scholarly journals Rhodovulum bhavnagarense sp. nov., a phototrophic alphaproteobacterium isolated from a pink pond

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2528-2532 ◽  
Author(s):  
A. Srinivas ◽  
K. Rahul ◽  
E. V. V. Ramaprasad ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Molecular Genetic ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
Molecular Genetic Evidence

An oval to rod-shaped, Gram-stain-negative, phototrophic bacterium, strain JA738T, was isolated from a sediment sample collected from a pink pond. Strain JA738T was non-motile and had vesicular-type intracellular photosynthetic membranes. Bacteriochlorophyll a and carotenoids of the spheroidene series were present as the major photosynthetic pigments. Strain JA738T required thiamine and pantothenate for growth. The major cellular fatty acids were C18 : 1ω7c, C18 : 1ω5c, C18 : 0 and C18 : 1ω7c11-methyl; minor amounts of C10 : 0 3-OH and C16 : 0 were also present. The major quinone was Q-10 and major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and two unidentified sulfolipids (SL1–2). Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA738T clustered with species of the genus Rhodovulum in the class Alphaproteobacteria . Strain JA738T was most closely related to Rhodovulum adriaticum DSM 2781T (96.4 % 16S rRNA gene sequence similarity) and other members of the genus Rhodovulum (<96.1 %). On the basis of phenotypic and molecular genetic evidence, it is proposed that strain JA738T should be classified as a novel species of the genus Rhodovulum for which the name Rhodovulum bhavnagarense sp. nov. is proposed. The type strain is JA738T ( = DSM 24766T = KCTC 15110T).

scholarly journals Noviherbaspirillum suwonense sp. nov., isolated from an air sample

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1552-1558 ◽  
Author(s):  
Soo-Jin Kim ◽  
Ji-Young Moon ◽  
Hang-Yeon Weon ◽  
Seung-Beom Hong ◽  
Soon-Ja Seok ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Air Sample ◽  
Bacterium Strain

A Gram-stain-negative bacterium, strain 5410S-62T, was isolated from an air sample collected in Suwon, Republic of Korea. It was aerobic, motile, mesophilic and formed rod-shaped cells. Colonies on R2A agar were convex, circular and pale orange with entire margins. Growth occurred at pH 5–9 (optimally at pH 7) and at 10–40 °C (optimally at 28 °C). It did not grow in the presence of 1 % NaCl. Comparative analyses of 16S rRNA gene sequences demonstrated that the novel strain was closely related to members of the genus Noviherbaspirillum . Strain 5410S-62T showed the highest sequence similarity (98.2 %) to Glaciimonas singularis A2-57T. It also showed high 16S rRNA gene sequence similarity (98.1–95.6 %) to members of the genus Noviherbaspirillum (98.1 % to Noviherbaspirillum aurantiacum SUEMI08T, 97.8 % to Noviherbaspirillum soli SUEMI10T and Noviherbaspirillum canariense SUEMI03T, 97.6 % to Noviherbaspirillum psychrotolerans PB1T and 95.6 % to Noviherbaspirillum malthae CC-AFH3T). The strain contained summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) as major fatty acids, Q-8 as the only ubiquinone and large amounts of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. Strain 5410S-62T revealed less than 70 % DNA–DNA relatedness with the type strains of closely related species of the genera Noviherbaspirillum and Herbaspirillum and Glaciimonas singularis . Based on the physiological, biochemical and chemotaxonomic data obtained in this study, it is proposed that strain 5410S-62T represents a novel species, Noviherbaspirillum suwonense sp. nov., with 5410S-62T ( = KACC 16657T =  NBRC 108944T) as the type strain.

Algoriphagus pacificus sp. nov. and Algoriphagus oliviformis sp. nov., isolated from a mariculture fishpond

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Huibin Lu ◽  
Zhipeng Cai ◽  
Tongchu Deng ◽  
Youfeng Qian ◽  
Meiying Xu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, non-flagellated, non-spore-forming and non-motile strains (YJ13CT and H41T) were isolated from a mariculture fishpond in PR China. Comparisons based on 16S rRNA gene sequences indicated that YJ13CT and H41T shared 16S rRNA gene sequences similarities between 92.6 and 99.2 % with species of the genus Algoriphagus . YJ13CT only shared 93.8 % 16S rRNA gene sequence similarity with H41T. The reconstructed phylogenetic and phylogenomic trees indicated that YJ13CT and H41T clustered closely with species of the genus Algoriphagus . The calculated pairwise orthologous average nucleotide identity with usearch (OrthoANIu) values between strains YJ13CT and H41T and other related strains were all less than 79.5 %. The OrthoANIu value between YJ13CT and H41T was only 69.9 %. MK-7 was the predominant respiratory quinone of YJ13CT and H41T and their major cellular fatty acids contained iso-C15 : 0, C16 : 1 ω7c and C17 : 1 ω9c. The polar lipids profiles of YJ13CT and H41T consisted of phosphatidylethanolamine and several kinds of unidentified lipids. Combining the above descriptions, strains YJ13CT and H41T represent two distinct novel species of the genus Algoriphagus , for which the names Algoriphagus pacificus sp. nov. (type strain YJ13CT=GDMCC 1.2178T=KCTC 82450T) and Algoriphagus oliviformis sp. nov. (type strain H41T=GDMCC 1.2179T=KCTC 82451T) are proposed.

