Molecular Diversity of Microcystis Strains (Cyanophyceae, Chroococcales) Based on 16S rDNA Sequences

2000 ◽  
Vol 70 (2) ◽  
pp. 275 ◽  
Author(s):  
Claire Lepere ◽  
Annick Wilmotte ◽  
Barbara Meyer
Keyword(s):  
16S Rdna ◽  
Molecular Diversity ◽  
Rdna Sequences ◽  
16S Rdna Sequences

scholarly journals Assessment of Molecular Diversity in Chickpea (Cicer arietinum L.) Rhizobia and Structural Analysis of 16S rDNA Sequences from Mesorhizobium ciceri

2013 ◽  
Vol 62 (3) ◽  
pp. 253-262 ◽  
Author(s):  
AKHILESH YADAV ◽  
ASHA LATA SINGH ◽  
GOVIND KUMAR RAI ◽  
MAJOR SINGH
Keyword(s):  
16S Rdna ◽  
Molecular Diversity ◽  
Variable Region ◽  
Phenotypic Characterization ◽  
Rflp Markers ◽  
Evolutionary Mechanisms ◽  
Minimal Free Energy ◽  
Mesorhizobium Ciceri ◽  
Rdna Sequences ◽  
16S Rdna Sequences

Molecular diversity studies of 19 rhizobia isolates from chickpea were conducted using simple sequence repeats (SSR) and 16S rDNA-RFLP markers. Phenotypic characterization with special reference to salinity and pH tolerance was performed. These isolates were identified as different strains of Mesorhizobium, Rhizobium, Bradyrhizobium, and Agrobacterium. Twenty SSR loci of Mesorhizobium ciceri, distributed across the other rhizobial genome, clearly differentiated 19 rhizobial isolates. Analogous clustering supported the results of 16S rDNA sequence-based phylogeny. Analysis of the 16S rDNA sequences from M. ciceri strains revealed that nucleotide variables (signature sites) were located at 20 different positions; most of them were present in the first 820 bp region from 5' terminal. Interestingly, 14 signature sites were located in two main regions, the variable region V1 (nt 527-584), and variable region V2 (nt 754-813). The secondary structure and minimal free energy were determined in these two regions. These results will be useful in characterizing the micro-evolutionary mechanisms of species formation and increase understanding of the symbiotic relationship.

scholarly journals The phylogeny of the genusYersiniabased on 16S rDNA sequences

1993 ◽  
Vol 114 (2) ◽  
pp. 173-177 ◽  
Author(s):  
A. Ibrahim ◽  
B.M. Goebel ◽  
W. Liesack ◽  
M. Griffiths ◽  
E. Stackebrandt
Keyword(s):  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences

scholarly journals Isolation and Identification of Hydrocarbon-Degrading Bacteria that Tolerant to Saponin of Sapindus Rarak Plant

2019 ◽  
Vol 4 (1) ◽  
pp. 79-88
Author(s):  
Evi Octaviany ◽  
Suharjono Suharjono ◽  
Irfan Mustafa
Keyword(s):  
Crude Oil ◽  
16S Rdna ◽  
Bacterial Isolates ◽  
High Concentration ◽  
Isolation And Identification ◽  
Rdna Sequences ◽  
Degrading Bacteria ◽  
16S Rdna Sequences ◽  
Petroleum Contaminated Soil ◽  
Cell Densities

