scholarly journals Colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the Japan Trench

2004 ◽  
Vol 54 (5) ◽  
pp. 1627-1631 ◽  
Author(s):  
Yuichi Nogi ◽  
Shoichi Hosoya ◽  
Chiaki Kato ◽  
Koki Horikoshi
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Japan Trench ◽  
Bottom Surface ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequence Analysis ◽  
Rapid Growth Rate ◽  
Definition Of ◽  
Reference Strains

Two strains of obligately piezophilic bacteria were isolated from sediment collected from the bottom surface of a small canyon on the seaward slope of the Japan Trench at a depth of 6278 m. The isolated strains, Y223GT and Y251E, are closely affiliated with members of the genus Colwellia on the basis of 16S rRNA gene sequence analysis. The G+C contents of both strains were about 39 mol%. DNA–DNA hybridization values between these strains and Colwellia reference strains were significantly lower than those accepted as the phylogenetic definition of a species. The novel strains are Gram-negative, polarly flagellated and facultatively anaerobic. The optimal pressure for growth was 60 MPa at both 4 and 10 °C; the most rapid growth rate was observed at 10 °C and 60 MPa. No growth occurred at 15 °C under any pressure studied. The major isoprenoid quinone is Q-8. The predominant cellular fatty acids are C16 : 0 and C16 : 1. Based on the taxonomic differences observed, the isolated strains appear to represent a novel obligately piezophilic Colwellia species. The name Colwellia piezophila sp. nov. (type strain Y223GT=JCM 11831T=ATCC BAA-637T) is proposed.

scholarly journals Aeromonas molluscorum sp. nov., isolated from bivalve molluscs

2004 ◽  
Vol 54 (6) ◽  
pp. 2073-2078 ◽  
Author(s):  
David Miñana-Galbis ◽  
Maribel Farfán ◽  
M. Carme Fusté ◽  
J. Gaspar Lorén
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Fragment Length Polymorphism ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Bivalve Molluscs ◽  
Gene Sequence Analysis ◽  
Indole Production ◽  
Reference Strains

Five Aeromonas strains (848TT, 93M, 431E, 849T and 869N), which were isolated from bivalve molluscs and were recognized previously by numerical taxonomy as members of an unknown Aeromonas taxon, were subjected to a polyphasic taxonomic study. DNA–DNA hybridization experiments showed that DNA of strain 848TT was <70 % similar (27–45 %) to that of the type/reference strains of the current Aeromonas hybridization groups (HGs), but 93 % similar to that of strain 93M. The DNA G+C content of the five strains ranged from 59·0 to 59·4 mol%. 16S rRNA gene sequence analysis confirmed that the strains belonged to the genus Aeromonas and showed high similarity to Aeromonas encheleia. Amplified fragment length polymorphism fingerprinting clustered the novel strains in a homogeneous group with low genotypic relatedness to other Aeromonas species. Useful phenotypic features for differentiating the five isolates from other Aeromonas species include their negative reactions in tests for indole production, lysine decarboxylase, gas from glucose and starch hydrolysis. From the results of this study, the name Aeromonas molluscorum sp. nov. is proposed for these strains, with the type strain 848TT (=CECT 5864T=LMG 22214T).

scholarly journals Psychromonas hadalis sp. nov., a novel piezophilic bacterium isolated from the bottom of the Japan Trench

2007 ◽  
Vol 57 (6) ◽  
pp. 1360-1364 ◽  
Author(s):  
Yuichi Nogi ◽  
Shoichi Hosoya ◽  
Chiaki Kato ◽  
Koki Horikoshi
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Gene Sequence ◽  
Unsaturated Fatty Acids ◽  
Japan Trench ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Temperature And Pressure ◽  
Definition Of ◽  
Reference Strains

An obligately piezophilic bacterium was isolated from sediment collected from the bottom of the Japan Trench at a depth of 7542 m. The isolated strain, designated K41GT, was closely affiliated with members of the genus Psychromonas on the basis of 16S rRNA gene sequence analysis. Levels of DNA–DNA relatedness between strain K41GT and Psychromonas reference strains were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of strain K41GT were 6 °C and 60 MPa, respectively. The DNA G+C content was 39.1 mol%. Whole-cell fatty acids consisted of significant amounts of unsaturated fatty acids C16 : 1 (37 %) and C14 : 1 (17 %), saturated fatty acid C16 : 0 (31 %) and polyunsaturated fatty acid C22 : 6 (8 %). Based on the taxonomic differences observed, strain K41GT is considered to represent a novel obligately piezophilic Psychromonas species. The name Psychromonas hadalis (type strain, K41GT=JCM 11830T=ATCC BAA-638T) is proposed. This is the second species of obligately piezophilic bacteria to be proposed in the genus Psychromonas.

