scholarly journals Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3841-3846 ◽  
Author(s):  
Xuyang Da ◽  
Fan Jiang ◽  
Xulu Chang ◽  
Lvzhi Ren ◽  
Xia Qiu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
South Shetland Islands ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests

A red-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, strain R2-28T, was isolated from a soil sample collected from Ardley Island, South Shetland Islands, Antarctica, and was characterized taxonomically by using a polyphasic approach. The organism grew optimally at 18 °C in TSB. On the basis of phylogenetic analyses of the 16S rRNA gene sequence, strain R2-28T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae. The highest levels of 16S rRNA gene sequence similarity were found with respect to Pedobacter alluvionis NWER-II11T (95.6 %) and Pedobacter terrae DS-57T (95.2 %). The DNA G+C content was 39.9 mol%, and MK-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine and a sphingolipid. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). These chemotaxonomic and phylogenetic data supported the allocation of strain R2-28T to the genus Pedobacter. Additionally, the results of physiological and biochemical tests allowed phenotypic differentiation of strain R2-28T from species of the genus Pedobacter with validly published names. Therefore, strain R2-28T represents a novel species within the genus Pedobacter, for which the name Pedobacter ardleyensis sp. nov. is proposed. The type strain is R2-28T ( = CCTCC AB 2013365T = LMG 28255T).

scholarly journals Flavisolibacter ginsengiterrae gen. nov., sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from ginseng cultivating soil

2007 ◽  
Vol 57 (8) ◽  
pp. 1834-1839 ◽  
Author(s):  
Min-Ho Yoon ◽  
Wan-Taek Im
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Separate Species

Two strains (Gsoil 492T and Gsoil 643T) isolated in Pocheon Province, South Korea, from soil used for ginseng cultivation were characterized using a polyphasic approach. Both isolates comprised Gram-negative, aerobic, non-motile, rod-shaped bacteria. They had similar chemotaxonomic characteristics, e.g. containing MK-7 as the major quinone, having a DNA G+C content in the range 42.5–43.3 mol% and possessing iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. A phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a tight cluster with several uncultured bacterial clones and with the established genera Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes but were clearly separate from these genera. The levels of 16S rRNA gene sequence similarity between the isolates and type strains of related genera ranged from 87.5 to 92.4 %. Furthermore, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from phylogenetically closely related species with validly published names. The level of 16S rRNA gene sequence similarity between the two strains was 99.5 %, whereas the DNA–DNA relatedness value was 44 %, indicating that they represent separate species. On the basis of the polyphasic evidence, a novel genus, Flavisolibacter gen. nov., and two novel species, Flavisolibacter ginsengiterrae sp. nov. (type strain Gsoil 492T=KCTC 12656T=DSM 18136T) and Flavisolibacter ginsengisoli sp. nov. (type strain Gsoil 643T=KCTC 12657T=DSM 18119T), are proposed. Flavisolibacter ginsengiterrae is the type species of the genus.

Terrabacter terrae sp. nov., a novel actinomycete isolated from soil in Spain

2005 ◽  
Vol 55 (6) ◽  
pp. 2491-2495 ◽  
Author(s):  
Marta Montero-Barrientos ◽  
Raúl Rivas ◽  
Encarna Velázquez ◽  
Enrique Monte ◽  
Manuel G. Roig
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Bacterium Strain

A Gram-positive, aerobic, long-rod-shaped, non-spore-forming bacterium (strain PPLBT) was isolated from soil mixed with Iberian pig hair. This actinomycete showed keratinase activity in vitro when chicken feathers were added to the culture medium. Strain PPLBT was oxidase-negative and catalase-positive and produced lipase and esterase lipase. This actinomycete grew at 40 °C on nutrient agar and in the same medium containing 5 % (w/v) NaCl. Growth was observed with many different carbohydrates as the sole carbon source. On the basis of 16S rRNA gene sequence similarity, strain PPLBT was shown to belong to the genus Terrabacter of the family Intrasporangiaceae. Strain PPLBT showed 98·8 % 16S rRNA gene sequence similarity to Terrabacter tumescens. Chemotaxonomic data, such as the main ubiquinone (MK-8), the main polar lipids (phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol) and the main fatty acids (i-C15 : 0, ai-C15 : 0, i-C16 : 0 and ai-C17 : 0) supported the affiliation of strain PPLBT to the genus Terrabacter. The G+C content of the DNA was 71 mol%. The results of DNA–DNA hybridization (36·6 % relatedness between Terrabacter tumescens and strain PPLBT) and physiological and biochemical tests suggested that strain PPLBT belongs to a novel species of the genus Terrabacter, for which the name Terrabacter terrae sp. nov. is proposed. The type strain is PPLBT (=CECT 3379T=LMG 22921T).

