scholarly journals Sphaerisporangium rufum sp. nov., an endophytic actinomycete from roots of Oryza sativa L

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1077-1082 ◽  
Author(s):  
Ratchanee Mingma ◽  
Kannika Duangmal ◽  
Savitr Trakulnaleamsai ◽  
Arinthip Thamchaipenet ◽  
Atsuko Matsumoto ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Rrna Gene ◽  
Content Type ◽  
Endophytic Actinomycete ◽  
Link Type ◽  
Physiological Properties ◽  
Actinomycete Strain ◽  
Phosphatidylinositol Mannosides ◽  
The 16S Rrna Gene

An endophytic actinomycete, strain R10-82T, isolated from surface-sterilized roots of rice (Oryza sativa L.) was studied using a polyphasic approach. Strain R10-82T produced branching substrate mycelia and developed spherical spore vesicles on aerial hyphae containing non-motile spores. The major cellular fatty acids were iso-C16 : 0, iso-C14 : 0 and 10-methyl C17 : 0. The predominant menaquinones were MK-9, MK-9(H2), MK-9(H4) and MK-9(H6). Rhamnose, ribose, madurose, mannose and glucose were detected in whole-cell hydrolysates. The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol mannosides, hydroxylphosphatidylethanolamine and ninhydrin-positive phosphoglycolipids. These morphological and chemotaxonomic data were similar to those of the genus Sphaerisporangium . Analysis of the 16S rRNA gene sequence revealed that strain R10-82T was related most closely to Sphaerisporangium cinnabarinum JCM 3291T (98.3 % similarity). The DNA G+C content of strain R10-82T was 74 mol%. DNA–DNA relatedness data in combination with differences in the biochemical and physiological properties suggested that strain R10-82T should be classified as representing a novel species of the genus Sphaerisporangium , for which the name Sphaerisporangium rufum is proposed. The type strain is R10-82T ( = BCC 51287T = NBRC 109079T). An emended description of the genus Sphaerisporangium is also provided.

Streptomyces wuyuanensis sp. nov., an actinomycete from soil

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2945-2950 ◽  
Author(s):  
Xuefang Zhang ◽  
Jianli Zhang ◽  
Jimei Zheng ◽  
Di Xin ◽  
Yuhua Xin ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
The Novel ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Actinomycete Strain ◽  
Phosphatidylinositol Mannosides ◽  
The 16S Rrna Gene ◽  
Phospholipid Profile

A novel actinomycete, strain FX61T, was isolated from a saline sample collected from the Inner Mongolian Autonomous Region in China and subjected to a taxonomic study using a polyphasic approach. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The major fatty acids were iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 1 H, C16 : 0, iso-C14 : 0 and anteiso-C17 : 0. The phospholipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two phosphatidylinositol mannosides and an unidentified phospholipid. The G+C content of the genomic DNA was 72 mol%. The 16S rRNA gene sequence of the isolate had greater than 98 % similarity with those of Streptomyces griseoincarnatus ATCC 23623T (98.2 %), Streptomyces labedae DSM 41446T (98.2 %), Streptomyces variabilis ATCC 19815T (98.2 %), Streptomyces erythrogriseus ATCC 27427T (98.2 %), Streptomyces matensis ATCC 23935T (98.2 %), Streptomyces althioticus ATCC 19724T (98.2 %) and Streptomyces luteosporeus ATCC 33049T (98.0 %), showing that the novel strain should be assigned to the genus Streptomyces . DNA–DNA hybridizations with the seven above-mentioned members of the genus Streptomyces showed 29.8, 28.5, 27.0, 25.5, 25.0, 23.5 and 22.0 % relatedness, respectively. On the basis of the phenotypic characteristics and genotypic distinctiveness, strain FX61T should be classified as a novel species of the genus Streptomyces , for which the name Streptomyces wuyuanensis sp. nov. is proposed. The type strain is FX61T ( = CGMCC 4.7042T = KCTC 29112T).

scholarly journals Cellulomonas endophytica sp. nov., isolated from Gastrodia elata Blume

