scholarly journals Nocardioides panacisoli sp. nov., isolated from the soil of a ginseng field

2010 ◽  
Vol 60 (2) ◽  
pp. 387-392 ◽  
Author(s):  
Chun Hwi Cho ◽  
Jung-Sook Lee ◽  
Dong-Shan An ◽  
Tae Woong Whon ◽  
Song-Gun Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Closely Related Species ◽  
The Family ◽  
Species Being

A Gram-positive, rod-shaped, non-spore-forming bacterium (Gsoil 346T) was isolated from the soil of a ginseng field in South Korea and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequences, strain Gsoil 346T was shown to belong to the genus Nocardioides in the family Nocardioidaceae, with the most closely related species being Nocardioides aquiterrae GW-9T (96.6 % 16S rRNA gene sequence similarity); however, the strain clustered in a distinct branch of the phylogenetic tree with Nocardioides kongjuensis A2-4T (96.2 %), Nocardioides aromaticivorans H-1T (96.1 %), Nocardioides nitrophenolicus NSP41T (96.1 %) and Nocardioides simplex ATCC 15799T (95.9 %). Strain Gsoil 346T was characterized chemotaxonomically and found to have ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, phosphatidylinositol and phosphatidylglycerol as the major polar lipids, MK-8(H4) as the predominant menaquinone and iso-C16 : 0, C18 : 1 ω9c and C17 : 1 ω8c as the major fatty acids. The G+C content of the genomic DNA of the novel strain was 73.0 mol%. These chemotaxonomic properties supported the placement of strain Gsoil 346T in the genus Nocardioides. The results of physiological and biochemical tests, along with the phylogenetic analysis, allowed strain Gsoil 346T to be differentiated genotypically and phenotypically from recognized species of the genus Nocardioides. Therefore, strain Gsoil 346T represents a novel species, for which the name Nocardioides panacisoli sp. nov. is proposed, with Gsoil 346T (=KCTC 19470T=DSM 21348T) as the type strain.

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

2006 ◽  
Vol 56 (8) ◽  
pp. 1939-1944 ◽  
Author(s):  
Qing-Mei Liu ◽  
Wan-Taek Im ◽  
Myungjin Lee ◽  
Deok-Chun Yang ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
The Family

A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, strain Gsoil 043T, was isolated from soil from a ginseng field in Pocheon province, South Korea. The novel isolate was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 043T was shown to belong to the family ‘Flexibacteraceae’ and was related to Dyadobacter fermentans (96.7 %), Dyadobacter crusticola (96.3 %) and Dyadobacter hamtensis (95.8 %). The 16S rRNA gene sequence similarity of the novel strain to other recognized species within the family ‘Flexibacteraceae’ was less than 87.0 %. The G+C content of genomic DNA was 48 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, C16 : 1 ω7c, iso-C15 : 0 and C16 : 0) supported the affiliation of strain Gsoil 043T to the genus Dyadobacter. The results of physiological and biochemical tests enabled strain Gsoil 043T to be differentiated genotypically and phenotypically from the three Dyadobacter species with validly published names. The novel isolate therefore represents a novel species for which the name Dyadobacter ginsengisoli sp. nov. is proposed, with the type strain Gsoil 043T (=KCTC 12589T=LMG 23409T).

scholarly journals Persicivirga ulvanivorans sp. nov., a marine member of the family Flavobacteriaceae that degrades ulvan from green algae

2011 ◽  
Vol 61 (8) ◽  
pp. 1899-1905 ◽  
Author(s):  
Tristan Barbeyron ◽  
Yannick Lerat ◽  
Jean-François Sassi ◽  
Sophie Le Panse ◽  
William Helbert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Green Algae ◽  
Electron Acceptor ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
The Family ◽  
Gliding Bacterium

A rod shaped, Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, non-gliding bacterium, designated strain PLRT, was isolated from faeces of the mollusc Aplysia punctata (Mollusca, Gastropoda) that had been fed with green algae belonging to the genus Ulva. The novel strain was able to degrade ulvan, a polysaccharide extracted from green algae (Chlorophyta, Ulvophyceae). The taxonomic position of strain PLRT was investigated by using a polyphasic approach. Strain PLRT was dark orange, oxidase-positive, catalase-positive and grew optimally at 25 °C, at pH 7.5 and in the presence of 2.5 % (w/v) NaCl with an oxidative metabolism using oxygen as the electron acceptor. Nitrate could not be used as the electron acceptor. Strain PLRT had a Chargaff’s coefficient (DNA G+C content) of 35.3 mol%. Phylogenetic analysis based on the sequence of the 16S rRNA gene placed the novel strain in the family Flavobacteriaceae (phylum ‘Bacteroidetes’), within a clade comprising Stenothermobacter spongiae, Nonlabens tegetincola, Sandarakinotalea sediminis, Persicivirga xylanidelens and Persicivirga dokdonensis. The closest neighbours of strain PLRT were P. xylanidelens and P. dokdonensis, sharing 95.2 and 95.5 % 16S rRNA gene sequence similarity, respectively. Phylogenetic inference and differential phenotypic characteristics demonstrated that strain PLRT represents a novel species of the genus Persicivirga, for which the name Persicivirga ulvanivorans sp. nov. is proposed. The type strain is PLRT ( = CIP 110082T = DSM 22727T).

Longimycelium tulufanense gen. nov., sp. nov., a filamentous actinomycete of the family Pseudonocardiaceae

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2813-2818 ◽  
Author(s):  
Zhan-Feng Xia ◽  
Tong-Wei Guan ◽  
Ji-Sheng Ruan ◽  
Ying Huang ◽  
Li-Li Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
North West ◽  
Link Type ◽  
The Family

A novel filamentous actinomycete strain, designated TRM 46004T, was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64′ N 89° 26′ E), north-west China. The isolate was characterized using a polyphasic approach. The isolate formed abundant aerial mycelium with few branches and vegetative mycelium, occasionally twisted and coiled; spherical sporangia containing one to several spherical spores developed at the ends of short sporangiophores on aerial mycelium. The G+C content of the DNA was 65.2 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and xylose, galactose and ribose as the major whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H10). The major fatty acids were iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TRM 46004T formed a distinct lineage within the family Pseudonocardiaceae and showed 91.7–96.1 % 16S rRNA gene sequence similarity with members of the family Pseudonocardiaceae . On the basis of the evidence from this polyphasic study, a novel genus and species, Longimycelium tulufanense gen. nov., sp. nov., are proposed. The type strain of Longimycelium tulufanense is TRM 46004T ( = CGMCC 4.5737T = NBRC 107726T).

scholarly journals Aeromicrobium panaciterrae sp. nov., isolated from soil of a ginseng field in South Korea

2007 ◽  
Vol 57 (4) ◽  
pp. 687-691 ◽  
Author(s):  
Ying-Shun Cui ◽  
Wan-Taek Im ◽  
Cheng-Ri Yin ◽  
Jung-Sook Lee ◽  
Keun Chul Lee ◽  
...  
Keyword(s):  
South Korea ◽  
Type Strain ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
The Novel ◽  
Biochemical Tests ◽  
The Family

A Gram-positive, rod-shaped, non-spore-forming and strictly aerobic bacterium (Gsoil 161T) was isolated from soil of a ginseng field in Pocheon Province, South Korea. The novel isolate was characterized using a polyphasic approach in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 161T was shown to belong to the family Nocardioidaceae and was related to Aeromicrobium marinum (98.0 % similarity to the type strain), Aeromicrobium alkaliterrae (97.6 %), Aeromicrobium fastidiosum (97.0 %) and Aeromicrobium erythreum (96.7 %); the sequence similarity with other species within the family was less than 94.4 %. It was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H4) as the predominant menaquinone and C16 : 0, 10-methyl C18 : 0 (tuberculostearic acid), C16 : 0 2-OH, 10-methyl C17 : 0 and 10-methyl-C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 65.5 mol%. These chemotaxonomic properties and phenotypic characteristics support the affiliation of strain Gsoil 161T to the genus Aeromicrobium. Results of physiological and biochemical tests enabled strain Gsoil 161T to be differentiated genotypically and phenotypically from currently known Aeromicrobium species. Therefore, strain Gsoil 161T represents a novel species, for which the name Aeromicrobium panaciterrae sp. nov. is proposed. The type strain is strain Gsoil 161T (=KCTC 19131T=DSM 17939T=CCUG 52476T).

