scholarly journals Demequina flava sp. nov. and Demequina sediminicola sp. nov., isolated from sea sediment

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 249-253 ◽  
Author(s):  
Moriyuki Hamada ◽  
Tomohiko Tamura ◽  
Hideki Yamamura ◽  
Ken-ichiro Suzuki ◽  
Masayuki Hayakawa
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Comparisons ◽  
Content Type ◽  
Monophyletic Cluster ◽  
Link Type ◽  
Type Strains

Two novel Gram-stain-positive bacteria, designated HR08-7T and HR08-43T, were isolated from a sea sediment sample from Rishiri Island, Hokkaido, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strains HR08-7T and HR08-43T and the members of the genus Demequina formed a monophyletic cluster with similarity range of 95.5–99.0 %. The peptidoglycan type of strains HR08-7T and HR08-43T was A4β. The predominant menaquinone of both strains was demethylmenaquinone DMK-9(H4) and the major fatty acid was anteiso-C15 : 0. The DNA G+C contents of strains HR08-7T and HR08-43T were 64.5 and 62.4 mol%, respectively. The results of phylogenetic analysis and DNA–DNA hybridization, along with differences of strains HR08-7T and HR08-43T from the recognized Demequina species in phenotypic characteristics, indicate that the two strains merit classification as representatives of two novel species of the genus Demequina , for which the names Demequina flava sp. nov. and Demequina sediminicola sp. nov. are proposed; the type strains are HR08-7T ( = NBRC 105854T = DSM 24865T) and HR08-43T ( = NBRC 105855T = DSM 24867T), respectively.

Agromyces iriomotensis sp. nov. and Agromyces subtropicus sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 833-838 ◽  
Author(s):  
Moriyuki Hamada ◽  
Chiyo Shibata ◽  
Yuumi Ishida ◽  
Tomohiko Tamura ◽  
Hideki Yamamura ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Three novel Gram-stain-positive bacteria, designated IY07-20T, IY07-56T and IY07-113, were isolated from soil samples from Iriomote Island, Okinawa, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the three isolates were closely related to the members of the genus Agromyces , with similarity range of 95.6–98.7 %. The isolates contained l-2,4-diaminobutylic acid, d-alanine, d-glutamic acid and glycine in their peptidoglycans. The predominant menaquinone was MK-12 and the major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C contents were 70.9–72.9 mol%. The chemotaxonomic characteristics of the isolates matched those described for members of the genus Agromyces . The results of phylogenetic analysis and DNA–DNA hybridization, along with differences in phenotypic characteristics between strains IY07-20T, IY07-56T and IY07-113 and the species of the genus Agromyces with validly published names, indicate that the three isolates merit classification as representatives of two novel species of the genus Agromyces , for which the names Agromyces iriomotensis sp. nov. and Agromyces subtropica sp. nov. are proposed; the type strains are IY07-20T ( = NBRC 106452T = DSM 26155T) and IY07-56T ( = NBRC 106454T = DSM 26153T), respectively.

scholarly journals Pseudovibrio axinellae sp. nov., isolated from an Irish marine sponge

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 141-145 ◽  
Author(s):  
John A. O’Halloran ◽  
Teresa M. Barbosa ◽  
John P. Morrissey ◽  
Jonathan Kennedy ◽  
Alan D. W. Dobson ◽  
...  
Keyword(s):  
Marine Sponge ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-negative, motile, rod-shaped bacterial strain, designated Ad2T, was isolated from a marine sponge, Axinella dissimilis, which was collected from a semi-enclosed marine lake in Ireland. Strain Ad2T grew optimally at 24 °C, at pH 7.0 and in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Ad2T clustered with members of the genus Pseudovibrio , and showed 97.3–98.2 % sequence similarity to the type strains of recognized Pseudovibrio species. DNA–DNA relatedness values between strain Ad2T and the type strains of other Pseudovibrio species were <27 %. The DNA G+C content of strain Ad2T was 50.5 mol%. The major fatty acid was 18 : 1ω7c. Differences in phenotypic properties, together with phylogenetic and DNA–DNA hybridization analyses, indicated that strain Ad2T represented a novel species of the genus Pseudovibrio . The name Pseudovibrio axinellae sp. nov. is proposed, with Ad2T ( = DSM 24994T = NCIMB 14761T) as the type strain.

