scholarly journals Alkalibacterium psychrotolerans sp. nov., a psychrotolerant obligate alkaliphile that reduces an indigo dye

2004 ◽  
Vol 54 (6) ◽  
pp. 2379-2383 ◽  
Author(s):  
Isao Yumoto ◽  
Kikue Hirota ◽  
Yoshinobu Nodasaka ◽  
Yuji Yokota ◽  
Tamotsu Hoshino ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Data ◽  
Novel Species ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Polygonum Tinctorium ◽  
Indigo Dye ◽  
Alkaliphilic Bacterium ◽  
Straight Rod

A psychrotolerant, obligately alkaliphilic bacterium, IDR2-2T, which is able to reduce indigo dye was isolated from a fermented polygonum indigo (Polygonum tinctorium Lour.) produced in Date, Hokkaido, using a traditional Japanese method. The isolate grew at pH 9–12 but not at pH 7–8. It was a Gram-positive, facultatively anaerobic, straight rod-shaped bacterium with peritrichous flagella. The isolate grew in 0–17 % (w/v) NaCl but not at NaCl concentrations higher than 18 % (w/v). Its major cellular fatty acids were C14 : 0, C16 : 0, C16 : 19c and C18 : 19c, and its DNA G+C content was 40·6 mol%. dl-lactic acid was the major end-product from d-glucose. No quinones could be detected. The peptidoglycan type was A4β, Orn–d-Glu. A phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain IDR2-2T is a member of the genus Alkalibacterium. DNA–DNA hybridization revealed low relatedness (less than 25 %) between the isolate and two phylogenetically related strains, Alkalibacterium olivapovliticus and Marinilactibacillus psychrotolerans. On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, the isolate merits classification as a novel species, for which the name Alkalibacterium psychrotolerans sp. nov. is proposed. The type strain is IDR2-2T (=JCM 12281T=NCIMB 13981T).

scholarly journals Alkalibacterium iburiense sp. nov., an obligate alkaliphile that reduces an indigo dye

2005 ◽  
Vol 55 (4) ◽  
pp. 1525-1530 ◽  
Author(s):  
Kenji Nakajima ◽  
Kikue Hirota ◽  
Yoshinobu Nodasaka ◽  
Isao Yumoto
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Data ◽  
Novel Species ◽  
Rrna Gene ◽  
Optimum Growth ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
Straight Rod

Three indigo-reducing obligately alkaliphilic strains, M3T, 41A and 41C, were isolated. The isolates grew at pH 9–12, but not at pH 7–8. They were Gram-positive, facultatively anaerobic, straight rod-shaped strains with peritrichous flagella. The isolates grew in 0–14 % (w/v) NaCl, with optimum growth at 3–13 %. They grew at temperatures between 10 and 45 °C, with optimum growth at around 30–37 °C. They did not hydrolyse starch or gelatin. dl-lactate was the major end-product from d-glucose. No quinones could be detected. The peptidoglycan type was A4β, Orn–d-Asp. The major cellular fatty acids were C16 : 0, C16 : 17c and C18 : 19c. The DNA G+C content was 42·6–43·2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that the isolates belong to the genus Alkalibacterium. DNA–DNA hybridization revealed low similarity (less than 16 %) of the isolates with respect to the two closest phylogenetically related strains, Alkalibacterium olivapovliticus and Alkalibacterium psychrotolerans. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic data and DNA–DNA relatedness, the isolates merit classification as a novel species of the genus Alkalibacterium, for which the name Alkalibacterium iburiense is proposed. The type strain is M3T (=JCM 12662T=NCIMB 14024T).

scholarly journals Plantactinospora sonchi sp. nov., an actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.)

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4895-4901 ◽  
Author(s):  
Zhaoxu Ma ◽  
Chongxi Liu ◽  
Jianlong Fan ◽  
Hairong He ◽  
Chuang Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Sonchus Oleraceus

A novel actinobacterium, designated strain NEAU-QY2T, was isolated from the leaves of Sonchus oleraceus L. specimen, collected from Wuchang, Heilongjiang Province, China. A polyphasic study was carried out to establish the taxonomic position of this strain. The organism formed single spores with rough surfaces on substrate mycelia. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-QY2T belonged to the genus Plantactinospora and formed a monophyletic clade with its closest related strains Plantactinospora endophytica YIM 68255T (99.2 % 16S rRNA gene sequence similarity), Plantactinospora veratri NEAU-FHS4T (98.8 %) and Plantactinospora mayteni YIM 61359T (98.7 %), an association that was supported by a bootstrap value of 90 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. However, DNA–DNA hybridization values between strain NEAU-QY2T and the three closely related strains were below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA–DNA hybridization results, strain NEAU-QY2T was distinguished from closely related strains and is classified as representing a novel species of the genus Plantactinospora, for which the name Plantactinospora sonchi sp. nov. is proposed. The type strain is NEAU-QY2T ( = CGMCC 4.7216T = JCM 30345T).

