scholarly journals Amycolatopsis samaneae sp. nov., isolated from roots of Samanea saman (Jacq.) Merr.

2011 ◽  
Vol 61 (4) ◽  
pp. 951-955 ◽  
Author(s):  
Kannika Duangmal ◽  
Ratchanee Mingma ◽  
Wasu Pathom-aree ◽  
Arinthip Thamchaipenet ◽  
Yuki Inahashi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Chemical Properties ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Samanea Saman

A novel actinomycete, designated strain RM287T, was isolated from surface-sterilized roots of Samanea saman (Jacq.) Merr., collected from Bangkok, Thailand. The status of the novel strain was determined using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism formed a distinct phyletic line within the radiation of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain RM287T was most closely related to Amycolatopsis mediterranei IMSNU 20056T (97.4 %), A. rifamycinica DSM 46095T (97.2 %), A. kentuckyensis NRRL B-24129T (97.2 %), A. pretoriensis DSM 44654T (97 %) and A. australiensis DSM 44671T (97 %). The novel organism was found to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the dignostic diamino acid in the cell-wall peptidoglycan and arabinose and galactose as the diagnostic sugars. The major menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 iso-C15 : 0, iso 2-OH-C16 : 0 and iso-C17 : 0. The DNA G+C content was 71.7 mol%. Phenotypic data clearly distinguished the novel isolate from its closest relatives. The combined genotypic and phenotypic data indicated that strain RM287T represented a novel species of the genus Amycolatopsis. The proposed name for this organism is Amycolatopsis samaneae sp. nov., with the type strain RM287T ( = TISTR 1919T = BCC 35842T = NBRC 106095T).

scholarly journals Aeromicrobium tamlense sp. nov., isolated from dried seaweed

2007 ◽  
Vol 57 (2) ◽  
pp. 337-341 ◽  
Author(s):  
Soon Dong Lee ◽  
Se Jae Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Octadecenoic Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hexadecanoic Acid ◽  
Phenotypic Data ◽  
Separate Branch

A Gram-positive, non-motile, rod-shaped actinomycete strain, designated SSW1-57T, was isolated from a dried seaweed sample from the coast of Jeju Island, Republic of Korea and subjected to a polyphasic taxonomic study. A neighbour-joining tree based on 16S rRNA gene sequences showed that the organism was related to members of the family Nocardioidaceae and formed a separate branch at the base of a taxon encompassing members of the genus Aeromicrobium, whereas it occupied an intermediate position between Aeromicrobium alkaliterrae–Aeromicrobium marinum and Aeromicrobium erythreum–Aeromicrobium fastidiosum clusters in maximum-parsimony and maximum-likelihood trees. The phylogenetic association of the isolate with the genus Aeromicrobium was supported by the following chemotaxonomic properties: ll-diaminopimelic acid in the peptidoglycan, MK-9(H4) as the major menaquinone and major fatty acids cis-9-octadecenoic acid, hexadecanoic acid, 10-methyl octadecanoic acid and 2-hydroxy hexadecanoic acid. The polar lipid profile contained phosphatidylinositol, diphosphatidylglycerol and phosphatidylglycerol. Levels of 16S rRNA gene sequence similarity between the novel organism and the type strains of the four recognized Aeromicrobium species were in the range 96.5–96.7 %. On the basis of phylogenetic analyses and phenotypic data, it is proposed that the organism should be classified as representing a novel species of the genus Aeromicrobium, with the name Aeromicrobium tamlense sp. nov. The type strain is SSW1-57T (=JCM 13811T=NRRL B-24466T).

scholarly journals Kineococcus gypseus sp. nov., isolated from saline sediment

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3703-3708 ◽  
Author(s):  
Qinyuan Li ◽  
Guiding Li ◽  
Xiu Chen ◽  
Fangji Xu ◽  
Yong Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

A novel Gram-stain-positive, aerobic, motile, non-spore-forming coccus-shaped actinomycete, designated strain YIM 121300T, was isolated from alkaline sediment in Yuanjiang, Yunnan province, south-west China. Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain YIM 121300T was affiliated to the genus Kineococcus, and was closely related to Kineococcus aurantiacus IFO 15268T (97.3 % similarity). 16S rRNA gene sequence similarity to other species of the genus Kineococcus was < 97 %. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugars contained arabinose, galactose, glucose, mannose and ribose. The predominant menaquinone was MK-9(H2). Mycolic acids were not detected. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unknown phospholipid. The predominant fatty acids were anteiso-C15 : 0 and anteiso-C15 : 1 A. The G+C content of the genomic DNA was 75.1 mol%. DNA–DNA relatedness (55 ± 4 % to K. aurantiacus IFO 15268T) and differential phenotypic data demonstrated that strain YIM 121300T was distinguished from all related species of the genus Kineococcus. On the basis of data from the present polyphasic study, the organism should be assigned to a novel species of the genus Kineococcus, for which the name Kineococcus gypseus sp. nov. is proposed. The type strain is YIM 121300T ( = CCTCC AA 2013232T = DSM 27627T).

