Flaviramulus ichthyoenteri sp. nov., an N-acylhomoserine lactone-degrading bacterium isolated from the intestine of a flounder (Paralichthys olivaceus), and emended descriptions of the genus Flaviramulus and Flaviramulus basaltis

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4477-4483 ◽  
Author(s):  
Yunhui Zhang ◽  
Kaihao Tang ◽  
Xiaochong Shi ◽  
Xiao-Hua Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Paralichthys Olivaceus ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Content Type ◽  
Acylhomoserine Lactone ◽  
Link Type ◽  
Degrading Bacterium

A Gram-stain-negative, strictly aerobic, yellow-pigmented, rod-shaped and N-acylhomoserine lactone-degrading bacterium, designated strain Th78T, was isolated from the intestine of a cultured flounder (Paralichthys olivaceus). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Th78T belonged to the genus Flaviramulus (family Flavobacteriaceae ) and showed the highest 16S rRNA gene sequence similarity to Flaviramulus basaltis H35T (96.70 %). Optimal growth occurred in the presence of 2–3 % (w/v) NaCl, at pH 7.0–8.0 and at 28 °C. The major fatty acids were iso-C15 : 0 3-OH, iso-C15 : 1 G and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and three unidentified polar lipids. Menaquinone 6 (MK-6) was the only respiratory quinone. The DNA G+C content of strain Th78T was 31.5 mol%. On the basis of polyphasic analysis, strain Th78T is considered to represent a novel species of the genus Flaviramulus , for which the name Flaviramulus ichthyoenteri sp. nov. is proposed. The type strain is Th78T ( = JCM 18634T = KCTC 32142T = DSM 26285T). Emended descriptions of the genus Flaviramulus and Flaviramulus basaltis are also proposed.

Glacieibacterium frigidum gen. nov., sp. nov., a novel member of the family Sphingosinicellaceae isolated from a glacier

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Qing Liu ◽  
Lei-Lei Yang ◽  
Hong-Can Liu ◽  
Guo-Qing Zhang ◽  
Yu-Hua Xin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel Gram-stain-negative, rod-shaped, yellow bacterium, designated as LB1R16T, was isolated from the Laigu glacier on the Tibetan Plateau, PR China. Strain LB1R16T was catalase-positive, oxidase-negative and grew at 0–28 °C, pH 6.0–8.0 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LB1R16T belongs to the family Sphingosinicellaceae but formed an independent lineage. The highest level of 16S rRNA gene sequence similarities were found to Polymorphobacter arshaanensis DJ1R-1T (95.24 %), Sphingoaurantiacus capsulatus YLT33T (94.78 %) and Sandarakinorhabdus limnophila DSM 17366T (94.67 %). The genomic DNA G+C content was 68.8 mol%. The main cellular fatty acids were summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), C16 : 0 and C12 : 0-OH. The respiratory quinone was ubiquinone-10. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid, one unidentified phospholipid and two unidentified polar lipids, which were different from the type strains of Polymorphobacter arshaanensis , Sphingoaurantiacus capsulatus and Sandarakinorhabdus limnophila . Based on a polyphasic approach, a novel species of a new genus, Glacieibacterium frigidum gen. nov., sp. nov., within the family Sphingosinicellaceae is proposed. The type strain is LB1R16T (=CGMCC 1.11941T=NBRC 113873T).

scholarly journals Zhongshania aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from marine sediment, and transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov.

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3768-3774 ◽  
Author(s):  
Naysim LO ◽  
Hyo Jung Kang ◽  
Che Ok Jeon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Degrading Bacterium

A Gram-staining-negative, facultatively aerobic bacterium, designated SM-2T, was isolated from a sea-tidal flat of Yellow Sea, South Korea. Cells were catalase- and oxidase-positive motile rods with a single polar flagellum. Growth of strain SM-2T was observed at 10–37 °C (optimum, 25–30 °C), at pH 5.5–8.5 (optimum, pH 7.0–7.5) and in the presence of 0–11 % (w/v) NaCl (optimum, 2 %). Strain SM-2T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and C17 : 1ω8c, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C17 : 0 and C18 : 1ω7c as the major fatty acids. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified lipid were identified as the major cellular polar lipids. The G+C content of the genomic DNA was 52.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SM-2T formed a tight phyletic lineage with Zhongshania antarctica ZS5-23T, Zhongshania guokunii ZS6-22T and Spongiibacter borealis CL-AS9T, but that S. borealis CL-AS9T was distinct from other species of the genus Spongiibacter . Based on 16S rRNA gene sequence similarities, strain SM-2T was most closely related to S. borealis CL-AS9T, Z. antarctica ZS5-23T and Z. guokunii ZS6-22T, with similarities of 99.5 %, 98.9 % and 98.7 %, respectively, but the DNA–DNA hybridization values among these species were clearly lower than 70 %. On the basis of chemotaxonomic data and molecular properties, we propose strain SM-2T represents a novel species of the genus Zhongshania with the name Zhongshania aliphaticivorans sp. nov. (type strain SM-2T = KACC 18120T = JCM 30138T). We also propose the transfer of Spongiibacter borealis Jang et al. 2011 to the genus Zhongshania as Zhongshania borealis comb. nov. (type strain CL-AS9T = KCCM 90094T = JCM 17304T).

Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 952-958 ◽  
Author(s):  
Richard A. Albert ◽  
Nancy E. Waas ◽  
Shawn C. Pavlons ◽  
Jamie L. Pearson ◽  
Laura Ketelboeter ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipid ◽  
Type Species ◽  
Lake Michigan ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Psychrophilic Bacterium ◽  
Content Type ◽  
Link Type

A psychrophilic, Gram-negative bacterium, designated MOL-1T, was isolated from water of Lake Michigan. 16S rRNA gene sequence analysis revealed that the sequence of strain MOL-1T has sequence similarity of 95.6, 94.8, 94.3, 94.3, 94.2 and 93.9 %, respectively, to the 16S rRNA gene sequences of Sphingobacterium shayense HS39T, S. lactis WCC 4512T, S. composti T5-12T, S. daejeonense TR6-04T, S. bambusae IBFC2009T and S. alimentarium WCC 4521T. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone MK-7 is the predominant respiratory quinone, while sym-homospermidine is the predominant polyamine. The polar lipid profile is composed of the predominant lipids phosphatidylethanolamine and unidentified polar lipid L2, with moderate amounts of unidentified polar lipids L1, L5 and L6 and unidentified aminophospholipids APL1 and APL2 and minor to trace amounts of unidentified polar lipids L3, L4, L7, L8, L9 and L10, unidentified phospholipid PL4 and unidentified aminophospholipid APL3. After molecular and phenotypic studies, including chemotaxonomic analyses, it was concluded that strain MOL-1T represents a novel Sphingobacterium species, for which the name Sphingobacterium psychroaquaticum sp. nov. is proposed. The type strain is MOL-1T ( = NRRL B-59232T  = DSM 22418T).

Psychroflexus halocasei sp. nov., isolated from a microbial consortium on a cheese

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1850-1856 ◽  
Author(s):  
Herbert Seiler ◽  
Anne Bleicher ◽  
Hans-Jürgen Busse ◽  
Josef Hüfner ◽  
Siegfried Scherer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A novel halophilic, Gram-reaction-negative, strictly aerobic, non-motile, rod-shaped and oxidase- and catalase-positive bacterial strain, designated WCC 4520T, was isolated from a semi-hard, Raclette-type cheese. The colonies were yellow–orange; flexirubin-type pigments were not found. The strain hydrolysed gelatin, hippurate, tyrosine and Tweens 20 and 80. Optimal growth was observed with 6–8 % (w/v) NaCl, at pH 7–8 and at 27–30 °C. The genomic DNA G+C content was 33.6 mol%. In phylogenetic analysis based on 16S rRNA gene sequences, strain WCC 4520T appeared to be a member of the family Flavobacteriaceae and the closest phylogenetic neighbours were identified as Psychroflexus gondwanensis DSM 5423T (94.0 % 16S rRNA gene sequence similarity) and Psychroflexus salinarum CCUG 56752T (94.0 %). The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The only detected quinone was MK-6 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified polar lipid. Minor polar lipids and traces of polyamines were also detected. On the basis of the data presented, strain WCC 4520T represents a novel species of the genus Psychroflexus , for which the name Psychroflexus halocasei sp. nov. is proposed. The type strain is WCC 4520T ( = LMG 25857T = CCUG 59705T).

scholarly journals Rhizobium flavum sp. nov., a triazophos-degrading bacterium isolated from soil under the long-term application of triazophos

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2017-2022 ◽  
Author(s):  
Tao Gu ◽  
Li Na Sun ◽  
Jun Zhang ◽  
Xin Hua Sui ◽  
Shun Peng Li
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Type Strains

