scholarly journals Actinoplanes luteus sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4227-4232 ◽  
Author(s):  
Chanwit Suriyachadkun ◽  
Wipaporn Ngaemthao ◽  
Suwanee Chunhametha ◽  
Jean-Jacques Sanglier
Keyword(s):  
Fatty Acids ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Evergreen Forest ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
Dry Evergreen Forest ◽  
The 16S Rrna Gene

A novel filamentous bacterial strain, A-T 5190T, which developed irregular sporangia at the end of sporangiophores on substrate mycelia, was isolated from dry evergreen forest soil collected in Thailand. The 16S rRNA gene sequence and phylogenetic analysis indicated that strain A-T 5190T belonged to the genus Actinoplanes and was related most closely to Actinoplanes palleronii NBRC 14916T (98.88 % similarity) and Actinoplanes rectilineatus NBRC 13941T (98.54 %). DNA–DNA relatedness values between strain A-T 5190T and its closest relatives were below 70 %. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained rhamnose, ribose, galactose and xylose. The predominant menaquinone was MK-9(H4). The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant cellular fatty acids were unsaturated fatty acid C17 : 1 and branched fatty acids iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 71.9 mol%. Evidence from phenotypic, chemotaxonomic and genotypic studies indicate that strain A-T 5190T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes luteus sp. nov. is proposed. The type strain is A-T 5190T ( = BCC 41582T = NBRC 109644T).

scholarly journals Amycolatopsis stemonae sp. nov., isolated from a Thai medicinal plant

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3894-3899 ◽  
Author(s):  
Nattaporn Klykleung ◽  
Somboon Tanasupawat ◽  
Pattama Pittayakhajonwut ◽  
Moriya Ohkuma ◽  
Takuji Kudo
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
Gene Sequence Analysis ◽  
Actinomycete Strain ◽  
Genotypic Characteristics ◽  
The 16S Rrna Gene

A novel actinomycete, strain ST1-08T, was isolated from the stem of Stemona sp. in Thailand. The taxonomic position of this isolate was determined by using a polyphasic approach. Strain ST1-08T contained meso-diaminopimelic acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars of the whole-cell hydrolysate, which are typical properties of members of the genus Amycolatopsis. Strain ST1-08T grew at 15–40 °C, pH 6–9 and on 5 % (w/v) NaCl. Gelatin liquefaction, starch hydrolysis and skimmed milk peptonization were positive. The strain utilized l-arabinose, d-glucose, glycerol, myo-inositol, d-mannitol and l-rhamnose. The predominant menaquinone was MK-9(H4) and the major cellular fatty acids were iso-C16 : 0 and iso-C15 : 0.The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyl-phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. The 16S rRNA gene sequence analysis revealed that the strain was closely related to Amycolatopsis pretoriensis JCM 12673T (98.99 %) and Amycolatopsis lexingtonensis JCM 12672T (98.87 %). The DNA G+C content of strain ST1-08T was 71.2 mol%. The DNA–DNA relatedness values among strain ST1-08T, A. pretoriensis JCM 12673T and A. lexingtonensis JCM 12672T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of phenotypic and genotypic characteristics, strain ST1-08T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis stemonae is proposed. The type strain is ST1-08T( = JCM 30050T = PCU 339T = TISTR 2278T).

scholarly journals Bacillus endolithicus sp. nov., isolated from pebbles

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4568-4573 ◽  
Author(s):  
B. Parag ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Strain JC267T was isolated from pebbles collected from Pingleshwar beach, Gujarat, India. Cells are Gram-stain-positive, facultatively anaerobic, non-motile rods forming sub-terminal endospores in swollen ellipsoidal to oval sporangia. Strain JC267T contains anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0 as major (>5 %) cellular fatty acids. Polar lipids include phosphatidylglycerol, phospholipids (PL1–3), glycolipids (GL1–2) and an unidentified lipid. Cell-wall amino acids are composed of diagnostic meso-diaminopimelic acid, dl-alanine and a small amount of d-glutamic acid. The genomic DNA G+C content of strain JC267T is 45.5 mol%. The 16S rRNA gene sequence of strain JC267T showed highest sequence similarities of < 98.41 % with all species of the genus Bacillus when subjected to EzTaxon-e blast analysis. The reassociation values based on DNA–DNA hybridization of strain JC267T with Bacillus halosaccharovorans IBRC-M 10095T and Bacillus niabensis JCM 16399T were 26 ± 1 % and 34 ± 3 %, respectively. Based on taxonomic data obtained using a polyphasic approach, strain JC267T represents a novel species of the genus Bacillus, for which the name Bacillus endolithicus sp. nov. is proposed. The type strain is JC267T ( = IBRC-M 10914T = KCTC 33579T).

scholarly journals Planotetraspora silvatica sp. nov. and emended description of the genus Planotetraspora

2004 ◽  
Vol 54 (6) ◽  
pp. 2053-2056 ◽  
Author(s):  
Tomohiko Tamura ◽  
Takeshi Sakane
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Subtropical Forest ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Monophyletic Cluster ◽  
Aerial Hyphae ◽  
Emended Description ◽  
The 16S Rrna Gene

An actinomycete that developed sporangia containing four spores in a single row at the ends of short sporangiophores on branched aerial hyphae was isolated from subtropical forest soil. The isolate contained menaquinone MK-9(H4), glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and madurose in the whole-cell hydrolysate. The 16S rRNA gene sequence indicated that the isolate formed a monophyletic cluster with Planotetraspora mira. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species of the genus Planotetraspora is proposed, Planotetraspora silvatica sp. nov. (type strain, TT 00-51T=NBRC 100141T=DSM 44746T).

