scholarly journals Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland

2006 ◽  
Vol 56 (12) ◽  
pp. 2887-2892 ◽  
Author(s):  
Mariane Schmidt ◽  
Anders Priemé ◽  
Peter Stougaard
Keyword(s):  
Gene Sequence ◽  
Unsaturated Fatty Acids ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Psychrophilic Bacterium ◽  
The Novel ◽  
Alkaliphilic Bacterium

A novel alkaliphilic and psychrophilic bacterium was isolated from the cold and alkaline ikaite tufa columns of the Ikka Fjord in south-west Greenland. According to 16S rRNA gene sequence analysis, strain GCM71T belonged to the family ‘Flexibacteraceae’ in the phylum Bacteroidetes. Strain GCM71T, together with five related isolates from ikaite columns, formed a separate cluster with 86–93 % gene sequence similarity to their closest relative, Belliella baltica. The G+C content of the DNA from strain GCM71T was 43.1 mol%, whereas that of B. baltica was reported to be 35 mol%. DNA–DNA hybridization between strain GCM71T and B. baltica was 9.5 %. The strain was red pigmented, Gram-negative, strictly aerobic with non-motile, rod-shaped cells. The optimal growth conditions for strain GCM71T were pH 9.2–10.0, 5 °C and 0.6 % NaCl. The fatty acid profile of the novel strain was dominated by branched and unsaturated fatty acids (90–97 %), with a high abundance of iso-C17 : 1 ω9c (17.5 %), iso-C17 : 0 3-OH (17.5 %) and summed feature 3, comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c (12.6 %). Phylogenetic, chemotaxonomic and physiological characteristics showed that the novel strain could not be affiliated to any known genus. A new genus, Rhodonellum gen. nov., is proposed to accommodate the novel strain. Strain GCM71T (=DSM 17998T=LMG 23454T) is proposed as the type strain of the type species, Rhodonellum psychrophilum sp. nov.

scholarly journals Litoribacter ruber gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a soda lake sediment

2010 ◽  
Vol 60 (12) ◽  
pp. 2996-3001 ◽  
Author(s):  
Shi-Ping Tian ◽  
Yong-Xia Wang ◽  
Bin Hu ◽  
Xiao-Xia Zhang ◽  
Wei Xiao ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Soda Lake ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Sequence Comparisons ◽  
Respiratory Quinone ◽  
Major Respiratory Quinone ◽  
Respective Type

A novel alkaliphilic, halotolerant, rod-shaped bacterium, designated strain YIM CH208T, was isolated from a soda lake in Yunnan, south-west China. The taxonomy of strain YIM CH208T was investigated by a polyphasic approach. Strain YIM CH208T was Gram-negative, strictly aerobic and non-motile and formed red colonies. Optimal growth conditions were 28 °C, pH 8.5 and 0.5–2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genus Echinicola in the phylum Bacteroidetes and was related to the species Echinicola pacifica and Rhodonellum psychrophilum, with sequence similarity of 91.7 and 91.6 % to the respective type strains. The DNA G+C content was 45.1 mol%. The major respiratory quinone was menaquinone-7 (MK-7). The predominant cellular fatty acids were iso-C17 : 1 ω9c (19.9 %), C15 : 0 3-OH (12.1 %), iso-C17 : 0 3-OH (11.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 10.7 %) and C17 : 1 ω6c (8.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain YIM CH208T represents a novel species of a new genus, for which the name Litoribacter ruber gen. nov., sp. nov. is proposed. The type strain of Litoribacter ruber is YIM CH208T (=ACCC 05414T =KCTC 22899T).

