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 Actinomadura rupiterrae sp. nov., isolated from cliff soil

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 990-995 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Mycolic Acids ◽  
Hybridization Data ◽  
Actinomycete Strain ◽  
Diamino Acid

A novel actinomycete strain, designated CS5-AC15T, was isolated from a soil sample collected from a cliff on Mara Island, Jeju, Republic of Korea, and subjected to a polyphasic taxonomic analysis. The isolate produced well-developed, yellow substrate mycelium and white aerial mycelium that differentiated into straight or flexuous chains of smooth-surfaced spores. 16S rRNA gene sequence analyses showed that the organism belonged to the family Thermomonosporaceae and formed a tight cluster with the type strain of Actinomadura oligospora (97.4 % sequence similarity). Chemotaxonomic characteristics were consistent with its assignment to the genus Actinomadura in that the isolate had meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall, madurose as the characteristic sugar, N-acetyl type of murein in the peptidoglycan, MK-9(H6) and MK-9(H8) as major menaquinones and a polar lipid profile containing diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown phospholipids. Mycolic acids were not detected. The predominant fatty acids were C16 : 0, C18 : 1ω9c and iso-C16 : 0. The DNA G+C content was 70.9 mol%. DNA relatedness of strain CS5-AC15T and A. oligospora JCM 10648T was 37.9±0.7 %. On the basis of the phenotypic, phylogenetic and DNA–DNA hybridization data, strain CS5-AC15T is assigned to a novel species of the genus Actinomadura, for which the name Actinomadura rupiterrae sp. nov. is proposed (type strain CS5-AC15T  = KCTC 19559T  = DSM 45251T).

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 Rubritalea halochordaticola sp. nov., a carotenoid-producing verrucomicrobial species isolated from a marine chordate

2011 ◽  
Vol 61 (7) ◽  
pp. 1515-1520 ◽  
Author(s):  
Jaewoo Yoon ◽  
Satoru Matsuda ◽  
Kyoko Adachi ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Sea Squirt ◽  
Cell Biomass ◽  
Taxonomic Approach

A Gram-negative-staining, obligately aerobic, non-motile, rod-shaped and chemoheterotrophic bacterium, designated strain MN1-1006T, was isolated from an ascidian (sea squirt) sample, and was studied using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the new isolate shared approximately 93–99% sequence similarity with recognized species of the genus Rubritalea within the phylum ‘Verrucomicrobia’. DNA–DNA hybridization values between strain MN1-1006T and Rubritalea squalenifaciens HOact23T and Rubritalea sabuli YM29-052T were 57% and 14.5%, respectively. Strain MN1-1006T produced carotenoid compounds that rendered the cell biomass a reddish pink colour. The strain also contained squalene. The cell-wall peptidoglycan of the novel strain contained muramic acid and meso-diaminopimelic acid. The DNA G+C content of strain MN1-1006T was 51.4 mol%. The major cellular fatty acids were iso-C14:0, iso-C16:0 and anteiso-C15:0. The major isoprenoid quinone was MK-9. On the basis of these data, it was concluded that strain MN1-1006T represents a novel species of the genus Rubritalea, for which the name Rubritalea halochordaticola sp. nov. is proposed. The type strain is MN1-1006T ( = KCTC 23186T = NBRC 107102T).

scholarly journals Haloactinopolyspora alkaliphila sp. nov., and emended description of the genus Haloactinopolyspora

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1945-1951 ◽  
Author(s):  
Yong-Guang Zhang ◽  
Qing Liu ◽  
Hong-Fei Wang ◽  
Dao-Feng Zhang ◽  
Yuan-Ming Zhang ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
North West ◽  
Link Type ◽  
Hybridization Data ◽  
Actinomycete Strain ◽  
Diamino Acid

A facultatively alkaliphilic actinomycete strain, designated EGI 80088T, was isolated from a saline-alkali soil sample from Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80088T formed fragmented aerial hyphae and short spore chains, and rod-like spores aggregated at maturity. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid as the diagnostic diamino acid, and glucosamine, mannose, galactose, glucose and rhamnose as the marker sugars. The major fatty acids identified (>5 %) were anteiso-C15 : 0, iso-C15 : 0, summed feature 4 (iso-C17 : 1I/anteiso-C17 : 1B), iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA of strain EGI 80088T was 70.6 mol%. EGI 80088T showed the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Haloactinopolyspora alba YIM 93246T (98.5 %). The DNA–DNA relatedness value of the strain EGI 80088T and H. alba YIM 93246T was 59.3±5.2 %. On the basis of morphological, chemotaxonomic and phylogenetic characteristics and DNA–DNA hybridization data, strain EGI 80088T represents a novel species of the genus Haloactinopolyspora , for which the name Haloactinopolyspora alkaliphila sp. nov. (type strain EGI 80088T = BCRC 16946T = JCM 19128T) is proposed. The description of the genus Haloactinopolyspora has also been emended.

