scholarly journals Rhizocola hellebori gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae containing 3,4-dihydroxydiaminopimelic acid in the cell-wall peptidoglycan

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2706-2711 ◽  
Author(s):  
Atsuko Matsumoto ◽  
Yoko Kawaguchi ◽  
Takuji Nakashima ◽  
Masato Iwatsuki ◽  
Satoshi Ōmura ◽  
...  
Keyword(s):  
Cell Wall ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Cell Wall Peptidoglycan ◽  
The Family ◽  
The 16S Rrna Gene

An actinomycete strain, K12-0602T, was isolated from the root of a Helleborus orientalis plant in Japan. The 16S rRNA gene sequence of strain K12-0602T showed that it had a close relationship with members of the family Micromonosporaceae and the 16S rRNA gene sequence similarity values between strain K12-0602T and type strains of type species of 27 genera belonging to the family Micromonosporaceae were below 96.2 %. MK-9 (H4) and MK-9 (H6) were detected as major menaquinones, and galactose, xylose, mannose and ribose were present in the whole-cell hydrolysate. The acyl type of the peptidoglycan was glycolyl. Major fatty acids were iso-C15 : 0, iso-C16 : 0, C17 : 1ω9c and anteiso-C17 : 0. Phosphatidylethanolamine was detected as the phospholipid corresponding to phospholipid type II. The G+C content of the genomic DNA was 67 mol%. Analyses of the cell-wall peptidoglycan by TLC and LC/MS showed that it was composed of alanine, glycine, hydroxylglutamic acid and an unknown amino acid, which was subsequently determined to be 3,4-dihydroxydiaminopimelic acid using instrumental analyses, including NMR and mass spectrometry. On the basis of the phylogenetic analysis and chemotaxonomic characteristics, strain K12-0602T represents a novel species of a new genus in the family Micromonosporaceae , for which the name Rhizocola hellebori gen. nov., sp. nov. is proposed. The type strain of the type species is K12-0602T ( = NBRC 109834T = DSM 45988T). This is the first report, to our knowledge, of 3,4-dihydroxydiaminopimelic acid being found as a diamino acid in bacterial cell-wall peptidoglycan.

Caldicellulosiruptor diazotrophicus sp. nov., a thermophilic, nitrogen-fixing fermentative bacterium isolated from a terrestrial hot spring in Japan

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Yuxin Chen ◽  
Arisa Nishihara ◽  
Takao Iino ◽  
Moriya Ohkuma ◽  
Shin Haruta
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
The 16S Rrna Gene

A novel nitrogen-fixing fermentative bacterium, designated as YA01T, was isolated from Nakabusa hot springs in Japan. The short-rod cells of strain YA01T were Gram-positive and non-sporulating. Phylogenetic trees of the 16S rRNA gene sequence and concatenated sequences of 40 single-copy ribosomal genes revealed that strain YA01T belonged to the genus Caldicellulosiruptor and was closely related to Caldicellulosiruptor hydrothermalis 108T, Caldicellulosiruptor bescii DSM 6725T and Caldicellulosiruptor kronotskyensis 2002T. The 16S rRNA gene sequence of strain YA01T shares less than 98.1 % identity to the known Caldicellulosiruptor species. The G+C content of the genomic DNA was 34.8 mol%. Strain YA01T shares low genome-wide average nucleotide identity (90.31–91.10 %), average amino acid identity (91.45–92.10 %) and <70 % digital DNA–DNA hybridization value (41.8–44.2 %) with the three related species of the genus Caldicellulosiruptor . Strain YA01T grew at 50–78 °C (optimum, 70 °C) and at pH 5.0–9.5 (optimum, pH 6.5). Strain YA01T mainly produced acetate by consuming d(+)-glucose as a carbon source. The main cellular fatty acids were iso-C17 : 0 (35.7 %), C16 : 0 (33.3 %), DMA16 : 0 (6.6 %) and iso-C15 : 0 (5.9 %). Based on its distinct phylogenetic position, biochemical and physiological characteristics, and the major cellular fatty acids, strain YA01T is considered to represent a novel species of the genus Caldicellulosiruptor for which the name Caldicellulosiruptor diazotrophicus sp. nov. is proposed (type strain YA01T=DSM 112098T=JCM 34253T).

scholarly journals Halovenus aranensis gen. nov., sp. nov., an extremely halophilic archaeon from Aran-Bidgol salt lake

