A two primers random amplified polymorphic DNA procedure to obtain polymerase chain reaction fingerprints of bacterial species

Rivas, Raúl; Velázquez, Encarna; Valverde, Ángel; Mateos, Pedro F.; Martínez‐Molina, Eustoquio

doi:10.1002/1522-2683()22:6<1086::aid-elps1086>3.0.co;2-6

Cited by 89 publications

(42 citation statements)

References 20 publications

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“…It had some more differences with the protein pattern of O. tritici LMG 18957 T TP-RAPD patterns. In a previous study we showed that TP-RAPD patterns allow the differentiation among rhizobial species (39) and that, within a species, the TP-RAPD pattern is identical for different strains. Figure 9 shows the TP-RAPD patterns of the strains isolated in the present study compared to those of O. anthropi and O. tritici.…”

Section: Downloaded Fromsupporting

confidence: 90%

“…GTTTGATCCTGGCTCAG-3Ј, Escherichia coli positions 8 to 27) and 1522R (5Ј-GGTTACCTTGTTACGACTT-3Ј, E. coli positions 1509 to 1491) were used at 2 M final concentration (39). PCR conditions were as follows: preheating at 95°C for 9 min; followed by 35 cycles of denaturing at 95°C for 1 min, annealing at 45°C for 1 min, and extension at 72°C for 2 min; with a final extension at 72°C for 7 min.…”

Section: Isolation From Plant Nodules Strains Lup21mentioning

confidence: 90%

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Nodulation ofLupinus albusby Strains ofOchrobactrum lupinisp. nov

Trujillo¹,

Willems

Abril

et al. 2005

Appl Environ Microbiol

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211

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The nodulation of legumes has for more than a century been considered an exclusive capacity of a group of microorganisms commonly known as rhizobia and belonging to the ␣-Proteobacteria. However, in the last 3 years four nonrhizobial species, belonging to ␣ and ␤ subclasses of the Proteobacteria, have been described as legume-nodulating bacteria. In the present study, two fast-growing strains, LUP21 and LUP23, were isolated from nodules of Lupinus honoratus. The phylogenetic analysis based on the 16S and 23S rRNA gene sequences showed that the isolates belong to the genus Ochrobactrum. The strains were able to reinfect Lupinus plants. A plasmid profile analysis showed the presence of three plasmids. The nodD and nifH genes were located on these plasmids, and their sequences were obtained. These sequences showed a close resemblance to the nodD and nifH genes of rhizobial species, suggesting that the nodD and nifH genes carried by strain LUP21 T were acquired by horizontal gene transfer. A polyphasic study including phenotypic, chemotaxonomic, and molecular features of the strains isolated in this study showed that they belong to a new species of the genus Ochrobactrum for which we propose the name Ochrobactrum lupini sp. nov. Strain LUP21 T (LMG 20667 T ) is the type strain.Plants from the family Leguminosae are usually capable of dinitrogen fixation because of their symbiotic interaction with nodulating bacteria belonging to the order Rhizobiales. Most bacteria that establish a symbiosis with legume plants, including some nonrhizobial species of Methylobacterium (16, 45) and Devosia (40, 41), belong to the ␣ subclass of Proteobacteria, although some species from genera of the ␤ subclass, such as Ralstonia and Burkholderia, can also nodulate legumes (6,32,53). In the last few years there has been an increasing amount of research focused on bacteria that nodulate stems or roots of tropical legume species. However, the identity of many of the endosymbionts of temperate legumes still remains unknown. The genus Lupinus groups up to 200 species of herbs and small shrubs, broadly distributed in the Mediterranean area and in the American continent, where they colonize very different environments. Despite the agronomic and ecological interest of Lupinus, this plant has been poorly studied with respect to its symbionts. Plants from the genus Lupinus are nodulated by fast-and slow-growing rhizobia; however, slow-growing rhizobia are more frequently isolated from this legume (3,5,21,30). The data obtained from the small-subunit (SSU) rRNA gene indicate a very close relationship between some bradyrhizobia isolated from Lupinus and Bradyrhizobium japonicum (3,12,30). However, bacterial strains nodulating Lupinus plants have been poorly characterized thus far, and fast-growing species nodulating this legume have not been not officially described; nevertheless, in the past the species Rhizobium lupini was proposed (15) and was later abandoned (14).During a study of rhizobia nodulating Lupinus plants in several geographical regi...

