DNA hybridization and phosphinothricin acetyltransferase gene sequence detection based on zirconia/nanogold film modified electrode

2008 ◽  
Vol 254 (15) ◽  
pp. 4750-4756 ◽  
Author(s):  
Wei Zhang ◽  
Tao Yang ◽  
Chen Jiang ◽  
Kui Jiao
Keyword(s):  
Modified Electrode ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Detection ◽  
Phosphinothricin Acetyltransferase

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

scholarly journals Pseudomonas coleopterorum sp. nov., a cellulase-producing bacterium isolated from the bark beetle Hylesinus fraxini

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2852-2858 ◽  
Author(s):  
Esther Menéndez ◽  
Martha H. Ramírez-Bahena ◽  
Anna Fabryová ◽  
José M. Igual ◽  
Oldrich Benada ◽  
...  
Keyword(s):  
Bark Beetle ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Arginine Dihydrolase

We isolated a strain coded Esc2AmT during a study focused on the microbial diversity of adult specimens of the bark beetle Hylesinus fraxini. Its 16S rRNA gene sequence had 99.4 % similarity with respect to its closest relative, Pseudomonas rhizosphaerae IH5T. The analysis of partial sequences of the housekeeping genes rpoB, rpoD and gyrB confirmed that strain Esc2AmT formed a cluster with P. rhizosphaerae IH5T clearly separated from the remaining species of the genus Pseudomonas. Strain Esc2AmT had polar flagella and could grow at temperatures from 4 °C to 30 °C. The respiratory quinone was Q9 and the main fatty acids were C16 : 0, C18 : 1ω7c and/or C18 : 1ω6c in summed feature 8 and C16 : 1ω7c and/or C16 : 1ω6c in summed feature 3. DNA–DNA hybridization results showed 51 % relatedness with respect to P. rhizosphaerae IH5T. Oxidase, catalase and urease-positive, the arginine dihydrolase system was present but nitrate reduction and β-galactosidase production were negative. Aesculin hydrolysis was positive. Based on the results from the genotypic, phenotypic and chemotaxonomic analyses, we propose the classification of strain Esc2AmT as representing a novel species of the genus Pseudomonas, for which we propose the name Pseudomonas coleopterorum sp. nov. The type strain is Esc2AmT ( = LMG 28558T = CECT 8695T).

scholarly journals Lysobacter novalis sp. nov., isolated from fallow farmland soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3131-3136 ◽  
Author(s):  
Hina Singh ◽  
Juan Du ◽  
Kyung-Hwa Won ◽  
Jung-Eun Yang ◽  
Shahina Akter ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Gliding Motility ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Farmland Soil ◽  
Major Respiratory Quinone

A novel bacterial strain, designated THG-PC7T, was isolated from fallow farmland soil in Yongin, South Korea. Cells of strain THG-PC7T were Gram-stain-negative, dark yellow, aerobic, rod-shaped and had gliding motility. Strain THG-PC7T grew optimally at 25–35 °C, at pH 7 and in the absence of NaCl. Comparative 16S rRNA gene sequence analysis identified strain THG-PC7T as belonging to the genus Lysobacter, exhibiting highest sequence similarity with Lysobacter ximonensis KCTC 22336T (98.7 %) followed by Lysobacter niastensis KACC 11588T (95.7 %). In DNA–DNA hybridization tests, DNA relatedness between strain THG-PC7T and its closest phylogenetic neighbour L. ximonensis was below 25 %. The DNA G+C content of the novel isolate was determined to be 62.5 mol%. Flexirubin-type pigments were found to be present. The major cellular fatty acids were determined to be iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C17 : 1ω9c. The major respiratory quinone was identified as ubiquonone-8 (Q8). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospolipid. On the basis of results from DNA–DNA hybridization and the polyphasic data, strain THG-PC7T represents a novel species of the genus Lysobacter, for which the name Lysobacter novalis sp. nov. is proposed. The type strain is THG-PC7T( = KACC 18276T = CCTCC AB 2014319T).

scholarly journals Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China

2019 ◽  
Vol 69 (4) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xiang-yue Zhou ◽  
Zeng-hong Gao ◽  
Mei-hong Chen ◽  
Mei-qi Jian ◽  
Li-hong Qiu
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Broad Leaved Forest ◽  
Gene Sequence Analysis ◽  
Leaved Forest

Cells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11T grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyella flagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyella humi DHG40T and Dyella nitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyella caseinilytica DHOB09T and Dyella mobilis DHON07T, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.

scholarly journals Halioglobus maricola sp. nov., isolated from coastal seawater

2020 ◽  
Vol 70 (3) ◽  
pp. 1868-1875 ◽  
Author(s):  
Shan-Hui Li ◽  
Jaeho Song ◽  
Yeonjung Lim ◽  
Yochan Joung ◽  
Ilnam Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6–97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA–DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-β-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus , for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).