2020 ◽  
Vol 70 (5) ◽  
pp. 3091-3095 ◽  
Author(s):  
Yan-Qiong Li ◽  
Hui Zhang ◽  
Min Xiao ◽  
Zhou-Yan Dong ◽  
Jing-Yi Zhang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Type Strain ◽  
Rrna Gene ◽  
Gastrodia Elata ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Pr China ◽  
Phosphatidylinositol Mannosides ◽  
The 16S Rrna Gene

A Gram-stain-positive, facultatively anaerobic and non-motile strain, designated SYSUP0004T, was isolated from the tubers of Gastrodia elata Blume collected from Yunnan Province, PR China. The 16S rRNA gene sequence result showed that the strain SYSUP0004T shared low similarity (97.7 %) with the type strain of Cellulomonas marina . SYSUP0004T grew at pH 6.0–9.0 (optimum, pH 8.0), temperature 4–30 °C (optimum, 28 °C) and could tolerate NaCl up to 4 % w/v (optimum in the absence of NaCl). The cell-wall peptidoglycan type was A4β with an interpeptide bridge l-ornithine–d-glutamic acid. Cell-wall sugars were mannose, ribose, glucose, galactose and fucose. The menaquinone was MK-9(H4). The major fatty acids were anteiso-C15:0, anteiso-C15 : 1 A, C16 : 0 and anteiso-C17 : 0. The polar lipids of SYSUP0004T were diphosphatidylglycerol, unidentified phosphoglycolipid, phosphatidylinositol mannosides and unidentified glycolipid. The genomic DNA G+C content was 76.5 %. The average nucleotide identity values between SYSUP0004T and members of the genus Cellulomonas were below the cut-off level (95–96 %) recommended as the ANI criterion for interspecies identity. Thus, based on the above results strain SYSUP0004T represents a novel species of the genus Cellulomonas , for which the name Cellulomonas endophytica sp. nov. is proposed. The type strain, SYSUP0004T (=KCTC 49025T=CGMCC 1.16405T).

Prauserella cavernicola sp. nov., isolated from cave rock

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Chanwit Suriyachadkun ◽  
Wipaporn Ngaemthao ◽  
Tawanmol Pujchakarn ◽  
Wuttichai Mhuantong ◽  
Suwanee Chunhametha
Keyword(s):  
Type Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Actinomycete Strain ◽  
Phosphatidylinositol Mannosides

A novel actinomycete, designated strain ASG 168T, was isolated from cave rock collected from Stegodon Sea Cave in Thailand. Long chains of non-motile spores that were oval or spherical in shape with a smooth surface developed on aerial mycelia. Substrate mycelia fragmented into irregular rod-shaped elements. A polyphasic taxonomic study showed that strain ASG 168T had typical characteristics of members of the genus Prauserella . 16S rRNA gene sequence analysis indicated that strain ASG 168T shared 97.5 % similarity with Prauserella marina MS498T and 96.7 % with Prauserella coralliicola SCSIO 11529T. Average nucleotide identity values with P. coralliicola SCSIO 11529T and P. marina MS498T were 82.98 and 76.08 %, respectively. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained ribose, arabinose and galactose. The predominant menaquinone was MK-9(H4). The predominant fatty acids were iso-C16 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). The phospholipid profile consisted of phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unknown phospholipids. The G+C content of the genomic DNA was 70.6 mol%. Differentiation of strain ASG 168T from closely related species was evident from digital DNA–DNA hybridization values of 29.2 and 21.3 % with P. coralliicola and P. marina , respectively. Based on comparative analysis of phenotypic, chemotaxonomic and genotypic data, the novel actinomycete strain ASG 168T (=TBRC 13679T=NBRC 114887T) is proposed to be the type strain of a novel species, Prauserella cavernicola sp. nov.