scholarly journals Lysobacter novalis sp. nov., isolated from fallow farmland soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3131-3136 ◽  
Author(s):  
Hina Singh ◽  
Juan Du ◽  
Kyung-Hwa Won ◽  
Jung-Eun Yang ◽  
Shahina Akter ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Gliding Motility ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Farmland Soil ◽  
Major Respiratory Quinone

A novel bacterial strain, designated THG-PC7T, was isolated from fallow farmland soil in Yongin, South Korea. Cells of strain THG-PC7T were Gram-stain-negative, dark yellow, aerobic, rod-shaped and had gliding motility. Strain THG-PC7T grew optimally at 25–35 °C, at pH 7 and in the absence of NaCl. Comparative 16S rRNA gene sequence analysis identified strain THG-PC7T as belonging to the genus Lysobacter, exhibiting highest sequence similarity with Lysobacter ximonensis KCTC 22336T (98.7 %) followed by Lysobacter niastensis KACC 11588T (95.7 %). In DNA–DNA hybridization tests, DNA relatedness between strain THG-PC7T and its closest phylogenetic neighbour L. ximonensis was below 25 %. The DNA G+C content of the novel isolate was determined to be 62.5 mol%. Flexirubin-type pigments were found to be present. The major cellular fatty acids were determined to be iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C17 : 1ω9c. The major respiratory quinone was identified as ubiquonone-8 (Q8). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospolipid. On the basis of results from DNA–DNA hybridization and the polyphasic data, strain THG-PC7T represents a novel species of the genus Lysobacter, for which the name Lysobacter novalis sp. nov. is proposed. The type strain is THG-PC7T( = KACC 18276T = CCTCC AB 2014319T).

scholarly journals Fuchsiella ferrireducens sp. nov., a novel haloalkaliphilic, lithoautotrophic homoacetogen capable of iron reduction, and emendation of the description of the genus Fuchsiella

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2432-2440 ◽  
Author(s):  
Tatyana N. Zhilina ◽  
Daria G. Zavarzina ◽  
Ekaterina N. Detkova ◽  
Ekaterina O. Patutina ◽  
Boris B. Kuznetsov
Keyword(s):  
Dna Hybridization ◽  
Iron Reduction ◽  
Gene Sequence ◽  
Soda Lake ◽  
Chloride Ions ◽  
Electron Donors ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequence Analysis ◽  
Ph Range

Two strains of haloalkaliphilic homoacetogenic bacteria capable of iron reduction, Z-7101T and Z-7102, were isolated from soda lake Tanatar III (Altai, Russia). Cells of both strains were flexible, motile, Gram-negative, spore-forming rods. The strains were mesophilic and obligately alkaliphilic: the pH range for growth was 8.5–10.2 (pHopt 9.8). Growth depended on carbonate and chloride ions. The strains were able to grow chemolithoautotrophically on H2+CO2, producing acetate as the only metabolic product. In medium with carbonates as the only potential electron acceptor, the following substrates were utilized for chemo-organotrophic growth: pyruvate, lactate, ethanol, 1-propanol, ethylene glycol and 1-butanol. Strain Z-7101T was able to reduce nitrate, selenate, thiosulfate and anthraquinone 2,6-disulfonate with ethanol as an electron donor. It was also able to reduce synthesized ferrihydrite to siderite with molecular hydrogen or organic compounds, including acetate and formate, as electron donors. It was able to reduce S0 with acetate or formate as electron donors. The DNA G+C content of strain Z-7101T was 34.6 mol%. 16S rRNA gene sequence analysis showed that strains Z-7101T and Z-7102 were members of the order Halanaerobiales and family Halobacteroidaceae, clustering with Fuchsiella alkaliacetigena Z-7100T (98.9–98.4 % similarity). DNA–DNA hybridization was 63.0 % between strain Z-7101T and F. alkaliacetigena Z-7100T. Based on morphological and physiological differences from F. alkaliacetigena Z-7100T and the results of phylogenetic analysis and DNA–DNA hybridization, it is proposed to assign strains Z-7101T and Z-7102 ( = DSM 26052 = VKM B-2790) to the novel species Fuchsiella ferrireducens sp. nov. The type strain is strain Z-7101T ( = DSM 26031T = VKM B-2766T).

