scholarly journals Brevibacterium samyangense sp. nov., an actinomycete isolated from a beach sediment

2006 ◽  
Vol 56 (8) ◽  
pp. 1889-1892 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Beach Sediment ◽  
Actinomycete Strain ◽  
Diamino Acid ◽  
Type Strains

A novel actinomycete, strain SST-8T, was isolated from sand sediment of Samyang Beach in Jeju, Korea, and subjected to a polyphasic taxonomic study. The organism, which produced opaque, circular, yellow colonies, with a coryneform morphology, showed the following chemotaxonomic characteristics: meso-diaminopimelic acid as the diamino acid in the peptidoglycan, MK-8(H2) as the major menaquinone, phosphatidylglycerol as the only polar lipid, anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids and a DNA G+C content of 70.7 mol%. The combination of morphological and chemotaxonomic features supported its classification in the genus Brevibacterium. Phylogenetic analyses, based on 16S rRNA gene sequence studies, showed that strain SST-8T formed an intermediate branch between the Brevibacterium luteolum/Brevibacterium otitidis and Brevibacterium mcbrellneri/Brevibacterium paucivorans clusters. Sequence similarity calculations based on a neighbour-joining analysis revealed that the closest relatives of strain SST-8T were the type strains of B. paucivorans (96.6 %), B. luteolum (96.5 %), B. mcbrellneri (96.3 %), Brevibacterium avium (96.0 %) and B. otitidis (95.9 %). Based on a broad set of phenotypic and genetic data, it was evident that the strain represents a novel species of the genus Brevibacterium. The name Brevibacterium samyangense sp. nov. is proposed, with SST-8T (=NRRL B-41420T=KCCM 42316T) as the type strain.

scholarly journals Micromonospora fluostatini sp. nov., isolated from marine sediment

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4417-4423 ◽  
Author(s):  
Wongsakorn Phongsopitanun ◽  
Takuji Kudo ◽  
Mihoko Mori ◽  
Kazuro Shiomi ◽  
Pattama Pittayakhajonwut ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Actinomycete Strain ◽  
Sequence Similarity Analysis ◽  
Type Strains

The novel actinomycete strain PWB-003T, which produced fluostatins B and C antibiotics, was isolated from nearshore sediment collected from Panwa Cape, Phuket Province, Thailand. Data from the present polyphasic study indicated that strain PWB-003T represented a member of the genus Micromonospora. It produced single spores on substrate mycelia and contained meso-diaminopimelic acid in the cell-wall peptidoglycan. Whole-cell hydrolysate contained ribose, xylose, arabinose, mannose and glucose. The predominant menaquinone was MK-10 (H4). Cellular fatty acids comprised C18 : 1ω9c, iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C17 : 0. On the basis of 16S rRNA gene sequence similarity analysis, the novel strain was closely related to Micromonospora eburnea LK2-10T (99.38 %), Micromonospora chaiyaphumensis MC5-1T (99.16 %), Micromonospora yangpuensis FXJ6.011T (98.97 %), Micromonospora echinaurantiaca DSM 43904T (98.97 %), Micromonospora pallida DSM 43817T (98.97 %), Micromonospora sagamiensis DSM 43912T and Micromonospora auratinigra JCM 12357T (both 98.97 %). The G+C content of the DNA was 74.5 mol%. DNA–DNA relatedness values among strain PWB-003T and related type strains ranged from 11.3 ± 1.3 to 38.8 ± 1.1 %. On the basis of these observations, strain PWB-003T could be distinguished from its closely related type strains and is considered to represent a novel species of the genus Micromonospora, for which the name Micromonospora fluostatini sp. nov. (type strain PWB-003T = JCM 30529T = PCU 341T = TISTR 2345T) is proposed.

scholarly journals Paenibacillus ripae sp. nov., isolated from bank side soil

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4757-4762 ◽  
Author(s):  
Ying Sun ◽  
Zhaohui Guo ◽  
Qi Zhao ◽  
Qiyu Gao ◽  
QinJian Xie ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Pr China ◽  
Diamino Acid