A commercial saponin as biosurfactant can reduce the surface tension of water and increase of hydrocarbon degradation. However, this saponin can be toxic to some hydrocarbonoclastic bac-teria. This study aimed to obtain bacterial isolates that were tolerant and incapable to degrade saponin, and to identify them based on 16S rDNA sequence. Bacteria were isolated from petroleum contaminated soil in Wonocolo Village, Bojonegoro Regency, East Java, Indonesia. The soil samples were acclimated using Bushnell-Haas (BH) broth with 0.5% crude oil at room temperature for 3 weeks. The culture was spread onto BH agar incubated at 30°C for 7 days. The first screened, isolates were grown in nutrient broth with addition of sap-onin 0%, 8%, and 12% (v/v) then incubated at 30°C for three days. The bacterial cell density was measured using a spectrophotometer. Second screened, the isolates were grown on BH broth with addition of 0.5% saponin as a sole carbon source, and their cell densities were measured. The selected isolates were identified based on 16S rDNA sequences. Among 34 bacterial isolates, nine isolates were tol-erant to 12% saponin. Three bacterial isolates IHT1.3, IHT1.5, and IHT3.24 tolerant to high concentration of saponin and did not use this substance as growth nutrition. The IHT1.3, IHT1.5, and IHT3.24 isolates were identified as Ochrobactrum pseudogrignonense (99% similarity), Pseudomonas mendocina (99%), and Ochrobactrum pi-tuitosum; (97%), respectively. Those three selected isolates are good candidates as hydrocarbon-degrading bacteria to bioremediation of soil contaminated crude oil. However, the combined activity of bacteria and saponin to degrade hydrocarbon needs further study. 

Identification of host-specific Bacteroidales 16S rDNA sequences from human sewage and ruminant feces

2011 ◽  
Vol 52 (3) ◽  
pp. 277-284 ◽  
Author(s):  
Siobhán Dorai-Raj ◽  
Justin O'Grady ◽  
Martin Cormican ◽  
Emer Colleran
Keyword(s):  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences

Human intestinal spirochetosis diagnosed with colonoscopy and analysis of partial 16S rDNA sequences of involved spirochetes

2001 ◽  
Vol 2 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Wolfgang Kraatz ◽  
Ulf Thunberg ◽  
Bertil Pettersson ◽  
Claes Fellström
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rdna Sequences ◽  
Intestinal Spirochetosis ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Human Intestinal Spirochetosis ◽  
Type Strains ◽  
Rrna Sequences

AbstractDNA was extracted from colonic biopsies of 33 patients with and three without evidence of intestinal spirochetosis (IS) in the large bowel. The biopsies were subjected to PCR. A pair of primers, generating a 207 bp fragment, were designed to detect specifically the 16S rDNA gene ofBrachyspira. PCR products of the expected size were obtained from 33 samples with histologic evidence of IS. The PCR amplicons were used for sequencing. The sequences obtained were aligned to the corresponding 16S rRNA sequences of five type strains ofBrachyspira. The sequences of 23 PCR products were 99–100% identical with the correspond-ingB.aalborgitype strain sequence. Two cases showed 99–100% sequence similarity with the type strain ofB.pilosicoliP43/6/78. Six cases could not be referred to any of the known species ofBrachyspira. Two PCR products gave incomplete sequences.

scholarly journals Mitocondrial COI and 16S rDNA sequences support morphological identification and biogeography of deep-sea red crabs of the genus Chaceon (Crustacea, Decapoda, Geryonidae) in the Eastern Central and South Atlantic Ocean

PLoS ONE ◽  
2019 ◽  
Vol 14 (2) ◽  
pp. e0211717
Author(s):  
Mariano Hernández ◽  
M. Virginia Martín ◽  
Pedro M. Herrador-Gómez ◽  
Sebastián Jiménez ◽  
Carlos Hernández-González ◽  
...  
Keyword(s):  
Atlantic Ocean ◽  
16S Rdna ◽  
Deep Sea ◽  
South Atlantic ◽  
South Atlantic Ocean ◽  
Morphological Identification ◽  
Rdna Sequences ◽  
16S Rdna Sequences

scholarly journals First report of Cedecea neteri Causing Yellow rot Disease in Pleurotus pulmonarius in China

Plant Disease ◽  
2020 ◽  
Author(s):  
Zeng-Liang LIU ◽  
Shuangyun Zhou ◽  
Wenlong Zhang ◽  
Shengjin Wu ◽  
Xuefeng Chen ◽  
...  
Keyword(s):  
16S Rdna ◽  
Morphological Characteristics ◽  
Soft Rot ◽  
Negative Control ◽  
Deionized Water ◽  
Fruiting Bodies ◽  
Pleurotus Pulmonarius ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Rot Disease