scholarly journals Paracoccus fistulariae sp. nov., a lipolytic bacterium isolated from bluespotted cornetfish, Fistularia commersonii

2010 ◽  
Vol 60 (12) ◽  
pp. 2908-2912 ◽  
Author(s):  
Young-Ok Kim ◽  
Hee Jeong Kong ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Kyung-Kil Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Type Strains

A Gram-stain-negative, non-motile, non-spore-forming and short rod- or rod-shaped bacterial strain, designated 22-5T, was isolated from a bluespotted cornetfish, Fistularia commersonii, and subjected to taxonomic study. Strain 22-5T grew optimally at 30 °C and in the presence of 2–5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 22-5T belonged to the genus Paracoccus and joined the cluster comprising Paracoccus homiensis DD-R11T and Paracoccus zeaxanthinifaciens ATCC 21588T, with which strain 22-5T exhibited 97.4 and 96.9 % 16S rRNA gene sequence similarity, respectively. Strain 22-5T exhibited 94.0–96.6 % 16S rRNA gene sequence similarity with the other type strains of species of the genus Paracoccus. Strain 22-5T contained Q-10 as the predominant menaquinone and C18 : 1 ω7c as the predominant fatty acid. In this study, P. zeaxanthinifaciens KCTC 22688T also contained Q-10 as the predominant isoprenoid quinone. The DNA G+C content of strain 22-5T was 63.6 mol%. Strain 22-5T exhibited 44 and 32 % DNA–DNA relatedness to P. homiensis KACC 11518T and P. zeaxanthinifaciens KCTC 22688T, respectively. On the basis of phenotypic, phylogenetic and genetic data, strain 22-5T is considered to represent a novel species of the genus Paracoccus, for which the name Paracoccus fistulariae sp. nov. is proposed. The type strain is 22-5T (=KCTC 22803T =CCUG 58401T).

scholarly journals Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 2089-2095 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Type Strains

Two Gram-negative, non-motile, pleomorphic bacterial strains, DS-40T and DS-45T, were isolated from a soil sample collected from Dokdo, Korea, and their exact taxonomic positions were investigated by using a polyphasic approach. Strains DS-40T and DS-45T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–1.0 % (w/v) NaCl. They contained MK-7 as the predominant menaquinone and possessed iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C contents of strains DS-40T and DS-45T were 36.0 and 36.8 mol%, respectively. Strains DS-40T and DS-45T shared a 16S rRNA gene sequence similarity of 96.7 % and demonstrated a mean DNA–DNA relatedness level of 12 %. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains DS-40T and DS-45T were most closely phylogenetically affiliated with the genus Pedobacter of the family Sphingobacteriaceae. Strains DS-40T and DS-45T exhibited 16S rRNA gene sequence similarity values of 91.4–93.7 and 89.9–91.6 % with respect to the type strains of Pedobacter and Sphingobacterium species, respectively. Phenotypic and chemotaxonomic properties, together with the phylogenetic data, support the assignment of strains DS-40T and DS-45T as two distinct species within the genus Pedobacter. On the basis of phenotypic, phylogenetic and genetic data, strains DS-40T and DS-45T represent two novel species of the genus Pedobacter, for which the names Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov. are proposed, respectively. The respective type strains are DS-40T (=KCTC 12875T=JCM 14593T) and DS-45T (=KCTC 12876T=JCM 14594T).

scholarly journals Photobacterium rosenbergii sp. nov. and Enterovibrio coralii sp. nov., vibrios associated with coral bleaching