Taibaiella koreensis sp. nov., isolated from soil of a ginseng field

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 1018-1023 ◽  
Author(s):  
Heung-Min Son ◽  
MooChang Kook ◽  
Ju-Han Kim ◽  
Tae-Hoo Yi
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Biochemical Tests ◽  
Phenotypic Data ◽  
Link Type ◽  
Gram Staining ◽  
The Republic

A Gram-staining-negative, strictly aerobic, motile (by gliding), non-spore-forming and rod-shaped bacterial strain, designated THG-DT86T, 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 10–35 °C, at pH 6.5–8.5 and with 0–1.5 % (w/v) NaCl on trypticase soy agar. Flexirubin-type pigments were found to be present. On the basis of 16S rRNA gene sequence similarity, strain THG-DT86T was shown to belong to the genus Taibaiella and was related to Taibaiella smilacinae PTJT-5T (95.3 %). The G+C content of the genomic DNA was 50.1 mol%. The only isoprenoid quinone detected in strain THG-DT86T was menaquinone-7 (MK-7) and the only polyamine was homospermidine. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0, iso-C15 : 1 G and iso-C17 : 0, and the major polar lipids were phosphatidylethanolamine, an unidentified aminophosphoglycolipid and an unidentified aminophospholipid. Phenotypic data and phylogenetic inference supported the affiliation of strain THG-DT86T to the genus Taibaiella , and a number of biochemical tests differentiated strain THG-DT86T from the recognized species of the genus Taibaiella . Therefore, the novel isolate represents a novel species, for which the name Taibaiella koreensis sp. nov. is proposed, with THG-DT86T as the type strain ( = KACC 17171T = JCM 18823T).

scholarly journals Chryseobacterium shandongense sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1860-1865 ◽  
Author(s):  
Fan Yang ◽  
Hong-ming Liu ◽  
Rong Zhang ◽  
Ding-bin Chen ◽  
Xiang Wang ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Rrna Gene Sequence ◽  
Yellow Orange ◽  
The 16S Rrna Gene

YF-3T is a Gram-stain-negative, non-motile, non-spore-forming, yellow–orange, rod-shaped bacterium. Optimal growth conditions were at 30 °C, pH 7.0 and 1 % (w/v) NaCl. Phylogenetic analysis, on the basis of the 16S rRNA gene sequence, showed that strain YF-3T was closely related to the strains Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T with 98.71 % and 96.93 % sequence similarity, respectively. Strain YF-3T contained MK-6 as the main menaquinone and had a polyamine pattern with sym-homospermidine as the major component. Its major polar lipid was phosphatidylethanolamine. The dominant fatty acids of strain YF-3T were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain YF-3T was 37 mol%. The DNA–DNA relatedness levels between strain YF-3T and the most closely related strains, C. hispalense AG13T and C. taiwanense Soil-3-27T, were 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively. Based on these results, a novel species named Chryseobacterium shandongense sp. nov. is proposed. The type strain is YF-3T ( = CCTCC AB 2014060T = JCM 30154T).

scholarly journals Thermocrinis jamiesonii sp. nov., a thiosulfate-oxidizing, autotropic thermophile isolated from a geothermal spring

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4769-4775 ◽  
Author(s):  
Jeremy A. Dodsworth ◽  
John C. Ong ◽  
Amanda J. Williams ◽  
Alice C. Dohnalkova ◽  
Brian P. Hedlund
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Growth Conditions ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Casamino Acids

An obligately thermophilic, chemolithotrophic, microaerophilic bacterium, designated strain GBS1T, was isolated from the water column of Great Boiling Spring, Nevada, USA. Thiosulfate was required for growth. Although capable of autotrophy, growth of GBS1T was enhanced in the presence of acetate, peptone or Casamino acids. Growth occurred at 70–85 °C with an optimum at 80 °C, at pH 6.50–7.75 with an optimum at pH 7.25, with 0.5–8 % oxygen with an optimum at 1–2 % and with ≤ 200 mM NaCl. The doubling time under optimal growth conditions was 1.3 h, with a final mean cell density of 6.2 ± 0.5 × 107 cells ml− 1. Non-motile, rod-shaped cells 1.4–2.4 × 0.4–0.6 μm in size occurred singly or in pairs. The major cellular fatty acids (>5 % of the total) were C20 : 1ω9c, C18 : 0, C16 : 0 and C20 : 0. Phylogenetic analysis of the GBS1T 16S rRNA gene sequence indicated an affiliation with Thermocrinis ruber and other species of the genus Thermocrinis, but determination of 16S rRNA gene sequence similarity ( ≤ 97.10 %) and in silico estimated DNA–DNA hybridization values ( ≤ 18.4 %) with the type strains of recognized Thermocrinis species indicate that the novel strain is distinct from described species. Based on phenotypic, genotypic and phylogenetic characteristics, a novel species, Thermocrinis jamiesonii sp. nov., is proposed, with GBS1T ( = JCM 19133T = DSM 27162T) as the type strain.

