scholarly journals Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10

2011 ◽  
Vol 61 (6) ◽  
pp. 1442-1447 ◽  
Author(s):  
Hideyuki Tamaki ◽  
Yasuhiro Tanaka ◽  
Hiroaki Matsuzawa ◽  
Mizuho Muramatsu ◽  
Xian-Ying Meng ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Aquatic Plant ◽  
Sequence Similarity ◽  
Limited Range ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Bacterium Strain ◽  
Ph Range

A novel aerobic, chemoheterotrophic bacterium, strain YO-36T, isolated from the rhizoplane of an aquatic plant (a reed, Phragmites australis) inhabiting a freshwater lake in Japan, was morphologically, physiologically and phylogenetically characterized. Strain YO-36T was Gram-negative and ovoid to rod-shaped, and formed pinkish hard colonies on agar plates. Strain YO-36T grew at 20–40 °C with optimum growth at 30–35 °C, whilst no growth was observed at 15 °C or 45 °C. The pH range for growth was 5.5–8.5 with an optimum at pH 6.5. Strain YO-36T utilized a limited range of substrates, such as sucrose, gentiobiose, pectin, gellan gum and xanthan gum. The strain contained C16 : 0, C16 : 1, C14 : 0 and C15 : 0 as the major cellular fatty acids and menaquinone-12 as the respiratory quinone. The G+C content of the genomic DNA was 62.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YO-36T belonged to the candidate phylum OP10 comprised solely of environmental 16S rRNA gene clone sequences except for two strains, P488 and T49 isolated from geothermal soil in New Zealand; strain YO-36T showed less than 80 % sequence similarity to strains P488 and T47. Based on the phylogetic and phenotypic findings, a new genus and species, Armatimonas rosea gen. nov., sp. nov., is proposed for the isolate (type strain YO-36T  = NBRC 105658T  = DSM 23562T). In addition, a new bacterial phylum named Armatimonadetes phyl. nov. is proposed for the candidate phylum OP10 represented by A. rosea gen. nov., sp. nov. and Armatimonadaceae fam. nov., Armatimonadales ord. nov., and Armatimonadia classis nov.

scholarly journals Chryseobacterium caeni sp. nov., isolated from bioreactor sludge

2007 ◽  
Vol 57 (1) ◽  
pp. 141-145 ◽  
Author(s):  
Zhe-Xue Quan ◽  
Kwang Kyu Kim ◽  
Myung-Kyum Kim ◽  
Long Jin ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
The Family ◽  
Bacterium Strain

A Gram-negative, non-spore-forming, yellow-pigmented bacterium, strain N4T, was isolated from a nickel-complexed cyanide-degrading bioreactor and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain N4T is affiliated to the genus Chryseobacterium of the family Flavobacteriaceae. The levels of 16S rRNA gene sequence similarity between strain N4T and the type strains of all known Chryseobacterium species were 93.2–95.8 %, suggesting that strain N4T represents a novel species within the genus Chryseobacterium. The strain contained iso-C15 : 0 and summed feature 4 as the major fatty acids and menaquinone MK-6 as the predominant respiratory quinone. The G+C content of the genomic DNA was 38.2 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain N4T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium caeni sp. nov. is proposed. The type strain is N4T (=KCTC 12506T=CCBAU 10201T=DSM 17710T).

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 Tenacibaculum geojense sp. nov., isolated from seawater

2012 ◽  
Vol 62 (1) ◽  
pp. 18-22 ◽  
Author(s):  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Motile By Gliding

A Gram-negative, non-flagellated, non-spore-forming bacterium, designated YCS-6T, that was motile by gliding, was isolated from seawater on the southern coast of Korea. Strain YCS-6T grew optimally at 30 °C and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YCS-6T fell within the genus Tenacibaculum and was most closely associated with Tenacibaculum litopenaei B-IT, with which the isolate exhibited 95.9 % 16S rRNA gene sequence similarity. Sequence similarity between strain YCS-6T and other members of the genus Tenacibaculum was 93.8–95.7 %. Strain YCS-6T contained menaquinone-6 (MK-6) as the predominant respiratory quinone and iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 3-OH and iso-C15 : 1 G as the major fatty acids. The DNA G+C content was 32.7 mol%. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain YCS-6T from all other members of the genus Tenacibaculum. On the basis of our phenotypic, chemotaxonomic and phylogenetic data, strain YCS-6T is considered to represent a novel species of the genus Tenacibaculum, for which the name Tenacibaculum geojense sp. nov. is proposed. The type strain is YCS-6T ( = KCTC 23423T  = CCUG 60527T).

scholarly journals Taeseokella kangwonensis gen. nov., sp. nov., isolated from a freshwater reservoir