scholarly journals Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska

2005 ◽  
Vol 55 (1) ◽  
pp. 473-478 ◽  
Author(s):  
Elena V. Pikuta ◽  
Damien Marsic ◽  
Asim Bej ◽  
Jane Tang ◽  
Paul Krader ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Optimum Growth ◽  
Facultative Anaerobe ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
Ph Range

A novel, psychrotolerant, facultative anaerobe, strain FTR1T, was isolated from Pleistocene ice from the permafrost tunnel in Fox, Alaska. Gram-positive, motile, rod-shaped cells were observed with sizes 0·6–0·7×0·9–1·5 μm. Growth occurred within the pH range 6·5–9·5 with optimum growth at pH 7·3–7·5. The temperature range for growth of the novel isolate was 0–28 °C and optimum growth occurred at 24 °C. The novel isolate does not require NaCl; growth was observed between 0 and 5 % NaCl with optimum growth at 0·5 % (w/v). The novel isolate was a catalase-negative chemoorganoheterotroph that used as substrates sugars and some products of proteolysis. The metabolic end products were acetate, ethanol and CO2. Strain FTR1T was sensitive to ampicillin, tetracycline, chloramphenicol, rifampicin, kanamycin and gentamicin. 16S rRNA gene sequence analysis showed 99·8 % similarity between strain FTR1T and Carnobacterium alterfunditum, but DNA–DNA hybridization between them demonstrated 39±1·5 % relatedness. On the basis of genotypic and phenotypic characteristics, it is proposed that strain FTR1T (=ATCC BAA-754T=JCM 12174T=CIP 108033T) be assigned to the novel species Carnobacterium pleistocenium sp. nov.

scholarly journals Streptomyces sparsus sp. nov., isolated from a saline and alkaline soil

2011 ◽  
Vol 61 (7) ◽  
pp. 1601-1605 ◽  
Author(s):  
Yi Jiang ◽  
Yan-Ru Cao ◽  
Jutta Wiese ◽  
Shu-Kun Tang ◽  
Li-Hua Xu ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Aerial Hyphae ◽  
Actinomycete Strain ◽  
The 16S Rrna Gene

A salt- and alkali-tolerant actinomycete strain, YIM 90018T, was isolated from a saline and alkaline soil sample collected from Qinghai, China. Aerial hyphae of strain YIM 90018T were only produced on YIM 82 agar. Vegetative hyphae were well developed and did not fragment. Straight or flexuous (rectiflexibiles) spore chains were produced. The isolate grew well with 25 % (w/v) MgCl2 . 6H2O and at pH 10. All of these characters indicated that strain YIM 90018T belonged to the genus Streptomyces. On the basis of phylogenetic analysis of the 16S rRNA gene sequence, DNA–DNA hybridization and phenotypic characteristics, strain YIM 90018T could be differentiated from all recognized species of the genus Streptomyces. A novel species, Streptomyces sparsus sp. nov., is proposed, with strain YIM 90018T ( = CCTCC AA204019T = DSM 41858T) as the type strain.

Agromyces iriomotensis sp. nov. and Agromyces subtropicus sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 833-838 ◽  
Author(s):  
Moriyuki Hamada ◽  
Chiyo Shibata ◽  
Yuumi Ishida ◽  
Tomohiko Tamura ◽  
Hideki Yamamura ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Three novel Gram-stain-positive bacteria, designated IY07-20T, IY07-56T and IY07-113, were isolated from soil samples from Iriomote Island, Okinawa, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the three isolates were closely related to the members of the genus Agromyces , with similarity range of 95.6–98.7 %. The isolates contained l-2,4-diaminobutylic acid, d-alanine, d-glutamic acid and glycine in their peptidoglycans. The predominant menaquinone was MK-12 and the major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C contents were 70.9–72.9 mol%. The chemotaxonomic characteristics of the isolates matched those described for members of the genus Agromyces . The results of phylogenetic analysis and DNA–DNA hybridization, along with differences in phenotypic characteristics between strains IY07-20T, IY07-56T and IY07-113 and the species of the genus Agromyces with validly published names, indicate that the three isolates merit classification as representatives of two novel species of the genus Agromyces , for which the names Agromyces iriomotensis sp. nov. and Agromyces subtropica sp. nov. are proposed; the type strains are IY07-20T ( = NBRC 106452T = DSM 26155T) and IY07-56T ( = NBRC 106454T = DSM 26153T), respectively.