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 Kocuria koreensis sp. nov., isolated from fermented seafood

2010 ◽  
Vol 60 (1) ◽  
pp. 140-143 ◽  
Author(s):  
Eun-Jin Park ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Mi-Ja Jung ◽  
Kee-Sun Shin ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
The 16S Rrna Gene

A Gram-positive, aerobic, non-motile and coccoid actinobacterium, designated P31T, was isolated from a traditional, fermented seafood. The strain was catalase-positive and oxidase-negative. Cells grew in the presence of 0–15.0 % (w/v) NaCl, and at pH 5–10 and 15–37 °C. Major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Strain P31T contained MK-7 as the predominant menaquinone. The DNA G+C content of the genomic DNA of strain P31T was 65.2 mol%. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain P31T was most closely related to Kocuria kristinae DSM 20032T, with 96.9 % similarity, and these two strains clustered together in constructed phylogenetic trees. The DNA–DNA hybridization value between strain P31T and K. kristinae DSM 20032T was 21.1 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it is suggested that strain P31T represents a novel species of the genus Kocuria, for which the name Kocuria koreensis sp. nov. is proposed. The type strain is P31T (=KCTC 19595T=JCM 15915T).

scholarly journals Nocardioides aestuarii sp. nov., isolated from tidal flat sediment

2004 ◽  
Vol 54 (6) ◽  
pp. 2151-2154 ◽  
Author(s):  
Hana Yi ◽  
Jongsik Chun
Keyword(s):  
Fatty Acids ◽  
Tidal Flat ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
Gene Sequence Analysis

A strictly aerobic, non-motile, rod-shaped actinomycete, designated strain JC2056T, was isolated from a sediment sample of getbol, the tidal flat of Korea. Results of 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Nocardioides, with the highest similarity being to Nocardioides luteus KCTC 9575T (95·7 %). The major menaquinone was MK-8(H4), and predominant cellular fatty acids were iso-16 : 0 and iso-16 : 1 H. The DNA G+C content was 70 mol%. Based on the morphological, physiological, biochemical and chemotaxonomical data presented in this study, strain JC2056T should be classified as a novel species, for which the name Nocardioides aestuarii sp. nov. is proposed; the type strain is JC2056T (=IMSNU 14029T=KCTC 9921T=JCM 12125T).

scholarly journals Nocardiopsis sinuspersici sp. nov., isolated from sandy rhizospheric soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2346-2352 ◽  
Author(s):  
Javad Hamedi ◽  
Fatemeh Mohammadipanah ◽  
Mathias von Jan ◽  
Gabriele Pötter ◽  
Peter Schumann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A polyphasic taxonomic study of a halotolerant bacterium, isolated from sandy rhizospheric soil in Sarbandar, Persian Gulf, Iran, revealed that strain HM6T represents a novel species within the genus Nocardiopsis. Results of the 16S rRNA gene sequence comparison revealed that strain HM6T clustered with strains of the genus Nocardiopsis, showing the highest degree of 16S rRNA gene sequence similarity to Nocardiopsis quinghaiensis (99.2 %), Nocardiopsis aegyptia (98.5 %) and Nocardiopsis halotolerans (98.3 %). However, DNA–DNA hybridization studies with these type strains revealed less than 39.6 % similarity. Rather than genotypic differences, there are some phenotypic discrepancies between strain HM6T and closely related species of the genus Nocardiopsis. Main morphological and chemotaxonomical features of strain HM6T include: (i) growth characteristics, i.e. the formation of a scant light-yellow to white aerial mycelium and the typical zig-zag form of the hyphae, which fragment during ageing into smooth rod-shaped spores; (ii) the presence of meso-diaminopimelic acid and glucose plus ribose in whole-cell hydrolysates; (iii) the presence of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol, together with three unknown Nocardiopsis-specific phospholipids (close to diphosphatidylglycerol in position) in polar lipid extracts; (iv) the presence of the major menaquinones MK-10(H0), MK-10(H2) and MK-9(H0) in the non-polar fraction; (v) the presence of iso/anteiso-branched plus 10-methyl-branched fatty acids, showing the diagnostic combination for species of the genus Nocardiopsis of iso-16 : 0 (31.1 %), anteiso-17 : 0 (19.2 %), 10-methyl-17 : 0 (5.8 %) and tuberculostearic acid (8.8 %); and (vi) the absence of mycolic acids. Analysis of the 16S rRNA gene sequence revealed that strain HM6T represents a distinct taxon within the genus Nocardiopsis. Based upon genotypic and phenotypic differences from other members of the genus, a novel species, Nocardiopsis sinuspersici sp. nov., is proposed. The type strain is HM6T (=UTMC 00102T =DSM 45277T =CCUG 57624T).