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4309-4314 ◽  
Author(s):  
Yochan Joung ◽  
Sunhee Hong ◽  
Haneul Kim ◽  
Heeyoung Kang ◽  
Christine E. Farrance ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New Genus ◽  
Lipid Analysis ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
The Family ◽  
Freshwater Reservoir

A Gram-stain-negative, non-motile and yellow-pigmented bacterium, designated HME8275T, was isolated from freshwater in Korea. The major fatty acids of strain HME8275T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and iso-C15 : 0. The only respiratory quinone was MK-7. Polar lipid analysis showed phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and three unidentified polar lipids. The DNA G+C content of strain HME8275T was 37.6 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME8275T formed a lineage within the family Cytophagaceae and was related to Lacihabitans soyangensis HME6675T (92.6 % 16S rRNA gene sequence similarity), Leadbetterella byssophila 4M15T (89.0 %), Fluviimonas pallidilutea TQQ6T (89.7 %) and Emticicia oligotrophica GPTSA100-15T (89.8 %). On the basis of the evidence presented in this study, strain HME8275T represents a novel species of a new genus in the family Cytophagaceae, for which the name Taeseokella kangwonensis, gen. nov., sp. nov. is proposed. The type strain of the type species is HME8275T ( = KACC 16933T = CECT 8198T).

scholarly journals Luteimonas soli sp. nov., isolated from farmland soil

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4809-4815 ◽  
Author(s):  
Xiang Wang ◽  
Hong-Xing Yang ◽  
Ying-Kun Zhang ◽  
Shi-Jun Zhu ◽  
Xiao-Wei Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Farmland Soil ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

A yellow-pigmented bacterial strain, designated Y2T, was isolated from farmland soil in Bengbu, Anhui province, China. Cells of strain Y2T were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Strain Y2T grew optimally at pH 7.0, 30 °C and in the presence of 2 % (w/v) NaCl. The DNA G+C content was 68.9 mol%. The major fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 0, summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c), iso-C11 : 0 3-OH and iso-C11 : 0. The major respiratory quinone was ubiquinone-8 (Q-8), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain Y2T was most closely related to Luteimonas mephitis B1953/27.1T (99.1 % 16S rRNA gene sequence similarity), followed by Luteimonas lutimaris G3T (98.6 %), Luteimonas abyssi XH031T (96.2 %) and Luteimonas aquatica RIB1-20T (96.0 %). Strain Y2T exhibited low DNA–DNA relatedness with Luteimonas mephitis B1953/27.1T (43.6 ± 0.5 %) and Luteimonas lutimaris G3T (43.9 ± 2.1 %). On the basis of phenotypic, genotypic and phylogenetic evidence, strain Y2T represents a novel species of the genus Luteimonas, for which the name Luteimonas soli sp. nov. is proposed. The type strain is Y2T ( = ACCC 19799T = KCTC 42441T).

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.

scholarly journals Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations

2004 ◽  
Vol 54 (6) ◽  
pp. 2185-2190 ◽  
Author(s):  
Hiroyuki Ohta ◽  
Reiko Hattori ◽  
Yuuji Ushiba ◽  
Hisayuki Mitsui ◽  
Masao Ito ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
High Sequence Similarity ◽  
Respiratory Quinone ◽  
Meat Extract ◽  
Low Concentrations ◽  
Bacterium Strain

The taxonomic position of a halo- and organo-sensitive, oligotrophic soil bacterium, strain S213T, was investigated. Cells were Gram-negative, non-motile, strictly aerobic, yellow-pigmented rods of short to medium length on diluted nutrient broth. When 0·1–0·4 % (w/v) NaCl was added to diluted media composed of peptone and meat extract, growth was inhibited with increasing NaCl concentration and the cells became long aberrant forms. When 6 mM CaCl2 was added, the cells grew quite normally and aberrant cells were no longer found at 0·1–0·5 % (w/v) NaCl. Chemotaxonomically, strain S213T contains chemical markers that indicate its assignment to the Sphingomonadaceae: the presence of ubiquinone Q-10 as the predominant respiratory quinone, C18 : 1 and C16 : 0 as major fatty acids, C14 : 0 2-OH as the major 2-hydroxy fatty acid and sphingoglycolipids. 16S rRNA gene sequence analysis indicated that strain S213T belongs to the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas mali IFO 15500T (98·3 %), Sphingomonas pruni IFO 15498T (98·0 %), Sphingomonas asaccharolytica IFO 15499T (97·9 %) and Sphingomonas echinoides DSM 1805T (97·8 %). The results of DNA–DNA hybridization experiments and its phenotypic characteristics clearly distinguished the strain from its nearest neighbours and demonstrate that strain S213T represents a novel Sphingomonas species, for which the name Sphingomonas oligophenolica sp. nov. is proposed. The type strain is S213T (=JCM 12082T=CIP 107926T).

scholarly journals Francisella salimarina sp. nov., isolated from coastal seawater

