scholarly journals Kibdelosporangium lantanae sp. nov., isolated from the rhizosphere soil of an ornamental plant, Lantana camara L.

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2581-2585 ◽  
Author(s):  
Dan Li ◽  
Yaojian Huang ◽  
Siyang Song ◽  
Ci Xue ◽  
Yingying Wu ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Ornamental Plant ◽  
Lantana Camara ◽  
Diaminopimelic Acid ◽  
Rrna Gene

Strain XMU 506T, isolated from the rhizosphere soil of an ornamental plant, Lantana camara L., collected from Xiamen City, China, was identified using a polyphasic approach to clarify its taxonomic position. The aerial mycelium of this organism formed long straight or curved chains of spores and sporangium-like structures. The optimum growth occurred at 28–30 °C, pH 7.0 with 0–1 % NaCl. Strain XMU 506T showed the highest 16S rRNA gene sequence similarity (96.5  %) to Kibdelosporangium philippinense DSM 44226T, and formed a monophyletic clade in the 16S rRNA gene phylogenetic tree together with the type strains of the genus Kibdelosporangium. The chemotaxonomic properties further supported the assignment of strain XMU 506T to the genus Kibdelosporangium: meso-diaminopimelic acid was the diagnostic amino acid in the cell wall peptidoglycan; mycolic acids were not present in the cell wall; the whole-cell hydrolysates contained arabinose, galactose, glucose and ribose. The major menaquinone was MK-9(H4); the phospholipids of the isolate comprised phosphatidylethanolamine, OH-phosphatidylethanolamine, diphosphatidylglycerol and unidentified amino-, glyco- and phospholipids; the major fatty acids of the strain were iso-C16 : 0, C17 : 1 ω6c and iso-C16 : 1 H. The G+C content of genomic DNA was 67.3 mol%. Based on the results of phylogenetic analysis, phenotypic and genotypic characterization, strain XMU 506T represents a novel species in the genus Kibdelosporangium, for which the name Kibdelosporangium lantanae sp. nov. is proposed. The type strain is XMU 506T ( = KCTC 29675T = MCCC 1K00430T).

scholarly journals Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant

2011 ◽  
Vol 61 (1) ◽  
pp. 190-193 ◽  
Author(s):  
Yu-Qin Zhang ◽  
Jie Chen ◽  
Hong-Yu Liu ◽  
Yue-Qin Zhang ◽  
Wen-Jun Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
Medicinal Plant ◽  
16S Rrna Gene ◽  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Good Growth

A novel actinobacterial strain, designated CPCC 201356T, was isolated from a rhizosphere soil sample of the medicinal plant Astragalus membranaceus and subjected to a polyphasic taxonomic analysis. Good growth occurred at 20–32 °C, at pH 7.0–7.5 and with 0–1 % (w/v) NaCl. Colonies on R2A and ISP 2 agar were light red to red, round and lacked aerial mycelium; cells adhered to the agar. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H4) and MK-9. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and C17 : 1 ω8c. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CPCC 201356T belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch with Geodermatophilus obscurus DSM 43160T. The organism showed 16S rRNA gene sequence similarity of 97.7 % with G. obscurus DSM 43160T. DNA–DNA hybridization between strain CPCC 201356T and G. obscurus DSM 43160T was 17.4 %. On the basis of evidence from this polyphasic taxonomic study, a novel species, Geodermatophilus ruber sp. nov., is proposed; the type strain is CPCC 201356T (=DSM 45317T =CCM 7619T).

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 Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis

2010 ◽  
Vol 60 (8) ◽  
pp. 1904-1908 ◽  
Author(s):  
Kannika Duangmal ◽  
Ratchanee Mingma ◽  
Arinthip Thamchaipenet ◽  
Atsuko Matsumoto ◽  
Yoko Takahashi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

The taxonomic position of a rhizosphere soil isolate, designated strain SR8.15T, was determined by using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence of the strain showed that it formed a well-separated sub-branch within the radiation encompassing the genus Saccharopolyspora. Highest levels of 16S rRNA gene sequence similarity were found between strain SR8.15T and Saccharopolyspora shandongensis CGMCC 4.3530T (98.9 %) and Saccharopolyspora spinosa DSM 44228T (98.5 %). However, these strains shared low levels of DNA–DNA relatedness (<26 %). Strain SR8.15T had chemical characteristics consistent with its classification in the genus Saccharopolyspora. It contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The diagnostic phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The main menaquinone was MK-9(H4). No mycolic acid was detected. The predominant cellular fatty acid was iso-C16 : 0. The G+C content of the genomic DNA of strain SR8.15T was 70.3 mol%. Strain SR8.15T had a phenotypic profile that readily distinguished it from recognized representatives of the genus Saccharopolyspora. It is evident from its combined genotypic and phenotypic properties that strain SR8.15T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora phatthalungensis sp. nov. is proposed. The type strain is SR8.15T (=TISTR 1921T=BCC 35844T=NRRL B-24798T).

