Arthrobacter cupressi sp. nov., an actinomycete isolated from the rhizosphere soil of Cupressus sempervirens

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2731-2736 ◽  
Author(s):  
Jian Zhang ◽  
Yuchao Ma ◽  
Huimin Yu
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Novel Species ◽  
Rrna Gene ◽  
Cupressus Sempervirens ◽  
Sequence Comparisons ◽  
Content Type ◽  
Hybridization Data ◽  
Diamino Acid

An actinobacterial strain, designated D48T, was isolated from the rhizosphere soil of a cypress tree collected from Mianyang in Sichuan province, China. The strain was Gram-stain-positive, catalase-positive, oxidase-negative and non-motile, with lysine as the peptidoglycan diagnostic diamino acid and acetyl as the peptidoglycan acyl type. The predominant menaquinone was MK-9(H2); small amounts of MK-7(H2), MK-10(H2) and MK-6 were also present. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The isolate underwent a rod–coccus morphological cycle, had a high DNA G+C content, was aerobic and grew between 12 and 37 °C (optimum, 28 °C). On the basis of the phenotypic and chemotaxonomic analyses, 16S rRNA gene sequence comparisons and DNA–DNA hybridization data, the isolate represents a novel species of the genus Arthrobacter , for which the name Arthrobacter cupressi sp. nov. is proposed. The type strain is D48T ( = DSM 24664T = CGMCC 1.10783T).

scholarly journals Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 587-592 ◽  
Author(s):  
Hien T. T. Ngo ◽  
KyungHwa Won ◽  
Juan Du ◽  
Heung-Min Son ◽  
YongJin Park ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Novel Species ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type

A Gram-stain negative, facultatively anaerobic, non-motile, rod-shaped bacterium, designated strain THG-A13T, was isolated from Aglaia odorata rhizosphere soil in Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-A13T had close similarity with Lysobacter niabensis GH34-4T (98.5 %), Lysobacter oryzae YC6269T (97.9 %) and Lysobacter yangpyeongensis GH19-3T (97.3 %). Chemotaxonomic data revealed that strain THG-A13T possesses ubiquinone-8 (Q8) as the predominant isoprenoid quinone and iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c as the major fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol) and diphosphatidylglycerol. The G+C content was 66.3 mol%. The DNA–DNA relatedness values between strain THG-A13T and its closest phylogenetic neighbours were below 18.0 %. These data corroborated the affiliation of strain THG-A13T to the genus Lysobacter . These data suggest that the isolate represents a novel species for which the name Lysobacter terrae sp. nov. is proposed, with THG-A13T as the type strain ( = KACC 17646T = JCM 19613T).

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.

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 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 Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China

2019 ◽  
Vol 69 (4) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xiang-yue Zhou ◽  
Zeng-hong Gao ◽  
Mei-hong Chen ◽  
Mei-qi Jian ◽  
Li-hong Qiu
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Broad Leaved Forest ◽  
Gene Sequence Analysis ◽  
Leaved Forest

Cells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11T grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyella flagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyella humi DHG40T and Dyella nitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyella caseinilytica DHOB09T and Dyella mobilis DHON07T, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.

scholarly journals Halioglobus maricola sp. nov., isolated from coastal seawater

2020 ◽  
Vol 70 (3) ◽  
pp. 1868-1875 ◽  
Author(s):  
Shan-Hui Li ◽  
Jaeho Song ◽  
Yeonjung Lim ◽  
Yochan Joung ◽  
Ilnam Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6–97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA–DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-β-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus , for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).

scholarly journals Herbidospora mongoliensis sp. nov., isolated from soil, and reclassification of Herbidospora osyris and Streptosporangium claviforme as synonyms of Herbidospora cretacea

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2322-2329 ◽  
Author(s):  
Ismet Ara ◽  
Baljinova Tsetseg ◽  
Damdinsuren Daram ◽  
Manabu Suto ◽  
Katsuhiko Ando
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Analyses ◽  
Content Type ◽  
Link Type ◽  
Phospholipid Profile

A Gram-reaction-positive aerobic actinomycete, designated strain MN08-A0118T, which produced short chains of non-motile spores on the tips of long sporophores and formed yellow–brown colonies with branched substrate mycelium, was studied in detail to determine its taxonomic position. On the basis of 16S rRNA gene sequence analyses, strain MN08-A0118T was grouped into the genus Herbidospora , being most closely related to Streptosporangium claviforme (98.2 %), Herbidospora osyris (98.2 %), Herbidospora daliensis (98.2 %), Herbidospora cretacea (97.9 %) and Herbidospora yilanensis (97.4 %). Chemotaxonomic data supported allocation of the strain to the genus Herbidospora . MK-10(H4) was the predominant menaquinone with minor amounts of MK-10(H6), MK-10(H2) and MK-9(H4); the fatty acid profile contained major amounts of iso-C16 : 0, C17 : 0 10-methyl, iso-C14 : 0 and iso-C16 : 0 2-OH; the phospholipid profile contained phosphatidylethanolamine, phosphatidylmethylethanolamine and glucosamine-containing phospholipids; and the whole-cell sugars included ribose, glucose, galactose, madurose and rhamnose (trace). The phylogenetic data, phenotypic and genotypic properties and DNA–DNA hybridization differentiated this strain from its closely related strains, S. claviforme (35–54 % DNA–DNA relatedness), H. osyris (39–51 %), H. daliensis (3–16 %), H. cretacea (34–39 %) and H. yilanensis (34–42 %). Thus, MN08-A0118T represents a novel species of the genus Herbidospora , for which the name Herbidospora mongoliensis sp. nov. is proposed, with MN08-A0118T ( = NBRC 105882T  = VTCC D9-22T) as the type strain. In addition, DNA–DNA hybridization results showed that S. claviforme and H. osyris are synonyms of H. cretacea .

scholarly journals Phenylobacterium kunshanense sp. nov., isolated from the sludge of a pesticide manufacturing factory

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 325-330 ◽  
Author(s):  
Cuiwei Chu ◽  
Cansheng Yuan ◽  
Xin Liu ◽  
Li Yao ◽  
Jianchun Zhu ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Ubiquinone 10 ◽  
Sequence Similarities

A novel aerobic, Gram-stain-negative, motile bacterium, designated strain BUT-10T, was isolated from the sludge of a pesticide manufacturing factory in Kunshan, China. Cells were rod-shaped (0.4–0.45×0.9–1.4 µm) and colonies were white, circular with entire edges and had a smooth surface. The strain grew at 25–37 °C, at pH 6.0–8.0 and with 0–0.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain BUT-10T was a member of the genus Phenylobacterium , and showed highest sequence similarities to Phenylobacterium muchangponense A8T (97.49 %), Phenylobacterium immobile DSM 1986T (97.14 %) and Phenylobacterium lituiforme FaiI3T (96.34 %). Major fatty acids (>5 %) were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The major isoprenoid quinone was ubiquinone-10. The DNA G+C content was 71.85 mol%. Strain BUT-10T showed low DNA–DNA relatedness with P. muchangponense A8T (15.7±2.9 %) and P. immobile DSM 1986T (12.8±1.1 %). On the basis of the phenotypic, phylogenetic and genotypic data, strain BUT-10T is considered to represent a novel species of the genus Phenylobacterium , for which the name Phenylobacterium kunshanense sp. nov. is proposed. The type strain is BUT-10T ( = CCTCC AB 2013085T = KCTC 42014T).

Roseomonas riguiloci sp. nov., isolated from wetland freshwater

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3024-3029 ◽  
Author(s):  
Keun Sik Baik ◽  
Seong Chan Park ◽  
Han Na Choe ◽  
Se Na Kim ◽  
Jae-Hak Moon ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach

A non-motile, coccobacillus-shaped and pink pigmented bacterium, designated strain 03SU10-PT, was isolated from wetland freshwater (Woopo wetland, Republic of Korea). Cells were Gram reaction-negative and catalase- and oxidase-positive. The major fatty acids (>10 % of total) were C18 : 1ω7c and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). The predominant respiratory lipoquinone was Q-10. The DNA G+C content was 68 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and an unknown aminolipid. Spermidine, putrescine and 1,3-diaminopropane were the major polyamines. A phylogenetic tree based on 16S rRNA gene sequence comparisons showed that strain 03SU10-PT formed an evolutionary lineage within the radiation enclosing the members of the genus Roseomonas . The nearest neighbour to the novel strain was Roseomonas stagni HS-69T (96.3 % gene sequence similarity). The evidence provided by the polyphasic taxonomic approach used in this study indicated that strain 03SU10-PT could not be assigned to any recognized species; therefore a novel species is proposed, Roseomonas riguiloci sp. nov., with 03SU10-PT ( = KCTC 23339T = JCM 17520T) as the type strain.

Mucilaginibacter mali sp. nov., isolated from rhizosphere soil of apple orchard

2021 ◽  
Author(s):  
Han Sol Kim ◽  
Keun Chul Lee ◽  
Min Kuk Suh ◽  
Ji-Sun Kim ◽  
Kook-Il Han ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Novel Species ◽  
Apple Orchard ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A novel Gram-negative bacterium, designated G2-14T, was isolated from rhizosphere soil sample collected from apple orchard in Chungju-si, Chungcheongbuk-do, Republic of Korea. Strain G2-14T was a strictly aerobic, non-spore-forming, non-motile and short-rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain G2-14T was closely related to Mucilaginibacter myungsuensis HMD1056T (96.9 %) and Mucilaginibacter boryungensis BDR-9T (96.8 %). The major cellular fatty acids (>10 %) of strain G2-14T were summed feature 3 (C16:1 ω6с and/or C16:1 ω7с) and iso-C15:0. The predominant quinone and the major polar lipid were menaquinone-7 and phosphatidylethanolamine, respectively. Strain G2-14T produced acetic acid. The DNA G+C content based on whole genome sequences was 46.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain G2-14T represents a novel species in the genus Mucilaginibacter , for which the name Mucilaginibacter mali sp. nov. is proposed. The type strain is G2-14T (=KCTC 72533T=NBRC 114179T).

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