scholarly journals Actinoallomurus oryzae sp. nov., an endophytic actinomycete isolated from roots of a Thai jasmine rice plant

2011 ◽  
Vol 61 (4) ◽  
pp. 737-741 ◽  
Author(s):  
Chantra Indananda ◽  
Arinthip Thamchaipenet ◽  
Atsuko Matsumoto ◽  
Yuki Inahashi ◽  
Kannika Duangmal ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rice Plant ◽  
Sequence Similarity ◽  
Chemical Properties ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Mycolic Acids ◽  
Jasmine Rice

The novel strain GMKU 370T was isolated from roots of a Thai jasmine rice plant (Oryza sativa L. ‘KDML 105’) collected from Pathum Thani Rice Research Center, Pathum Thani province, Thailand. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GMKU 370T formed a distinct clade within the genus Actinoallomurus. Strain GMKU 370T contained meso-diaminopimelic acid and lysine in the cell-wall peptidoglycan and galactose and madurose as whole-cell sugars. No mycolic acids were detected. The predominant menaquinones were MK-9(H6) and MK-9(H8). The polar phospholipids consisted of phosphatidylglycerol and phosphatidylinositol. These chemical properties reveal that strain GMKU 370T belongs to the genus Actinoallomurus. Strain GMKU 370T is distinct from the phylogenetically closely related type strains Actinoallomurus iriomotensis NBRC 103685T and Actinoallomurus coprocola NBRC 103688T (99.20 % 16S rRNA gene sequence similarity to both) in terms of differences in phenotypic characteristics and DNA–DNA relatedness (51 and 17 %, respectively). It is proposed that strain GMKU 370T represents a novel species of the genus Actinoallomurus, for which the name Actinoallomurus oryzae sp. nov. is proposed. The type strain is GMKU 370T ( = BCC 31373T  = NBRC 105246T).

Amycolatopsis magusensis sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1254-1260 ◽  
Author(s):  
Mustafa Camas ◽  
Nevzat Sahin ◽  
Anil Sazak ◽  
Cathrin Spröer ◽  
Hans-Peter Klenk
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

A novel actinomycete, designated strain KT2025T, was isolated from arid soil collected from Magusa, northern Cyprus. The taxonomic position of the novel strain was established by using a polyphasic approach. The organism had chemical and morphological features consistent with its classification in the genus Amycolatopsis . Phylogenetic analyses based on 16S rRNA gene sequences supported the classification of the isolate in the genus Amycolatopsis and showed that the organism formed a cluster with Amycolatopsis nigrescens CSC17-Ta-90T, Amycolatopsis minnesotensis 32U-2T, Amycolatopsis sacchari DSM 44468T and Amycolatopsis dongchuanensis YIM 75904T. 16S rRNA gene sequence similarity analysis indicated that strain KT2025T was most closely related to Amycolatopsis lurida DSM 43134T (97.5 %), Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409T (97.4 %), Amycolatopsis keratiniphila subsp. nogabecina DSM 44586T (97.1 %), Amycolatopsis nigrescens DSM 44992T (97.1 %), Amycolatopsis azurea DSM 43854T (97.1 %) and Amycolatopsis minnesotensis DSM 44988T (96.9 %). The organism was found to have chemical features typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and hydroxy-phosphatidylethanolamine. The major fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0. The G+C content of the genomic DNA was 70.8 mol%. Phenotypic data clearly distinguished the isolate from its closest relatives. The combined genotypic and phenotypic data and low levels of DNA–DNA relatedness with its closest relatives indicated that strain KT2025T represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis magusensis sp. nov. is proposed. The type strain is KT2025T ( = DSM 45510T = KCTC 29056T).

scholarly journals Brachybacterium phenoliresistens sp. nov., isolated from oil-contaminated coastal sand

2007 ◽  
Vol 57 (11) ◽  
pp. 2674-2679 ◽  
Author(s):  
Jui-Hsing Chou ◽  
Kuan-Yin Lin ◽  
Mei-Chun Lin ◽  
Shih-Yi Sheu ◽  
Yu-Hong Wei ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Sand Sample ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Coastal Sand