2020 ◽  
Vol 70 (5) ◽  
pp. 3264-3272 ◽  
Author(s):  
Liang-Hui Li ◽  
Hai-Min Luo ◽  
Jun-Hui Feng ◽  
Yu-Zhen Ming ◽  
Min-Ling Zheng ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Protein Marker ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Ph Range

Four strains (SYSU SYW-1T, SYW-2, SYW-3 and XLW-1) were isolated from seawater near the shore in Guangdong Province, China. Cells were Gram-stain-negative, aerobic, non-motile and non-spore-forming. Growth was observed at a temperature range of 16–40 °C (optimum, 32 °C), a pH range of 4–8 (optimum, pH 7) and in the presence of up to 10 % (w/v) NaCl. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified phospholipid. The respiratory quinone was ubiquinone 8 (UQ-8), and the predominant fatty acids were C18 : 0 3-OH, C10 : 0, C14 : 0 and C18 : 1ω9c. Comparison of 16S rRNA gene and genome sequences confirmed that these strains represented a novel member of the genus Francisella , with less than 98.8 % 16S rRNA gene sequence similarity and less than 95 % genomic average nucleotide identity to recognized Francisella species. The phylogenetic tree based on 16S rRNA gene sequences and the protein-concatamer tree based on a concatenation of 28 protein marker sequences both indicated that the strains clustered with ‘Francisella salina’ TX07-7308 and ‘Francisella marina’ E95-16, but formed a distinct lineage group among the other members of the genus Francisella . The DNA G+C contents of the four strains were determined to be 32.9, 32.7, 32.9 and 32.9 %, respectively (genome). On the basis of phenotypic and genotypic features, the strains are considered to represent a novel species of the genus Francisella , for which the name Francisella salimarina sp. nov. is proposed. The type strain is SYSU SYW-1T (=CGMCC 1.17031T=NBRC 113781T).

scholarly journals Pedobacter nanyangensis sp. nov., isolated from herbicide-contaminated soil

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3517-3521 ◽  
Author(s):  
Hao Zhang ◽  
Jing Zhang ◽  
Man Song ◽  
Ming-gen Cheng ◽  
Ya-dong Wu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Soil ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Physiological And Biochemical Characteristics ◽  
Ph Range

A Gram-stain-negative, strictly aerobic, non-spore-forming, motile, rod-shaped bacterium, designated Q-4T, was isolated from a herbicide-contaminated soil sample in Nanyang, Henan province, China. Strain Q-4T grew optimally in the LB medium without NaCl supplement at a pH range of 6.0–7.0 and a temperature of 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Q-4T was most closely related to ‘Pedobacter zeaxanthinifaciens’ TDMA-5 (97.4 % 16S rRNA gene sequence similarity), followed by Pedobacter xixiisoli S27T (95.8 %). The genomic DNA G+C content of strain Q-4T was 41.8 mol%. MK-7 was the major respiratory quinone. Phosphatidylethanolamine and phosphoaminolipid were the major polar lipids. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω6c and/or C16 : 1ω7c (summed feature 3) and C16 : 1ω7c/C16 : 1ω6c (summed feature 3). Strain Q-4T showed low DNA–DNA relatedness with ‘P. zeaxanthinifaciens’ TDMA-5 (21.4 ± 0.6 %). Physiological and biochemical characteristics are able to distinguish strain Q-4T from the most closely related species of the genus Pedobacter. On the basis of genotypic and phenotypic data, strain Q-4T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter nanyangensis sp. nov. is proposed. The type strain is Q-4T ( = KCTC 42442T = ACCC 19798T).

scholarly journals Nocardioides marinus sp. nov.

2007 ◽  
Vol 57 (4) ◽  
pp. 775-779 ◽  
Author(s):  
Dong Han Choi ◽  
Hye Min Kim ◽  
Jae-Hoon Noh ◽  
Byung Cheol Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Diamino Acid ◽  
Ph Range ◽  
Type Strains

A Gram-positive, slightly halophilic, rod-shaped bacterium, designated CL-DD14T, was isolated from seawater of the East Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CL-DD14T belongs to the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between strain CL-DD14T and the type strains of recognized species of the genus Nocardioides were low (94.1–97.1 %). Strain CL-DD14 T grew over the pH range 6–9 and temperature range 10–40 °C. The strain grew at NaCl concentrations of 0.5–8 % (w/v) with optimum growth at 1–3 % and no growth was observed after 3 weeks on nutrient agar without any salts. It contained ll-diaminopimelic acid as the diamino acid in the cell wall. The major isoprenoid quinone was MK-8(H4) and the major cellular fatty acids were iso-C16 : 0 and 10-methyl C17 : 0. The DNA G+C content was 72.9 mol%. On the basis of phenotypic and phylogenetic data, strain CL-DD14T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides marinus sp. nov. is proposed. The type strain is CL-DD14T (=KCCM 42321T=DSM 18248T).

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