scholarly journals Desulfoplanes formicivorans gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a blackish meromictic lake, and emended description of the family Desulfomicrobiaceae

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1902-1907 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Meromictic Lake ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
The Novel ◽  
Sulfate Reducing ◽  
The Family ◽  
The 16S Rrna Gene

A novel sulfate-reducing bacterium, designated strain Pf12BT, was isolated from sediment of meromictic Lake Harutori in Japan. Cells were vibroid (1.0 × 3.0–4.0 μm), motile and Gram-stain-negative. For growth, the optimum pH was 7.0–7.5 and the optimum temperature was 42–45 °C. Strain Pf12BT used sulfate, thiosulfate and sulfite as electron acceptors. The G+C content of the genomic DNA was 55.4 mol%. Major cellular fatty acids were C16 : 0 and C18 : 0. The strain was desulfoviridin-positive. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the order Desulfovibrionales in the class Deltaproteobacteria. The closest relative was Desulfomicrobium baculatum DSM 4028T with which it shared 91  % 16S rRNA gene sequence similarity. On the basis of phylogenetic and phenotypic characterization, a novel species of a new genus belonging to the family Desulfomicrobiaceae is proposed, Desulfoplanes formicivorans gen. nov., sp. nov. The type strain of Desulfoplanes formicivorans is Pf12BT ( = NBRC 110391T = DSM 28890T).

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 Maribius salinus gen. nov., sp. nov., isolated from a solar saltern and Maribius pelagius sp. nov., cultured from the Sargasso Sea, belonging to the Roseobacter clade

2007 ◽  
Vol 57 (2) ◽  
pp. 270-275 ◽  
Author(s):  
Dong H. Choi ◽  
Jang-Cheon Cho ◽  
Brian D. Lanoil ◽  
Stephen J. Giovannoni ◽  
Byung C. Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Sargasso Sea ◽  
The Novel ◽  
Solar Saltern ◽  
The Family

Two strictly aerobic, Gram-negative bacteria, designated strains CL-SP27T and B5-6T, were isolated from the hypersaline water of a solar saltern in Korea and from the surface water of the Sargasso Sea, respectively. The two strains were rod-shaped, non-motile and grew on marine agar 2216 as beige colonies. Phylogenetic analyses of 16S rRNA gene sequences revealed a clear affiliation of the novel strains to the family Rhodobacteraceae. However, the novel strains were only distantly related to members of the Roseobacter clade, forming a distinct lineage. Although the 16S rRNA gene sequence similarity between strains CL-SP27T and B5-6T was very high (99.6 %), DNA–DNA relatedness between the strains was 48.4 %, suggesting that the strains be categorized as two genospecies. Additionally, the two novel strains could be differentiated by DNA G+C contents, fatty acid profiles, carbon source utilization patterns, antibiotic susceptibilities and biochemical characteristics. Based on taxonomic data obtained in this study, strains CL-SP27T and B5-6T represent separate species within a novel genus of the family Rhodobacteraceae, for which the names Maribius salinus gen. nov., sp. nov. (type species) and Maribius pelagius sp. nov. are proposed. The type strains of Maribius salinus and Maribius pelagius are CL-SP27T (=KCCM 42113T=JCM 13037T) and B5-6T (=KCCM 42336T=JCM 14009T), respectively.

Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2224-2228 ◽  
Author(s):  
Hiromi Uchida ◽  
Koei Hamana ◽  
Masayuki Miyazaki ◽  
Takao Yoshida ◽  
Yuichi Nogi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-negative, aerobic, motile, orange-pigmented, slightly halophilic, rod-shaped bacterium, designated strain JAMH 0132T, was isolated from the trophosome of a tubeworm in Kagoshima Bay, Japan, and its taxonomic position was investigated using a polyphasic approach. The novel strain grew optimally at 28–30 °C and with about 2.0 % (w/v) NaCl. Chemotaxonomic analysis showed that Q-10 was the predominant respiratory quinone and that C18 : 1ω7c, C16 : 0 2-OH and C16 : 0 were the major fatty acids. Sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. The genomic DNA G+C content was 60.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JAMH 0132T belonged to the family Sphingomonadaceae , within the class Alphaproteobacteria . The novel strain appeared most closely related to Sphingopyxis baekryungensis SW-150T (95.1 % 16S rRNA gene sequence similarity) and showed less sequence similarity with representatives of the genera Blastomonas , Sphingomonas , Sphingosinicella and Novosphingobium (<94.8 %). In having no detectable polyamine, strain JAMH 0132T differed from members of all genera currently in the family Sphingomonadaceae . On the basis of its phenotypic properties and phylogenetic distinctiveness, strain JAMH 0132T represents a novel species of a new genus in the family Sphingomonadaceae for which the name Parasphingopyxis lamellibrachiae gen. nov., sp. nov. is proposed. The type strain of Parasphingopyxis lamellibrachiae gen. nov., sp. nov. is JAMH 0132T ( = JCM 15549T  = NCIMB 14486T).

Lysobacter dokdonensis sp. nov., isolated from soil

2011 ◽  
Vol 61 (5) ◽  
pp. 1089-1093 ◽  
Author(s):  
Ki-Hoon Oh ◽  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Closely Related Species ◽  
The Family ◽  
Type Strains

A Gram-negative, non-motile, rod-shaped bacterial strain, DS-58T, was isolated from a soil sample from Dokdo, an island of Korea, and its taxonomic position was investigated. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-58T fell within the family Xanthomonadaceae. The isolate showed 96.9 % 16S rRNA gene sequence similarity with its closest phylogenetic neighbour, Lysobacter niastensis GH41-7T, and 93.4–95.7 % 16S rRNA gene sequence similarity with other members of the genus Lysobacter. Strain DS-58T contained Q-8 as the predominant ubiquinone and iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1ω9c as the major fatty acids. The DNA G+C content was 68.1 mol%. Strain DS-58T could be distinguished phenotypically from type strains of closely related species of the genus Lysobacter and phylogenetically from all members of the genus Lysobacter. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DS-58T is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter dokdonensis sp. nov. is proposed. The type strain is DS-58T ( = KCTC 12822T  = DSM 17958T).

scholarly journals Phycicoccus jejuensis gen. nov., sp. nov., an actinomycete isolated from seaweed

2006 ◽  
Vol 56 (10) ◽  
pp. 2369-2373 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Mycolic Acids ◽  
The Family ◽  
Novel Genus And Species ◽  
The Republic

A marine actinomycete strain, designated KSW2-15T, was isolated from a dried seaweed sample collected from a sandy beach on the coast of Jeju in the Republic of Korea. The organism produced non-motile, non-endospore-forming, Gram-positive, coccoid cells. The colonies were circular, translucent and yellow in colour with entire margins. meso-Diaminopimelic acid was present as the diamino acid of the peptidoglycan. The acyl type of the muramic acid was acetyl. Mycolic acids were not present. The predominant menaquinone was MK-8(H4). The polar lipids were phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were of the saturated, unsaturated and iso-branched methyl types. The DNA G+C content was 74 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain KSW2-15T formed a loose association with ‘Candidatus Nostocoida limicola’, within the radiation of the family Intrasporangiaceae of the suborder Micrococcineae. The organism showed the highest levels of sequence similarity with ‘Candidatus Nostocoida limicola’ (96.1 %), Terrabacter tumescens (96.1 %) and Terrabacter terrae (96.0 %). The levels of 16S rRNA gene sequence similarity between the isolate and members of other genera of the family Intrasporangiaceae were in the range 92.1–95.5 %. On the basis of the polyphasic evidence, the isolate should be classified within a novel genus and species, for which the name Phycicoccus jejuensis gen. nov., sp. nov. is proposed. The type strain of Phycicoccus jejuensis is strain KSW2-15T (=KCCM 42315T=NRRL B-24460T).

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