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confidence: 90%

Section: Isolation From Plant Nodules Strains Lup21mentioning

confidence: 90%

Nodulation ofLupinus albusby Strains ofOchrobactrum lupinisp. nov

Trujillo¹,

Willems

Abril

et al. 2005

Appl Environ Microbiol

Self Cite

211

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“…DNA extraction was carried out as described previously (Rivas et al, 2001). PCR amplification of 16S rDNA was carried out using primers 59-AGAGTTTGATCTGGCTCAG-39 and 59-AAGGAGGTGATCCANCCRCA-39 under conditions described previously (Velázquez et al, 2001).…”

Section: Methodsmentioning

confidence: 99%

Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra)

Rivas

Sánchez

Trujillo

et al. 2003

International Journal of Systematic and Evolutionary Microbiology

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“…It has been reported that bacterial strains that show identical patterns in TP-RAPD analysis belong to the same species, whereas different species have distinct patterns (Rivas et al, 2001). In the present study, strain CCBAU 25048 T , S. granuli JCM 13254 T , S. zoogloeoides JCM 20728 T , Rhizobium etli CFN 42 T , Rhizobium leguminosarum USDA 2370 T , Ensifer meliloti USDA 1002 T and Mesorhizobium loti NZP 2213 T were incubated in YMA medium (Vincent, 1970) at 28 u C. DNA extracted from these strains with the method of Terefework et al (2001) was used in TP-RAPD analysis as described previously (Trujillo et al, 2005).…”

mentioning

confidence: 99%

Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea

Lin

Wang

Tang

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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Bacterial strain CCBAU 25048 T was isolated from root nodules of Kummerowia stipulacea grown in Shandong province of China. Cells of the strain were Gram-negative, strictly aerobic, nonspore-forming, motile short rods. Phylogeny of 16S rRNA gene sequences revealed that the strain belonged to the genus Shinella, a member of family Rhizobiaceae. Its closest phylogenetic relatives were Shinella granuli Ch06 T and Shinella zoogloeoides IAM 12669 T , respectively showing 98.3 and 98.9 % 16S rRNA gene sequence similarity. Strain CCBAU 25048 T had DNA-DNA relatedness of 43.5 and 34.8 %, respectively, with S. zoogloeoides JCM 20728 T and S. granuli JCM 13254 T . In addition, in TP-RAPD analysis, different patterns were obtained for these three strains and some rhizobial strains. The nifH, nodC and nodD sequences of CCBAU 25048 T were identical or very similar to those of bean-nodulating Rhizobium tropici strains. Several phenotypic characteristics, including the use of citrate and D-ribose as carbon sources and growth at pH 11.0, as well as the fatty acid composition, could differentiate CCBAU 25048 T from the two defined Shinella species. Therefore, a novel species Shinella kummerowiae sp. nov. is proposed, with strain CCBAU 25048 T (5JCM 14778 T 5LMG 24136 T ) as the type strain.Rhizobia are soil bacteria capable of eliciting nodules on leguminous plant roots and/or stems in which the bacteria fix nitrogen. In addition to species in the genera Allorhizobium, Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium and Ensifer (former Sinorhizobium species), symbiotic strains belonging to a wide range of bacterial genera have been reported recently from root nodules of several legume species, including Devosia neptuniae In a survey of Kummerowia rhizobia , we isolated strain CCBAU 25048 T from a root nodule of Kummerowia stipulacea grown in Shandong province of China. This strain was related only distantly to Rhizobium giardinii and was quite different from the defined species of Bradyrhizobium, Rhizobium and Ensifer in the 16S rRNA gene phylogeny . Therefore, it might represent a novel lineage of symbiotic bacteria. With the aim of clarifying the taxonomic position of this strain, we made a serial of analyses, including reconstruction of the 16S rRNA gene phylogenetic tree by adding the recently defined Shinella species, detection and sequencing of symbiotic genes from CCBAU 25048 T , DNA-DNA hybridization, twoprimers randomly amplified polymorphic DNA (TP-RAPD) analysis and phenotypic characterization.The 16S rRNA gene sequence of strain CCBAU 25048 T was closely related to those of Shinella species, recently described members of the family Rhizobiaceae , in the phylogenetic tree of 16S rRNA gene sequences (Fig. 1) reconstructed with the neighbourjoining method and bootstrapped with 1000 replications using MEGA program version 3.1 (Kumar et al., 2004). In this tree, CCBAU 25048 T was most similar to Shinella Abbreviation: TP-RAPD, two-primers randomly amplified polymorphic DNA.The GenBank/EMBL/DDBJ accession number fo...

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A two primers random amplified polymorphic DNA procedure to obtain polymerase chain reaction fingerprints of bacterial species

Cited by 89 publications

References 20 publications

Nodulation ofLupinus albusby Strains ofOchrobactrum lupinisp. nov

Nodulation ofLupinus albusby Strains ofOchrobactrum lupinisp. nov

Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra)

Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea

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