scholarly journals Tistlia consotensis gen. nov., sp. nov., an aerobic, chemoheterotrophic, free-living, nitrogen-fixing alphaproteobacterium, isolated from a Colombian saline spring

2010 ◽  
Vol 60 (6) ◽  
pp. 1437-1443 ◽  
Author(s):  
C. Díaz-Cárdenas ◽  
B. K. C. Patel ◽  
S. Baena
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Chromosomal Dna ◽  
Colombian Andes ◽  
Gene Sequence Analysis ◽  
Novel Genus And Species ◽  
Curved Rods ◽  
Saline Spring

A Gram-negative, aerobic, mesophilic, non-spore-forming, chemotrophic, chlorophyll-lacking, nitrogen-fixing bacterium, designated strain USBA 355T, was isolated from the saline spring ‘Salado de Consotá’ situated in the Colombian Andes. The non-flagellated cells of strain USBA 355T were straight to slightly curved rods (0.6–0.7 × 3.0–3.5 μm). Growth occurred optimally at 30 °C (growth temperature range between 20 and 40 °C), at pH 6.5–6.7 (pH growth range between 5.0 and 8.0) and at 0.5 % NaCl (w/v) (range between 0 and 4 %). The major quinone present was Q-10 and the predominant fatty acids identified were C19 : 0 cyclo ω8c, C18 : 1 ω7c and C18 : 0. The G+C content of the chromosomal DNA was 71±1 mol%. 16S rRNA gene sequence analysis indicated that strain USBA 355T formed a distant phylogenetic line of descent with members of the genus Thalassobaculum, family Rhodospirillaceae, class Alphaproteobacteria (90 % gene sequence similarity). Comparison of the phylogenetic, chemotaxonomic and physiological features of strain USBA 355T with all other members of the family Rhodospirillaceae suggested that it represents a novel genus and species for which the name Tistlia consotensis gen. nov., sp. nov. is proposed. The type strain of the type species is USBA 355T (=JCM 15529T=KCTC 22406T).

scholarly journals Dethiosulfovibrio salsuginis sp. nov., an anaerobic, slightly halophilic bacterium isolated from a saline spring

2010 ◽  
Vol 60 (4) ◽  
pp. 850-853 ◽  
Author(s):  
C. Díaz-Cárdenas ◽  
G. López ◽  
B. K. C. Patel ◽  
S. Baena
Keyword(s):  
Halophilic Bacterium ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Chromosomal Dna ◽  
Colombian Andes ◽  
Gene Sequence Analysis ◽  
Curved Rods ◽  
Slightly Halophilic Bacterium ◽  
Nitrate And Nitrite ◽  
Saline Spring

A mesophilic, strictly anaerobic, slightly halophilic bacterium, designated strain USBA 82T, was isolated from a terrestrial saline spring in the Colombian Andes. The non-spore-forming curved rods (5–7×1.3 μm) with pointed or rounded ends, stained Gram-negative and were motile by means of laterally inserted flagella. The strain grew optimally at 30 °C (growth range 20–40 °C), pH 7.3 (growth range pH 5.5–8.5) and 2 % (w/v) NaCl (growth range 0.1–7 % NaCl). The strain fermented peptides, amino acids and a few organic acids, but growth was not observed on carbohydrates, alcohols or fatty acids. The strain reduced thiosulfate and sulfur to sulfide. Sulfate, sulfite, nitrate and nitrite were not used as electron acceptors. On peptone alone, acetate, succinate, propionate and traces of ethanol were formed, but in the presence of thiosulfate, acetate and succinate were formed. The G+C content of the chromosomal DNA was 52 mol% (T m).16S rRNA gene sequence analysis indicated that strain USBA 82T was affiliated to Dethiosulfovibrio peptidovorans within the phylum Synergistetes with a similarity value of approximately 93 %. Based on the differences between the new strain and the type species of the genus Dethiosulfovibrio, we suggest that strain USBA 82T represents a novel species of the genus for which the name Dethiosulfovibrio salsuginis sp. nov. is proposed. The type strain is USBA 82T (=DSM 21565T=KCTC 5659T).