A Gram-stain-variable, rod-shaped, non-motile and endospore-forming bacterium, designated strain HZ1T, was isolated from a sample of bank side soil from Hangzhou city, Zhejiang province, PR China. On the basis of 16S rRNA gene sequence analysis, strain HZ1T was closely related to members of the genus Paenibacillus, sharing the highest levels of sequence similarity with Paenibacillus agarexedens DSM 1327T (94.4 %), Paenibacillus sputi KIT00200-70066-1T (94.4 %). Growth occurred at 15–42 °C (optimum 30–37 °C), pH 5.0–9.5 (optimum pH 7.0–8.0) and NaCl concentrations of up to 6.0 % (w/v) were tolerated (optimum 0.5 %). The dominant respiratory quinone was MK-7 and the DNA G+C content was 40.1 mol%. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids of strain HZ1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain HZ1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus ripae sp. nov. (type strain HZ1T = CCTCC AB 2014276T = LMG 28639T) is proposed.

Terrabacter carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete

2011 ◽  
Vol 61 (3) ◽  
pp. 482-486 ◽  
Author(s):  
Sung M. Kim ◽  
Sae W. Park ◽  
Sang T. Park ◽  
Young M. Kim
Keyword(s):  
Carbon Monoxide ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Diamino Acid ◽  
Type Strains

A bacterial strain, PY2T, capable of oxidizing carbon monoxide, was isolated from a soil sample collected from a roadside at Yonsei University, Seoul, Korea. On the basis of 16S rRNA gene sequence analysis, strain PY2T was shown to belong to the genus Terrabacter and was most closely related to Terrabacter lapilli LR-26T (99.1 % similarity). Strain PY2T was characterized chemotaxonomically as having iso-C15 : 0 as the predominant fatty acid, MK-8(H4) as the major menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid of the cell wall, as possessing a polar lipid profile that included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and unknown amino-containing phosphoglycolipids, and having a DNA G+C content of 75.6 mol%. DNA–DNA relatedness values between strain PY2T and the type strains of T. lapilli, Terrabacter tumescens, Terrabacter terrae and Terrabacter aerolatus were 20.0 %, 22.9 %, 35.9 % and 64.5 %, respectively. Based on the combined evidence from the phylogenetic analyses, chemotaxonomic data and DNA–DNA hybridization experiments, it is proposed that strain PY2T represents a novel species for which the name Terrabacter carboxydivorans sp. nov. is proposed. The type strain is PY2T (=KCCM 42922T=JCM 16259T).

scholarly journals Blastococcus jejuensis sp. nov., an actinomycete from beach sediment, and emended description of the genus Blastococcus Ahrens and Moll 1970

2006 ◽  
Vol 56 (10) ◽  
pp. 2391-2396 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Separate Species ◽  
Beach Sediment ◽  
Actinomycete Strain ◽  
Type Strains

A novel actinomycete, strain KST3-10T, was isolated from sand sediment of a beach in Jeju, Korea, and was subjected to polyphasic taxonomic characterization. The organism produced circular, smooth, translucent, apricot-coloured colonies comprising coccoid- or rod-shaped cells. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch outside the radiation of the genus Blastococcus. The organism showed 16S rRNA gene sequence similarity values of 98.2 % with respect to Blastococcus aggregatus DSM 4725T and 98.1 % with respect to Blastococcus saxobsidens BC444T. The type strains of the two Blastococcus species shared 98.2 % sequence similarity with respect to each other, whereas the levels of sequence similarity between the novel organism and the type strains of the less closely related neighbours, Modestobacter multiseptatus and Geodermatophilus obscurus, were in the range 96.2–96.9 %. The physiological, biochemical and chemotaxonomic data revealed that the novel organism can be readily differentiated from members of the genus Blastococcus and that it merits separate species status. On the basis of the phenotypic and genotypic evidence, strain KST3-10T represents a novel species of the genus Blastococcus, for which the name Blastococcus jejuensis sp. nov. is proposed. The type strain is KST3-10T (=NRRL B-24440T=KCCM 42251T).

