scholarly journals Whole-Genome Sequence Data Analysis of Anoxybacillus kamchatkensis NASTPD13 Isolated from Hot Spring of Myagdi, Nepal

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Punam Yadav ◽  
Shikha Sharma ◽  
Tribikram Bhattarai ◽  
Lakshmaiah Sreerama ◽  
Gandham S. Prasad ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Whole Genome ◽  
Rrna Gene Sequence ◽  
Anoxybacillus Kamchatkensis

Anoxybacillus kamchatkensis NASTPD13 isolated from Paudwar hot spring of Myagdi, Nepal, upon morphological and biochemical analysis revealed to be Gram-positive, straight or slightly curved, rod-shaped, spore-forming, catalase, and oxidase-positive facultative anaerobes. It grows over a wide range of pH (5.0-11) and temperature (37-75°C), which showed growth in different reduced carbon sources such as starch raffinose, glucose, fructose, inositol, trehalose, sorbitol, mellobiose, and mannitol in aerobic conditions. Furthermore, the partial sequence obtained upon sequencing showed 99% sequence similarity in 16S rRNA gene sequence with A. kamchatkensis JW/VK-KG4 and was suggested to be Anoxybacillus kamchatkensis. Moreover, whole-genome analysis of NASTPD13 revealed 2,866,796 bp genome with a G+C content of 41.6%. Analysis of the genome revealed the presence of 102 RNA genes, which includes sequences coding for 19 rRNA and 79 tRNA genes. While the 16S rRNA gene sequence of strain NASTPD13 showed high similarity (>99%) to those of A. kamchatkensis JW/VK-KG4, RAST analysis of NASTPD13 genome suggested that A. kamchatkensis G10 is actually the closest neighbor in terms of sequence similarity. The genome annotation by RAST revealed various genes encoding glycoside hydrolases supporting that it can utilize several reduced carbon sources as observed and these genes could be important for carbohydrate-related industries. Xylanase pathway, particularly the genomic region encoding key enzymes for xylan depolymerization and xylose metabolism, further confirmed the presence of the complete gene in xylan metabolism. In addition, the complete xylose utilization gene locus analysis of NASTPD13 genome revealed all including D-xylose transport ATP-binding protein XylG and XylF, the xylose isomerase encoding gene XylA, and the gene XylB coding for a xylulokinase supported the fact that the isolate contains a complete set of genes related to xylan degradation, pentose transport, and metabolism. The results of the present study suggest that the isolated A. kamchatkensis NASTPD13 containing xylanase-producing genes could be useful in lignocellulosic biomass-utilizing industries where pentose polymers could also be utilized along with the hexose polymers.

scholarly journals Paucibacter toxinivorans gen. nov., sp. nov., a bacterium that degrades cyclic cyanobacterial hepatotoxins microcystins and nodularin

2005 ◽  
Vol 55 (4) ◽  
pp. 1563-1568 ◽  
Author(s):  
Jarkko Rapala ◽  
Katri A. Berg ◽  
Christina Lyra ◽  
R. Maarit Niemi ◽  
Werner Manz ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Thirteen bacterial isolates from lake sediment, capable of degrading cyanobacterial hepatotoxins microcystins and nodularin, were characterized by phenotypic, genetic and genomic approaches. Cells of these isolates were Gram-negative, motile by means of a single polar flagellum, oxidase-positive, weakly catalase-positive and rod-shaped. According to phenotypic characteristics (carbon utilization, fatty acid and enzyme activity profiles), the G+C content of the genomic DNA (66·1–68·0 mol%) and 16S rRNA gene sequence analysis (98·9–100 % similarity) the strains formed a single microdiverse genospecies that was most closely related to Roseateles depolymerans (95·7–96·3 % 16S rRNA gene sequence similarity). The isolates assimilated only a few carbon sources. Of the 96 carbon sources tested, Tween 40 was the only one used by all strains. The strains were able to mineralize phosphorus from organic compounds, and they had strong leucine arylamidase and chymotrypsin activities. The cellular fatty acids identified from all strains were C16 : 0 (9·8–19 %) and C17 : 1 ω7c (<1–5·8 %). The other predominant fatty acids comprised three groups: summed feature 3 (<1–2·2 %), which included C14 : 0 3-OH and C16 : 1 iso I, summed feature 4 (54–62 %), which included C16 : 1 ω7c and C15 : 0 iso OH, and summed feature 7 (8·5–28 %), which included ω7c, ω9c and ω12t forms of C18 : 1. A more detailed analysis of two strains indicated that C16 : 1 ω7c was the main fatty acid. The phylogenetic and phenotypic features separating our strains from recognized bacteria support the creation of a novel genus and species, for which the name Paucibacter toxinivorans gen. nov., sp. nov. is proposed. The type strain is 2C20T (=DSM 16998T=HAMBI 2767T=VYH 193597T).