scholarly journals Desulfosoma caldarium gen. nov., sp. nov., a thermophilic sulfate-reducing bacterium from a terrestrial hot spring

2011 ◽  
Vol 61 (4) ◽  
pp. 732-736 ◽  
Author(s):  
Sandra Baena ◽  
Natalia Perdomo ◽  
Catalina Carvajal ◽  
Carolina Díaz ◽  
Bharat K. C. Patel
Keyword(s):  
Gene Sequence ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Terminal Electron Acceptor ◽  
Sulfate Reducing ◽  
Colombian Andes ◽  
Gene Sequence Analysis ◽  
Lactate Degradation ◽  
Terrestrial Hot Spring

A thermophilic, sulfate-reducing bacterium, designated strain USBA-053T, was isolated from a terrestrial hot spring located at a height of 2500 m in the Colombian Andes (5° 45′ 33.29″ N 73° 6′ 49.89″ W), Colombia. Cells of strain USBA-053T were oval- to rod-shaped, Gram-negative and motile by means of a single polar flagellum. The strain grew autotrophically with H2 as the electron donor and heterotrophically on formate, propionate, butyrate, valerate, isovalerate, lactate, pyruvate, ethanol, glycerol, serine and hexadecanoic acid in the presence of sulfate as the terminal electron acceptor. The main end products from lactate degradation, in the presence of sulfate, were acetate, CO2 and H2S. Strain USBA-053T fermented pyruvate in the absence of sulfate and grew optimally at 57 °C (growth temperature ranged from 50 °C to 62 °C) and pH 6.8 (growth pH ranged from 5.7 to 7.7). The novel strain was slightly halophilic and grew in NaCl concentrations ranging from 5 to 30 g l−1, with an optimum at 25 g l−1 NaCl. Sulfate, thiosulfate and sulfite were used as electron acceptors, but not elemental sulfur, nitrate or nitrite. The G+C content of the genomic DNA was 56±1 mol%. 16S rRNA gene sequence analysis indicated that strain USBA-053T was a member of the class Deltaproteobacteria, with Desulfacinum hydrothermale MT-96T as the closest relative (93 % gene sequence similarity). On the basis of physiological characteristics and phylogenetic analysis, it is suggested that strain USBA-053T represents a new genus and novel species for which the name Desulfosoma caldarium gen. nov., sp. nov. is proposed. The type strain of the type species is USBA-053T ( = KCTC 5670T = DSM 22027T).

scholarly journals Parapedobacter koreensis gen. nov., sp. nov.

2007 ◽  
Vol 57 (6) ◽  
pp. 1336-1341 ◽  
Author(s):  
Myung Kyum Kim ◽  
Ju-Ryun Na ◽  
Dong Ha Cho ◽  
Nak-Kyun Soung ◽  
Deok-Chun Yang
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Physiological And Biochemical

Strain Jip14T, a Gram-negative, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from dried rice straw and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Jip14T belongs to the family Sphingobacteriaceae, and the highest degree of sequence similarity was determined to be to Pedobacter saltans DSM 12145T (88.5 %), Pedobacter africanus DSM 12126T (87.6 %), Pedobacter heparinus DSM 2366T (87.1 %) and Pedobacter caeni LMG 22862T (86.9 %). Chemotaxonomic data revealed that strain Jip14T possesses menaquinone MK-7 and the predominant fatty acids C15 : 0 iso, C16 : 0, C16 : 0 10-methyl, C17 : 0 iso 3-OH and summed feature 3 (C15 : 0 iso 2-OH/C16 : 1 ω7c). The results of physiological and biochemical tests clearly demonstrated that strain Jip14T represents a distinct species. Based on these data, Jip14T should be classified within a novel genus and species, for which the name Parapedobacter koreensis gen. nov., sp. nov. is proposed. The type strain of Parapedobacter koreensis is Jip14T (=KCTC 12643T=LMG 23493T).

scholarly journals Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur- and thiosulfate-reducing spirochaete isolated from a saline spring