A coccoid- to ovoid-shaped, Gram-positive, non-motile bacterial strain, designated phenol-AT, was isolated from an oil-contaminated coastal sand sample collected from Pingtung County, southern Taiwan, and characterized by use of a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Brachybacterium in the family Dermabacteraceae, class Actinobacteria. The closest neighbours were Brachybacterium rhamnosum LMG 19848T (96.9 % 16S rRNA gene sequence similarity), Brachybacterium nesterenkovii DSM 9573T (97.0 %) and Brachybacterium muris C3H-21T (96.3 %). The peptidoglycan type of strain phenol-AT was variation A4γ with meso-diaminopimelic acid as the diagnostic cell-wall diamino acid. The isolate contained MK-7 as the major component of the quinone system. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, and unidentified phospholipids and glycolipids. The predominant fatty acid was anteiso-C15 : 0 (59.5 %); significant amounts of iso-C16 : 0 (9.4 %), iso-C14 : 0 (9.5 %) and anteiso-C17 : 0 (10.8 %) were also present. The isolate was also distinguished from recognized members of the genus Brachybacterium on the basis of several phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data that isolate phenol-AT represents a novel species of the genus Brachybacterium, for which the name Brachybacterium phenoliresistens sp. nov. is proposed. The type strain is phenol-AT (=LMG 23707T=BCRC 17589T).

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 Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1334-1338 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Keun Chul Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-positive, non-motile and rod- or coccoid-shaped bacterial strain, MDN22T, was isolated from a soil sample from Korea. Strain MDN22T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MDN22T was phylogenetically most closely related to the genera Nocardioides and Marmoricola. In the neighbour-joining phylogenetic tree, strain MDN22T was most closely related to Nocardioides jensenii KCTC 9134T, with which it exhibited 98.3 % 16S rRNA gene sequence similarity. The strain exhibited 93.1–96.9 % and 95.3–95.9 % 16S rRNA gene sequence similarities to the type strains of other species of the genera Nocardioides and Marmoricola, respectively. The chemotaxonomic properties of strain MDN22T were consistent with those of the genus Nocardioides; the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, the predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0 and C17 : 1. The DNA G+C content was 68.7 mol%. DNA–DNA relatedness data and differential phenotypic properties suggested that strain MDN22T could be differentiated from N. jensenii and Nocardioides dubius. On the basis of the data obtained, strain MDN22T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides daedukensis sp. nov., is proposed. The type strain is MDN22T (=KCTC 19601T=CCUG 57505T).

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.

Lacibacterium aquatile gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a freshwater lake

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4797-4804 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yi-Ling Chen ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Link Type ◽  
The Family

A bacterial strain designated LTC-2T was isolated from a freshwater lake in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain LTC-2T were Gram-reaction-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming, slightly curved rods surrounded by a thick capsule and formed creamy white colonies. Growth occurred at 10–37 °C (optimum, 20–30 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-10 and the DNA G+C content was 58.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, two uncharacterized phospholipids and two uncharacterized aminophospholipids. The major polyamines were putrescine, homospermidine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LTC-2T forms a distinct lineage with respect to closely related genera in the family Rhodospirillaceae , most closely related to the genera Elstera and Dongia , and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 94 %. On the basis of the genotypic and phenotypic data, strain LTC-2T represents a novel genus and species of the family Rhodospirillaceae , for which the name Lacibacterium aquatile gen. nov., sp. nov. is proposed. The type strain is LTC-2T ( = BCRC 80445T = LMG 26999T = KCTC 32017T).

scholarly journals Nocardioides iriomotensis sp. nov., an actinobacterium isolated from forest soil

2011 ◽  
Vol 61 (9) ◽  
pp. 2205-2209 ◽  
Author(s):  
Hideki Yamamura ◽  
Shin-ya Ohkubo ◽  
Youji Nakagawa ◽  
Yuumi Ishida ◽  
Moriyuki Hamada ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soil ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data

An actinomycete strain, designated IR27-S3T, was isolated from a forest soil sample collected from Iriomote Island, Okinawa, Japan. Cells of the isolate were Gram-stain-positive, aerobic, non-sporulating, non-motile coccoids or short rods. The strain grew in the presence of 0–7 % (w/v) NaCl, at pH 6–8 and at 12–37 °C, with optimum growth at 30 °C. Chemotaxonomically, the strain contained ll-diaminopimelic acid as the diagnostic diamino acid and MK-8(H4) as the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. The major cellular fatty acids were iso-C16 : 0, C17 : 1 cis-9, C15 : 0 and iso-C15 : 0. The DNA G+C content was 73.7 mol%. On the basis of 16S rRNA gene sequence analysis, strain IR27-S3T was closely related to Nocardioides mesophilus MSL-22T (98.1 % 16S rRNA gene sequence similarity), Marmoricola bigeumensis MSL-05T (97.2 %) and Nocardioides jensenii DSM 20641T (96.5 %). On the basis of fatty acid analysis, phylogenetic analysis and phenotypic data, the isolate should be classified in a novel species of the genus Nocardioides, for which the name Nocardioides iriomotensis sp. nov. is proposed. The type strain is IR27-S3T ( = NBRC 105384T  = KACC 14926T).

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