scholarly journals Chelativorans multitrophicus gen. nov., sp. nov. and Chelativorans oligotrophicus sp. nov., aerobic EDTA-degrading bacteria

2010 ◽  
Vol 60 (5) ◽  
pp. 1044-1051 ◽  
Author(s):  
Nina V. Doronina ◽  
Elena N. Kaparullina ◽  
Yuri A. Trotsenko ◽  
Bernd Nörtemann ◽  
Margarete Bucheli-Witschel ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Phenotypic Properties ◽  
Mesorhizobium Loti ◽  
Degrading Bacteria

Two previously isolated strains (DSM 9103T and LPM-4T) able to grow with EDTA (facultatively and obligately, respectively) as the source of carbon, nitrogen and energy were investigated in order to clarify their taxonomic positions. The strains were strictly aerobic, Gram-negative, asporogenous and non-motile rods that required biotin for growth. Reproduction occurred by binary fission. The strains were mesophilic and neutrophilic. Their major fatty acids were summed feature 7 (consisting of C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t) and C19 : 0 cyclo ω8c. The polyamine pattern revealed homospermidine as a major polyamine. Predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine and diphosphatidylglycerol. Mesorhizobium-specific ornithine lipid was absent. The predominant isoprenoid quinone was Q-10. The DNA G+C values were 60.8 and 63.1 mol% (T m) for strains LPM-4T and DSM 9103T, respectively. The level of 16S rRNA gene sequence similarity between these EDTA-utilizers was 99.3 % while the DNA–DNA hybridization value was only 37 %. Both strains were phylogenetically related to members of the genera Aminobacter and Mesorhizobium (95–97 % sequence similarity). However, DNA–DNA hybridization values between the novel EDTA-degrading strains and Aminobacter aminovorans DSM 7048T and Mesorhizobium loti DSM 2626T were low (10–11 %). Based on their genomic and phenotypic properties, the new alphaproteobacterial strains are assigned to a novel genus, Chelativorans gen. nov., with the names Chelativorans multitrophicus sp. nov. (type strain DSM 9103T=VKM B-2394T) and Chelativorans oligotrophicus sp. nov. (type strain LPM-4T=VKM B-2395T=DSM 19276T).

scholarly journals Roseovarius nanhaiticus sp. nov., a member of the Roseobacter clade isolated from marine sediment

2010 ◽  
Vol 60 (6) ◽  
pp. 1289-1295 ◽  
Author(s):  
Baojiang Wang ◽  
Fengqin Sun ◽  
Qiliang Lai ◽  
Yaping Du ◽  
Xiupian Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Gram Staining

An aerobic, Gram-staining-negative, rod or ovoid-shaped bacterial isolate, strain NH52JT, was isolated from a sandy sediment sample from the South China Sea. Strain NH52JT exhibited tumbling motility, formed beige or faint pink colonies, gave a positive reaction in tests for catalase and oxidase and required NaCl for growth. Optimal growth was observed at pH 7.8–9.3, at 30 °C and in the presence of 2.0–4.0 % (w/v) NaCl. The novel strain did not synthesize bacteriochlorophyll a, and the DNA G+C content was 62 %. The major fatty acids were C18 : 1 ω7c, C16 : 0 and C18 : 1 ω7c 11-methyl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NH52JT was affiliated to the genus Roseovarius of the class Alphaproteobacteria. Roseovarius pacificus and Roseovarius aestuarii were the most closely related recognized species to strain NH52JT with 16S rRNA gene sequence similarity values of 95.0 and 95.7 %, respectively. Sequence similarity values between strain NH52JT and other phylogenetically related species were all below 95.0 %. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain NH52JT is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius nanhaiticus sp. nov. is proposed. The type strain is NH52JT (=LMG 24840T=CCTCC AB 208317T=MCCC 1A03543T).