A Gram-stain-negative, non-motile, pale yellow, rod-shaped bacterial strain, YW14T, was isolated from soil and its taxonomic position was investigated by a polyphasic study. Strain YW14T did not form nodules on three different legumes, and the nodD and nifH genes were not detected by PCR. Strain YW14T contained Q-10 as the predominant ubiquinone. The major cellular fatty acid was C18 : 1ω7c. Phylogenetic analyses based on 16S rRNA gene sequences and seven housekeeping gene sequences (recA, atpD, glnII, gyrB, rpoB, dnaK and thrC) showed that strain YW14T belonged to the genus Rhizobium . Strain YW14T showed 16S rRNA gene sequence similarity of 93.4–97.3 % to the type strains of recognized species of the genus Rhizobium . DNA–DNA relatedness between strain YW14T and the type strains of Rhizobium sullae IS123T and Rhizobium yanglingense CCBAU 71623T was 19.6–25.7 %, indicating that strain YW14T was distinct from them genetically. Strain YW14T could also be differentiated from these phylogenetically related species of the genus Rhizobium by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain YW14T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium flavum sp. nov. is proposed. The type strain is YW14T ( = KACC 17222T = CCTCC AB2013042T).

scholarly journals Haemophilus seminalis sp. nov., isolated from human semen

2020 ◽  
Vol 70 (4) ◽  
pp. 2588-2595 ◽  
Author(s):  
Min-ling Zheng ◽  
Liang-hui Li ◽  
Bin Liu ◽  
Yu-bo Lin ◽  
Xiao-tuan Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Human Semen ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Two Haemophilus -like isolates with similar biochemical characteristics, designated strains SZY H1T and SZY H2, were isolated from human semen specimens. Cells were Gram-negative, non-motile, non-acid-fast, pleomorphic rods or coccobacilli. The major fatty acids (>10 %) were C16 : 0, C14 : 0, iso-C16 : 0 and/or C14 : 0 3-OH and C16 : 1 ω6c and/or C16 : 1 ω7c. The polar lipids were determined to be phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminophospholipid, two unidentified polar lipids and four unidentified aminolipids. The major polyamine was found to be cadaverine. The near-full-length (1462 nt) 16S rRNA gene sequences analysis showed the two isolates were nearly identical (>99.8 %), and closely matched Haemophilus haemolyticus ATCC 33390T with 98.9–99.1 % sequence similarities. Phylogenetic analysis based on 16S rRNA gene sequences and concatenation of 30 protein markers also revealed that the isolates clustered together with H. haemolyticus ATCC 33390T, and formed a distinct lineage well separated from the other members of the genus Haemophilus . Further, the average nucleotide identity values between the two isolates and their related species were below the established cut-off values for species delineation (95 %). Based on these findings, the two isolates are considered to represent a new species of the genus Haemophilus , for which name Haemophilus seminalis sp. nov. is proposed. The type strain is SZY H1T (=NBRC 113782T=CGMCC 1.17137T).

scholarly journals Zoogloea oleivorans sp. nov., a floc-forming, petroleum hydrocarbon-degrading bacterium isolated from biofilm

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 274-279 ◽  
Author(s):  
Milán Farkas ◽  
András Táncsics ◽  
Balázs Kriszt ◽  
Tibor Benedek ◽  
Erika M. Tóth ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Petroleum Hydrocarbon ◽  
Sequence Similarity ◽  
Contaminated Site ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium

A floc-forming, Gram-stain-negative, petroleum hydrocarbon-degrading bacterial strain, designated BucT, was isolated from a petroleum hydrocarbon-contaminated site in Hungary. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BucT formed a distinct phyletic lineage within the genus Zoogloea . Its closest relative was found to be Zoogloea caeni EMB43T (97.2 % 16S rRNA gene sequence similarity) followed by Zoogloea oryzae A-7T (95.9 %), Zoogloea ramigera ATCC 19544T (95.5 %) and Zoogloea resiniphila DhA-35T (95.4 %). The level of DNA–DNA relatedness between strain BucT and Z. caeni EMB43T was 31.6 %. Cells of strain BucT are facultatively aerobic, rod-shaped, and motile by means of a polar flagellum. The strain grew at temperatures of 5–35 °C (optimum 25–28 °C), and at pH 6.0–9.0 (optimum 6.5–7.5). The predominant fatty acids were C16 : 0, C10 : 0 3-OH, C12 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major respiratory quinone was ubiquinone-8 (Q-8) and the predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 63.2 mol%. On the basis of the chemotaxonomic, molecular and phenotypic data, isolate BucT is considered to represent a novel species of the genus Zoogloea , for which the name Zoogloea oleivorans sp. nov. is proposed. The type strain is BucT ( = DSM 28387T = NCAIM B 02570T).

scholarly journals Ammoniibacillus agariperforans gen. nov., sp. nov., a thermophilic, agar-degrading bacterium isolated from compost

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 570-577 ◽  
Author(s):  
Masao Sakai ◽  
Daigo Deguchi ◽  
Akifumi Hosoda ◽  
Tomohiro Kawauchi ◽  
Makoto Ikenaga
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
The Family