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1331-1336 ◽  
Author(s):  
A. Makhdoumi-Kakhki ◽  
M. A. Amoozegar ◽  
A. Ventosa
Keyword(s):  
Type Species ◽  
New Genus ◽  
Gene Sequence ◽  
Salt Lake ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel red-pigmented halophilic archaeon, strain EB27T, was isolated from Aran-Bidgol salt lake, a hypersaline playa in Iran. Cells of strain EB27T were non-motile and pleomorphic (rods to triangular or disc-shaped). Strain EB27T required at least 2.5 M NaCl and 0.1 M MgCl2 for growth. Optimal growth was achieved at 4 M NaCl and 0.5 M MgCl2. The optimum pH and temperature for growth were pH 7.5 and 40 °C; it was able to grow at pH 6.0–8.0 and 25–50 °C. 16S rRNA gene sequence analysis showed that strain EB27T is a member of the family Halobacteriaceae ; however, levels of 16S rRNA gene sequence similarity were as low as 90.0, 89.3 and 89.1 % to the most closely related haloarchaeal taxa, namely Halalkalicoccus tibetensis DS12T, Halosimplex carlsbadense 2-9-1T and Halorhabdus utahensis AX-2T, respectively. The DNA G+C content of strain EB27T was 61 mol%. Strain EB27T contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, common phospholipids found in haloarchaea, together with two minor phospholipids. The only quinone present was MK-8(II-H2). Physiological, biochemical and phylogenetic differences between strain EB27T and recognized genera of extremely halophilic archaea suggest that this strain represents a novel species in a new genus within the family Halobacteriaceae , for which the name Halovenus aranensis gen. nov., sp. nov. is proposed. The type strain of Halovenus aranensis, the type species of the new genus, is strain EB27T ( = IBRC-M 10015T = CGMCC 1.11001T).

Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of Leifsonia kribbensis Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov.

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1403-1410 ◽  
Author(s):  
Yun-Hee Jang ◽  
Soo-Jin Kim ◽  
Tomohiko Tamura ◽  
Moriyuki Hamada ◽  
Hang-Yeon Weon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-positive, non-motile rod, designated strain SGM3-12T, was isolated from paddy soil in Suwon, Republic of Korea. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Microbacteriaceae . The nearest phylogenetic neighbour was Leifsonia kribbensis MSL-13T (97.4 % 16S rRNA gene sequence similarity). Strain SGM3-12T and Leifsonia kribbensis MSL-13T formed a distinct cluster within the family Microbacteriaceae . Strain SGM3-12T contained MK-12(H2) and MK-11(H2) as the predominant menaquinones with moderate amounts of MK-12 and MK-11; anteiso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids (>10 % of total); and diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids as the polar lipids. The peptidoglycan type of the isolate was B1δ with l-Lys as the diagnostic cell-wall diamino acid. On the basis of these results, strain SGM3-12T represents a novel species within a new genus, for which the name Lysinimonas soli gen. nov., sp. nov. is proposed (the type strain of the type species is SGM3-12T = KACC 13362T = NBRC 107106T). It is also proposed that Leifsonia kribbensis be transferred to this genus as Lysinimonas kribbensis comb. nov. (the type strain is MSL-13T = DSM 19272T = JCM 16015T = KACC 21108T = KCTC 19267T).

Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov.

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 208-211 ◽  
Author(s):  
Lourdes Martínez-Aguilar ◽  
Jesús Caballero-Mellado ◽  
Paulina Estrada-de los Santos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Phylogenetic analysis of the 16S rRNA gene sequences of strains TE26T and K6 belonging to Wautersia numazuensis Kageyama et al. 2005 showed the strains to be deeply intermingled among the species of the genus Cupriavidus . The comparison showed that strain TE26T was closely related to the type strains of Cupriavidus pinatubonensis (99.1 % 16S rRNA gene sequence similarity), C. basilensis (98.7 %), C. necator (98.7 %) and C. gilardii (98.0 %). However, DNA–DNA hybridization experiments (less than 20 % relatedness) demonstrated that strain TE26T is different from these Cupriavidus species. A comparative phenotypic and chemotaxonomic analysis (based on fatty acid profiles) in combination with the 16S rRNA gene sequence phylogenetic analysis and the DNA–DNA hybridization results supported the incorporation of Wautersia numazuensis into the genus Cupriavidus as Cupriavidus numazuensis comb. nov.; the type strain is TE26T ( = LMG 26411T  = DSM 15562T  = CIP 108892T).