Zhihengliuella flava sp. nov., an actinobacterium isolated from sea sediment, and emended description of the genus Zhihengliuella

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4760-4764 ◽  
Author(s):  
Moriyuki Hamada ◽  
Chiyo Shibata ◽  
Tomohiko Tamura ◽  
Ken-ichiro Suzuki
Keyword(s):  
Dna Hybridization ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Emended Description ◽  
Diamino Acid ◽  
Sequence Similarities

A novel Gram-staining-positive actinobacterium, designated H85-3T, was isolated from a sea sediment sample and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain H85-3T was closely related to the members of the genus Zhihengliuella with pairwise sequence similarities of 97.4–98.6 %. The peptidoglycan of strain H85-3T was found to be of the A4α type with lysine as the diagnostic diamino acid. The menaquinones were MK-9, MK-10 and MK-8 (56 : 30 : 14) and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. These data supported the affiliation of strain H85-3T to the genus Zhihengliuella . Meanwhile, the results of DNA–DNA hybridization, along with the differences in some phenotypic characteristics, indicated that strain H85-3T should be distinguished from the recognized species of the genus Zhihengliuella . Therefore, strain H85-3T represents a novel species of the genus Zhihengliuella , for which the name Zhihengliuella flava sp. nov. is proposed; the type strain is H85-3T ( = NBRC 109021T = DSM 26152T). An emended description of the genus Zhihengliuella is also proposed.

Paraoerskovia sediminicola sp. nov., an actinobacterium isolated from sea sediment, and emended description of the genus Paraoerskovia

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2637-2641 ◽  
Author(s):  
Moriyuki Hamada ◽  
Tomohiko Tamura ◽  
Chiyo Shibata ◽  
Hideki Yamamura ◽  
Masayuki Hayakawa ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Hybridization Data ◽  
Emended Description ◽  
Diamino Acid

A novel Gram-stain-positive actinobacterium, designated H25-14T, was isolated from a sea sediment sample, and its taxonomic position was investigated by a polyphasic approach. The peptidoglycan type of strain H25-14T was A4α and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-9(H4) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain H25-14T was closely related to Paraoerskovia marina NBRC 104352T (98.3 %). However, DNA–DNA hybridization data and phenotypic characteristics revealed that strain H25-14T differed from P. marina NBRC 104352T. Therefore, strain H25-14T represents a novel species of the genus Paraoerskovia , for which the name Paraoerskovia sediminicola sp. nov. is proposed. The type strain is H25-14T ( = NBRC 108565T = DSM 25477T). An emended description of the genus Paraoerskovia is also proposed.

scholarly journals Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1151-1154 ◽  
Author(s):  
Moriyuki Hamada ◽  
Chiyo Shibata ◽  
Arif Nurkanto ◽  
Shanti Ratnakomala ◽  
Puspita Lisdiyanti ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Diamino Acid

A novel Gram-stain-positive actinobacterium, designated PS-14-7T, was isolated from the rhizosphere of a mangrove on Pramuka Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. The peptidoglycan type of strain PS-14-7T was A4α and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-8(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The DNA G+C content was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain PS-14-7T was closely related to Serinibacter salmoneus Kis4-28T (99.6 %). However, DNA–DNA hybridization and phenotypic characteristics revealed that strain PS-14-7T differed from Serinibacter salmoneus . Therefore, strain PS-14-7T represents a novel species of the genus Serinibacter , for which the name Serinibacter tropicus sp. nov. is proposed. The type strain is PS-14-7T ( = NBRC 110108T = InaCC A 515T). An emended description of the genus Serinibacter is also proposed.

scholarly journals Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide–degrading bacterium isolated from activated sludge

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2573-2578 ◽  
Author(s):  
Qing Chen ◽  
Jun Zhang ◽  
Cheng-Hong Wang ◽  
Jin Jiang ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Activated Sludge ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Sequence Similarities