2011 ◽  
Vol 61 (1) ◽  
pp. 110-117 ◽  
Author(s):  
Galina Dubinina ◽  
Margarita Grabovich ◽  
Natalia Leshcheva ◽  
Frederick A. Rainey ◽  
Ekaterina Gavrish
Keyword(s):  
Gene Sequence ◽  
Elemental Sulfur ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Saline Spring

A novel strain of fermenting, aerotolerant, chemo-organoheterotrophic spirochaete designated PT was isolated from a sulfur ‘Thiodendron’ mat in a saline spring at the Staraya Russa resort (Novgorod Region, Russia). Cells of strain PT exhibited a helical shape. The spirochaete required sulfide in the growth medium and was able to oxidize it non-enzymically to elemental sulfur via the interaction of H2O2 with sulfide and deposit it in the periplasmic space. Growth occurred at 4–32 °C (optimum at 28–30 °C), pH 6.0–8.5 (optimum pH 7.0–7.5), and in 0.1–1 M NaCl (optimum 0.35 M). The isolate used several sugars and polysaccharides as carbon or energy sources but did not use peptides, amino acids, organic acids or alcohols. The products of glucose fermentation were formate, acetate, ethanol, pyruvate, CO2 and H2. The genomic DNA G+C content was 41.7 mol%. 16S rRNA gene sequence analysis showed that strain PT fell within a group of species in the genus Spirochaeta, including Spirochaeta litoralis, S. isovalerica and S. cellobiosiphila, with which it shared less then 89 % sequence similarity. On the basis of its morphology, physiology and other phenotypic properties, as well as its phylogenetic position, the new isolate is considered to represent a novel species of the genus Spirochaeta, for which the name Spirochaeta perfilievii sp. nov. is proposed. The type strain is PT (=DSM 19205T =VKM B-2514T).

scholarly journals Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the ‘Betaproteobacteria’

2005 ◽  
Vol 55 (6) ◽  
pp. 2329-2332 ◽  
Author(s):  
Hee-Chan Yang ◽  
Wan-Taek Im ◽  
Dong-Shan An ◽  
Woo-shin Park ◽  
In S. Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Novel Genus And Species

A taxonomic study was carried out on a bacterial strain, designated KM-45T, isolated from forest soil collected near Daejeon, South Korea. Comparative 16S rRNA gene sequence analysis indicated a clear affiliation of this bacterium to the ‘Betaproteobacteria’ and that it was related most closely to Chitinibacter tainanensis BCRC 17254T, Formivibrio citricus DSM 6150T and Iodobacter fluviatilis ATCC 33051T (92·4, 91·2 and 88·9 % 16S rRNA gene sequence similarity, respectively). Cells were Gram-negative, facultatively anaerobic, motile and rod-shaped. The strain grew well on R2A medium and utilized a broad spectrum of carbon sources. The G+C content of the genomic DNA was 58 mol% and the predominant ubiquinone was Q-8. Major fatty acids were C16 : 0, C16 : 1 ω7c/iso-C15 : 0 2-OH, C18 : 1 ω7c/ω9t/ω12t and C17 : 0 cyclo. On the basis of the evidence presented, it is proposed that strain KM-45T should be placed in a novel genus and species, for which the name Silvimonas terrae gen. nov., sp. nov. is proposed. The type strain is KM-45T (=KCTC 12358T=NBRC 100961T).

scholarly journals Martelella mediterranea gen. nov., sp. nov., a novel α-proteobacterium isolated from a subterranean saline lake

2005 ◽  
Vol 55 (2) ◽  
pp. 955-959 ◽  
Author(s):  
Raúl Rivas ◽  
Salud Sánchez-Márquez ◽  
Pedro F. Mateos ◽  
Eustoquio Martínez-Molina ◽  
Encarna Velázquez
Keyword(s):  
Gene Sequence ◽  
Saline Lake ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Novel Genus ◽  
Gene Sequence Analysis ◽  
Novel Genus And Species ◽  
Separate Line ◽  
Aurantimonas Coralicida