scholarly journals Perexilibacter aurantiacus gen. nov., sp. nov., a novel member of the family ‘Flammeovirgaceae’ isolated from sediment

2007 ◽  
Vol 57 (5) ◽  
pp. 964-968 ◽  
Author(s):  
Jaewoo Yoon ◽  
Shu Ishikawa ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
The Family ◽  
Republic Of Palau ◽  
The 16S Rrna Gene

A strictly aerobic, Gram-negative, gliding, dull-orange-pigmented, rod-shaped bacterium, designated strain Shu-F-UV2-2T, was isolated from sediment (Carp Island, Republic of Palau) and was the focus of a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated to the family ‘Flammeovirgaceae’ of the phylum Bacteroidetes and that it showed highest sequence similarity (85.5 %) to Flammeovirga yaeyamensis NBRC 100898T. The novel isolate could be differentiated phenotypically and physiologically from recognized members of the family ‘Flammeovirgaceae’. The G+C content of the DNA was 43.0 mol%, MK-7 was the major menaquinone and iso-C15 : 0, C16 : 1 ω7c and C16 : 1 ω5c were the major fatty acids. On the basis of this polyphasic evidence, it was concluded that strain Shu-F-UV2-2T represents a novel species in a new genus of the family ‘Flammeovirgaceae’, for which the name Perexilibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain is Shu-F-UV2-2T (=MBIC06993T=IAM 15413T=KCTC 12867T).

scholarly journals Roseithermus sacchariphilus gen. nov., sp. nov. and proposal of Salisaetaceae fam. nov., representing new family in the order Rhodothermales

2019 ◽  
Vol 69 (4) ◽  
pp. 1213-1219 ◽  
Author(s):  
Mi-Jeong Park ◽  
Ji Hye Oh ◽  
Sung-Hyun Yang ◽  
Kae Kyoung Kwon
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Growth Conditions ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A novel bacterium with cells that were pinkish-cream-coloured, aerobic, rod-shaped, 0.62–1.00 µm wide and 2.3–3.3 µm long, designated as strain MEBiC09517T, was isolated from Buksung-Po, a small port in Incheon, Republic of Korea. Strain MEBiC09517T had low 16S rRNA gene sequence similarity to validly reported strains; among them, Rubrivirga profundi SAORIC-476T displayed highest sequence similarity (89.9 %). Nevertheless, the novel strain shared a phylogenetic line with members of the genus Rhodothermus , not the genus Rubrivirga . Optimum growth conditions of strain MEBiC09517T were at 50–55 °C, pH 7 and in 2.0–4.0 % salt concentration. Strain MEBiC09517T was found to be an obligate marine bacterium that requires KCl, MgCl2 and CaCl2 as well as NaCl for growth. A phosphatidylethanolamine, a diphosphatidylglycerol, three glycolipids and four unidentified lipids were the strain's predominant polar lipid components. The fatty acid of the cell wall mainly consisted of carbons with 16 or 18 chain lengths such as C16 : 0, C18 : 0, C18 : 1 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The predominant menaquinone was MK-7. The DNA G+C content is 68.65 mol%. Strain MEBiC09517T differs from genera of the order Rhodothermales in terms of fatty acid composition, growth conditions, and range of carbon source utilization. Based on phylogenetic analysis using the strain's 16S rRNA gene sequence and results of physiological tests, strain MEBiC09517T (KCCM=43267T, JCM=32374T) is proposed as Roseithermus sacchariphilus gen. nov., sp. nov. Additionally, the novel family Salisaetaceae fam. nov. based on phylogenetic analysis and physiological characteristics is suggested.