Flammeovirga pacifica sp. nov., isolated from deep-sea sediment

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 937-941 ◽  
Author(s):  
Hui Xu ◽  
Yuanyuan Fu ◽  
Ning Yang ◽  
Zhixin Ding ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Strain WPAGA1T was isolated from marine sediment of the west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Flammeovirga . Strain WPAGA1T exhibited highest 16S rRNA gene sequence similarity with Flammeovirga yaeyamensis NBRC 100898T (98.1 %) and lower sequence similarity with Flammeovirga arenaria IFO 15982T (94.6 %) and other members of the genus Flammeovirga (<94.2 %). DNA–DNA relatedness studies showed that strain WPAGA1T was distinct from F. yaeyamensis NBRC 100898T and F. arenaria NBRC 15982T (43±4 % and 32±2 % relatedness values, respectively). Strain WPAGA1T could be distinguished from all known members of the genus Flammeovirga by a number of phenotypic features. However, the dominant fatty acids of strain WPAGA1T (iso-C15 : 0, C16 : 0 and C20 : 4ω6,9,12,15c), the major polyamine (cadaverine) and the G+C content of the chromosomal DNA (32.9 mol%) were consistent with those of members of the genus Flammeovirga . Based on phenotypic and chemotaxonomic features and 16S rRNA gene sequences, strain WPAGA1T can be assigned to the genus Flammeovirga as a representative of a novel species, for which the name Flammeovirga pacifica sp. nov. is proposed; the type strain is WPAGA1T ( = CCTCC AB 2010364T = LMG 26175T = DSM 24597T = MCCC 1A06425T).

Ferrimonas sediminum sp. nov., isolated from coastal sediment of an amphioxus breeding zone

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 977-981 ◽  
Author(s):  
Shiqi Ji ◽  
Rui Zhao ◽  
Zhao Li ◽  
Bingyu Li ◽  
Xiaochong Shi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Coastal Sediment ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Breeding Zone ◽  
Isoprenoid Quinones

A Gram-stain-negative, facultatively anaerobic rod with a polar flagellum, designated strain JYr13T, was isolated from coastal sediment of an amphioxus breeding zone located in Qingdao, China. The isolate utilized Fe(III) oxyhydroxide, Fe(III) citrate, SeO3 2– and SeO4 2– as electron acceptors. Strain JYr13T grew optimally at 25–28 °C, pH 7.0–8.0 and in presence of 3 % (w/v) NaCl. Strain JYr13T contained menaquinone-7 and ubiquinones Q-7 and Q-8 as the predominant isoprenoid quinones, and C18 : 1ω9c, iso-C15 : 0, C17 : 1ω8c and C16 : 0 as the major fatty acids. The DNA G+C content of strain JYr13T was 59 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the closest phylogenetic neighbour of strain JYr13T was Ferrimonas kyonanensis DSM 18153T (96.0 % 16S rRNA gene sequence similarity). Based on the phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain JYr13T is considered to represent a novel species of the genus Ferrimonas , for which the name Ferrimonas sediminum sp. nov. is proposed. The type strain is JYr13T ( = DSM 23317T = LMG 25564T).

scholarly journals Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., isolated from alpine glacier cryoconite

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2662-2668 ◽  
Author(s):  
Rosa Margesin ◽  
Cathrin Spröer ◽  
De-Chao Zhang ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Alpine Glacier ◽  
Dna Relatedness ◽  
Link Type

