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 Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3′-dithiodipropionic acid

2006 ◽  
Vol 56 (6) ◽  
pp. 1305-1310 ◽  
Author(s):  
Jan Hendrik Wübbeler ◽  
Tina Lütke-Eversloh ◽  
Stefanie Van Trappen ◽  
Peter Vandamme ◽  
Alexander Steinbüchel
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Rrna Gene Sequence ◽  
Nearest Neighbours ◽  
The 16S Rrna Gene

In this study, a novel betaproteobacterium, strain DPN7T, was isolated under mesophilic conditions from compost because of its capacity to utilize the organic disulfide 3,3′-dithiodipropionic acid. Analysis of the 16S rRNA gene sequence of strain DPN7T revealed 98.5 % similarity to that of Tetrathiobacter kashmirensis LMG 22695T. Values for sequence similarity to members of the genera Alcaligenes, Castellaniella and Taylorella, the nearest neighbours of the genus Tetrathiobacter, were about 95 % or less. The DNA G+C content of strain DPN7T was 55.1 mol%. The level of DNA–DNA hybridization between strain DPN7T and T. kashmirensis LMG 22695T was 41 %, whereas it was much lower between strain DPN7T and Alcaligenes faecalis LMG 1229T (7 %) or Castellaniella defragrans LMG 18538T (5 %). This genotypic divergence was supported by differences in biochemical and chemotaxonomic characteristics. For this reason, and because of the differences in the protein and fatty acid profiles, strain DPN7T should be classified within a novel species of Tetrathiobacter, for which the name Tetrathiobacter mimigardefordensis sp. nov. is proposed. The type strain is strain DPN7T (=DSM 17166T=LMG 22922T).

scholarly journals Agromyces arachidissp. nov. Isolated from a Peanut (Arachis hypogaea) Crop Field

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Chandandeep Kaur ◽  
Anil Kumar Pinnaka ◽  
Nitin Kumar Singh ◽  
Monu Bala ◽  
Shanmugam Mayilraj
Keyword(s):  
Arachis Hypogaea ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Crop Field ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A Gram-positive, yellowish bacterium strain AK-1Twas isolated from soil sample collected from peanut (Arachis hypogaea) crop field and studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genusAgromyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain AK-1Twas closely related toAgromyces aurantiacus(98.6%) followed byAgromyces soli(98.3%),Agromyces tropicus(97.6%),Agromyces ulmi(97.3%),Agromyces flavus(97.2%), andAgromyces italicus(97.0%), whereas the sequence similarity values with respect to the otherAgromycesspecies with validly published names were between 95.3 and 96.7 %. However, the DNA-DNA hybridization values obtained between strain AK-1Tand other related strains were well below the threshold that is required for the proposal of a novel species. The DNAG+Ccontent of the strain is 71.8 mol%. The above data in combination with the phenotypic distinctiveness of AK-1Tclearly indicate that the strain represents a novel species, for which the nameAgromyces arachidissp. nov. is proposed. The type strain is AK-1T(=MTCC 10524T= JCM 19251T).

scholarly journals Paenibacillus mendelii sp. nov., from surface-sterilized seeds of Pisum sativum L.

2005 ◽  
Vol 55 (6) ◽  
pp. 2351-2354 ◽  
Author(s):  
Jakub Šmerda ◽  
Ivo Sedláček ◽  
Zdena Páčová ◽  
Eva Durnová ◽  
Alexandra Smíšková ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Garden Pea ◽  
Phenotypic Profile ◽  
Pisum Sativum L ◽  
The 16S Rrna Gene

A Gram-variable, facultatively anaerobic, endospore-forming bacterium was isolated from surface-sterilized seeds of the garden pea and characterized with phenotypic and molecular methods. A PCR with the Paenibacillus-specific primer PAEN515F and the 16S rRNA gene sequence indicated that strain C/2T belongs to the genus Paenibacillus and is closely related to Paenibacillus phyllosphaerae (94·0 % sequence similarity). Strain C/2T generated a unique phenotypic profile, in particular for the production of acid from substrates. The DNA G+C content (50·8 mol%) and the major fatty acid (anteiso-C15 : 0) are consistent with the genus Paenibacillus. DNA–DNA hybridization distinguished strain C/2T from other phylogenetically related Paenibacillus species and, therefore, strain C/2T (=CCM 4839T=LMG 23002T) is here described as the type strain of a novel species, for which the name Paenibacillus mendelii sp. nov. is proposed.

scholarly journals Saccharothrix ecbatanensis sp. nov., an actinobacterium isolated from soil

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4544-4549 ◽  
Author(s):  
Fatemeh Mohammadipanah ◽  
Javad Hamedi ◽  
Peter Schumann ◽  
Cathrin Spröer ◽  
María del Carmen Montero-Calasanz ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Unknown Phospholipid ◽  
Hamedan Province