Strain BUT-14T, a Gram-reaction-negative, non-spore-forming, ellipse-shaped bacterium, was isolated from activated sludge of a chloroacetamide-herbicides-manufacturing wastewater treatment facility. The strain was able to degrade more than 90 % of butachlor, acetochlor and alachlor (100 mg l−1) within 5 days of incubation. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BUT-14T was a member of the genus Novosphingobium and showed the highest sequence similarities to Novosphingobium soli DSM 22821T (97.9 %), N. naphthalenivorans KACC 15258T (97.4 %), N. pentaromativorans JCM 12182T (97.4 %) and N. barchaimii DSM 25411T (97.1 %) and lower (<97 %) sequence similarities to all other species of the genus Novosphingobium . Chemotaxonomic analysis revealed that strain BUT-14T possessed Q-10 as the predominant ubiquinone, spermidine as the major polyamine and C18 : 1ω7c (46.9 %), C17 : 1ω6c (17.9 %), summed feature 3, C14 : 0 2-OH (4.4 %), C15 : 0 2-OH (3.1 %) and C16 : 0 (5.51 %) as the major fatty acids. The polar lipids included lipid, glycolipid, phosphatidylglycerol, phospholipid, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and phospatidyldimethylethanolamine. Strain BUT-14T showed low DNA–DNA relatedness with N. soli DSM 22821T (41.5±2.9 %), N. naphthalenivorans JCM 12182T (49.2±4.2 %), N. pentaromativorans KACC 12295T (53.2±1.9 %) and N. barchaimii DSM 25411 (51.2±4.5 %). The DNA G+C content was 66±0.3 mol%. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic data and DNA–DNA hybridization supports the suggestion that strain BUT-14T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium chloroacetimidivorans sp. nov. is proposed. The type strain is BUT-14T ( = CCTCC AB 2013086T = KACC 17147T = JCM 19923T).

Paenibacillus tianjinensis sp. nov., isolated from corridor air

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Hongxiang Liu ◽  
Lijing Lu ◽  
Sijin Wang ◽  
Meng Yu ◽  
Xiaoyun Cao ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Type Strains

A Gram-stain-positive, facultatively anaerobic, non-motile, endospore-forming and rod-shaped bacterium, occurring singly or in pairs, designated TB2019T, was isolated from environmental monitoring samples of corridor air collected at the Tianjin Institute for Drug Control, Tianjin Province (PR China). The isolate was able to grow at 15–40 °C (optimum growth at 37 °C), pH 6.0–8.0 (pH 7.0) and in the presence of 0–2% (w/v) NaCl (0% NaCl). Comparison of 16S rRNA gene sequences indicated that TB2019T was most closely related to Paenibacillus typhae CGMCC 1.11012T (98.63%), Paenibacillus albidus Q4-3T (98.19%), Paenibacillus borealis DSM 13188T (97.55%), Paenibacillus helianthi P26ET (97.33%) and Paenibacillus odorifer DSM 15391T (97.19%). The digital DNA–DNA hybridization and the average nucleotide identity values between TB2019T and the five type strains mentioned above ranged from 20.7 to 25.0% and 75.2 to 81.3%, respectively, and the genomic DNA G+C content was 49.52 mol%. The diagnostic cell-wall sugar was ribose, and the diagnostic amino acid was meso-diaminopimelic acid. The polar lipids of TB2019T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. MK-7 was the predominant menaquinone, and anteiso-C15:0 (30.6%) was the major fatty acid. Based on the polyphasic taxonomic data, strain TB2019T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus tianjinensis sp. nov. is proposed. The type strain is TB2019T (=CICC 25065T=JCM 34610T).

Catenulispora graminis sp. nov., a rhizobacterium from bamboo (Phyllostachys nigro var. henonis) rhizosphere soil

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2589-2592 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Song-Ih Han ◽  
Kyung-Sook Whang
Keyword(s):  
Type Species ◽  
Rhizosphere Soil ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Isoprenoid Quinones ◽  
Type Strains

A novel actinobacterium, designated strain BR-34T, was isolated from rhizosphere soil of bamboo (Phyllostachys nigro var. henonis) sampled in Damyang, Korea. The strain was found to have morphological and chemotaxonomic characteristics typical of the genus Catenulispora . The strain contained iso-C16 : 0 as the major fatty acid and MK-9(H4), MK-9(H6) and MK-9(H8) as major isoprenoid quinones. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BR-34T formed a cluster separate from members of the genus Catenulispora and was related most closely to Catenulispora acidiphila ID139908T (97.4 % similarity), Catenulispora rubra Aac-30T (97.3 %), Catenulispora yoronensis TT N02-20T (97.3 %) and Catenulispora subtropica TT 99-48T (97 %). However, the level of DNA–DNA relatedness between strain BR-34T and C. acidiphila ID139908T was only 45.32 %. Based on DNA–DNA relatedness, morphological and phenotypic data, strain BR-34T could be distinguished from the type strains of phylogenetically related species. It is therefore considered to represent a novel species of the genus Catenulispora , for which the name Catenulispora graminis sp. nov. is proposed. The type strain is BR-34T ( = KACC 15070T = NBRC 107755T).

scholarly journals Marinomonas mangrovi sp. nov., isolated from mangrove sediment

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1537-1541 ◽  
Author(s):  
De-Chao Zhang ◽  
Rosa Margesin
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Mangrove Sediment ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Content Sharing ◽  
Link Type ◽  
Curved Rods ◽  
Sequence Similarities

A Gram-stain-negative, Na+-requiring bacterial strain, designated B20-1T, was isolated from soil of the root system of mangrove forest. Cells were curved rods and motile by means of a polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B20-1T belonged to the genus Marinomonas , sharing highest sequence similarities with Marinomonas rhizomae IVIA-Po-145T (97.6 %), Marinomonas dokdonensis DSW10-10T (97.0 %) and Marinomonas foliarum IVIA-Po-155T (96.9 %). The predominant cellular fatty acids of strain B20-1T were C10 : 0 3-OH, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. The predominant ubiquinone was Q-8. The genomic DNA G+C content of strain B20-1T was 46.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas mangrovi sp. nov., is proposed with B20-1T ( = DSM 28136T = LMG 28077T) as the type strain.

scholarly journals Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1790-1798 ◽  
Author(s):  
V. Venkata Ramana ◽  
S. Kalyana Chakravarthy ◽  
P. Shalem Raj ◽  
B. Vinay Kumar ◽  
E. Shobha ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rhodopseudomonas Palustris ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Geographical Regions ◽  
Emended Description ◽  
Type Strains

Four strains (JA310T, JA531T, JA447 and JA490) of red to reddish brown pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from soil and freshwater sediment samples from different geographical regions of India. All strains contained bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The major cellular fatty acid of strains JA310T and JA531T was C18 : 1ω7c, the quinone was Q-10 and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminohopanoid and an unidentified aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that all strains clustered with species of the genus Rhodopseudomonas in the class Alphaproteobacteria . Strains JA531T, JA447 and JA490 were genotypically (>80 % related based on DNA–DNA hybridization) and phenotypically closely related to each other and the three strains were distinct from strain JA310T (33 % related). Furthermore, all four strains had less than 48 % relatedness (DNA–DNA hybridization) with type strains of members of the genus Rhodopseudomonas , i.e. Rhodopseudomonas palustris ATCC 17001T, Rhodopseudomonas faecalis JCM 11668T and Rhodopseudomonas rhenobacensis DSM 12706T. The genomic DNA G+C contents of strains JA310T and JA531T were 63.8 and 62.4 mol%, respectively. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, it is proposed that strains JA310T ( = NBRC 106083T = KCTC 5839T) and JA531T ( = NBRC 107575T = KCTC 5841T) be classified as the type strains of two novel species of the genus Rhodopseudomonas , Rhodopseudomonas parapalustris sp. nov. and Rhodopseudomonas harwoodiae sp. nov., respectively. In addition, we propose that strain DSM 123T ( = NBRC 100419T) represents a novel species, Rhodopseudomonas pseudopalustris sp. nov., since this strain differs genotypically and phenotypically from R. palustris ATCC 17001T and other members of the genus Rhodopseudomonas . An emended description of R. palustris is also provided.

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