The taxonomic positions of two Gram-staining-negative, psychrophilic bacteria, which were isolated from alpine glacier cryoconite and designated strains Cr4-12T and Cr4-35T, were investigated using a polyphasic approach. Both novel strains contained ubiquinone Q-8 as the sole quinone, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the dominant cellular fatty acids, putrescine and 2-hydroxyputrescine as the major polyamines, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C contents of strains Cr4-12T and Cr4-35T were 61.3 mol% and 60.7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the genus Polaromonas . Although the 16S rRNA gene sequences of strains Cr4-12T and Cr4-35T were very similar (98.7 % sequence similarity), hybridizations indicated a DNA–DNA relatedness value of only 26.9 % between the two novel strains. In pairwise comparisons with the type strains of recognized Polaromonas species, strains Cr4-12T and Cr4-35T showed 16S rRNA gene sequence similarities of 96.4–98.5 % and 96.5–98.4 %, respectively. Based on the phenotypic and phylogenetic evidence and DNA–DNA relatedness data, strains Cr4-12T and Cr4-35T represent two novel species within the genus Polaromonas , for which the names Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., respectively, are proposed. The type strain of Polaromonas glacialis sp. nov. is Cr4-12T ( = DSM 24062T  = LMG 26049T  = KACC 15089T) and that of Polaromonas cryoconiti sp. nov. is Cr4-35T ( = DSM 24248T  = LMG 26050T  = KACC 15090T).

Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1902-1907 ◽  
Author(s):  
Bédis Dridi ◽  
Marie-Laure Fardeau ◽  
Bernard Ollivier ◽  
Didier Raoult ◽  
Michel Drancourt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Human Faeces ◽  
Link Type

During attempts to obtain novel, human-associated species of the domain Archaea , a coccoid micro-organism, designated strain B10T, was isolated in pure culture from a sample of human faeces collected in Marseille, France. On the basis of its phenotypic characteristics and 16S rRNA and mcrA gene sequences, the novel strain was classified as a methanogenic archaeon. Cells of the strain were non-motile, Gram-staining-positive cocci that were approximately 850 nm in diameter and showed autofluorescence at 420 nm. Cells were lysed by 0.1 % (w/v) SDS. With hydrogen as the electron donor, strain B10T produced methane by reducing methanol. The novel strain was unable to produce methane when hydrogen or methanol was the sole energy source. In an atmosphere containing CO2, strain B10T could not produce methane from formate, acetate, trimethylamine, 2-butanol, 2-propanol, cyclopentanol, 2-pentanol, ethanol, 1-propanol or 2,3-butanediol. Strain B10T grew optimally with 0.5–1.0 % (w/v) NaCl, at pH 7.6 and at 37 °C. It required tungstate-selenite for growth. The complete genome of the novel strain was sequenced; the size of the genome was estimated to be 2.05 Mb and the genomic DNA G+C content was 59.93 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the highest sequence similarities (98.0–98.7 %) were seen between strain B10T and several uncultured, methanogenic Archaea that had been collected from the digestive tracts of a cockroach, a chicken and mammals. In the same analysis, the non-methanogenic ‘Candidatus Aciduliprofundum boonei’ DSM 19572 was identified as the cultured micro-organism that was most closely related to strain B10T (83.0 % 16S rRNA gene sequence similarity). Each of the three treeing algorithms used in the analysis of 16S rRNA gene sequences indicated that strain B10T belongs to a novel order that is distinct from the Thermoplasmatales . The novel strain also appeared to be distinct from Methanosphaera stadtmanae DSM 3091T (72.9 % 16S rRNA gene sequence similarity), another methanogenic archaeon that was isolated from human faeces and can use methanol in the presence of hydrogen. Based on the genetic and phenotypic evidence, strain B10T represents a novel species of a new genus for which the name Methanomassiliicoccus luminyensis gen. nov., sp. nov. is proposed. The type strain of the type species is B10T ( = DSM 24529T = CSUR P135T).

Hymenobacter ginsengisoli sp. nov., isolated from soil of a ginseng field

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 661-666 ◽  
Author(s):  
Van-An Hoang ◽  
Yeon-Ju Kim ◽  
Ngoc Lan Nguyen ◽  
Deok-Chun Yang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, red bacterium, designated DCY57T, was isolated from soil of a ginseng field in a mountainous region of Chungnam province in South Korea. Strain DCY57T grew with 0–1 % (w/v) NaCl and the optimum temperature for growth was 30 °C. Strain DCY57T contained MK-7 as the predominant menaquinone. The polyamine was sym-homospermidine. The major fatty acids were C16:1ω5c, iso-C15:0, anteiso-C15:0 and summed feature 3 (containing C16:1ω7c and/or C16:1ω6c). The major polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids. The DNA G+C content was 58.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DCY57T was most closely related to members of the genus Hymenobacter . The isolate exhibited 91.7 % 16S rRNA gene sequence similarity with H. soli PB17T, 94.5 % with H. flocculans A2-50AT and 95.8 % with H. metalli A2-91T. On the basis of the evidence presented in this study, strain DCY57T represents a novel species within the genus Hymenobacter , for which the name Hymenobacter ginsengisoli sp. nov. is proposed. The type strain is DCY57T ( = KCTC 23674T = JCM 17841T).