Geodermatophilus taihuensis sp. nov., isolated from the interfacial sediment of a eutrophic lake

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4108-4112 ◽  
Author(s):  
Jian-Hang Qu ◽  
Ming Hui ◽  
Jian-Ying Qu ◽  
Fu-Fang Wang ◽  
Hai-Feng Li ◽  
...  
Keyword(s):  
Type Species ◽  
Taihu Lake ◽  
Eutrophic Lake ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Phosphatidylinositol Mannosides ◽  
Taxonomic Characterization ◽  
The 16S Rrna Gene

A novel actinobacterial strain, 3-wff-81T, was isolated from interfacial sediment of the eutrophic Taihu Lake in Jiangsu Province (China) and subjected to polyphasic taxonomic characterization. The strain formed pale orange-pigmented colonies comprising rod-shaped cells on R2A agar. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain 3-wff-81T belonged to the genus Geodermatophilus , with Geodermatophilus soli PB34T (99.1 % similarity) and Geodermatophilus terrae PB261T (98.3 % similarity) as closest relatives. The major fatty acids were 16 : 0 iso, 15 : 0 iso, 17 : 1ω8c and 14 : 0 iso. The predominant menaquinones were MK-9(H4) and MK-9. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The genomic DNA G+C content was 73.2 mol%. DNA–DNA relatedness values with G. soli PB34T and G. terrae PB261T were 42.8 % and 39.6 %, respectively. Based on the physiological, biochemical and chemotaxonomic data, it is proposed that strain 3-wff-81T represents a novel species named Geodermatophilus taihuensis sp. nov. with 3-wff-81T ( = CGMCC 1.12303T = NBRC 109416T) as the type strain.

Lactobacillus oryzae sp. nov., isolated from fermented rice grain (Oryza sativa L. subsp. japonica)

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2957-2962 ◽  
Author(s):  
Masanori Tohno ◽  
Maki Kitahara ◽  
Tomohiro Irisawa ◽  
Hidehiko Inoue ◽  
Ryuichi Uegaki ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Type Species ◽  
Oryza Sativa L ◽  
Taxonomic Position ◽  
Rrna Gene ◽  
Rice Grain ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Micro Organisms

The taxonomic position of three Lactobacillus -like micro-organisms (strains SG293T, SG296 and SG310) isolated from fermented rice grain (Oryza sativa L. subsp. japonica) in Japan was investigated. These heterofermentative lactic acid bacteria were Gram-stain-positive, rod-shaped, facultatively anaerobic, non-motile, non-spore-forming and did not show catalase activity. 16S rRNA gene sequence analysis of strain SG293T revealed that the type strains of Lactobacillus malefermentans (98.3 %), Lactobacillus odoratitofui (96.2 %), Lactobacillus similis (96.1 %), Lactobacillus kimchicus (96.1 %), Lactobacillus paracollinoides (95.9 %) and Lactobacillus collinoides (95.7 %) were the closest neighbours. Additional phylogenetic analysis on the basis of pheS and rpoA gene sequences, as well as biochemical and physiological characteristics, indicated that these three strains were members of the genus Lactobacillus and that the novel isolates had a unique taxonomic position. The predominant cellular fatty acids were C18 : 1ω9c and C19 : 1 cyclo 9,10. Because low DNA–DNA hybridization values among the isolates and Lactobacillus malefermentans JCM 12497T were observed, it is proposed that these unidentified isolates be classified as a novel species of the genus Lactobacillus , Lactobacillus oryzae sp. nov. The type strain is SG293T ( = JCM 18671T = DSM 26518T).

scholarly journals Oceanitalea nanhaiensis gen. nov., sp. nov., an actinobacterium isolated from seawater

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2490-2494 ◽  
Author(s):  
Yingnan Fu ◽  
Qipei Li ◽  
Keshao Liu ◽  
Yongle Xu ◽  
Yanan Wang ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Diamino Acid ◽  
Unknown Phospholipid ◽  
Phosphatidylinositol Mannosides ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-positive, motile, short-rod-shaped bacterium, designated strain JLT1488T, was isolated from the South China Sea and investigated in a taxonomic study using a polyphasic approach. The peptidoglycan type determined for strain JLT1488T was A4α with lysine as the diagnostic cell-wall diamino acid and an interpeptide bridge of l-Lys–l-Glu. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unknown glycolipid and an unknown phospholipid. The only detected menaquinone was MK-8(H4), and the major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) , C16 : 0 and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c); significant amounts of C12 : 0 3-OH, C10 : 0 and C19 : 0 cyclo ω8c were also present. The G+C content of the genomic DNA was 62.3 mol%. Comparison of the 16S rRNA gene sequence of strain JLT1488T with those of related type strains demonstrated that it represented a novel lineage within the family Bogoriellaceae , suborder Micrococcineae , being closely related to species of the genera Georgenia , Bogoriella and Cellulomonas (94.6–96.8 % sequence similarity). These results demonstrate that strain JLT1488T is a member of a new genus, for which the name Oceanitalea nanhaiensis gen. nov., sp. nov. is proposed. The type strain of the type species is JLT1488T ( = JCM 17755T = CGMCC 1.10826T).

