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Roberto Defez - One of the best experts on this subject based on the ideXlab platform.
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use of nodulation pattern stress tolerance nodc gene amplification rapd pcr and rflp 16s rDNA Analysis to discriminate genotypes of rhizobium leguminosarum biovar viciae
Systematic and Applied Microbiology, 2005Co-Authors: Giancarlo Moschetti, Anna Lucia Peluso, Andrea Protopapa, Marilena Anastasio, Olimpia Pepe, Roberto DefezAbstract:Twenty-seven new Rhizobium isolates were obtained from root nodules of wild and crop legumes belonging to the genera Vicia, Lathyrus and Pisum from different agroecological areas in central and southern Italy. A polyphasic approach including phenotypic and genotypic techniques was used to study their diversity and their relationships with other biovars and species of rhizobia. Analysis of symbiotic properties and stress tolerance tests revealed that wild isolates showed a wide spectrum of nodulation and a marked variation in stress tolerance compared with reference strains tested in this study. All rhizobial isolates (except for the isolate CG4 from Galega officinalis) were presumptively identified as Rhizobium leguminosarum biovar viciae both by their symbiotic properties and the specific amplification of the nodC gene. In particular, we found that the nodC gene could be used as a diagnostic molecular marker for strains belonging to the bv. viciae. RFLP-PCR 16S rDNA Analysis confirms these results, with the exception of two strains that showed different RFLP-genotypes from those of the reference strains of R. leguminosarum bv. viciae. Analysis of intraspecies relationship among strains by using the RAPD-PCR technique showed a high level of genetic polymorphism, grouping our isolates and reference strains into six different major clusters with a similarity level of 20%. Data from seven parameters of phenotypic and genotypic analyses were evaluated by using principal component Analysis which indicated the differences among strains and allowed them to be divided into seven different groups.
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Use of nodulation pattern, stress tolerance, nodC gene amplification, RAPD-PCR and RFLP–16S rDNA Analysis to discriminate genotypes of Rhizobium leguminosarum biovar viciae
Systematic and Applied Microbiology, 2005Co-Authors: Giancarlo Moschetti, Anna Lucia Peluso, Andrea Protopapa, Marilena Anastasio, Olimpia Pepe, Roberto DefezAbstract:Twenty-seven new Rhizobium isolates were obtained from root nodules of wild and crop legumes belonging to the genera Vicia, Lathyrus and Pisum from different agroecological areas in central and southern Italy. A polyphasic approach including phenotypic and genotypic techniques was used to study their diversity and their relationships with other biovars and species of rhizobia. Analysis of symbiotic properties and stress tolerance tests revealed that wild isolates showed a wide spectrum of nodulation and a marked variation in stress tolerance compared with reference strains tested in this study. All rhizobial isolates (except for the isolate CG4 from Galega officinalis) were presumptively identified as Rhizobium leguminosarum biovar viciae both by their symbiotic properties and the specific amplification of the nodC gene. In particular, we found that the nodC gene could be used as a diagnostic molecular marker for strains belonging to the bv. viciae. RFLP-PCR 16S rDNA Analysis confirms these results, with the exception of two strains that showed different RFLP-genotypes from those of the reference strains of R. leguminosarum bv. viciae. Analysis of intraspecies relationship among strains by using the RAPD-PCR technique showed a high level of genetic polymorphism, grouping our isolates and reference strains into six different major clusters with a similarity level of 20%. Data from seven parameters of phenotypic and genotypic analyses were evaluated by using principal component Analysis which indicated the differences among strains and allowed them to be divided into seven different groups.
Jongsik Chun - One of the best experts on this subject based on the ideXlab platform.
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archaeal diversity in tidal flat sediment as revealed by 16s rDNA Analysis
Journal of Microbiology, 2005Co-Authors: Huynmyung Oh, Hojeong Kang, Jongsik ChunAbstract:: During the past ten years, Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages. More recently, the presence of novel archaeal phylogenetic lineages has been discovered in coastal marine environments, freshwater lakes, polar seas, and deep-sea hydrothermal vents. Therefore, we conducted an investigation into the archaeal community existing in tidal flat sediment collected from Ganghwa Island, Korea. Phylogenetic Analysis of archaeal 16S rDNA amplified directly from tidal flat sediment DNA revealed the presence of two major lineages, belonging to the Crenarchaeota (53.9%) and Euryarchaeota (46.1%) phyla. A total of 102 clones were then sequenced and analyzed by comprehensive phylogenetic Analysis. The sequences determined in our samples were found to be closely related to the sequences of clones which had been previously obtained from a variety of marine environments. Archaeal clones exhibited higher similarities (83.25-100%) to sequences from other environments in the public database than did those (75.22-98.46%) of previously reported bacterial clones obtained from tidal flat sediment. The results of our study suggest that the archaeal community in tidal flat sediment is remarkably diverse.
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remarkable bacterial diversity in the tidal flat sediment as revealed by 16s rDNA Analysis
Journal of Microbiology and Biotechnology, 2004Co-Authors: Huynmyung Oh, Hojeong Kang, Seok Soon Park, Jongsik ChunAbstract:A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community Analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.
Giancarlo Moschetti - One of the best experts on this subject based on the ideXlab platform.