Actinoallomurus acaciae sp. nov., an endophytic actinomycete isolated from Acacia auriculiformis A. Cunn. ex Benth.

2010 ◽  
Vol 60 (3) ◽  
pp. 554-559 ◽  
Author(s):  
Arinthip Thamchaipenet ◽  
Chantra Indananda ◽  
Chakrit Bunyoo ◽  
Kannika Duangmal ◽  
Atsuko Matsumoto ◽  
...  
Keyword(s):  
Novel Species ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Acacia Auriculiformis ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Endophytic Actinomycete ◽  
Phyletic Line ◽  
Actinomycete Strain ◽  
Short Spiral

A novel endophytic actinomycete, strain GMKU 931T, was isolated from the root of a wattle tree, Acacia auriculiformis A. Cunn. ex Benth., collected at Kasetsart University, Bangkok, Thailand. Strain GMKU 931T produced short spiral chains of smooth-surfaced spores on the aerial mycelium. Lysine and meso-diaminopimelic acid were present in the cell-wall peptidoglycan. Whole-cell hydrolysates contained galactose, madurose and mannose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major fatty acids were iso-C16 : 0 and iso-C16 : 1. The major phospholipids were phosphatidylinositol and phosphatidylglycerol. A phylogenetic analysis based on 16S rRNA gene sequences suggested that strain GMKU 931T forms a distinct phyletic line within the recently proposed genus Actinoallomurus. The significant differences in phenotypic and genotypic data indicate that strain GMKU 931T represents a novel species of the genus Actinoallomurus, for which the name Actinoallomurus acaciae sp. nov. is proposed. The type strain is GMKU 931T (=BCC 28622T =NBRC 104354T =NRRL B-24610T).

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 Pelagicoccus croceus sp. nov., a novel marine member of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’ isolated from seagrass

2007 ◽  
Vol 57 (12) ◽  
pp. 2874-2880 ◽  
Author(s):  
Jaewoo Yoon ◽  
Naoya Oku ◽  
Satoru Matsuda ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
Cell Wall ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Antibiotic Susceptibility Test ◽  
The Family ◽  
Lactam Antibiotic

An obligately aerobic, spherical, non-motile, pale-yellow pigmented bacterium was isolated from a piece of leaf of seagrass, Enhalus acoroides (L.f.) Royle, grown in Okinawa, Japan and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolate N5FB36-5T shared approximately 96–98 % sequence similarity with the species of the genus Pelagicoccus of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’. The DNA–DNA relatedness values of strain N5FB36-5T with Pelagicoccus mobilis 02PA-Ca-133T and Pelagicoccus albus YM14-201T were below 70 %, which is accepted as the phylogenetic definition of a novel species. β-Lactam antibiotic susceptibility test and amino acid analysis of the cell wall hydrolysates indicated the absence of muramic acid and diaminopimelic acid in the cell walls, which suggested that this strain lacks an ordinary Gram-negative type of peptidoglycan in the cell wall. The DNA G+C content of strain N5FB36-5T was 51.6 mol%; MK-7 was the major menaquinone; and the presence of C16 : 0, C16 : 1 ω7c and anteiso-C15 : 0 as the major cellular fatty acids supported the identification of the novel isolate as a member of the genus Pelagicoccus. On the basis of polyphasic taxonomic data, it was concluded that this strain should be classified as a novel species of the genus Pelagicoccus, for which the name Pelagicoccus croceus sp. nov. is proposed. The type strain is N5FB36-5T (=MBIC08282T=KCTC 12903T).

scholarly journals Nocardiopsis nikkonensis sp. nov., isolated from a compost sample

2010 ◽  
Vol 60 (12) ◽  
pp. 2967-2971 ◽  
Author(s):  
Hideki Yamamura ◽  
Shin-ya Ohkubo ◽  
Yuumi Ishida ◽  
Misa Otoguro ◽  
Tomohiko Tamura ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Morphological Characterization ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Compost Sample ◽  
Actinomycete Strain ◽  
Biochemical Analyses