2005 ◽  
Vol 55 (2) ◽  
pp. 913-917 ◽  
Author(s):  
F. L. Thompson ◽  
C. C. Thompson ◽  
S. Naser ◽  
B. Hoste ◽  
K. Vandemeulebroecke ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Six new Vibrio-like isolates originating from different species of bleached and healthy corals around Magnetic Island (Australia) were investigated using a polyphasic approach. Phylogenetic analyses based on 16S rRNA, recA and rpoA gene sequences split the isolates in two new groups. Strains LMG 22223T, LMG 22224, LMG 22225, LMG 22226 and LMG 22227 were phylogenetic neighbours of Photobacterium leiognathi LMG 4228T (95·6 % 16S rRNA gene sequence similarity), whereas strain LMG 22228T was related to Enterovibrio norvegicus LMG 19839T (95·5 % 16S rRNA gene sequence similarity). The two new groups can be distinguished from closely related species on the basis of several phenotypic features, including fermentation of d-mannitol, melibiose and sucrose, and utilization of different compounds as carbon sources, arginine dihydrolase activity, nitrate reduction, resistance to the vibriostatic agent O/129 and the presence of fatty acids 15 : 0 iso and 17 : 0 iso. The names Photobacterium rosenbergii sp. nov. (type strain LMG 22223T=CBMAI 622T=CC1T) and Enterovibrio coralii sp. nov. (type strain LMG 22228T=CBMAI 623T=CC17T) are proposed to accommodate these new isolates. The G+C contents of the DNA of the two type strains are respectively 47·6 and 48·2 mol%.

Actinoplanes couchii sp. nov.

2007 ◽  
Vol 57 (4) ◽  
pp. 721-724 ◽  
Author(s):  
Peter Kämpfer ◽  
Birgit Huber ◽  
Kathrin Thummes ◽  
Iris Grün-Wollny ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Closely Related Species ◽  
Bacterium Strain

A Gram-positive bacterium, strain GW8-1761T, was isolated from soil close to the Marmore waterfalls, Terni, Italy. 16S rRNA gene sequence similarity studies showed that strain GW8-1761T belonged to the genus Actinoplanes, being most closely related to Actinoplanes italicus JCM 3165T (98.9 %), A. rectilineatus IFO 13941T (98.5 %), A. palleronii JCM 7626T (97.8 %), A. utahensis IFO 13244T (97.6 %) and A. cyaneus DSM 46137T (97.6 %). Strain GW8-1761T could be distinguished from any other Actinoplanes species with validly published names by 16S rRNA gene sequence similarity values of less than 97.5 %. Chemotaxonomic data [major menaquinone MK-9(H4); major polar lipids diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol, with phosphatidylcholine and aminoglycolipids absent; major fatty acids C15 : 0, C16 : 0, C16 : 0 iso, C17 : 1 ω8c and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH)] supported the affiliation of strain GW8-1761T to the genus Actinoplanes. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW8-1761T from the most closely related species. Strain GW8-1761T therefore merits species status, and we propose the name Actinoplanes couchii sp. nov., with the type strain GW8-1761T (=DSM 45050T=CIP 109316T).

scholarly journals Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1334-1338 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Keun Chul Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-positive, non-motile and rod- or coccoid-shaped bacterial strain, MDN22T, was isolated from a soil sample from Korea. Strain MDN22T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MDN22T was phylogenetically most closely related to the genera Nocardioides and Marmoricola. In the neighbour-joining phylogenetic tree, strain MDN22T was most closely related to Nocardioides jensenii KCTC 9134T, with which it exhibited 98.3 % 16S rRNA gene sequence similarity. The strain exhibited 93.1–96.9 % and 95.3–95.9 % 16S rRNA gene sequence similarities to the type strains of other species of the genera Nocardioides and Marmoricola, respectively. The chemotaxonomic properties of strain MDN22T 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 acids were iso-C16 : 0 and C17 : 1. The DNA G+C content was 68.7 mol%. DNA–DNA relatedness data and differential phenotypic properties suggested that strain MDN22T could be differentiated from N. jensenii and Nocardioides dubius. On the basis of the data obtained, strain MDN22T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides daedukensis sp. nov., is proposed. The type strain is MDN22T (=KCTC 19601T=CCUG 57505T).

scholarly journals Streptococcus rupicaprae sp. nov., isolated from a Pyrenean chamois (Rupicapra pyrenaica)

