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).

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 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 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).

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).

scholarly journals Amycolatopsis salitolerans sp. nov., a filamentous actinomycete isolated from a hypersaline habitat

2012 ◽  
Vol 62 (1) ◽  
pp. 23-27 ◽  
Author(s):  
Tong-Wei Guan ◽  
Zhan-Feng Xia ◽  
Shu-Kun Tang ◽  
Nan Wu ◽  
Zheng-Jun Chen ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
West China ◽  
North West ◽  
Actinomycete Strain

A novel actinomycete strain, designated TRM F103T, was isolated from a hypersaline habitat of the Tarim basin in Xinjiang province, north-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Amycolatopsis and was most closely related to Amycolatopsis halophila YIM 93223T (99.3 % 16S rRNA gene sequence similarity). However, DNA–DNA relatedness between these two strains, based on triplicate experiments, was only 31.6 %. The isolate contained meso-diaminopimelic acid and ribose, glucose and galactose as the major whole-cell sugars. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C16 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and glucosamine-containing phospholipids. The G+C content of the genomic DNA was 66.4 mol%. The phenotypic data clearly distinguished the isolate from its closest relatives. The combined phylogenetic, chemotaxonomic and phenotypic data indicate that the isolate represents a novel species of the genus Amycolatopsis. The proposed name is Amycolatopsis salitolerans sp. nov., with TRM F103T ( = JCM 15899T = CCTCC AB 208326T) as the type strain.

Devosia subaequoris sp. nov., isolated from beach sediment

2007 ◽  
Vol 57 (10) ◽  
pp. 2212-2215 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Bacterium ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Natural Seawater ◽  
Phenotypic Data ◽  
Beach Sediment ◽  
Type Strains

A novel marine bacterium was isolated from a sediment sample from Hwasun Beach in Jeju, Republic of Korea. The cells were found to be Gram-negative, aerobic, oxidase-positive, catalase-positive, motile rods. The organism required natural seawater or artificial sea salts for growth. The temperature and pH ranges for growth were 20–42 °C and pH 5.1–12.1, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the order Rhizobiales and formed a robust cluster with members of the genus Devosia. Its phylogenetic neighbours were the type strains of Devosia riboflavina (96.8 % 16S rRNA gene sequence similarity), Devosia neptuniae (96.7 %), Devosia soli (96.5 %) and Devosia limi (96.2 %), ‘Devosia terrae’ DCY11 (96.2 %) and ‘Candidatus Devosia euplotis’ (96.2 %). The predominant ubiquinone was Q-10, the major fatty acids were C18 : 1, C18 : 0 and C16 : 0 and the G+C content of the DNA was 59.1 mol%. On the basis of phenotypic data and the results of phylogenetic analyses, strain HST3-14T represents a novel species of the genus Devosia, for which the name Devosia subaequoris sp. nov. is proposed. The type strain is strain HST3-14T (=KCTC 12772T =JCM 14206T).

Reclassification of Marinococcus albus Hao et al. 1985 as Salimicrobium album gen. nov., comb. nov. and Bacillus halophilus Ventosa et al. 1990 as Salimicrobium halophilum comb. nov., and description of Salimicrobium luteum sp. nov.

2007 ◽  
Vol 57 (10) ◽  
pp. 2406-2411 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New Genus ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Separate Species ◽  
Diamino Acid

A Gram-positive, non-motile, coccoid-shaped, non-spore-forming halophilic bacterial strain, BY-5T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated by using a polyphasic approach. The novel strain grew optimally at 37 °C and in the presence of 10 % (w/v) NaCl. Strain BY-5T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone and anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C content was 47.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BY-5T formed a coherent cluster with Bacillus halophilus and Marinococcus albus. Strain BY-5T exhibited 16S rRNA gene sequence similarity values of 98.7 and 97.4 % to the type strains of B. halophilus and M. albus, respectively. Strain BY-5T was distinguished from B. halophilus and M. albus by several phenotypic properties and DNA–DNA relatedness data. On the basis of the combined chemotaxonomic and phylogenetic data, it is proposed that M. albus, B. halophilus and strain BY-5T should be placed in a new genus as three separate species. Marinococcus albus and Bacillus halophilus are reclassified in a new genus, Salimicrobium gen. nov., as Salimicrobium album comb. nov. and Salimicrobium halophilum comb. nov., respectively. The type species of the new genus is Salimicrobium album. Strain BY-5T (=KCTC 3989T=CIP 108918T) is placed in the genus Salimicrobium as a novel species Salimicrobium luteum sp. nov.

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