scholarly journals Shewanella donghaensis sp. nov., a psychrophilic, piezosensitive bacterium producing high levels of polyunsaturated fatty acid, isolated from deep-sea sediments

2007 ◽  
Vol 57 (2) ◽  
pp. 208-212 ◽  
Author(s):  
Sung-Hyun Yang ◽  
Jung-Hyun Lee ◽  
Ji-Sun Ryu ◽  
Chiaki Kato ◽  
Sang-Jin Kim
Keyword(s):  
Dna Hybridization ◽  
Deep Sea ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Psychrophilic Bacterium ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Shewanella Frigidimarina ◽  
Deep Sea Sediments

A Gram-negative, motile, rod-shaped, psychrophilic bacterium, LT17T, was isolated from deep-sea sediments (3300 m depth) of the East Sea (Sea of Japan). Optimal growth of LT17T requires the presence of 2.5 % (w/v) NaCl, a pH of 7.0–7.5 and a temperature of 17 °C. The isolate grows optimally under a hydrostatic pressure of 10 MPa and growth is possible between 0.1 and <30 MPa. The novel strain is positive in tests for catalase, oxidase, lipase, β-glucosidase and gelatinase activities and reduces nitrate to nitrate. The predominant cellular fatty acids are iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 1ω7 and C20 : 5ω3. The DNA G+C content of strain LT17T is 38.8 mol%. Phylogenetic analysis of 16S rRNA gene sequences places this bacterium in the class Gammaproteobacteria, within the genus Shewanella. The closest relatives of strain LT17T are Shewanella japonica (97.8 % gene sequence similarity), Shewanella pacifica (97.5 %), Shewanella olleyana (96.8 %), Shewanella frigidimarina (96.5 %) and Shewanella gelidimarina (95.4 %). The DNA–DNA hybridization levels between the novel isolate and its closest known phylogenetic relatives, S. japonica and S. pacifica, are lower than 14 %. On the basis of this polyphasic evidence, strain LT17T represents a novel species of the genus Shewanella, for which the name Shewanella donghaensis sp. nov. is proposed. The type strain is LT17T (=KCTC 10635BPT=JCM 12524T).

scholarly journals Salegentibacter flavus sp. nov.

2006 ◽  
Vol 56 (3) ◽  
pp. 583-586 ◽  
Author(s):  
Elena P. Ivanova ◽  
John P. Bowman ◽  
Richard Christen ◽  
Natalia V. Zhukova ◽  
Anatoly M. Lysenko ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Unsaturated Fatty Acids ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Tween 80 ◽  
Optimal Growth ◽  
Rrna Gene ◽  
The Novel ◽  
Straight Chain ◽  
Branched Chain

A yellow-pigmented, non-motile, Gram-negative bacterium, designated Fg 69T, was isolated from a sediment sample collected in Chazhma Bay (Sea of Japan). The novel organism grew at 10–35 °C, was neutrophilic and required 3–10 % NaCl for optimal growth. Strain Fg 69T was able to degrade starch and to hydrolyse gelatin and Tween 80 weakly but not casein or agar. Predominant cellular fatty acids comprised n-C15 and n-C16 branched-chain and straight-chain saturated and unsaturated fatty acids, including iso-C15 : 0 (5 %), anteiso-C15 : 0 (11 %), C15 : 0 (9 %), iso-C15 : 1 (5 %), iso-C16 : 0 (8 %), C16 : 0 (5 %) and C16 : 1 ω7 (5 %) and iso- and anteiso-branched 2-OH and 3-OH C15 : 0 to C17 : 0 fatty acids (26 % in total). The G+C content of the DNA was 40·4 mol%. 16S rRNA gene sequence data indicated that strain Fg 69T belonged to the genus Salegentibacter but was distinct from recognized Salegentibacter species (94–95 % sequence similarity). Based on these results, a novel species, Salegentibacter flavus sp. nov., is proposed. The type strain is Fg 69T (=KMM 6000T=CIP 107843T).

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