scholarly journals Streptomyces mimosae sp. nov., an endophytic actinomycete isolated from the root of Mimosa pudica in Thailand

2020 ◽  
Vol 70 (5) ◽  
pp. 3316-3322 ◽  
Author(s):  
Nattaporn Klykleung ◽  
Masahiro Yuki ◽  
Takuji Kudo ◽  
Moriya Ohkuma ◽  
Wongsakorn Phongsopitanun ◽  
...  
Keyword(s):  
Type Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Mimosa Pudica ◽  
Content Type ◽  
Endophytic Actinomycete ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
Actinomycete Strain

An endophytic actinomycete, strain 3MP-10T, isolated from the root of Mimosa pudica was taxonomically studied based upon polyphasic approaches. This strain formed spiral spore chains on aerial mycelia. ll-Diaminopimelic acid, glucose and ribose were found in the whole-cell hydrolysates. It belonged to the genus Streptomyces and was closely related to Streptomyces zhaozhouensis DSM 42101T (98.9 %) and Streptomyces sedi JCM 16909T (98.6 %) based on 16S rRNA gene sequence analysis results. The major menaquinones were MK-10(H8), MK-10(H6) and MK-9(H8). The predominant cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The detected phospholipids were diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, phosphatidylethanolamine and phosphatidylglycerol. Strain 3MP-10T had a genome size of 7.2 Mb with a genome G+C content of 73.4 mol%. Results of in silico genome-based similarity analysis revealed ANIb values of 84.94 and 84.77 %, ANIm values of 88.01 and 87.92 %, and dDDH values of 29.9 and 29.6 % when compared with S. zhaozhouensis DSM 42101T and S. sedi JCM 16909T, respectively. Based on the polyphasic approach, digital DNA–DNA relatedness and average nucleotide identity, we propose that the novel actinomycete represents a novel species, Streptomyces mimosae, with type strain 3MP-10T (=JCM 33328T=TISTR 2646T).

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

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).

Nocardiopsis coralli sp. nov. a novel actinobacterium isolated from the coral Galaxea astreata

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Fenfa Li ◽  
Qingyi Xie ◽  
Shuangqing Zhou ◽  
Fandong Kong ◽  
Yun Xu ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Phosphatidylinositol Mannosides

Strain HNM0947T, representing a novel actinobacterium, was isolated from the coral Galaxea astreata collected from the coast of Wenchang, Hainan, China. The strain was found to have morphological and chemotaxonomic characteristics consistent with the genus Nocardiopsis . The organism formed abundant fragmented substrate mycelia and aerial mycelia which differentiated into non-motile, rod-shaped spores. Whole-cell hydrolysates contained meso-diaminopimelic acid and no diagnostic sugars. The major menaquinones were MK-10(H8), MK-10(H6) and MK-10(H4). The major phospholipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16:0, anteiso-C17:0, C18:0, C18:0 10-methyl (TBSA) and anteiso-C15:0. The G+C content was 71.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HNM0947T belonged to the genus Nocardiopsis and shared highest sequence similarity to Nocardiopsis salina YIM 90010T (98.8%), Nocardiopsis xinjiangensis YIM 90004T(98.5%) and Nocardiopsis kunsanensis DSM 44524T (98.3%). The strain HNM0947T was distinguished from its closest type strain by low average nucleotide identity (90.8%) and dDDH values (60.4%) respectively. Based on genotypic, chemotaxonomic and phenotypic characteristics, it was concluded that strain HNM0947T represents a novel species of the genus Nocardiopsis whose name was proposed as Nocardiopsis coralli sp. nov. The type strain was HNM0947T (=CCTCC AA 2020015 T=KCTC 49525 T).

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