scholarly journals Nocardiopsis arvandica sp. nov., isolated from sandy soil

2011 ◽  
Vol 61 (5) ◽  
pp. 1189-1194 ◽  
Author(s):  
Javad Hamedi ◽  
Fatemeh Mohammadipanah ◽  
Gabriele Pötter ◽  
Cathrin Spröer ◽  
Peter Schumann ◽  
...  
Keyword(s):  
Sandy Soil ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Actinomycete Strain ◽  
Taxonomic Approach

An actinomycete strain, HM7T, was isolated from sandy soil from the banks of the Arvand River, Khoramshahr, Iran. In a study conducted using a polyphasic taxonomic approach, it was found that this strain represented a novel species in the genus Nocardiopsis. Strain HM7T had long, branched substrate mycelia and the aerial mycelium completely fragmented to long chains of rod-shaped spores. The cell wall of strain HM7T contained meso-diaminopimelic acid, galactose and ribose. The predominant phospholipids were phosphatidylglycerol, phosphatidylethanolamine diphosphatidylglycerol, and phosphatidylcholine. The main menaquinones were MK-10(H2), MK-10(H4), MK-10(H0) and MK-9(H2). Strain HM7T showed the highest degree of 16S rRNA gene sequence similarity with Nocardiopsis sinuspersici UTMC 00102T (99.8 %) and Nocardiopsis quinghaiensis YIM 28A4T (99.3 %), but differed significantly from these type strains based on DNA–DNA hybridization data (37.6 and 38.9 % relatedness, respectively). Physiological, biochemical and phenotypic characteristics allowed strain HM7T to be differentiated from related species. On the basis of results from phenotypic and phylogenetic analyses, strain HM7T is considered to represent a novel species of the genus Nocardiopsis, for which the name Nocardiopsis arvandica sp. nov. is proposed; the type strain of this species is HM7T ( = UTMC 00103T = DSM 45278T = CCUG 58831T).

scholarly journals Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum ‘Verrucomicrobia’ isolated from seawater in Japan

2007 ◽  
Vol 57 (5) ◽  
pp. 959-963 ◽  
Author(s):  
Jaewoo Yoon ◽  
Mina Yasumoto-Hirose ◽  
Atsuko Katsuta ◽  
Hiroshi Sekiguchi ◽  
Satoru Matsuda ◽  
...  
Keyword(s):  
Cell Wall ◽  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hard Coral ◽  
The 16S Rrna Gene

An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24T, was isolated from seawater surrounding the hard coral Galaxea fascicularis L., collected at Majanohama, Akajima, Japan, and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the phylum ‘Verrucomicrobia’ and shared 84–95 % sequence similarity with cultivated strains of ‘Verrucomicrobia’ subdivision 4. Amino acid analysis of the cell-wall hydrolysate indicated the absence of muramic acid and diaminopimelic acid, which suggested that the strain did not contain peptidoglycan in the cell wall. The G+C content of the DNA was 53.9 mol%. MK-7 was the major menaquinone and C14 : 0, C18 : 1 ω9c and C18 : 0 were the major fatty acids. On the basis of these data, it was concluded that strain 04OKA010-24T represents a novel species in a new genus in subdivision 4 of the phylum ‘Verrucomicrobia’, for which the name Coraliomargarita akajimensis gen. nov., sp. nov. is proposed. The type strain of Coraliomargarita akajimensis is 04OKA010-24T (=MBIC06463T=IAM 15411T=KCTC 12865T).

scholarly journals Mucilaginibacter boryungensis sp. nov., isolated from soil

2011 ◽  
Vol 61 (7) ◽  
pp. 1549-1553 ◽  
Author(s):  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Ki-Hoon Oh ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-stain-negative, non-motile, non-spore-forming bacterial strain, BDR-9T, was isolated from soil collected from Boryung on the west coast of the Korean peninsula, and its taxonomic position was investigated by using a polyphasic study. Strain BDR-9T grew optimally at 25 °C, at pH 6.0–7.5 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BDR-9T fell within the clade comprising species of the genus Mucilaginibacter within the phylum Bacteroidetes. 16S rRNA gene sequence similarity values between strain BDR-9T and the type strains of species of the genus Mucilaginibacter were in the range 94.0–95.6 %. Strain BDR-9T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The DNA G+C content was 44.3 mol%. Differential phenotypic properties and phylogenetic distinctiveness of strain BDR-9T demonstrated that this strain is distinguishable from species of the genus Mucilaginibacter. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain BDR-9T is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter boryungensis sp. nov. is proposed. The type strain is BDR-9T ( = KCTC 23157T  = CCUG 59599T).