scholarly journals Luteipulveratus halotolerans sp. nov., an actinobacterium (Dermacoccaceae) from forest soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4113-4120 ◽  
Author(s):  
Holed Juboi ◽  
Ann Anni Basik ◽  
Sunita Sara Gill Shamsul ◽  
Phil Arnold ◽  
Esther K. Schmitt ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Monophyletic Clade ◽  
Phenotypic Characteristics ◽  
Pacbio Rs Ii ◽  
The Family ◽  
The 16S Rrna Gene

The taxonomic position of an actinobacterium strain, C296001T, isolated from a soil sample collected in Sarawak, Malaysia, was established using a polyphasic approach. Phylogenetically, strain C296001T was closely associated with the genus Luteipulveratus and formed a distinct monophyletic clade with the only described species, Luteipulveratus mongoliensis NBRC 105296T. The 16S rRNA gene sequence similarity between strain C296001T and L. mongoliensis was 98.7 %. DNA–DNA hybridization results showed that the relatedness of strain C296001T to L. mongoliensis was only 21.5 %. The DNA G+C content of strain C296001T was 71.7 mol%. Using a PacBio RS II system, whole genome sequences for strains C296001T and NBRC 105296T were obtained. The genome sizes of 4.5 Mbp and 5.4 Mbp determined were similar to those of other members of the family Dermacoccaceae. The cell-wall peptidoglycan contained lysine, alanine, aspartic acid, glutamic acid and serine, representing the peptidoglycan type A4α l-Lys-l-Ser-d-Asp. The major menaquinones were MK-8(H4), MK-8 and MK-8(H2). Phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol and phosphoglycolipid were the polar lipids, while the whole-cell sugars were glucose, fucose and lesser amounts of ribose and galactose. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, anteiso-C17 : 1ω9c, iso-C18 : 0 and 10-methyl C17 : 0. Chemotaxonomic analyses showed that C296001T had typical characteristics of members of the genus Luteipulveratus, with the main differences occurring in phenotypic characteristics. On the basis of the phenotypic and chemotaxonomic evidence, it is proposed that strain C296001T be classified as a representative of a novel species in the genus Luteipulveratus, for which the name Luteipulveratus halotolerans sp. nov. is recommended. The type strain is C296001T ( = ATCC TSD-4T = JCM 30660T).

scholarly journals Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4655-4661 ◽  
Author(s):  
Yong Hua Li ◽  
Rui Wang ◽  
Xiao Xia Zhang ◽  
J. Peter. W. Young ◽  
En Tao Wang ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Lablab Purpureus ◽  
Phenotypic Characteristics ◽  
Slow Growing ◽  
Type Strains

Seven slow-growing rhizobia isolated from effective nodules of Arachis hypogaea were assigned to the genus Bradyrhizobium based on sharing 96.3–99.9 % 16S rRNA gene sequence similarity with the type strains of recognized Bradyrhizobium species. Multilocus sequence analysis of glnII, recA, gyrB and dnaK genes indicated that the seven strains belonged to two novel species represented by CCBAU 51649T and CCBAU 53363T. Strain CCBAU 51649T shared 94, 93.4, 92.3 and 94.9 % and CCBAU 53363T shared 91.4, 94.5, 94.6 and 97.7 % sequence similarity for the glnII, recA, gyrB and dnaK genes, respectively, with respect to the closest related species Bradyrhizobium manausense BR 3351T and Bradyrhizobium yuanmingense CCBAU 10071T. Summed feature 8 and C16 : 0 were the predominant fatty acid components for strains CCBAU 51649T and CCBAU 53363T. DNA–DNA hybridization and analysis of phenotypic characteristics also distinguished these strains from the closest related Bradyrhizobium species. The strains formed effective nodules on Arachis hypogaea, Lablab purpureus and Aeschynomene indica, and they had identical nodA genes to Bradyrhizobium sp. PI237 but were phylogenetically divergent from other available nodA genes at less than 66 % similarity. Based in these results, strains CCBAU 51649T ( = CGMCC 1.15034T = LMG 28620T) and CCBAU 53363T ( = CGMCC 1.15035T = LMG 28621T) are designated the type strains of two novel species, for which the names Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov. are proposed, respectively.