Bacillus composti sp. nov. and Bacillus thermophilus sp. nov., two thermophilic, Fe(III)-reducing bacteria isolated from compost

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3030-3036 ◽  
Author(s):  
Guiqin Yang ◽  
Ming Chen ◽  
Zhen Yu ◽  
Qin Lu ◽  
Shungui Zhou
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Two novel thermophilic bacteria, designated SgZ-9T and SgZ-10T, were isolated from compost. Cells of the two strains were catalase-positive, endospore-forming and Gram-staining-positive rods. Strain SgZ-9T was oxidase-positive and non-motile, and strain SgZ-10T was oxidase-negative and motile. The highest 16S rRNA gene sequence similarity for both strains SgZ-9T and SgZ-10T was observed with Bacillus fortis (97.5 % and 96.9 %, respectively). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SgZ-9T formed a cluster with B. fortis R-6514T and Bacillus fordii R-7190T, and SgZ-10T formed a cluster with Bacillus farraginis R-6540T. The DNA–DNA pairing studies showed that SgZ-9T displayed 41.6 % and 30.7 % relatedness to the type strains of B. fortis and B. fordii , respectively. The 16S rRNA gene sequence similarity between strains SgZ-9T and SgZ-10T was 97.2 %, and the level of DNA–DNA relatedness between them was 39.2 %. The DNA G+C content of SgZ-9T and SgZ-10T was 45.3 and 47.9 mol%, respectively. Chemotaxonomic analysis revealed that both strains contained the menaquinone 7 (MK-7) as the predominant respiratory quinone. The major cellular fatty acids (>5 %) were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C17 : 0 in SgZ-9T and iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0 and iso-C16 : 0 in SgZ-10T. Based on the phenotypic characteristics, chemotaxonomic features, DNA–DNA hybridization with the nearest phylogenetic neighbours and phylogenetic analysis based on the 16S rRNA gene sequences, the two strains were determined to be two distinct novel species in the genus Bacillus , and the names proposed are Bacillus composti sp. nov. SgZ-9T ( = CCTCC AB2012109T = KACC 16872T) and Bacillus thermophilus sp. nov. SgZ-10T (CCTCC AB2012110T = KACC 16873T).

scholarly journals Luteimonas cucumeris sp. nov., isolated a from cucumber leaf

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2916-2920 ◽  
Author(s):  
Zhan-Bin Sun ◽  
Hui Zhang ◽  
Xing-Fang Yuan ◽  
Yin-Xian Wang ◽  
Dong-Mei Feng ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Pr China

A Gram-negative, aerobic and non-motile rod, designated Y4T, was isolated from a cucumber leaf from Pinggu District, east Beijing, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Y4T was most closely related to Luteimonas aquatica RIB1-20T (96.7 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain Y4T and L. aquatica RIB1-20T was 42.5±3.9 %. The predominant fatty acids were iso-C15 : 0, iso-C17 : 1ω9c, iso-C16 : 0 and iso-C17 : 0. The major ubiquinone was Q-8. The DNA G+C content of the type strain was 69.9 mol%. Based on the evidence above, strain Y4T represents a novel species of the genus Luteimonas , for which the name Luteimonas cucumeris sp. nov. is proposed. The type strain is Y4T ( = CGMCC 1.10821T = KCTC 23627T).

scholarly journals Bradymonas sediminis gen. nov., sp. nov., isolated from coastal sediment, and description of Bradymonadaceae fam. nov. and Bradymonadales ord. nov.

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1542-1549 ◽  
Author(s):  
Zong-Jie Wang ◽  
Qian-Qian Liu ◽  
Li-Hua Zhao ◽  
Zong-Jun Du ◽  
Guan-Jun Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Coastal Sediment ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

A novel Gram-stain-negative, rod-shaped, gliding, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated FA350T, was isolated from coastal sediment from Xiaoshi Island, Weihai, China. Strain FA350T showed growth on modified nutrient agar supplemented with 0.1 % d-(+)-trehalose and with distilled water replaced by seawater. Optimal growth occurred at 33 °C and pH 8.5 with 4 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FA350T belongs to a novel bacterial order in the class Deltaproteobacteria , and the most closely related type strains belong to the order Desulfuromonadales , with 85.1–85.6 % 16S rRNA gene sequence similarity. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and two unknown phospholipids. Major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω10c and menaquinone MK-7 was the sole respiratory quinone. The DNA G+C content of strain FA350T was 60.3 mol%. The isolate and closely related environmental clones formed a novel order-level clade in the class Deltaproteobacteria . Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain FA350T may represent a novel order of the Deltaproteobacteria . Here, we propose the name Bradymonas sediminis gen. nov., sp. nov. to accommodate strain FA350T. The type strain of Bradymonas sediminis is FA350T ( = DSM 28820T = CICC 10904T); Bradymonadales ord. nov. and Bradymonadaceae fam. nov. are also proposed to accommodate the novel taxon.

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