scholarly journals Nocardioides terrigena sp. nov., isolated from soil

2007 ◽  
Vol 57 (11) ◽  
pp. 2472-2475 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Type Strains

A Gram-positive, rod- or coccoid-shaped bacterial strain, DS-17T, was isolated from a soil in Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-17T grew optimally at around pH 8.0 and 30 °C in the presence of 0.5–1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-17T belonged to the genus Nocardioides. The chemotaxonomic properties of strain DS-17T were consistent with those of the genus Nocardioides: the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0, C17 : 1 ω8c and C17 : 0 were the major fatty acids. The DNA G+C content was 71.5 mol%. Strain DS-17T exhibited 16S rRNA gene sequence similarity values of 94.5–96.9 % to the type strains of recognized Nocardioides species. Strain DS-17T could be distinguished from recognized Nocardioides species by differences in phenotypic characteristics. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DS-17T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides terrigena sp. nov. is proposed. The type strain is DS-17T (=KCTC 19217T=JCM 14582T).

scholarly journals Stenotrophomonas dokdonensis sp. nov., isolated from soil

2006 ◽  
Vol 56 (6) ◽  
pp. 1363-1367 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Hyun Woo Oh ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, rod-shaped, Stenotrophomonas-like bacterial strain, DS-16T, was isolated from soil from Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-16T grew optimally at pH 6.0–7.0 and 30 °C in the presence of 0.5 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c as the major fatty acids. The DNA G+C content was 65.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-16T joined the cluster comprising Stenotrophomonas species. The levels of 16S rRNA gene sequence similarity between strain DS-16T and the type strains of Stenotrophomonas species ranged from 95.5 to 97.5 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness of strain DS-16T, demonstrated that this novel strain differs from Stenotrophomonas species with validly published names. On the basis of phenotypic, phylogenetic and genetic data, strain DS-16T (=KCTC 12543T=CIP 108839T) should be classified in the genus Stenotrophomonas as a member of a novel species, for which the name Stenotrophomonas dokdonensis sp. nov. is proposed.

scholarly journals Agrococcus carbonis sp. nov., isolated from soil of a coal mine

2011 ◽  
Vol 61 (6) ◽  
pp. 1253-1258 ◽  
Author(s):  
Soniya Dhanjal ◽  
Ishwinder Kaur ◽  
Suresh Korpole ◽  
Peter Schumann ◽  
Swaranjit Singh Cameotra ◽  
...  
Keyword(s):  
Coal Mine ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Diamino Acid ◽  
Taxonomic Characterization ◽  
Type Strains

An actinobacterial strain, designated G4T, isolated from a coal mine was subjected to polyphasic taxonomic characterization. Cells were Gram-stain-positive, yellow-pigmented, non-motile and non-spore-forming cocci. This organism possessed a type B peptidoglycan with diaminobutyric acid as diagnostic diamino acid. The major respiratory quinones were MK-9, MK-10 and MK-11. The major fatty acids were anteiso-C15 : 0 (41.6  %) and anteiso-C17 : 0 (32.8 %). The predominant cellular polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Cell wall sugars comprised galactose, glucose, ribose and rhamnose. 16S rRNA gene sequence analysis of strain G4T showed high similarity with Agrococcus baldri (98.9 %), Agrococcus citreus (97.8 %), Agrococcus jenensis (97.3 %) and Agrococcus terreus (97.0 %). Sequence similarity with the type strains of the other species of the genus Agrococcus was less than 97.0 %. The DNA–DNA relatedness of strain G4T with the type strains of Agrococcus baldri, Agrococcus citreus, Agrococcus jenensis and Agrococcus terreus was less than 70 %. On the basis of the physiological, biochemical and chemotaxonomic characteristics, strain G4T should be classified as the type strain of a novel species of the genus Agrococcus, for which the name Agrococcus carbonis sp. nov. is proposed. The type strain is G4T ( = MTCC 10213T  = DSM 22965T).

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