.5 (optimum, pH 7.5) and salinity of 5.0 g l−1 NaCl. The results of 16S rRNA gene sequence analysis revealed that strain Marseille-Q3039T was closely related to Selenomonas infelix ATCC 43532T (98.42 % similarity), Selenomonas dianae ATCC 43527T (97.25 %) and Centipedia periodontii DSM 2778T (97.19 %). The orthologous average nucleotide identity and digital DNA–DNA hybridization relatedness between strain Q3039T and its closest phylogenetic neighbours were respectively 84.57 and 28.2 % for S. infelix ATCC 43532T and 83.93 and 27.2 % for C. periodontii DSM 2778T. The major fatty acids were identified as C13 : 0 (27.7 %), C15 : 0 (24.4 %) and specific C13 : 0 3-OH (12.3 %). Genome sequencing revealed a genome size of 2 351 779 bp and a G+C content of 57.2 mol%. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3039T represents a novel species of the genus Selenomonas , for which the name Selenomonas timonae sp. nov. is proposed (=CSUR Q3039=CECT 30128).

scholarly journals Herbidospora mongoliensis sp. nov., isolated from soil, and reclassification of Herbidospora osyris and Streptosporangium claviforme as synonyms of Herbidospora cretacea

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2322-2329 ◽  
Author(s):  
Ismet Ara ◽  
Baljinova Tsetseg ◽  
Damdinsuren Daram ◽  
Manabu Suto ◽  
Katsuhiko Ando
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Analyses ◽  
Content Type ◽  
Link Type ◽  
Phospholipid Profile

A Gram-reaction-positive aerobic actinomycete, designated strain MN08-A0118T, which produced short chains of non-motile spores on the tips of long sporophores and formed yellow–brown colonies with branched substrate mycelium, was studied in detail to determine its taxonomic position. On the basis of 16S rRNA gene sequence analyses, strain MN08-A0118T was grouped into the genus Herbidospora , being most closely related to Streptosporangium claviforme (98.2 %), Herbidospora osyris (98.2 %), Herbidospora daliensis (98.2 %), Herbidospora cretacea (97.9 %) and Herbidospora yilanensis (97.4 %). Chemotaxonomic data supported allocation of the strain to the genus Herbidospora . MK-10(H4) was the predominant menaquinone with minor amounts of MK-10(H6), MK-10(H2) and MK-9(H4); the fatty acid profile contained major amounts of iso-C16 : 0, C17 : 0 10-methyl, iso-C14 : 0 and iso-C16 : 0 2-OH; the phospholipid profile contained phosphatidylethanolamine, phosphatidylmethylethanolamine and glucosamine-containing phospholipids; and the whole-cell sugars included ribose, glucose, galactose, madurose and rhamnose (trace). The phylogenetic data, phenotypic and genotypic properties and DNA–DNA hybridization differentiated this strain from its closely related strains, S. claviforme (35–54 % DNA–DNA relatedness), H. osyris (39–51 %), H. daliensis (3–16 %), H. cretacea (34–39 %) and H. yilanensis (34–42 %). Thus, MN08-A0118T represents a novel species of the genus Herbidospora , for which the name Herbidospora mongoliensis sp. nov. is proposed, with MN08-A0118T ( = NBRC 105882T  = VTCC D9-22T) as the type strain. In addition, DNA–DNA hybridization results showed that S. claviforme and H. osyris are synonyms of H. cretacea .

Nibribacter koreensis gen. nov., sp. nov., isolated from estuarine water

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4663-4668 ◽  
Author(s):  
Ji Young Kang ◽  
Jeesun Chun ◽  
Kwang Yeop Jahng
Keyword(s):  
Type Species ◽  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-reaction-negative, rod-shaped, non-motile, red-pigmented bacterium, designated strain GSR3061T, was isolated from a water sample of the Mangyung estuary enclosed by the Saemangeum Embankment in JEOLlabuk-do of South Korea, and characterized using a polyphasic approach. 16S rRNA gene sequence analysis of strain GSR3061T indicated that the isolate belonged to the phylum Bacteroidetes and exhibited similarity levels of 94.7 % to Rufibacter tibetensis NRRL B-51285T, 92.4 % to Adhaeribacter terreus KACC 14257T and 91.9 % to Pontibacter korlensis KACC 15371T. Growth was observed at 15–40 °C and pH 6.5–9.5. The major cellular fatty acids of the novel strain were summed feature 4 (comprising iso-C17 : 1 I and/or anteiso-C17 : 1 B), iso-C15 : 0, C17 : 1ω6c and iso-C16 : 1 H. Flexirubin-type pigments were absent. The DNA G+C content of strain GSR3061T was 44.9 mol% and the major quinone was MK-7. The polar lipid profile consisted mainly of phosphatidylethanolamine; three unidentified lipids, two unknown aminolipids, two unknown phospholipids, an unknown aminophospholipid and an unknown glycolipid were also present. On the basis of the evidence presented, it is concluded that strain GSR3061T represents a novel species of a new genus, for which the name Nibribacter koreensis gen. nov., sp. nov. is proposed. The type strain of Nibribacter koreensis is GSR3061T ( = KACC 16450T = JCM 17917T).