A bacterial strain was isolated from the water of Lake Martel in Mallorca (Spain). The isolate, designated MACL11T, was halotolerant and strictly aerobic. The cells were non-motile, non-spore-forming, Gram-negative short rods. Comparative 16S rRNA gene sequence analysis revealed that MACL11T represents a separate line of descent within the order ‘Rhizobiales’ of the class ‘Alphaproteobacteria’. Strain MACL11T was most closely related to the genera Rhizobium (93·3 % sequence similarity to Rhizobium rhizogenes), Aurantimonas (90·3 % sequence similarity to Aurantimonas coralicida) and Fulvimarina (90·3 % sequence similarity to Fulvimarina pelagi). Chemotaxonomically, strain MACL11T was characterized by the presence of Q-10 as the major respiratory lipoquinone. The major fatty acids detected were C19 : 0 cycloω8c, C18 : 1 ω7c, C16 : 0 and 11-methyl C18 : 1 ω7c. The G+C content of the DNA was 57·4 mol%. Oxidase and catalase activities were present. Growth with many different carbohydrates as the sole carbon source was observed. The data from this polyphasic study suggest that this bacterium belongs to a novel genus of the order ‘Rhizobiales’ and is not associated with any of the known families of this order. It is proposed that isolate MACL11T should be classified in a novel genus and species, Martelella mediterranea gen. nov., sp. nov., with MACL11T (=LMG 22193T=CECT 5861T) as the type strain.

scholarly journals Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2831-2837 ◽  
Author(s):  
Peter Kämpfer ◽  
Karin Martin ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
High Sequence Similarity ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).

scholarly journals Lactobacillus hammesii sp. nov., isolated from French sourdough

2005 ◽  
Vol 55 (2) ◽  
pp. 763-767 ◽  
Author(s):  
Rosica Valcheva ◽  
Maher Korakli ◽  
Bernard Onno ◽  
Hervé Prévost ◽  
Iskra Ivanova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Fragment Length Polymorphism ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Different Strains

Twenty morphologically different strains were chosen from French wheat sourdough isolates. Cells were Gram-positive, non-spore-forming, non-motile rods. The isolates were identified using amplified-fragment length polymorphism, randomly amplified polymorphic DNA and 16S rRNA gene sequence analysis. All isolates were members of the genus Lactobacillus. They were identified as representing Lactobacillus plantarum, Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus spicheri and Lactobacillus sakei. However, two isolates (LP38T and LP39) could be clearly discriminated from recognized Lactobacillus species on the basis of genotyping methods. 16S rRNA gene sequence similarity and DNA–DNA relatedness data indicate that the two strains belong to a novel Lactobacillus species, for which the name Lactobacillus hammesii is proposed. The type strain is LP38T (=DSM 16381T=CIP 108387T=TMW 1.1236T).

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 Paenibacillus ripae sp. nov., isolated from bank side soil

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4757-4762 ◽  
Author(s):  
Ying Sun ◽  
Zhaohui Guo ◽  
Qi Zhao ◽  
Qiyu Gao ◽  
QinJian Xie ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Pr China ◽  
Diamino Acid

A Gram-stain-variable, rod-shaped, non-motile and endospore-forming bacterium, designated strain HZ1T, was isolated from a sample of bank side soil from Hangzhou city, Zhejiang province, PR China. On the basis of 16S rRNA gene sequence analysis, strain HZ1T was closely related to members of the genus Paenibacillus, sharing the highest levels of sequence similarity with Paenibacillus agarexedens DSM 1327T (94.4 %), Paenibacillus sputi KIT00200-70066-1T (94.4 %). Growth occurred at 15–42 °C (optimum 30–37 °C), pH 5.0–9.5 (optimum pH 7.0–8.0) and NaCl concentrations of up to 6.0 % (w/v) were tolerated (optimum 0.5 %). The dominant respiratory quinone was MK-7 and the DNA G+C content was 40.1 mol%. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids of strain HZ1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain HZ1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus ripae sp. nov. (type strain HZ1T = CCTCC AB 2014276T = LMG 28639T) is proposed.

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