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use of nodulation pattern stress tolerance nodc gene amplification rapd pcr and rflp 16s rDNA Analysis to discriminate genotypes of rhizobium leguminosarum biovar viciae
Systematic and Applied Microbiology, 2005Co-Authors: Giancarlo Moschetti, Anna Lucia Peluso, Andrea Protopapa, Marilena Anastasio, Olimpia Pepe, Roberto DefezAbstract:Twenty-seven new Rhizobium isolates were obtained from root nodules of wild and crop legumes belonging to the genera Vicia, Lathyrus and Pisum from different agroecological areas in central and southern Italy. A polyphasic approach including phenotypic and genotypic techniques was used to study their diversity and their relationships with other biovars and species of rhizobia. Analysis of symbiotic properties and stress tolerance tests revealed that wild isolates showed a wide spectrum of nodulation and a marked variation in stress tolerance compared with reference strains tested in this study. All rhizobial isolates (except for the isolate CG4 from Galega officinalis) were presumptively identified as Rhizobium leguminosarum biovar viciae both by their symbiotic properties and the specific amplification of the nodC gene. In particular, we found that the nodC gene could be used as a diagnostic molecular marker for strains belonging to the bv. viciae. RFLP-PCR 16S rDNA Analysis confirms these results, with the exception of two strains that showed different RFLP-genotypes from those of the reference strains of R. leguminosarum bv. viciae. Analysis of intraspecies relationship among strains by using the RAPD-PCR technique showed a high level of genetic polymorphism, grouping our isolates and reference strains into six different major clusters with a similarity level of 20%. Data from seven parameters of phenotypic and genotypic analyses were evaluated by using principal component Analysis which indicated the differences among strains and allowed them to be divided into seven different groups.
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Use of nodulation pattern, stress tolerance, nodC gene amplification, RAPD-PCR and RFLP–16S rDNA Analysis to discriminate genotypes of Rhizobium leguminosarum biovar viciae
Systematic and Applied Microbiology, 2005Co-Authors: Giancarlo Moschetti, Anna Lucia Peluso, Andrea Protopapa, Marilena Anastasio, Olimpia Pepe, Roberto DefezAbstract:Twenty-seven new Rhizobium isolates were obtained from root nodules of wild and crop legumes belonging to the genera Vicia, Lathyrus and Pisum from different agroecological areas in central and southern Italy. A polyphasic approach including phenotypic and genotypic techniques was used to study their diversity and their relationships with other biovars and species of rhizobia. Analysis of symbiotic properties and stress tolerance tests revealed that wild isolates showed a wide spectrum of nodulation and a marked variation in stress tolerance compared with reference strains tested in this study. All rhizobial isolates (except for the isolate CG4 from Galega officinalis) were presumptively identified as Rhizobium leguminosarum biovar viciae both by their symbiotic properties and the specific amplification of the nodC gene. In particular, we found that the nodC gene could be used as a diagnostic molecular marker for strains belonging to the bv. viciae. RFLP-PCR 16S rDNA Analysis confirms these results, with the exception of two strains that showed different RFLP-genotypes from those of the reference strains of R. leguminosarum bv. viciae. Analysis of intraspecies relationship among strains by using the RAPD-PCR technique showed a high level of genetic polymorphism, grouping our isolates and reference strains into six different major clusters with a similarity level of 20%. Data from seven parameters of phenotypic and genotypic analyses were evaluated by using principal component Analysis which indicated the differences among strains and allowed them to be divided into seven different groups.
Erko Stackebrandt - One of the best experts on this subject based on the ideXlab platform.
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the phylogenetic diversity of thermophilic members of the genus bacillus as revealed by 16s rDNA Analysis
Fems Microbiology Letters, 1994Co-Authors: Fred A Rainey, Dagmar Fritze, Erko StackebrandtAbstract:Sixteen thermophilic strains of the genus Bacillus, representing eight validly described and six invalidly described species, as well as one unassigned strain, were investigated by comparative 16S rDNA analyses and the sequences compared to the existing database for the genera Bacillus and Alicyclobacillus. The majority of strains were found to cluster in two groups represented by B. stearothermophilus and B. pallidus. Bacillus smithii, B. thermocloacae, and B. thermoruber are phylogenetically well separated and cluster within the radiation of mesophilic bacilli. The as yet undescribed taxon ‘B. flavothermus’ warrants species status. B. schlegelii and B. tusciae group peripherally with members of Alicyclobacillus and may be reclassified when more phenotypic data support their phylogenetic position.
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16s rDNA Analysis reveals phylogenetic diversity among the polysaccharolytic clostridia
Fems Microbiology Letters, 1993Co-Authors: Frederick A Rainey, Erko StackebrandtAbstract:Small subunit rDNA sequences were determined for 13 mesophilic, polysaccharolytic, mainly cellulolytic species of the genus Clostridium and one cellulolytic Eubacterium specues. Sequences were compared to those of 36 representatives of mesophilic and thermophilic clostridia, including those of nine thermophilic polysaccharolytic species published previously. The majority of strains group with 23S rRNA clusters I and III, while the others group with the thermophilic polysaccharolytic clostridia, i.e. C. stercorarium, C. thermolacticum and C. thermocellum. Lack of close genetic relationships between the various polysaccharolytic species is unexpected and may indicate that these biotechnologically important organisms differ with respect to the enzymology of polysaccharolytic degradation as well.
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bacterial diversity in a soil sample from a subtropical australian environment as determined by 16s rDNA Analysis
The FASEB Journal, 1993Co-Authors: Erko Stackebrandt, