scholarly journals Limnochorda pilosa gen. nov., sp. nov., a moderately thermophilic, facultatively anaerobic, pleomorphic bacterium and proposal of Limnochordaceae fam. nov., Limnochordales ord. nov. and Limnochordia classis nov. in the phylum Firmicutes

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2378-2384 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Moderately Thermophilic ◽  
Facultatively Anaerobic ◽  
Novel Taxa

A novel facultatively anaerobic bacterium, strain HC45T, was isolated from sediment of a brackish meromictic lake in Japan, Lake Harutori. Cells were pleomorphic, and filamentous bodies were 5–100 μm in length. For growth, the optimum pH was 7.0 and the optimum temperature was 45–50 °C. The G+C content of the genomic DNA was 71 mol%. iso-C15 : 0 and anteiso-C15 : 0 were the major components in the cellular fatty acid profile. The predominant respiratory quinone was MK-7. Strain HC45T shared very low 16S rRNA gene sequence similarity with cultivated strains ( ≤ 85 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was distantly related to members of the family Symbiobacteriaceae and family XVII Incertae Sedis in the class Clostridia, and they formed a cluster separate from canonical species of the phylum Firmicutes. These results indicated that strain HC45T should not be placed in any existing class of the phylum Firmicutes. On the basis of phylogenetic and phenotypic characterization, Limnochorda pilosa gen. nov., sp. nov. is proposed with HC45T ( = NBRC 110152T = DSM 28787T) as the type strain, as the first representative of novel taxa, Limnochordales ord. nov., Limnochordaceae fam. nov. in Limnochordia classis. nov.

scholarly journals Aquipluma nitroreducens gen. nov. sp. nov., a novel facultatively anaerobic bacterium isolated from a freshwater lake

2020 ◽  
Vol 70 (12) ◽  
pp. 6408-6413 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Freshwater Lake ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Facultatively Anaerobic ◽  
The Family

A novel facultatively anaerobic, nitrate-reducing bacterium, designated MeG22T, was isolated from a freshwater lake in Japan. Cells of the strain were straight rods (0.8×2.5–10 µm), motile, and Gram-stain-negative. For growth, the optimum NaCl concentration was 0 % and the optimum temperature was 30 °C. Under anoxic conditions, strain MeG22T reduced nitrate to nitrite. Major cellular fatty acids were C15 : 1 ω6c (13.6 %), C17 : 0 (11.9 %), anteiso-C15 : 0 (10.6 %) and iso-C15 : 0 (10.6 %). The major respiratory quinone was menaquinone-7. The genome sequence of strain MeG22T consists of 5 712 279 bp with a G+C content of 40.3 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Prolixibacteraceae within the phylum Bacteroidetes . The closest relative of strain MeG22T was Sunxiuqinia faeciviva strain JAM-BA0302T with a 16S rRNA gene sequence similarity of 90.9 %. On the basis of phylogenetic and phenotypic characterization, Aquipluma nitroreducens, gen. nov., sp. nov., belonging to the family Prolixibacteraceae is proposed with the type strain MeG22T (=NBRC 112896T=DSM 106262T).

Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.

2011 ◽  
Vol 61 (1) ◽  
pp. 105-109 ◽  
Author(s):  
Geun Cheol Song ◽  
Muhammad Yasir ◽  
Fehmida Bibi ◽  
Eu Jin Chung ◽  
Che Ok Jeon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Sand Dunes ◽  
Endophytic Bacterium ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Gram Staining

A Gram-staining-positive, coccoid to rod-shaped bacterium, designated strain YC6903T, was isolated from a halophytic plant (Carex scabrifolia Steud.) collected from sand dunes at Namhae Island, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain YC6903T grew optimally at 30 °C and at pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6903T belongs to the genus Nocardioides in the family Nocardioidaceae. Strain YC6903T was related most closely to Nocardioides pyridinolyticus OS4T (97.0 % 16S rRNA gene sequence similarity), Nocardioides dokdonensis FR1436T (96.6 %), Nocardioides aquiterrae GW-9T (96.6 %) and Nocardioides hankookensis DS-30T (96.6 %). The cell-wall peptidoglycan contained ll-diaminopimelic acid and MK-8(H4) was the major respiratory quinone. The mean (±sd) level of DNA–DNA relatedness between strain YC6903T and N. pyridinolyticus OS4T was 53.5±5.5 %. The predominant cellular fatty acid of strain YC6903T was iso-C16 : 0 (28.9 %). The DNA G+C content was 71.7 mol%. Phenotypic, phylogenetic and chemotaxonomic data indicated that strain YC6903T represents a novel species of the genus Nocardioides, for which the name Nocardioides caricicola sp. nov. is proposed. The type strain is YC6903T (=KACC 13778T =DSM 22177T).

scholarly journals Altererythrobacter ishigakiensis sp. nov., an astaxanthin-producing bacterium isolated from a marine sediment

2011 ◽  
Vol 61 (12) ◽  
pp. 2956-2961 ◽  
Author(s):  
Mitsufumi Matsumoto ◽  
Daisuke Iwama ◽  
Atsushi Arakaki ◽  
Akira Tanaka ◽  
Tsuyoshi Tanaka ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Rrna Gene Sequencing

A Gram-negative, non-motile, non-spore-forming, halophilic rod, designated JPCCMB0017T, was isolated from a marine sediment of the coastal area of Okinawa, Japan. The isolate formed orange–red colonies on marine agar. Bacteriochlorophyll α was absent and sphingoglycolipid 1 and other carotenoids, including astaxanthin, adonixanthin and zeaxanthin, were present. Ubiquinone-10 (Q-10) was the main respiratory quinone and C18 : 1ω7c was the major cellular fatty acid. The G+C content of DNA was 59.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Altererythrobacter in the family Erythrobacteraceae. Strain JPCCMB0017T exhibited 96.8 % 16S rRNA gene sequence similarity with Altererythrobacter marinus H32T. Unlike other members of the genus Altererythrobacter, strain JPCCMB0017T reduced nitrate. On the basis of genotypic and phenotypic data, a novel species is proposed to accommodate this isolate, with the name Altererythrobacter ishigakiensis sp. nov. The type strain is JPCCMB0017T ( = NITE-AP48T = ATCC BAA-2084T = NBRC 107699T).

scholarly journals Donghicola tyrosinivorans sp. nov., a tyrosine-degrading bacterium isolated from seawater

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4140-4145 ◽  
Author(s):  
Hye-Ri Sung ◽  
Jin-Man Lee ◽  
Mibang Kim ◽  
Bo-ram Yun ◽  
Kee-Sun Shin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Respiratory Quinone ◽  
Degrading Bacterium

A Gram-stain-negative, non-motile, aerobic bacterium, strain 13-93-B1T, was isolated from seawater off Jeju Island, Republic of Korea, and was subjected to polyphasic taxonomic study. Cells formed ivory colonies and were ovoid to rod-shaped. The strain was catalase-positive, oxidase-negative and grew optimally at 30 °C, in the presence of 1–2 % (w/v) NaCl and at pH 7.0–7.5. It did not synthesize bacteriochlorophyll a. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain 13-93-B1T clustered with the type strain Donghicola eburneus SW-277T (97.0 % 16S rRNA gene sequence similarity). DNA–DNA hybridization between strain 13-93-B1T and D. eburneus KCTC 12735T was 33.1 ± 1.4 % (35.2 ± 2.8 % in a reciprocal experiment). The predominant cellular fatty acid was summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 76.9 %). The major respiratory quinone was ubiquinone Q-10 and polar lipids detected in strain 13-93-B1T were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified aminolipid and unidentified lipids. The DNA G+C content of strain 13-93-B1T was 60.4 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain 13-93-B1T is considered to represent a novel species of the genus Donghicola, for which the name Donghicola tyrosinivorans sp. nov. is proposed. The type strain is 13-93-B1T ( = DSM 100212T = KCTC 42571T)

scholarly journals Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5

2021 ◽  
Vol 9 (4) ◽  
pp. 768
Author(s):  
Karel Kopejtka ◽  
Yonghui Zeng ◽  
David Kaftan ◽  
Vadim Selyanin ◽  
Zdenko Gardian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Close Phylogenetic Relationship

An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Tyrolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). Its genomic DNA G + C content is 65.9%. Further, in silico DNA-DNA hybridization and calculation of the average nucleotide identity speaks for the close phylogenetic relationship of AAP5 and Sphingomonas glacialis. The high percentage (76.2%) of shared orthologous gene clusters between strain AAP5 and Sphingomonas paucimobilis NCTC 11030T, the type species of the genus, supports the classification of the two strains into the same genus. Strain AAP5 was found to contain C18:1ω7c (64.6%) as a predominant fatty acid (>10%) and the polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, six unidentified glycolipids, one unidentified phospholipid, and two unidentified lipids. The main respiratory quinone was ubiquinone-10. Strain AAP5 is a facultative photoheterotroph containing type-2 photosynthetic reaction centers and, in addition, contains a xathorhodopsin gene. No CO2-fixation pathways were found.

scholarly journals Marinobacter gudaonensis sp. nov., isolated from an oil-polluted saline soil in a Chinese oilfield

2007 ◽  
Vol 57 (2) ◽  
pp. 250-254 ◽  
Author(s):  
Jun Gu ◽  
Hua Cai ◽  
Su-Lin Yu ◽  
Ri Qu ◽  
Bin Yin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Saline Soil ◽  
Sequence Similarity ◽  
Eastern China ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Shengli Oilfield ◽  
Major Respiratory Quinone ◽  
Reference Strains