scholarly journals Photobacterium rosenbergii sp. nov. and Enterovibrio coralii sp. nov., vibrios associated with coral bleaching

2005 ◽  
Vol 55 (2) ◽  
pp. 913-917 ◽  
Author(s):  
F. L. Thompson ◽  
C. C. Thompson ◽  
S. Naser ◽  
B. Hoste ◽  
K. Vandemeulebroecke ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Six new Vibrio-like isolates originating from different species of bleached and healthy corals around Magnetic Island (Australia) were investigated using a polyphasic approach. Phylogenetic analyses based on 16S rRNA, recA and rpoA gene sequences split the isolates in two new groups. Strains LMG 22223T, LMG 22224, LMG 22225, LMG 22226 and LMG 22227 were phylogenetic neighbours of Photobacterium leiognathi LMG 4228T (95·6 % 16S rRNA gene sequence similarity), whereas strain LMG 22228T was related to Enterovibrio norvegicus LMG 19839T (95·5 % 16S rRNA gene sequence similarity). The two new groups can be distinguished from closely related species on the basis of several phenotypic features, including fermentation of d-mannitol, melibiose and sucrose, and utilization of different compounds as carbon sources, arginine dihydrolase activity, nitrate reduction, resistance to the vibriostatic agent O/129 and the presence of fatty acids 15 : 0 iso and 17 : 0 iso. The names Photobacterium rosenbergii sp. nov. (type strain LMG 22223T=CBMAI 622T=CC1T) and Enterovibrio coralii sp. nov. (type strain LMG 22228T=CBMAI 623T=CC17T) are proposed to accommodate these new isolates. The G+C contents of the DNA of the two type strains are respectively 47·6 and 48·2 mol%.

scholarly journals Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the ‘Betaproteobacteria’

2005 ◽  
Vol 55 (6) ◽  
pp. 2329-2332 ◽  
Author(s):  
Hee-Chan Yang ◽  
Wan-Taek Im ◽  
Dong-Shan An ◽  
Woo-shin Park ◽  
In S. Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Novel Genus And Species

A taxonomic study was carried out on a bacterial strain, designated KM-45T, isolated from forest soil collected near Daejeon, South Korea. Comparative 16S rRNA gene sequence analysis indicated a clear affiliation of this bacterium to the ‘Betaproteobacteria’ and that it was related most closely to Chitinibacter tainanensis BCRC 17254T, Formivibrio citricus DSM 6150T and Iodobacter fluviatilis ATCC 33051T (92·4, 91·2 and 88·9 % 16S rRNA gene sequence similarity, respectively). Cells were Gram-negative, facultatively anaerobic, motile and rod-shaped. The strain grew well on R2A medium and utilized a broad spectrum of carbon sources. The G+C content of the genomic DNA was 58 mol% and the predominant ubiquinone was Q-8. Major fatty acids were C16 : 0, C16 : 1 ω7c/iso-C15 : 0 2-OH, C18 : 1 ω7c/ω9t/ω12t and C17 : 0 cyclo. On the basis of the evidence presented, it is proposed that strain KM-45T should be placed in a novel genus and species, for which the name Silvimonas terrae gen. nov., sp. nov. is proposed. The type strain is KM-45T (=KCTC 12358T=NBRC 100961T).

scholarly journals Thermoanaerobacterium aciditolerans sp. nov., a moderate thermoacidophile from a Kamchatka hot spring

2007 ◽  
Vol 57 (2) ◽  
pp. 260-264 ◽  
Author(s):  
I. V. Kublanov ◽  
M. I. Prokofeva ◽  
N. A. Kostrikina ◽  
T. V. Kolganova ◽  
T. P. Tourova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Polar Flagellum ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Wide Range

An anaerobic, moderately thermoacidophilic bacterium, strain 761-119T, was isolated from an acidic hot spring in the Orange Field of the Uzon Caldera (Kamchatka, far-eastern Russia). Cells were spore-forming, Gram-positive rods, possessing one polar flagellum. Growth of strain 761-119T was observed between 37 and 68 °C and in the pH20 °C range 3.2–7.1. No growth was observed within 5 days of incubation at or below 35 °C and at or above 70 °C, as well as at or below pH20 °C 2.8 and at or above pH20 °C 7.5. The optimal temperature and pH20 °C for growth were 55 °C and pH20 °C 5.7, respectively. A wide range of carbohydrates and polysaccharides were fermented, as well as peptides and proteinaceous substrates. The main products of glucose fermentation were acetate, ethanol, lactate, H2 and CO2. The DNA G+C content was 34 (±0.5) mol%. 16S rRNA gene sequence analysis indicated that strain 761-119T belonged to the genus Thermoanaerobacterium. The level of 16S rRNA gene sequence similarity with other Thermoanaerobacterium species was 86.5–97.8 %, with the only moderately acidophilic member of this genus, Thermoanaerobacterium aotearoense, being one of its closest relatives. DNA–DNA hybridization with T. aotearoense showed 33 % relatedness. Thus, morphological (one polar flagellum) and physiological characteristics (lower pH limit of growth at pH20 °C 3.2 compared with T. aotearoense) and 16S rRNA gene sequence analyses revealed that strain 761-119T represents a novel species in the genus Thermoanaerobacterium, for which the name Thermoanaerobacterium aciditolerans sp. nov. is proposed, with the type strain 761-119T (=DSM 16487T=VKM B-2363T).