Halobacillus fulvus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi) in Thailand

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Auttaporn Booncharoen ◽  
Wonnop Visessanguan ◽  
Nattakorn Kuncharoen ◽  
Supalurk Yiamsombut ◽  
Pannita Santiyanont ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Halophilic Bacterium ◽  
Rrna Gene ◽  
Content Type ◽  
Moderately Halophilic ◽  
Link Type ◽  
Moderately Halophilic Bacterium

An aerobic, Gram-stain-positive, endospore-forming, rod-shaped and moderately halophilic strain SKP4-6T, was isolated from shrimp paste (Ka-pi) collected from Samut Sakhon Province, Thailand. Phylogenetic analysis revealed that strain SKP4-6T belonged to the genus Halobacillus and was most closely related to Halobacillus salinus JCM 11546T (98.6 %), Halobacillus locisalis KCTC 3788T (98.6 %) and Halobacillus yeomjeoni KCTC 3957T (98.6 %) based on 16S rRNA gene sequence similarity. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKP4-6T and its related species were 18.2–19.3 % and 69.84–84.51 %, respectively, which were lower than the threshold recommended for species delineation. The strain grew optimally at 30–40 °C, at pH 7.0 and with 10–15 % (w/v) NaCl. It contained l-Orn–d-Asp in the cell wall peptidoglycan. The DNA G+C content was 44.8 mol%. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The predominant isoprenoid quinone was MK-7. Phosphatidylglycerol and diphosphatidylglycerol were present as major polar lipids. Based on this polyphasic approach, digital DNA–DNA relatedness and ANI values, strain SKP4-6T represents a novel species of the genus Halobacillus , for which the name Halobacillus fulvus sp. nov. is proposed. The type strain is SKP4-6T (=JCM 32624T=TISTR 2595T).

Isolation and description of Selenomonas timonae sp. nov., a novel Selenomonas species detected in a gingivitis patient

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Angéline Antezack ◽  
Manon Boxberger ◽  
Mariem Ben Khedher ◽  
Bernard La Scola ◽  
Virginie Monnet-Corti
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
Optimum Ph

A Gram-stain-negative bacterium, designated strain Marseille-Q3039T, was isolated from subgingival dental plaque of a woman with gingivitis in Marseille, France. Strain Marseille-Q3039T was found to be an anaerobic, motile and spore-forming crescent-shaped bacterium that grew at 25–41.5 °C (optimum, 37 °C), pH 5.5–8.5 (optimum, pH 7.5) and salinity of 5.0 g l−1 NaCl. The results of 16S rRNA gene sequence analysis revealed that strain Marseille-Q3039T was closely related to Selenomonas infelix ATCC 43532T (98.42 % similarity), Selenomonas dianae ATCC 43527T (97.25 %) and Centipedia periodontii DSM 2778T (97.19 %). The orthologous average nucleotide identity and digital DNA–DNA hybridization relatedness between strain Q3039T and its closest phylogenetic neighbours were respectively 84.57 and 28.2 % for S. infelix ATCC 43532T and 83.93 and 27.2 % for C. periodontii DSM 2778T. The major fatty acids were identified as C13 : 0 (27.7 %), C15 : 0 (24.4 %) and specific C13 : 0 3-OH (12.3 %). Genome sequencing revealed a genome size of 2 351 779 bp and a G+C content of 57.2 mol%. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3039T represents a novel species of the genus Selenomonas , for which the name Selenomonas timonae sp. nov. is proposed (=CSUR Q3039=CECT 30128).

Graphene-modified electrode for DNA detection via PNA–DNA hybridization

2013 ◽  
Vol 186 ◽  
pp. 563-570 ◽  
Author(s):  
Danxin Du ◽  
Shuang Guo ◽  
Lina Tang ◽  
Yong Ning ◽  
Qunfeng Yao ◽  
...  
Keyword(s):  
Modified Electrode ◽  
Dna Hybridization ◽  
Dna Detection

Terrabacter carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete

2011 ◽  
Vol 61 (3) ◽  
pp. 482-486 ◽  
Author(s):  
Sung M. Kim ◽  
Sae W. Park ◽  
Sang T. Park ◽  
Young M. Kim
Keyword(s):  
Carbon Monoxide ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Diamino Acid ◽  
Type Strains

A bacterial strain, PY2T, capable of oxidizing carbon monoxide, was isolated from a soil sample collected from a roadside at Yonsei University, Seoul, Korea. On the basis of 16S rRNA gene sequence analysis, strain PY2T was shown to belong to the genus Terrabacter and was most closely related to Terrabacter lapilli LR-26T (99.1 % similarity). Strain PY2T was characterized chemotaxonomically as having iso-C15 : 0 as the predominant fatty acid, MK-8(H4) as the major menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid of the cell wall, as possessing a polar lipid profile that included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and unknown amino-containing phosphoglycolipids, and having a DNA G+C content of 75.6 mol%. DNA–DNA relatedness values between strain PY2T and the type strains of T. lapilli, Terrabacter tumescens, Terrabacter terrae and Terrabacter aerolatus were 20.0 %, 22.9 %, 35.9 % and 64.5 %, respectively. Based on the combined evidence from the phylogenetic analyses, chemotaxonomic data and DNA–DNA hybridization experiments, it is proposed that strain PY2T represents a novel species for which the name Terrabacter carboxydivorans sp. nov. is proposed. The type strain is PY2T (=KCCM 42922T=JCM 16259T).

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