A novel actinomycete, designated HM 537T, was isolated from soil in Hamedan Province, Iran. Cell-wall hydrolysates of strain HM 537T contained meso-diaminopimelic acid, and whole-cell hydrolysates contained ribose, glucose, galactose, rhamnose and traces of mannose. The main phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and an unknown phospholipid. MK-9(H4), an unknown MK and MK-10(H4) were the predominant menaquinones. The major fatty acids included iso-C16 : 0, iso-C15 : 0, iso-C16 : 1 G and 9(?)-methyl C16 : 0. Strain HM 537T had the highest 16S rRNA gene sequence similarity to Saccharothrix hoggarensis DSM 45457T (99.5 %) and Saccharothrix saharensis DSM 45456T (99.0 %). DNA–DNA hybridization studies showed relatedness values of 13.8 ± 3.3 % with S. hoggarensis DSM 45457T and 16.3 ± 3.5 % with S. saharensis DSM 45456T. Based on the results of phenotypic and genotypic studies, strain HM 537T represents a novel species of the genus Saccharothrix, for which the name Saccharothrix ecbatanensis sp. nov. is proposed. The type strain is HM 537T ( = DSM 45486T = UTMC 00537T = CCUG 63021T).

Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana)

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2951-2956 ◽  
Author(s):  
Sei Joon Oh ◽  
Na-Ri Shin ◽  
Dong-Wook Hyun ◽  
Pil Soo Kim ◽  
Joon Yong Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod- or coccoid-shaped bacterium, designated strain ORY33T, was isolated from the gut of a camel cricket (Diestrammena coreana). The 16S rRNA gene sequence analysis showed that strain ORY33T belonged to the genus Weissella , with highest sequence similarity to Weissella koreensis S-5623T (97.7 %). The strain grew optimally at 30 °C and pH 7 in the presence of 0 % (w/v) NaCl. Catalase and oxidase activities were negative. The genomic DNA G+C content of strain ORY33T was 45.1 mol%. DNA–DNA hybridization values between strain ORY33T and closely related members of the genus Weissella were less than 27 %. The major fatty acids of strain ORY33T were C18 : 1ω9c, C16 : 0 and C14 : 0. Based on these phenotypic, phylogenetic and genotypic analyses, strain ORY33T represents a novel species belonging to the genus Weissella , for which the name Weissella diestrammenae sp. nov. is proposed. The type strain is ORY33T ( = KACC 16890T = JCM 18559T).

scholarly journals Streptomyces mangrovi sp. nov., an actinomycete from mangrove soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3086-3090 ◽  
Author(s):  
Ying Wang ◽  
Huiqin Huang ◽  
Weidao Yuan ◽  
Hua Wei ◽  
Yuqing Chen ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Mangrove Soil

A novel aerobic actinomycete, designated HA11110T, was isolated from a mangrove soil sample collected in Haikou, China. It formed white aerial mycelium and pale yellow substrate mycelium on Gause's synthetic agar no. 1. Scanning electron microscopy revealed that cells of HA11110T produced straight to spiral spore chains with spiny spores. Chemotaxonomic tests showed that the cell wall contained ll-diaminopimelic acid and the major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C14 : 0.16S rRNA gene sequence similarity showed that strain HA11110T belonged to the genus Streptomyces, most closely related to Streptomyces fenghuangensis GIMN4.003T (99.1 %), Streptomyces nanhaiensis SCSIO 01248T (98.8 %) and Streptomyces radiopugnans R97T (98.8 %). However, DNA–DNA hybridization studies of strain HA11110T with these three closest relatives showed relatedness values of 58.4, 49.7 and 47.2 %, respectively. On the basis of phenotypic and genotypic data, strain HA11110T represents a novel species of the genus Streptomyces, for which the name Streptomyces mangrovi sp. nov. is proposed. The type strain is HA11110T ( = CGMCC 4.7117T = DSM 42113T).

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).

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).

scholarly journals Tumebacillus ginsengisoli sp. nov., isolated from soil of a ginseng field

2011 ◽  
Vol 61 (7) ◽  
pp. 1715-1719 ◽  
Author(s):  
Sang-Hoon Baek ◽  
Yingshun Cui ◽  
Sun-Chang Kim ◽  
Chang-Hao Cui ◽  
Chengri Yin ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

A Gram-reaction-positive, rod-shaped, spore-forming bacterium, designated Gsoil 1105T, was isolated from soil of a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the order Bacillales, showing the highest level of sequence similarity with respect to Tumebacillus permanentifrigoris Eur1 9.5T (94.6 %). The phylogenetic distances from other described species with validly published names within the order Bacillales were greater than 9.0 %. Strain Gsoil 1105T had a genomic DNA G+C content of 55.6 mol% and menaquinone 7 (MK-7) as the major respiratory quinone. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1105T represents a novel species of the genus Tumebacillus, for which the name Tumebacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 1105T ( = KCTC 13942T  = DSM 18389T).

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