Kaistia defluvii sp. nov., isolated from river sediment

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2878-2882 ◽  
Author(s):  
Long Jin ◽  
Kwang Kyu Kim ◽  
Hyung-Gwan Lee ◽  
Chi-Yong Ahn ◽  
Hee-Mock Oh
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
River Sediment ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

A Gram-stain-negative, aerobic, non-motile, rod- and coccus-shaped bacterium, designated strain B6-12T, was isolated from sediment collected from the River Geumho in South Korea. In comparative 16S rRNA gene sequence analysis, the novel strain appeared to be affiliated with the class Alphaproteobacteria and to be most closely related to Kaistia adipata KCTC 12095T, Kaistia dalseonensis DSM 18800T, Kaistia geumhonensis DSM 18799T, Kaistia granuli KCTC 12575T, Kaistia soli KACC 12605T and Kaistia terrae KACC 12910T, with sequence similarities of 96.2–99.1 %. The predominant ubiquinone in the isolate was Q-10, major fatty acids were C18 : 0, C18 : 1ω7c and C19 : 0ω8c cyclo, and genomic DNA G+C content was 63.0 mol%. Based on the phylogenetic and chemotaxonomic evidence and the results of DNA–DNA hybridizations, strain B6-12T represents a novel species in the genus Kaistia , for which the name Kaistia defluvii sp. nov. is proposed. The type strain is B6-12T ( = KCTC 23766T  = JCM 18034T).

scholarly journals Streptomyces smaragdinus sp. nov., isolated from the gut of the fungus growing-termite Macrotermes natalensis

2020 ◽  
Vol 70 (11) ◽  
pp. 5806-5811 ◽  
Author(s):  
Jan W. Schwitalla ◽  
René Benndorf ◽  
Karin Martin ◽  
John Vollmers ◽  
Anne-Kristin Kaster ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type ◽  
A Value ◽  
Gene Sequence Analysis

The taxonomic position of a novel aerobic, Gram-positive actinobacteria, designated strain RB5T, was determined using a polyphasic approach. The strain, isolated from the gut of the fungus-farming termite Macrotermes natalensis, showed morphological, physiological and chemotaxonomic properties typical of the genus Streptomyces . Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbour of RB5T was Streptomyces polyrhachis DSM 42102T (98.87 %). DNA–DNA hybridization experiments between strain RB5T and S. polyrhachis DSM 42102T resulted in a value of 27.4 % (26.8 %). The cell wall of strain RB5T contained ll-diaminopimelic acid as the diagnostic amino acid. Mycolic acids and diagnostic sugars in whole-cell hydrolysates were not detected. The strain produced the following major phospholipids: diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol-mannoside and phosphatidylserine. The menaquinone profile showed hexa- and octahydrogenated menaquinones containing nine isoprene units [MK-9(H6) and MK-9(H8)]. The strain exhibited a fatty acid profile containing the following major fatty acids: 12-methyltridecanoic acid (iso-C14 : 0) 12-methyltetradecanoic acid (anteiso-C15 : 0), 13-methyltetradecanoic acid (iso-C15 : 0) and 14-methylpentadecanoic acid (iso-C16 : 0). Here, we propose a novel species of the genus Streptomyces – Streptomyces smaragdinus with the type strain RB5T (=VKM Ac-2839T=NRRL B65539T).

Actinoplanes siamensis sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3037-3042 ◽  
Author(s):  
Chanwit Suriyachadkun ◽  
Wipaporn Ngaemthao ◽  
Suwanee Chunhametha ◽  
Chitti Thawai ◽  
Jean-Jacques Sanglier
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A Gram-positive filamentous bacterial strain that developed large campanulate sporangia at the ends of sporangiophores on substrate mycelium was isolated from bamboo forest soil in Thailand. According to the results of a polyphasic taxonomic study, our isolate had typical characteristics of members of the genus Actinoplanes . The 16S rRNA gene sequence analysis also indicated that strain A-T 6646T belonged to the genus Actinoplanes , being most closely related to Actinoplanes liguriensis DSM 43865T (97.61 %) and Actinoplanes octamycinicus NBRC 14524T (97.52 %). The DNA–DNA relatedness values, which differentiate the new strain from the most closely related species, were significantly below 70 %. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained xylose and arabinose. The predominant menaquinone was MK-9(H4). The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and anteiso-C15 : 0. Following an evaluation of phenotypic, chemotaxonomic and genotypic studies, the isolate is proposed to represent a novel species to be named Actinoplanes siamensis sp. nov. The type strain is A-T 6646T ( = BCC 46194T = NBRC 109076T).

Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3848-3853 ◽  
Author(s):  
Heung-Min Son ◽  
Jung-Eun Yang ◽  
YongJin Park ◽  
Chang-Kyun Han ◽  
Song-Gun Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain THG-B283T, which has β-glucosidase activity, was isolated from soil of a ginseng field. Cells were Gram-reaction-negative, oxidase- and catalase-positive, aerobic, motile with one polar flagellum and rod-shaped. The strain was subjected to a polyphasic taxonomic study. Strain THG-B283T grew optimally at around pH 7.0, at 25–28 °C and in the absence of NaCl on R2A agar. 16S rRNA gene sequence analysis revealed that strain THG-B283T belongs to the family Sphingomonadaceae and is closely related to Sphingomonas melonis DAPP-PG 224T (98.2 %), S. aquatilis JSS7T (98.1 %), S. insulae DS-28T (97.6 %), S. mali IFO 15500T (97.1 %) and S. pruni IFO 15498T (97.0 %). Strain THG-B283T contained Q-10 as the predominant ubiquinone. The major fatty acids included summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C14 : 0 2-OH and C16 : 0. The DNA G+C content was 72.2 mol%. The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipid, diphosphatidylglycerol, an unidentified glycolipid, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Genomic and chemotaxonomic data supported the affiliation of strain THG-B283T to the genus Sphingomonas . DNA–DNA relatedness between strain THG-B283T and its closest phylogenetic neighbours was below 23 %. On the basis of phenotypic, phylogenetic and genetic data, strain THG-B283T represents a novel species of genus Sphingomonas , for which the name Sphingomonas kyungheensis sp. nov. is proposed. The type strain is THG-B283T ( = KACC 16224T = LMG 26582T).

Mycetocola miduiensis sp. nov., a psychrotolerant bacterium isolated from Midui glacier

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2661-2665 ◽  
Author(s):  
Lang Zhu ◽  
Qing Liu ◽  
Hongcan Liu ◽  
Yuguang Zhou ◽  
Yuhua Xin ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Psychrotolerant Bacterium ◽  
Sequence Similarities

An aerobic, asporous, flagellated, Gram-stain-positive, rod-shaped bacterium MD-T1-10-2T was isolated from the topsoil of Midui Glacier, Tibet Province, China. Phylogenetic analysis based on 16S rRNA gene sequence analysis placed the strain in a clade containing Mycetocola manganoxydans CCTCC AB 209002T, Mycetocola reblochoni DSM 18580T, Mycetocola tolaasinivorans JCM 11656T, Mycetocola lacteus JCM 11654T and Mycetocola saprophilus JCM 11655T, with the sequence similarities of 99.2, 98.1, 96.7, 96.6 and 96.4 %, respectively. DNA–DNA hybridization analysis indicated that strain MD-T1-10-2T represented a new member of this genus. The optimal ranges of temperature and pH for growth were 20–25 °C and 7.0–9.0, respectively; the strain could even grow at 0 °C. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinones were MK-10 and MK-11. The cell wall amino acids were lysine, alanine, glycine and glutamic acids. The DNA G+C content was 65.9 mol%. Based on the genotypic and phenotypic data, strain MD-T1-10-2T for which the name Mycetocola miduiensis sp. nov. is proposed; the type strain is MD-T1-10-2T ( = CGMCC 1.11101T = NBRC 107877T).

Williamsia sterculiae sp. nov., isolated from a Chinese medicinal plant

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4158-4162 ◽  
Author(s):  
Xiao-Mei Fang ◽  
Jing Su ◽  
Hao Wang ◽  
Yu-Zhen Wei ◽  
Tao Zhang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Chinese Medicinal Plant

Two actinobacterial strains, CPCC 203464T and CPCC 203448, isolated from surface-sterilized stems of medicinal plants were subjected to a polyphasic taxonomic study. These two aerobic organisms formed pale yellow colonies on tryptic soy agar (TSA). Cells were Gram-stain-positive, non-acid-fast, non-motile, rod- or coccoid-like elements. Comparative 16S rRNA gene sequence analysis indicated that strains CPCC 203464T and CPCC 203448 were most closely related to the type strains of the species of the genus Williamsia . Chemotaxonomic properties such as containing meso-diaminopimelic acid in the cell wall, arabinose, galactose and ribose being the whole-cell hydrolysate sugars, phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the phospholipids, and C16 : 0, 10-methyl C18 : 0, C18 : 1ω9c, C16 : 1ω7c and/or iso-C15 : 0 2-OH as major fatty acids supported the affiliation of strains CPCC 203464T and CPCC 203448 to the genus Williamsia . The DNA–DNA hybridization values in combination with differentiating chemotaxonomic and physiological characteristics strongly suggested that these two isolates should be classified as representatives of a novel species of the genus Williamsia . The name Williamsia sterculiae sp. nov. is proposed, with strain CPCC 203464T ( = DSM 45741T = KCTC 29118T) as the type strain.

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