Pleurotus pulmonarius is a popular edible fungus and widely cultivated in many areas of China. In June 2018, yellow rot (more than 10% incidence) was found on the first crop of P. pulmonarius fruiting bodies in a mushroom factory in Nanning, Guangxi Province, China. At first, yellow water-soaked lesions appeared in the infected fruiting bodies. Lesions then spread and purulent tissues were formed. Severe rot induced production of deformed fruiting bodies and offensive odor. Internal sections of the diseased tissue (approximately 0.5 × 0.5 cm) were sterilized in 75% alcohol for 30 s, rinsed three times with sterilized and deionized water, crushed and suspended in sterilized and deionized water. The suspension was spread on the Luria-Bertani (LB) medium. After incubation at 30°C for 2 days, dominant bacterial colonies were oyster white, smooth, convex, and circular. Individual colonies were transferred two times to LB medium using the conventional streak plate techniques to obtain the pure cultures. The cells were gram-negative, short rods, motile, and no capsules or endospores were observed. Using a BoJian Gram-negative bacteria biochemical analysis kit (5 CARDS, Hopebio, Qingdao, China), data were obtained and analyzed, showing that the isolated strain belongs to the Cedecea genus (positive for β-galactosidase, citric acid, arginine, sucrose, mannitol, sorbitol, D-glucose, gelatin hydrolysis and VP test but negative for H2S, urease, oxidase, indole, rhamnose, melibiose, amygdalin, lysine, ornithine, lactose, inositol and arabinose). Amplified 16S rDNA gene sequences (1,424 bp, GenBank accession No. MT925570) of the isolate using the universal primers 27f and 1492r (Lane 1991) exhibited 99.86% identity with Cedecea neteri M006 (CP009458.1). Based on its morphological characteristics, 16S rDNA sequences, and biochemical test results, the strain was identified as C. neteri. Pathogenicity tests for this strain were performed with bacterial suspensions (approximately 1 × 108 CFU/ml) after growing for 24 h in LB medium at 30°C. Mycelia of P. pulmonarius were cultivated for 60 days in plastic bags. Then young fruiting bodies were formed after induced with low temperature stimulation to serve as a host source. The prepared bacterial suspensions were directly sprayed onto the surface of three bags of fruiting bodies; another three bags were sprayed with sterilized and deionized water as negative control. All inoculated fruiting bodies were then incubated at 20°C with 90 to 95% relative humidity. All experiments were repeated three times. After 2 days, all the fruiting bodies inoculated with the bacterial suspensions showed yellow water-soaked lesions, and the normal growth of the fruiting bodies was inhibited. An offensive odor then developed along with a severe soft rot that was similar to the disease symptoms observed under natural conditions. The fruiting bodies of negative control were growing healthily with no symptoms. Koch's postulates were fulfilled by isolating bacteria from lesions on artificially inoculated fruiting bodies that were identical to the original isolates based on morphological characteristics, 16S rDNA sequences and biochemical test results. C. neteri was formally reported as a pathogen to humans that could cause bacteremia (Farmer et al. 1982). Recently, it has also been reported causing soft rot disease on mushrooms of Pholiota nameko (Yan et al. 2018) and yellow sticky disease on mushrooms of Flammulina velutipes (Yan et al. 2019). However, to the best of our knowledge, this is the first report of C. neteri-induced yellow rot disease of P. pulmonarius in China.

scholarly journals Obtaining long 16S rDNA sequences using multiple primers and its application on dioxin-containing samples

2015 ◽  
Vol 16 (Suppl 18) ◽  
pp. S13 ◽  
Author(s):  
Yi-Lin Chen ◽  
Chuan-Chun Lee ◽  
Ya-Lan Lin ◽  
Kai-Min Yin ◽  
Chung-Liang Ho ◽  
...  
Keyword(s):  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences
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