scholarly journals Oceanobacillus oncorhynchi sp. nov., a halotolerant obligate alkaliphile isolated from the skin of a rainbow trout (Oncorhynchus mykiss), and emended description of the genus Oceanobacillus

2005 ◽  
Vol 55 (4) ◽  
pp. 1521-1524 ◽  
Author(s):  
Isao Yumoto ◽  
Kikue Hirota ◽  
Yoshinobu Nodasaka ◽  
Kenji Nakajima
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Dna Hybridization ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Emended Description ◽  
Alkaliphilic Bacterium

A halotolerant, obligately alkaliphilic bacterium, R-2T, was isolated from the skin of a rainbow trout (Oncorhynchus mykiss), a freshwater fish. The strain is Gram-positive, ferments several carbohydrates, is rod-shaped and motile by peritrichous flagella and produces ellipsoidal spores. The isolate grows at pH 9–10 but not at pH 7–8. This micro-organism grows in 0–22 % (w/v) NaCl at pH 10. Its major cellular fatty acids are iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, the major isoprenoid quinone is MK-7 and the DNA G+C content is 38·5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicates that strain R-2T is a member of the genus Oceanobacillus. DNA–DNA hybridization reveals low relatedness between the isolate and Oceanobacillus iheyensis (21·0 %). On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, the isolate should be designated as a novel species, for which the name Oceanobacillus oncorhynchi sp. nov. is proposed. The type strain is R-2T (=JCM 12661T=NCIMB 14022T).

scholarly journals Nesterenkonia sandarakina sp. nov. and Nesterenkonia lutea sp. nov., novel actinobacteria, and emended description of the genus Nesterenkonia

2005 ◽  
Vol 55 (1) ◽  
pp. 463-466 ◽  
Author(s):  
Wen-Jun Li ◽  
Hua-Hong Chen ◽  
Chang-Jin Kim ◽  
Yu-Qin Zhang ◽  
Dong-Jin Park ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
Emended Description

Two novel actinobacteria isolates, designated YIM 70009T and YIM 70081T, were characterized in order to determine their taxonomic position. Cells of strains YIM 70009T and YIM 70081T were cocci, although only the latter were motile. The G+C contents of their DNAs were 64·0 and 64·5 mol%, respectively. On the basis of chemotaxonomic characteristics and 16S rRNA gene sequence analysis, the two isolates were classified in the genus Nesterenkonia. DNA–DNA hybridization and comparison of phenotypic characteristics revealed that strains YIM 70009T and YIM 70081T differed from each other and from known species. Therefore, it is proposed that they represent two separate novel species of the genus Nesterenkonia: Nesterenkonia sandarakina sp. nov. (type strain, YIM 70009T=CCTCC AA 203007T=DSM 15664T=KCTC 19011T) and Nesterenkonia lutea sp. nov. (type strain, YIM 70081T=CCTCC AA 203010T=DSM 15666T=KCTC 19013T).

scholarly journals Pseudomonas reinekei sp. nov., Pseudomonas moorei sp. nov. and Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid

2007 ◽  
Vol 57 (5) ◽  
pp. 923-931 ◽  
Author(s):  
Beatriz Cámara ◽  
Carsten Strömpl ◽  
Susanne Verbarg ◽  
Cathrin Spröer ◽  
Dietmar H. Pieper ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Phenotypic Characteristics ◽  
Isopimaric Acid ◽  
Gene Sequence Analysis

Three bacterial strains, designated MT1T, RW10T and IpA-2T, had been isolated previously for their ability to degrade chlorosalicylates or isopimaric acid. 16S rRNA gene sequence analysis demonstrated that these bacteria are related to species of the genus Pseudomonas. Analysis of the results of DNA–DNA hybridization with several close phylogenetic neighbours revealed a low level of hybridization (less than 57 %). On the basis of phenotypic characteristics, phylogenetic analysis, DNA–DNA relatedness data and chemotaxonomic analysis, it is concluded that these isolates represent separate novel species, for which the names Pseudomonas reinekei sp. nov. (type strain MT1T =DSM 18361T=CCUG 53116T), Pseudomonas moorei sp. nov. (type strain RW10T =DSM 12647T=CCUG 53114T) and Pseudomonas mohnii sp. nov. (type strain IpA-2T =DSM 18327T=CCUG 53115T) are proposed.

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