Melghirimyces profundicolus sp. nov., isolated from a deep-sea sediment

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4552-4556 ◽  
Author(s):  
Jie Li ◽  
Sheng Qin ◽  
Zhi-Qing You ◽  
Li-Juan Long ◽  
Xin-Peng Tian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel filamentous bacterium, strain SCSIO 11153T, was isolated from a sediment sample collected from the Indian Ocean (80° 03.099′ E 01° 03.300′ N) at a depth of 4593 m. Good growth was observed at 50–55 °C and pH 7.0 with 3 % NaCl. It formed ivory–white colonies with radial wrinkles. Aerial mycelium was absent on the media tested. Phenotypic characteristics and 16S rRNA gene sequence analysis indicated that strain SCSIO 11153T belonged to the family Thermoactinomycetaceae . It exhibited 96.4 % and 96.2 % 16S rRNA gene sequence similarities to Melghirimyces algeriensis NariEXT and Melghirimyces thermohalophilus Nari11AT, respectively, while lower sequence similarity values (<95.4 %) were observed between strain SCSIO 11153T and other species of genera in the family Thermoactinomycetaceae . The menaquinone type was MK-7. Major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain SCSIO 11153T was 52.6 mol%. On the basis of the genotypic and phenotypic characteristics, it is proposed that strain SCSIO 11153T represents a novel species of the genus Melghirimyces with the name Melghirimyces profundicolus sp. nov. The type strain is SCSIO 11153T ( = DSM 45787T = CCTCC AA 2012007T = NBRC 109068T).

Aquimarina agarilytica sp. nov., an agarolytic species isolated from a red alga

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 869-873 ◽  
Author(s):  
Bokun Lin ◽  
Guoyong Lu ◽  
Yandan Zheng ◽  
Wei Xie ◽  
Shengkang Li ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Red Alga ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

A novel yellow-pigmented, agarolytic bacterial strain, designated ZC1T, was isolated from the surface of the marine red alga Porphyra haitanensis collected near Nan Ao Island, Guangdong province, China. The isolate was Gram-stain-negative, strictly aerobic and rod-shaped and displayed β-galactosidase, alkaline phosphatase, catalase and oxidase activities. The predominant cellular fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and iso-C17 : 0 3-OH. The major menaquinone was menaquinone 6 (MK-6). The DNA G+C content was 32.8 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain ZC1T was closely related to members of the genus Aquimarina in the family Flavobacteriaceae , phylum Bacteroidetes . Based on phylogenetic and phenotypic evidence, strain ZC1T ( = CCTCC AB 2010229T  = NBRC 107695T) represents the type strain of a novel species in the genus Aquimarina , for which the name Aquimarina agarilytica sp. nov. is proposed.

‘Candidatus Phytoplasma balanitae’ associated with witches’ broom disease of Balanites triflora

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 636-640 ◽  
Author(s):  
Nang Kyu Kyu Win ◽  
Seung-Yeol Lee ◽  
Assunta Bertaccini ◽  
Shigetou Namba ◽  
Hee-Young Jung
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

A phytoplasma was identified in naturally infected wild Balanites triflora plants exhibiting typical witches’ broom symptoms (Balanites witches’ broom: BltWB) in Myanmar. The 16S rRNA gene sequence revealed that BltWB phytoplasma had the highest similarity to that of ‘Candidatus Phytoplasma ziziphi’ and it was also closely related to that of ‘Candidatus Phytoplasma ulmi ’. Phylogenetic analysis of the 16S rRNA gene sequences indicated that the BltWB phytoplasma clustered as a discrete subclade with Elm yellows phytoplasmas. RFLP analysis of the 16S rRNA gene including the 16S–23S spacer region differentiated the BltWB phytoplasma from ‘Ca. P. ziziphi ’, ‘Ca. P. ulmi ’ and ‘Candidatus Phytoplasma trifolii ’. Analysis of additional ribosomal protein (rp) and translocase protein (secY) gene sequences and phylogenetic analysis of BltWB showed that this phytoplasma was clearly distinguished from those of other ‘Candidatus Phytoplasma ’ taxa. Taking into consideration the unique plant host and the restricted geographical occurrence in addition to the 16S rRNA gene sequence similarity, the BltWB phytoplasma is proposed to represent a novel taxon, ‘Candidatus Phytoplasma balanitae’.

Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3848-3853 ◽  
Author(s):  
Heung-Min Son ◽  
Jung-Eun Yang ◽  
YongJin Park ◽  
Chang-Kyun Han ◽  
Song-Gun Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain THG-B283T, which has β-glucosidase activity, was isolated from soil of a ginseng field. Cells were Gram-reaction-negative, oxidase- and catalase-positive, aerobic, motile with one polar flagellum and rod-shaped. The strain was subjected to a polyphasic taxonomic study. Strain THG-B283T grew optimally at around pH 7.0, at 25–28 °C and in the absence of NaCl on R2A agar. 16S rRNA gene sequence analysis revealed that strain THG-B283T belongs to the family Sphingomonadaceae and is closely related to Sphingomonas melonis DAPP-PG 224T (98.2 %), S. aquatilis JSS7T (98.1 %), S. insulae DS-28T (97.6 %), S. mali IFO 15500T (97.1 %) and S. pruni IFO 15498T (97.0 %). Strain THG-B283T contained Q-10 as the predominant ubiquinone. The major fatty acids included summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C14 : 0 2-OH and C16 : 0. The DNA G+C content was 72.2 mol%. The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipid, diphosphatidylglycerol, an unidentified glycolipid, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Genomic and chemotaxonomic data supported the affiliation of strain THG-B283T to the genus Sphingomonas . DNA–DNA relatedness between strain THG-B283T and its closest phylogenetic neighbours was below 23 %. On the basis of phenotypic, phylogenetic and genetic data, strain THG-B283T represents a novel species of genus Sphingomonas , for which the name Sphingomonas kyungheensis sp. nov. is proposed. The type strain is THG-B283T ( = KACC 16224T = LMG 26582T).

scholarly journals Amycolatopsis nivea sp. nov., isolated from a Yellow River sample

2020 ◽  
Vol 70 (5) ◽  
pp. 3084-3090 ◽  
Author(s):  
Ming-Ming Niu ◽  
Hong Ming ◽  
Li-Jiao Cheng ◽  
Zhuo-Li Zhao ◽  
Wei-Li Ji ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Yellow River ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

A novel actinobacterium, designated strain CFH S0261T, was isolated from a sediment sample of the Yellow River. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of strain CFH S0261T were Gram-reaction-positive, aerobic, non-motile. Growth occurs at 15–37 °C, pH 6.0–8.0 and with 0–9.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CFH S0261T was a member of the genus Amycolatopsis . The 16S rRNA gene sequence similarity indicated that strain CFH S0261T is most closely related to the type strains of Amycolatopsis niigatensis LC11T (98.95 %), Amycolatopsis echigonensis LC2T (98.81 %) and Amycolatopsis albidoflavus IMSNU 22139T (98.73 %). The whole-genome of CFH S0261T showed a G+C content of 69.5 mol%. The ANI values and in silico DDH values between CFH S0261T and the other species of the genus Amycolatopsis were found to be low (ANIb <90.61 % and DDH <53.40 %). The cell wall diamino acid in the peptidoglycan of strain CFH S0261T was meso-diaminopimelic acid and the whole-cell hydrolysate comprised arabinose, galactose, glucose, rhamnose and ribose. The predominant menaquinone was MK-9(H4). The major cellular fatty acids were C16 : 0, iso-C15 : 0 and iso-C16 : 0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and four unidentified glycolipids. On the basis of phenotypic, genotypic and phylogenetic data, strain CFH S0261T represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis nivea sp. nov. is proposed. The type strain is CFH S0261T (=KCTC 39515T =CCTCC AA 2014028T).

scholarly journals Paucihalobacter ruber gen. nov., sp. nov., isolated from a haloalkaline lake sediment sample

2020 ◽  
Vol 70 (10) ◽  
pp. 5373-5381 ◽  
Author(s):  
Shu-ge Wu ◽  
Jing-jing Wang ◽  
Jia-ning Wang ◽  
Qi Chen ◽  
Zong-jun Du ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacterium, designated CWB-1T, was isolated from a haloalkaline lake sediment sample collected from the bottom of Chaiwopu Lake, Urumchi, Xinjiang Province, PR China. Strain CWB-1T grew at 4–40 °C (optimum, 30–35 °C), pH 6.5–9.0 (optimum, pH 6.5–7.0) and with 0.5–5.5 % (w/v) NaCl (optimum, 2.5–3.0 %). Phylogenetic analyses based on the 16S rRNA gene sequence and the whole genome sequence both revealed that strain CWB-1T belonged to the family Flavobacteriaceae . The strain had the highest similarity of the 16S rRNA gene sequence to Psychroserpens jangbogonensis PAMC 27130T (92.8 %). The genome of strain CWB-1T was 3 548 011 bp long with 36.3 % DNA G+C content. The predominant fatty acids (>10 %) in the CWB-1T cells were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 1 (iso-C15 : 1 H/C13 : 0 3-OH). The major respiratory quinone was menaquinone-6 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. Based on the phylogenetic analyses, as well as the phenotypic characteristics, a novel genus and species of the family Flavobacteriaceae , Paucihalobacter ruber gen. nov., sp. nov., is proposed. The type strain is CWB-1T (=KCTC 72450T=CGMCC 1.17149T).

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