An actinomycete strain, designated YU1183-22T, was isolated from a compost sample collected in Nikko, Japan. The isolate formed white aerial mycelium with relatively long aerial hyphae showing chains of arthrospores. Strain YU1183-22T grew with 0–10 % (w/v) NaCl, at pH 6–11 and at 10–37 °C (optimum 30 °C). Strain YU1183-22T contained meso-diaminopimelic acid and no diagnostic sugars. The predominant menaquinones were MK-10(H10) and MK-10(H8). The polar lipids were phosphatidylcholine and phosphatidylglycerol. The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0 and tuberculostearic acid. The G+C content of the DNA was 72.3 mol%. Chemotaxonomic and morphological characterization clearly demonstrated that strain YU1183-22T belonged to the genus Nocardiopsis. Phylogenetic analysis using 16S rRNA gene sequences showed that the isolate was closely related to Nocardiopsis salina YIM 90010T (98.0 % 16S rRNA gene sequence similarity), Nocardiopsis xinjiangensis YIM 90004T (97.9 %) and Nocardiopsis kunsanensis HA-9T (97.3 %). However, DNA–DNA relatedness as well as physiological and biochemical analyses showed that strain YU1183-22T could be differentiated from its closest phylogenetic relatives. It is proposed that this strain be classified as a representative of a novel species of the genus Nocardiopsis, with the name Nocardiopsis nikkonensis sp. nov. The type strain is YU1183-22T (=NBRC 102170T =KCTC 19666T).

scholarly journals Micromonospora fluminis sp. nov., isolated from mountain river sediment

2020 ◽  
Vol 70 (12) ◽  
pp. 6428-6436 ◽  
Author(s):  
Miladis Isabel Camacho Pozo ◽  
Anneleen D. Wieme ◽  
Suyén Rodríguez Pérez ◽  
Gabriel Llauradó Maury ◽  
Charlotte Peeters ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Novel Species ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Santiago De Cuba ◽  
Actinomycete Strain

During a bioprospection of bacteria with antimicrobial activity, the actinomycete strain A38T was isolated from a sediment sample of the Carpintero river located in the Gran Piedra Mountains, Santiago de Cuba province (Cuba). This strain was identified as a member of the genus Micromonospora by means of a polyphasic taxonomy study. Strain A38T was an aerobic Gram-positive filamentous bacterium that produced single spores in a well-developed vegetative mycelium. An aerial mycelium was absent. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were glucose, mannose, ribose and xylose. The major cellular fatty acids were isoC15:0, 10 methyl C17:0, anteiso-C17:0 and iso-C17:0. The predominant menaquinones were MK-10(H4) and MK-10(H6). Phylogenetic analysis of 16S rRNA gene sequences revealed that this strain was closely related to Micromonospora tulbaghiae DSM 45142T (99.5 %), Micromonospora citrea DSM 43903T (99.4 %), Micromonospora marina DSM 45555T (99.4 %), Micromonospora maritima DSM 45782T (99.3 %), Micromonospora sediminicola DSM 45794T (99.3 %), Micromonospora aurantiaca DSM 43813T (99.2 %) and Micromonospora chaiyaphumensis DSM 45246T (99.2 %). The results of OrthoANIu analysis showed the highest similarity to Micromonospora chalcea DSM 43026T (96.4 %). However, the 16S rRNA and gyrB gene sequence-based phylogeny and phenotypic characteristics provided support to distinguish strain A38T as a novel species. On the basis of the results presented here, we propose to classify strain A38T (=LMG 30467T=CECT 30034T) as the type strain of the novel species Micromonospora fluminis sp. nov.

Planobispora siamensis sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2649-2654 ◽  
Author(s):  
Wipaporn Ngaemthao ◽  
Chanwit Suriyachadkun ◽  
Suwanee Chunhametha ◽  
Tomohiko Tamura ◽  
Jean-Jacques Sanglier
Keyword(s):  
Novel Species ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Evergreen Forest ◽  
Rrna Gene ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Actinomycete Strain

A novel actinomycete strain, A-T 4600T, which developed cylindrical sporangia containing a longitudinal pair of motile spores forming singly or in bundles on short ramifications of the aerial mycelium, was isolated from soil collected from an evergreen forest in Thailand. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained ribose, madurose, mannose and glucose. The predominant menaquinones were MK-9(H2). Mycolic acids were not detected. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylglycerol, phosphatidylinositol mannoside, diphosphatidylglycerol and aminophosphoglycolipid. The predominant cellular fatty acids were unsaturated C17 : 1, C18 : 1, saturated C16 : 0, and C17 : 0. The G+C content of the DNA was 70.8 mol%. Phenotypic and chemotaxonomic analyses showed that the isolate had the typical characteristics of members of the genus Planobispora . Furthermore, 16S rRNA gene sequence analysis also indicated that this strain belonged to the genus Planobispora but as a putative novel species. DNA–DNA relatedness values that differentiate the isolate from previously described members of the genus Planobispora were significantly below 70 %. Following an evaluation of phenotypic, chemotaxonomic and genotypic studies, it is proposed that the isolate represents a novel species, Planobispora siamensis sp. nov.; the type strain is A-T 4600T ( = BCC 39469T = NBRC 107568T).

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