scholarly journals Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska

2005 ◽  
Vol 55 (1) ◽  
pp. 473-478 ◽  
Author(s):  
Elena V. Pikuta ◽  
Damien Marsic ◽  
Asim Bej ◽  
Jane Tang ◽  
Paul Krader ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Optimum Growth ◽  
Facultative Anaerobe ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
Ph Range

A novel, psychrotolerant, facultative anaerobe, strain FTR1T, was isolated from Pleistocene ice from the permafrost tunnel in Fox, Alaska. Gram-positive, motile, rod-shaped cells were observed with sizes 0·6–0·7×0·9–1·5 μm. Growth occurred within the pH range 6·5–9·5 with optimum growth at pH 7·3–7·5. The temperature range for growth of the novel isolate was 0–28 °C and optimum growth occurred at 24 °C. The novel isolate does not require NaCl; growth was observed between 0 and 5 % NaCl with optimum growth at 0·5 % (w/v). The novel isolate was a catalase-negative chemoorganoheterotroph that used as substrates sugars and some products of proteolysis. The metabolic end products were acetate, ethanol and CO2. Strain FTR1T was sensitive to ampicillin, tetracycline, chloramphenicol, rifampicin, kanamycin and gentamicin. 16S rRNA gene sequence analysis showed 99·8 % similarity between strain FTR1T and Carnobacterium alterfunditum, but DNA–DNA hybridization between them demonstrated 39±1·5 % relatedness. On the basis of genotypic and phenotypic characteristics, it is proposed that strain FTR1T (=ATCC BAA-754T=JCM 12174T=CIP 108033T) be assigned to the novel species Carnobacterium pleistocenium sp. nov.

scholarly journals Variovorax soli sp. nov., isolated from greenhouse soil

2006 ◽  
Vol 56 (12) ◽  
pp. 2899-2901 ◽  
Author(s):  
Byung-Yong Kim ◽  
Hang-Yeon Weon ◽  
Seung-Hee Yoo ◽  
Seon-Young Lee ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Greenhouse Soil ◽  
Variovorax Paradoxus ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Sequence Similarities

A Gram-negative, rod-shaped, non-spore-forming bacterium, strain GH9-3T, isolated from greenhouse soil, was investigated in a polyphasic study. The novel organism grew at 10–35 °C, 0–3 % NaCl and pH 5–9. It had ubiquinone 8 (Q-8) as the predominant isoprenoid quinone and possessed C16 : 0, summed feature 3, C17 : 0 cyclo and C18 : 1 ω7c as the major fatty acids (together representing 87.4 % of the total). The DNA G+C content was 67.1 mol%. 16S rRNA gene sequence analysis of strain GH9-3T showed that it grouped within the Variovorax cluster, with highest sequence similarities to Variovorax paradoxus IAM 12373T (98.3 %) and Variovorax dokdonensis DS-43T (98.0 %). DNA–DNA hybridization values between strain GH9-3T and V. paradoxus DSM 30034T and V. dokdonensis DS-43T were 38 and 29 %, respectively. Based on phenotypic, chemotaxonomic and phylogenetic features, it is proposed that strain GH9-3T represents a novel species of the genus Variovorax with the name Variovorax soli sp. nov. The type strain is GH9-3T (=KACC 11579T=DSM 18216T).

scholarly journals Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan

2006 ◽  
Vol 56 (7) ◽  
pp. 1607-1613 ◽  
Author(s):  
Masayuki Miyazaki ◽  
Yuichi Nogi ◽  
Ron Usami ◽  
Koki Horikoshi
Keyword(s):  
Deep Sea ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Suruga Bay ◽  
Deep Sea Sediment ◽  
Gene Sequence Analysis ◽  
Definition Of ◽  
Reference Strains

Six strains representing three novel species were isolated from deep-sea sediment in Suruga Bay, Japan, at a depth of 2406–2409 m. On the basis of 16S rRNA gene sequence analysis, the isolated strains, c931T, c941T, d943, c952, d954 and c959T, are closely affiliated with members of the genus Shewanella. The hybridization values for DNA–DNA relatedness between these strains and Shewanella reference strains were significantly lower than that which is accepted as the phylogenetic definition of a species. On the basis of their distinct taxonomic characteristics, the isolated strains represent three novel Shewanella species, for which the names Shewanella kaireitica sp. nov. (three strains, type strain c931T=JCM 11836T=DSM 17170T), Shewanella abyssi sp. nov. (two strains, type strain c941T=JCM 13041T=DSM 17171T) and Shewanella surugensis sp. nov. (type strain c959T=JCM 11835T=DSM 17177T) are proposed.

scholarly journals Micromonospora zhanjiangensis sp. nov., isolated from mangrove forest soil