2011 ◽  
Vol 61 (8) ◽  
pp. 1989-1993 ◽  
Author(s):  
A. I. Vela ◽  
G. Mentaberre ◽  
I. Marco ◽  
R. Velarde ◽  
S. Lavín ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Pyrenean Chamois

Biochemical and molecular genetic studies were performed on an unknown Gram-stain-positive, catalase-negative, coccus-shaped organism isolated from clinical samples of a Pyrenean chamois. The micro-organism was identified as a streptococcal species based on its cellular morphological and biochemical tests. 16S rRNA gene sequence comparison studies confirmed its identification as a member of the genus Streptococcus, but the organism did not correspond to any species of this genus. The nearest phylogenetic relative of the unknown coccus from chamois was Streptococcus ovis (95.9 % 16S rRNA gene sequence similarity). The rpoB and sodA sequence analysis showed sequence similarity values of less than 85.7 % and 83.0 %, respectively, with the currently recognized species of the genus Streptococcus. The novel bacterial isolate was distinguished from S. ovis and other species of the genus Streptococcus using biochemical tests. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be classified as a novel species of the genus Streptococcus, Streptococcus rupicaprae sp. nov., with the type strain 2777-2-07T ( = CECT 7718T  = CCUG 59652T).

scholarly journals Yonghaparkia alkaliphila gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an alkaline soil

2006 ◽  
Vol 56 (10) ◽  
pp. 2415-2420 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Peter Schumann ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
The Family

Two Gram-positive, non-motile, non-spore-forming and rod-shaped actinomycete strains, KSL-113T and KSL-133, were isolated from an alkaline soil in Korea, and their taxonomic positions were investigated by using a polyphasic approach. The strains grew optimally at 30 °C and pH 9.0. Phenotypic, phylogenetic and genetic similarities indicated that strains KSL-113T and KSL-133 represent the same species. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains KSL-113T and KSL-133 fell within the family Microbacteriaceae of the suborder Micrococcineae, the highest 16S rRNA gene sequence similarity values (98.2 %) being obtained with respect to Microcella putealis CV-2T. The 16S rRNA gene sequence similarities between strains KSL-113T and KSL-133 and the other members of the family Microbacteriaceae used in the phylogenetic analysis were less than 96.0 %. Strains KSL-113T and KSL-133 could be clearly distinguished from members of the family Microbacteriaceae on the basis of differences in chemotaxonomic properties, including the predominant menaquinone type, the cell-wall peptidoglycan type and the fatty acid profile. Accordingly, on the basis of the combined phenotypic, chemotaxonomic and phylogenetic data, strains KSL-113T and KSL-133 constitute a novel genus and species of the family Microbacteriaceae, for which the name Yonghaparkia alkaliphila gen. nov., sp. nov. is proposed. The type strain of Yonghaparkia alkaliphila is KSL-113T (=KCTC 19126T=CIP 108920T).

scholarly journals Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro

2011 ◽  
Vol 61 (2) ◽  
pp. 417-421 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Han-Su You ◽  
Dong-Heon Lee ◽  
Duck-Chul Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sponge ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence

A Gram-stain-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated, non-gliding and oxidase- and catalase-positive bacterium, designated A6T, was isolated from a marine sponge, Halichondria oshoro, collected on the coast of Jeju Island, South Korea. Phylogenetic analysis based on the nearly complete 16S rRNA gene sequence revealed that strain A6T was a member of the family Flavobacteriaceae. The closest relatives were Aquimarina intermedia LMG 23204T, A. latercula ATCC 23177T, A. brevivitae SMK-19T and A. muelleri KMM 6020T, with which strain A6T shared 95.7, 95.1, 94.7 and 94.6 % 16S rRNA gene sequence similarity, respectively. The dominant fatty acids of strain A6T were iso-C15 : 0 (32.2 %), iso-C17 : 0 3-OH (20.0 %), iso-C15 : 0 3-OH (12.3 %), iso-C15 : 1 G (7.2 %) and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 6.8 %). The DNA G+C content of strain A6T was 36.0 mol% and the major respiratory quinone was MK-6. On the basis of combined phenotypic and phylogenetic analyses, strain A6T represents a novel species of the genus Aquimarina, for which the name Aquimarina spongiae sp. nov. is proposed. The type strain is A6T (=KCTC 22663T =DSM 22623T).

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