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 Humicoccus flavidus gen. nov., sp. nov., isolated from soil

2007 ◽  
Vol 57 (1) ◽  
pp. 56-59 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Seo-Youn Jung ◽  
Tae-Kwang Oh
Keyword(s):  
Fatty Acids ◽  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Diamino Acid

A Gram-positive, non-motile, spherical, non-spore-forming bacterial strain, DS-52T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 °C and pH 6.0–7.0. Strain DS-52T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and galactose, mannose, xylose and rhamnose as whole-cell sugars. It contained MK-8(H4) and MK-9(H4) as the predominant menaquinones and anteiso-C15 : 0, iso-C15 : 0 and C17 : 0 as major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyldimethylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-52T is most closely related to the genus Nakamurella of the suborder Frankineae. Strain DS-52T exhibited 16S rRNA gene sequence similarity values of 96.5 % to Nakamurella multipartita JCM 9543T and 92.0–93.9 % to other members of the suborder Frankineae. The diagnostic diamino acid type and polar lipid profile of strain DS-52T were the same as those of the genus Nakamurella. However, strain DS-52T could be clearly distinguished from the genus Nakamurella by differences in predominant menaquinones, major fatty acids and cell-wall sugars. Accordingly, based on combined phenotypic, chemotaxonomic and phylogenetic data, strain DS-52T (=KCTC 19127T=CIP 108919T) is proposed as the type strain of a novel species in a new genus, Humicoccus flavidus gen. nov., sp. nov.

scholarly journals Kribbella mirabilis sp. nov., isolated from rhizosphere soil of a herbaceous plant, Mirabilis jalapa L.

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3143-3147 ◽  
Author(s):  
Dan Li ◽  
Jiaojiao Song ◽  
Yaojian Huang ◽  
Siyang Song ◽  
Yingying Wu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Threshold Value ◽  
Genetic Distances ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Herbaceous Plant ◽  
Mirabilis Jalapa

Strain XMU 706T, isolated from the rhizosphere soil of a herbaceous plant, Mirabilis jalapa L., collected from Xiamen City, China, was characterized using a polyphasic approach to clarify its taxonomic position. Strain XMU 706T shared the highest 16S rRNA gene sequence similarity with Kribbella antibiotica YIM 31530T (97.2 %), and formed a distinct branch in the subclade of the genus Kribbella in the 16S rRNA gene phylogenetic tree. The genetic distances of gyrase subunit B gene (gyrB) sequence between strain XMU 706T and other species of the genus Kribbella ranged from 0.045 to 0.116, greater than the threshold value of 0.014 for species delineation of this genus. DNA–DNA hybridization experiments gave a DNA–DNA relatedness value of 34.82 ± 6.31 % between strain XMU 706T and K. antibiotica YIM 31530T. The chemotaxonomic properties further supported the assignment of strain XMU 706T to the genus Kribbella. ll-Diaminopimelic acid was the diagnostic amino acid in the cell-wall peptidoglycan and cell hydrolysates contained ribose and glucose. The major menaquinone was MK-9(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and other unidentified phospholipids and lipids. The major fatty acids of the strain were anteiso-C15 : 0 and iso-C15 : 0, and the G+C content of the genomic DNA was 67.3 mol%. Based on the results of phylogenetic analysis, phenotypic and genotypic characterization, strain XMU 706T represents a novel species of the genus Kribbella, for which the name Kribbella mirabilis sp. nov. is proposed. The type strain is XMU 706T ( = KCTC 29676T = MCCC 1K00429T).

scholarly journals Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake

2010 ◽  
Vol 60 (5) ◽  
pp. 1073-1078 ◽  
Author(s):  
Shu-Kun Tang ◽  
Yun Wang ◽  
Tong-Wei Guan ◽  
Jae-Chan Lee ◽  
Chang-Jin Kim ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Salt Lake ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
North West ◽  
Halophilic Actinomycete ◽  
Type Strains

A novel halophilic actinomycete, designated strain YIM 93223T, was isolated from a salt lake in Xinjiang Province, north-west China, and was subjected to a polyphasic taxonomic study. The isolate grew at 25–45 °C, at pH 6–8 and in the presence of 1–15 % (w/v) NaCl; no growth was observed in the absence of NaCl. Strain YIM 93223T contained meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids, and glucose and galactose as major whole-cell-wall sugars. Major fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1 ω7c/iso-C15 : 0 2-OH. MK-8(H4) was the predominant menaquinone. The genomic DNA G+C content was 66.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 93223T belongs to the genus Amycolatopsis. It shared highest 16S rRNA gene sequence similarity with Amycolatopsis palatopharyngis 1BDZT (96.6 %) and Amycolatopsis marina Ms392AT (96.4 %), but lower values (94.5–96.2 %) with the type strains of other recognized species of the genus Amycolatopsis. On the basis of the data from this polyphasic study, strain YIM 93223T is considered to represent a novel species of the genus Amycolatopsis, for which the name Amycolatopsis halophila sp. nov. is proposed. The type strain is YIM 93223T (=DSM 45216T =KCTC 19403T).