scholarly journals Paenibacillus sepulcri sp. nov., isolated from biodeteriorated mural paintings in the Servilia tomb

2006 ◽  
Vol 56 (10) ◽  
pp. 2341-2344 ◽  
Author(s):  
Jakub Šmerda ◽  
Ivo Sedláček ◽  
Zdena Páčová ◽  
Eva Krejčí ◽  
Ladislav Havel
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Mural Paintings ◽  
The 16S Rrna Gene

In 2001, a Gram-variable, facultatively anaerobic, endospore-forming bacterium isolated from biodeteriorated mural paintings in the Servilia tomb of the Roman necropolis of Carmona was deposited as Paenibacillus strain LMG 19508. Subsequently, the strain was characterized in detail using phenotypic and molecular methods. The 16S rRNA gene sequence confirmed that the strain belongs to the genus Paenibacillus and indicated its relationship to Paenibacillus mendelii CCM 4839T (96.7 % sequence similarity). The predominant menaquinone was MK-7. The cell wall contained meso-diaminopimelic acid of the A1γ type. The DNA G+C content (50 mol%) and the major fatty acid (anteiso-C15 : 0) of strain LMG 19508T were also consistent with its affiliation to the genus Paenibacillus. DNA–DNA hybridization distinguished strain LMG 19508T from other phylogenetically related Paenibacillus species. Therefore, the isolate represents a novel species, for which the name Paenibacillus sepulcri sp. nov. is proposed. The type strain is CCM 7311T (=LMG 19508T).

scholarly journals Rheinheimera nanhaiensis sp. nov., isolated from marine sediments, and emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007

2011 ◽  
Vol 61 (5) ◽  
pp. 1016-1022 ◽  
Author(s):  
Hui-Juan Li ◽  
Xi-Ying Zhang ◽  
Yan-Jiao Zhang ◽  
Ming-Yang Zhou ◽  
Zhao-Ming Gao ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Cellular Fatty Acids ◽  
Emended Description ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, facultatively aerobic, oxidase- and catalase-positive, rod-shaped bacterium, designated strain E407-8T, was isolated from a sediment sample from the South China Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain E407-8T was affiliated with the genus Rheinheimera, sharing the highest sequence similarity with Rheinheimera pacifica KMM 1406T (97.5 %) and Rheinheimera aquimaris SW-353T (97.4 %) and showing less than 97 % sequence similarity to the type strains of other recognized Rheinheimera species. Levels of DNA–DNA relatedness of strain E407-8T to R. pacifica DSM 17616T and R. aquimaris JCM 14331T were 25.2 % (25.3 % in the duplicate measurement) and 9.4 % (6.5 %), respectively. The bacterium could grow at 10–48 °C (optimum 37 °C) and in the presence of 0–8 % (w/v) NaCl (optimum 0.5–2.5 %). The major cellular fatty acids of strain E407-8T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C17 : 1ω8c, C16 : 0 and C18 : 1ω7c. The predominant respiratory quinone was ubiquinone Q-8. The DNA G+C content was 51.0 mol%. Based on the results of our polyphasic taxonomic study, strain E407-8T represents a novel species in the genus Rheinheimera, for which the name Rheinheimera nanhaiensis sp. nov. is proposed. The type strain is E407-8T ( = CCTCC AB 209089T  = KACC 14030T). An emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007 is also proposed.

scholarly journals Paenibacillus algorifonticola sp. nov., isolated from a cold spring

2011 ◽  
Vol 61 (9) ◽  
pp. 2167-2172 ◽  
Author(s):  
Qi-Yong Tang ◽  
Na Yang ◽  
Jian Wang ◽  
Yu-Qing Xie ◽  
Biao Ren ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Cold Spring ◽  
Xinjiang Uyghur Autonomous Region ◽  
The 16S Rrna Gene

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated XJ259T, was isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region, China. The isolate grew optimally at 20–30 °C and pH 7.3–7.8. Comparative analysis of the 16S rRNA gene sequence showed that isolate XJ259T belonged phylogenetically to the genus Paenibacillus, and was most closely related to Paenibacillus xinjiangensis B538T (with 96.6 % sequence similarity), Paenibacillus glycanilyticus DS-1T (96.3 %) and Paenibacillus castaneae Ch-32T (96.1 %), sharing less than 96.0 % sequence similarity with all other members of the genus Paenibacillus. Chemotaxonomic analysis revealing menaquinone-7 (MK-7) as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phosphoglycolipids as the major cellular polar lipids, a DNA G+C content of 47.0 mol%, and anteiso-C15 : 0 and C16 : 0 as the major fatty acids supported affiliation of the new isolate to the genus Paenibacillus. Based on these data, isolate XJ259T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus algorifonticola sp. nov. is proposed. The type strain is XJ259T ( = CGMCC 1.10223T  = JCM 16598T).

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