Pseudomonas toyotomiensis sp. nov., a psychrotolerant facultative alkaliphile that utilizes hydrocarbons

2011 ◽  
Vol 61 (8) ◽  
pp. 1842-1848 ◽  
Author(s):  
Kikue Hirota ◽  
Keiko Yamahira ◽  
Kenji Nakajima ◽  
Yoshinobu Nodasaka ◽  
Hidetoshi Okuyama ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A psychrotolerant, facultatively alkaliphilic strain, HT-3T, was isolated from a sample of soil immersed in hot-spring water containing hydrocarbons in Toyotomi, Hokkaido, Japan. 16S rRNA gene sequence-based phylogeny suggested that strain HT-3T is a member of the genus Pseudomonas and belongs to the Pseudomonas oleovorans group. Cells of the isolate were Gram-negative, aerobic, straight rods, motile by a single polar flagellum. The strain grew at 4–42 °C, with optimum growth at 35 °C at pH 7, and at pH 6–10. It hydrolysed Tweens 20, 40, 60 and 80, but not casein, gelatin, starch or DNA. Its major isoprenoid quinone was ubiquinone-9 (Q-9) and the DNA G+C content was 65.1 mol%. The whole-cell fatty acid profile consisted mainly of C16 : 0, C16 : 1ω9c and C18 : 1ω9c. Phylogenetic analyses based on gyrB, rpoB and rpoD sequences revealed that the isolate could be discriminated from Pseudomonas species that exhibited more than 97 % 16S rRNA gene sequence similarity and phylogenetic neighbours belonging to the P. oleovorans group including the closest relative of the isolate, Pseudomonas alcaliphila. DNA–DNA hybridization with P. alcaliphila AL15-21T revealed 51±5 % relatedness. Owing to differences in phenotypic properties and phylogenetic analyses based on multilocus gene sequence analysis and DNA–DNA relatedness data, the isolate merits classification in a novel species, for which the name Pseudomonas toyotomiensis sp. nov. is proposed. The type strain is HT-3T ( = JCM 15604T  = NCIMB 14511T).

scholarly journals Caldicellulosiruptor changbaiensis sp. nov., a cellulolytic and hydrogen-producing bacterium from a hot spring

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 293-297 ◽  
Author(s):  
Wei Bing ◽  
Honglei Wang ◽  
Baisong Zheng ◽  
Feng Zhang ◽  
Guangshan Zhu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A novel thermophilic bacterial strain, CBS-ZT, was isolated from a terrestrial hot spring in the Changbai Mountains, PR China. Cells of strain CBS-ZT were short straight rods without flagella and had Gram-positive cell walls. Growth was observed at 40–90 °C (optimum 75 °C) and at pH 5.6–8.6 (optimum pH 7.8). The primary end-products from the fermentation of filter paper by strain CBS-ZT were acetate, lactate, H2, and CO2. The main cellular fatty acids were iso-C17 : 0, iso-C14 : 0 3-OH and C16 : 0. The G+C content of the genomic DNA was 36.08 mol%. Multiple sequence alignment of the 16S rRNA gene sequence and phylogenetic analyses indicated that strain CBS-ZT belongs to the genus Caldicellulosiruptor and the most similar micro-organism was Caldicellulosiruptor saccharolyticus DSM 8903T (96.36 % 16S rRNA gene sequence similarity); the 16S rRNA gene sequence similarity of strain CBS-ZT to other species was below 95 %. Based on its phylogenetic and phenotypic characteristics, strain CBS-ZT represents a novel species of the genus Caldicellulosiruptor , for which the name Caldicellulosiruptor changbaiensis sp. nov. is proposed. The type strain is CBS-ZT ( = DSM 26941T = CGMCC 1.5180T).

scholarly journals Meiothermus hypogaeus sp. nov., a moderately thermophilic bacterium isolated from a hot spring

2012 ◽  
Vol 62 (1) ◽  
pp. 112-117 ◽  
Author(s):  
Koji Mori ◽  
Takao Iino ◽  
Jun-ichiro Ishibashi ◽  
Hiroyuki Kimura ◽  
Moriyuki Hamada ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Thermophilic Bacterium ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Moderately Thermophilic