Two novel strains, SL014B61AT and SL014B11A, were isolated from an oil-polluted saline soil from Gudao in the coastal Shengli Oilfield, eastern China. Cells of strains SL014B61AT and SL014B11A were motile, Gram-negative and rod-shaped. Growth occurred at NaCl concentrations of between 0 and 15 % and at temperatures of between 10 and 45 °C. Strain SL014B61AT had Q9 as the major respiratory quinone and C16 : 0 (21.2 %), C18 : 1ω9c (20.3 %), C16 : 1ω7c (7.3 %) and C16 : 1ω9c (6.4 %) as predominant fatty acids. The G+C content of the DNA was 57.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SL014B61AT belonged to the genus Marinobacter in the class Gammaproteobacteria. Strain SL014B61AT showed the highest 16S rRNA gene sequence similarity with Marinobacter bryozoorum (97.9 %) and showed 97.8 % sequence similarity to Marinobacter lipolyticus. DNA–DNA relatedness to the reference strains Marinobacter bryozoorum and Marinobacter lipolyticus was 35.5 % and 33.8 %, respectively. On the basis of these data, it is proposed that strains SL014B61AT and SL014B11A represent a novel species, Marinobacter gudaonensis sp. nov. The type strain is strain SL014B61AT (=DSM 18066T=LMG 23509T=CGMCC 1.6294T).

scholarly journals Effusibacillus dendaii sp. nov. isolated from farm soil

2021 ◽  
Author(s):  
Tomoyuki Konishi ◽  
Tomohiko Tamura ◽  
Toru Tobita ◽  
Saori Sakai ◽  
Namio Matsuda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Genome Analyses

Abstract Gram-positive, rod-shaped, spore-forming, thermophilic, acidophilic bacterium, designated strain skT53T, was isolated from farm soil in Tokyo, Japan. The strain grew aerobically at 37–55°C (optimum 50°C) and pH 4.0–6.0 (optimum 5.0). Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate was most closely related to the type strain of Effusibacillus consociatus (94.3% similarity). The G + C content of the genomic DNA was 48.22 mol%. MK-7 was the predominant respiratory quinone. The major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0 and C18:3ω6c. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain skT53T as representing a novel species of Effusibacillus dendaii sp. nov. is proposed. The type strain is strain skT53T (= NBRC 114101T = TBRC 11241T).

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.

Luteimonas deserti sp. nov., a novel strain isolated from desert soil

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Xiao-Xian Huang ◽  
Jia Shang ◽  
Lian Xu ◽  
Rui Yang ◽  
Ji-Quan Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Desert Soil ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16T, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16T grew at pH 6.0–11.0 (optimum, pH 8.0–9.0), 4–40 °C (optimum, 30–35 °C) and in the presence of 0–8 % (w/v) NaCl (optimum, 0–2 %). The strain was negative for catalase and positive for oxidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SJ-16T clustered with Luteimonas chenhongjianii 100111T and Luteimonas terrae THG-MD21T, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains L. chenhongjianii 100111T, L. terrae THG-MD21T, L. aestuarii B9T and all other type strains of the genus Luteimonas , respectively. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1  ω9c). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids, and ubiquinone-8 was the only respiratory quinone. The genomic DNA G+C content was 69.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values of strain SJ-16T to L. chenhongjianii 100111T, L. terrae THG-MD21T, L. rhizosphaerae 4-12T and L. aestuarii B9T were 36.9, 37.5, 24.0 and 21.1 %, and 80.9, 80.6, 80.7 and 76.3 %, respectively. Based on phenotypic, physiological and phylogenetic results, strain SJ-16T represents a novel species of the genus Luteimonas , for which the name Luteimonas deserti is proposed. The type strain is SJ-16T (=CGMCC 1.17694T=KCTC 82207T).

scholarly journals Sediminicola luteus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae

2006 ◽  
Vol 56 (4) ◽  
pp. 841-845 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Golden Yellow ◽  
The Family

The taxonomic position of four Gram-negative, rod-shaped, golden-yellow-coloured bacteria isolated from marine sediments was determined. Analysis of the almost complete 16S rRNA gene sequences indicated that these isolates belong to the family Flavobacteriaceae. An unclassified bacterium, NBRC 15975, was found to be the closest relative, showing 16S rRNA gene sequence similarity of 93 %; other related genera shared only 87·9–90·5 % similarity. In contrast, the four isolates shared high levels of 16S rRNA gene sequence similarity (99·3–99·7 %) and high DNA–DNA reassociation values (93–104 %). The isolates could be differentiated phenotypically from other genera by the abilities to reduce nitrate and to degrade gelatin, casein and starch. The only respiratory quinone was MK-6, and the major fatty acids were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. The DNA G+C content was 38–40 mol%. Differentiating phenotypic characteristics and large phylogenetic distances between the isolates and previously published genera indicated that the isolates constitute a novel genus, for which the name Sediminicola gen. nov. is proposed. The type species is Sediminicola luteus sp. nov. (type strain CNI-3T=NBRC 100966T=LMG 23246T).

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