scholarly journals Haloechinothrix alba gen. nov., sp. nov., a halophilic, filamentous actinomycete of the suborder Pseudonocardineae

2010 ◽  
Vol 60 (9) ◽  
pp. 2154-2158 ◽  
Author(s):  
Shu-Kun Tang ◽  
Yun Wang ◽  
Hua Zhang ◽  
Jae-Chan Lee ◽  
Kai Lou ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Salt Lake ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
North West ◽  
Novel Genus And Species

A novel halophilic, filamentous actinomycete strain, designated YIM 93221T, was isolated from a salt lake in Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. The isolate grew with 9–23 % (w/v) NaCl and did not grow without NaCl. The isolate formed spiny aerial mycelium and did not form spores at maturity. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and glucose, glucosamine, mannose and an unknown sugar as the major whole-cell sugars. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unknown phospholipid. MK-8(H4) was the predominant menaquinone. The major fatty acid was iso-C16 : 0. The DNA G+C content was 68.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 93221T formed a distinct lineage within the suborder Pseudonocardineae and showed 91.9–94.8 % 16S rRNA gene sequence similarity with members of the suborder Pseudonocardineae. On the basis of the evidence from this polyphasic study, a novel genus and species, Haloechinothrix alba gen. nov., sp. nov., are proposed. The type strain of Haloechinothrix alba is YIM 93221T (=DSM 45207T =CCTCC AB 208140T).

scholarly journals Halobacillus campisalis sp. nov., containing meso-diaminopimelic acid in the cell-wall peptidoglycan, and emended description of the genus Halobacillus

2007 ◽  
Vol 57 (9) ◽  
pp. 2021-2025 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Tae-Kwang Oh
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Cell Wall Peptidoglycan ◽  
Type Strains

A Gram-positive or variable, motile and coccoid or oval-shaped bacterial strain, ASL-17T, was isolated from a marine solar saltern of the Yellow Sea in Korea and its exact taxonomic position was investigated by a polyphasic approach. Strain ASL-17T grew optimally at pH 7.0–8.0 and 37 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ASL-17T is most closely affiliated phylogenetically to the genus Halobacillus. Strain ASL-17T exhibited 16S rRNA gene sequence similarity values of 97.7–98.6 % to the type strains of recognized Halobacillus species. Interestingly, strain ASL-17T had cell-wall peptidoglycan based on meso-diaminopimelic acid, unlike other Halobacillus species. It contained MK-7 as the predominant menaquinone. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 42.1 mol%. DNA–DNA relatedness data and differential phenotypic properties demonstrated that strain ASL-17T can be differentiated from recognized Halobacillus species. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain ASL-17T represents a novel species of the genus Halobacillus, for which the name Halobacillus campisalis sp. nov. is proposed. The type strain is ASL-17T (=KCTC 13144T =CCUG 54360T).

scholarly journals Actinomadura scrupuli sp. nov., isolated from rock

2010 ◽  
Vol 60 (11) ◽  
pp. 2647-2651 ◽  
Author(s):  
Dong Wan Lee ◽  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Agricultural Field ◽  
The Family ◽  
Small Stone

A novel actinomycete, designated strain R-Ac121T, was isolated from a small stone collected from an agricultural field in Jeju, Republic of Korea. The organism formed abundant vegetative mycelium that was branched and twisted. The reverse colour of colonies was brownish-yellow. Non-motile, wrinkled arthrospores were produced directly on the substrate mycelium. Aerial mycelium and sporangia were not observed. A neighbour-joining tree based on 16S rRNA gene sequences indicated that the isolate formed a distinct clade within the radiation of the family Thermomonosporaceae. The highest 16S rRNA gene sequence identity was found with the type strain of Spirillospora rubra (97.3 % sequence similarity) followed by those of Actinoallomurus purpureus (97.0 %), Actinomadura alba (96.5 %), Actinomadura fibrosa (96.5 %) and Actinomadura echinospora (96.4 %). The cell wall contained meso-diaminopimelic acid. The whole-cell sugars were rhamnose, glucose, ribose, xylose and arabinose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The major menaquinone was MK-9(H6) and the predominant fatty acids were iso-C16 : 0, C16 : 0, C17 : 1 ω8c and 10-methyl C17 : 0. The DNA G+C content was 71.8 mol%. The combination of morphological, chemotaxonomic and phylogenetic data clearly supports the separation of the organism from recognized species of the genus Actinomadura and related genera. On the basis of the data presented here, strain R-Ac121T represents a novel species of the genus Actinomadura, for which the name Actinomadura scrupuli sp. nov. is proposed. The type strain is strain R-Ac121T (=KCTC 19488T =DSM 45225T).

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