A novel moderately thermophilic, red-pigmented bacterium, designated strain AZM34c11T, was isolated from the bottom of a 1000 m-deep drilled well located in a Japanese hot spring. Cells were Gram-negative and grew optimally at 50 °C, at pH 7.6 and with 0–0.3 % (w/v) NaCl. Analysis of the 16S rRNA gene sequence revealed that the isolate belonged to the genus Meiothermus. Levels of 16S rRNA gene sequence similarity between strain AZM34c11T and the type strains of recognized Meiothermus species were 88.2–94.8 %. Strain AZM34c11T was distinguished from recognized Meiothermus species by its cellular fatty acid profile: iso-C16 : 0 was one of the predominant components and hydroxy fatty acids were present only in trace amounts. The strain could also be differentiated based on its growth substrate preferences and characteristic enzyme reactions. On the basis of these results, strain AZM34c11T is considered to represent a novel species of the genus Meiothermus, for which the name Meiothermus hypogaeus sp. nov. is proposed. The type strain is AZM34c11T ( = NBRC 106114T  = DSM 23238T).

scholarly journals Thermus amyloliquefaciens sp. nov., isolated from a hot spring sediment sample

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2491-2495 ◽  
Author(s):  
Tian-Tian Yu ◽  
Hong Ming ◽  
Ji-Cheng Yao ◽  
En-Min Zhou ◽  
Dong-Jin Park ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence

A Gram-stain-negative, aerobic bacterium, designated strain YIM 77409T, was isolated from the Niujie hot spring in the Eryuan county of Dali, Yunnan province, south-west China. Cells of the strain were rod-shaped and colonies were yellow and circular. The strain grew at pH 6.0–8.0 (optimum, pH 7.0) and 50–70°C (optimum, 60–65°C). The predominant menaquinone was MK-8 and the DNA G+C content was 66.4 mol%. Major fatty acids (>10 %) were iso-C15 : 0 and iso-C17 : 0.The polar lipids consisted of one aminophospholipid, one phospholipid and two glycolipids. 16S rRNA gene sequence analysis showed that strain YIM 77409T formed a cluster with Thermus scotoductus DSM 8553T, Thermus antranikianii DSM 12462T, Thermus caliditerrae YIM 77925T and Thermus tengchongensis YIM 77924T, with highest 16S rRNA gene sequence similarity to T. scotoductus DSM 8553T (97.57 %). However, DNA–DNA hybridization indicated that strain YIM 77409T should be viewed as a representative of a novel species, as there was only 30.6 ± 1.6 % reassociation with T. scotoductus DSM 8553T. On the basis of the morphological and chemotaxonomic characteristics, as well as the genotypic data, it is proposed that strain YIM 77409T represents a novel species of the genus Thermus, with the name Thermus amyloliquefaciens sp. nov. The type strain is YIM 77409T ( = DSM 25898T = KCTC 32024T).

scholarly journals Methylobacterium gossipiicola sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the cotton phyllosphere

2012 ◽  
Vol 62 (1) ◽  
pp. 162-167 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Selvaraj Poonguzhali ◽  
Murugaiyan Senthilkumar ◽  
Jung-Sook Lee ◽  
Keun-Chul Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Rrna Gene Sequence

A pink, aerobic, facultatively methylotrophic, motile, Gram-negative rod, designated Gh-105T, was isolated from the phyllosphere of cotton from Coimbatore (Tamilnadu, India). 16S rRNA gene sequence analysis showed clearly that the isolate belonged to the Methylobacterium cluster. Strain Gh-105T was most closely related to Methylobacterium adhaesivum AR27T (99 % 16S rRNA gene sequence similarity) and Methylobacterium iners 5317S-33T (97.5 %). The isolate grew with C1 compounds such as methanol and dichloromethane, but not with formaldehyde, formate, methylamine, trimethylamine or methane, as sole carbon sources and carried mxaF, which encodes methanol dehydrogenase and supports methylotrophic metabolism. The major fatty acid was C18 : 1ω7c and the G+C content of the genomic DNA was 64.2 mol%. Physiological and biochemical data and DNA–DNA relatedness with M. adhaesivum KACC 12195T and M. iners KACC 11765T revealed clear phenotypic and genotypic differences. For this reason, we propose that strain Gh-105T ( = CCM 7572T  = NRRL B-51692T) represents the type strain of a novel species, with the name Methylobacterium gossipiicola sp. nov.

scholarly journals Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach

2021 ◽  
Author(s):  
Shadi Khodamoradi ◽  
Richard L. Hahnke ◽  
Yvonne Mast ◽  
Peter Schumann ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bioinformatic Analysis ◽  
Biosynthetic Gene Cluster ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Polar Lipid Profile

AbstractStrain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.

Sign in / Sign up

Export Citation Format

Share Document