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4880-4885 ◽  
Author(s):  
Li Zhang ◽  
Lei Li ◽  
Zixin Deng ◽  
Kui Hong
Keyword(s):  
Dna Hybridization ◽  
Mangrove Forest ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Hybridization Data ◽  
Reference Strains ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

A novel actinomycete, designated strain 2902at01T was isolated from soil collected at a mangrove forest in Zhanjiang, Guangdong province, China. The strain was identified using a polyphasic classification method. The 16S rRNA gene sequence of strain 2902at01T showed the highest similarity to Micromonospora equina Y22T (98.3 %) and Micromonospora pattaloongensis TJ2-2T (98.1 %). Phylogenetic analysis based on the gyrB gene sequence also clearly showed that the strain was different from any previously discovered species of the genus Micromonospora. The characteristic whole-cell sugars were ribose and xylose. The cell-wall hydrolysates contained alanine, asparagine, glycine and meso-diaminopimelic acid. MK-10(H6) and MK-10(H8) were the major menaquinones of the novel strain. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The characteristic polar lipids of strain 2902at01T were phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and diphosphatidylglycerol. The DNA G+C content was 70.2 mol%. DNA–DNA hybridization data combined with other physiological and biochemical features could distinguish strain 2902at01T from the reference strains M. equina Y22T and M. pattaloongensis TJ2-2 T. On the basis of these phenotypic and genotypic data, strain 2902at01T represents a novel species of the genus Micromonospora, for which the name Micromonospora zhanjiangensis sp. nov. is proposed. The type strain is 2902at01T ( = CCTCC AA2014018T = DSM 45902T).

scholarly journals Castellaniella gen. nov., to accommodate the phylogenetic lineage of Alcaligenes defragrans, and proposal of Castellaniella defragrans gen. nov., comb. nov. and Castellaniella denitrificans sp. nov.

2006 ◽  
Vol 56 (4) ◽  
pp. 815-819 ◽  
Author(s):  
P. Kämpfer ◽  
K. Denger ◽  
A. M. Cook ◽  
S.-T. Lee ◽  
U. Jäckel ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Gene Sequence Analysis ◽  
Distinct Genus

Comparative 16S rRNA gene sequence analysis indicates that two distinct sublineages exist within the genus Alcaligenes: the Alcaligenes faecalis lineage, comprising Alcaligenes aquatilis and A. faecalis (with the three subspecies A. faecalis subsp. faecalis, A. faecalis subsp. parafaecalis and A. faecalis subsp. phenolicus), and the Alcaligenes defragrans lineage, comprising A. defragrans. This phylogenetic discrimination is supported by phenotypic and chemotaxonomic differences. It is proposed that the A. defragrans lineage constitutes a distinct genus, for which the name Castellaniella gen. nov. is proposed. The type strain for Castellaniella defragrans gen. nov., comb. nov. is 54PinT (=CCUG 39790T=CIP 105602T=DSM 12141T). Finally, on the basis of data from the literature and new DNA–DNA hybridization and phenotypic data, the novel species Castellaniella denitrificans sp. nov. (type strain NKNTAUT=DSM 11046T=CCUG 39541T) is proposed for two strains previously identified as strains of A. defragrans.

scholarly journals Microbacterium ulmi sp. nov., a xylanolytic, phosphate-solubilizing bacterium isolated from sawdust of Ulmus nigra

2004 ◽  
Vol 54 (2) ◽  
pp. 513-517 ◽  
Author(s):  
Raúl Rivas ◽  
Martha E. Trujillo ◽  
Manuel Sánchez ◽  
Pedro F. Mateos ◽  
Eustoquio Martínez-Molina ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Phosphate Solubilizing ◽  
Type Strains

A xylanolytic and phosphate-solubilizing bacterium isolated from sawdust of Ulmus nigra in Salamanca was characterized by a polyphasic approach. The novel strain, designated XIL02T, was Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped and non-motile. Phylogenetically and chemotaxonomically, it was related to members of the genus Microbacterium. According to 16S rRNA gene sequence analysis, it is closely related to Microbacterium arborescens and Microbacterium imperiale; however, DNA–DNA hybridization showed reassociation values less than 70 % with the type strains of these species. In chemotaxonomic analyses, the major menaquinones detected were MK-12, MK-13 and MK-11 and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0; the peptidoglycan was of the type B2β. The G+C content determined was 69 mol%. Based on the present data, it is proposed that strain XIL02T (=LMG 20991T=CECT 5976T) be classified as the type strain of a novel Microbacterium species, for which the name Microbacterium ulmi sp. nov. is proposed.

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