A thermophilic, agar-degrading bacterium, strain FAB2T, was isolated from sewage sludge compost. According to phylogenetic analysis based on 16S rRNA gene sequences, strain FAB2T belonged to the family Paenibacillaceae within the phylum Firmicutes . However, FAB2T was different enough at the genus level from closely related species. The percentages of 16S rRNA gene sequence similarity with related organisms were 90.4 % for Thermobacillus xylanilyticus , 91.8 % for Paenibacillus barengoltzii , 89.4 % for Cohnella lupini , 90.1 % for Fontibacillus aquaticus , and 89.0 % for Saccharibacillus sacchari . Morphological and physiological analyses revealed that the strain was motile, rod-shaped, Gram-stain-positive, aerobic and able to form oval endospores in swollen sporangia. Ammonium was required as a nitrogen source while nitrate, nitrite, urea and glutamate were not utilized. Catalase and oxidase activities were weakly positive and positive, respectively. The bacterium grew in the temperature range of 50–65 °C and in media with pH 7.5 to 9.0. Optimal growth occurred at 60 °C and pH 8.0–8.6. Growth was inhibited at pH≤7.0 and NaCl concentrations ≥2.5 % (w/v). In chemotaxonomic characterization, MK-7 was identified as the dominant menaquinone. Major fatty acids were iso-C16 : 0 and C16 : 0. Dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phosphatidylcholine was present in a moderate amount. The diamino acid in the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 49.5 mol% in a nucleic acid study. On the basis of genetic and phenotypic characteristics, strain FAB2T ( = NBRC 109510T = KCTC 33130T) showed characteristics suitable for classification as the type strain of a novel species of a new genus in the family Paenibacillaceae , for which the name Ammoniibacillus agariperforans gen. nov., sp. nov. is proposed.

scholarly journals Nocardioides soli sp. nov., a carbendazim-degrading bacterium isolated from soil under the long-term application of carbendazim

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2047-2052 ◽  
Author(s):  
Li-Na Sun ◽  
Jun Zhang ◽  
Fen-Fen Gong ◽  
Xiang Wang ◽  
Gang Hu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium

The taxonomic status of a carbendazim-degrading strain, mbc-2T, isolated from soil under the long-term application of carbendazim in China was determined by means of a polyphasic study. The cells were Gram-stain-positive, motile and rod-shaped. Strain mbc-2T grew optimally at pH 7.0, 30–35 °C and in the presence of 1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain mbc-2T fell within the genus Nocardioides , forming a coherent cluster with the type strain of Nocardioides hankookensis , with which it exhibited 16S rRNA gene sequence similarity values of 97.9 %. The chemotaxonomic properties of strain mbc-2T were consistent with those of the genus Nocardioides : the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, the predominant menaquinone was MK-8 (H4) and the major fatty acid was iso-C16 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, unknown phospholipids and an unknown aminolipid. The DNA G+C content was 72 mol%. Strain mbc-2T exhibited DNA–DNA relatedness values of 12.5±1.5 %, 23.7±2.7 % and 26.3±3.2 % with respect to Nocardioides hankookensis DS-30T, Nocardioides aquiterrae GW-9T and Nocardioides pyridinolyticus OS4T. On the basis of the data obtained, strain mbc-2T represents a novel species of the genus Nocardioides , for which the name Nocardioides soli sp. nov. is proposed. The type strain is mbc-2T ( = KACC 17152T = CCTCC AB 2012934T).

scholarly journals Achromobacter sediminum sp. nov., isolated from deep subseafloor sediment of South Pacific Gyre

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2244-2249 ◽  
Author(s):  
Zenghu Zhang ◽  
Xiaoyang Fan ◽  
Xin Gao ◽  
Xiao-Hua Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
South Pacific ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Lateral Flagellum ◽  
South Pacific Gyre

A Gram-stain-negative, facultatively anaerobic, rod-shaped, motile bacterium with a subpolar or lateral flagellum, designated strain XH089T, was isolated from deep-sea sediment sample collected from the South Pacific Gyre (41°51′ S 153°06′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH089T belonged to the genus Achromobacter and showed the highest 16S rRNA gene sequence similarities with Achromobacter ruhlandii ATCC 15749T (96.95 %), Achromobacter denitrificans DSM 30026T (96.70 %) and Achromobacter marplatensis B2T (96.66 %). The DNA G+C content of strain XH089T was 66.5 mol%. The major fatty acids were C16 : 0 and C17 : 0 cyclo. The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, three unknown phospholipids and four unknown polar lipids. On the basis of data from the polyphasic analysis, strain XH089T is considered to represent a novel species of the genus Achromobacter , for which the name Achromobacter sediminum sp. nov. is proposed. The type strain is XH089T ( = DSM 27279T = JCM 19223T).

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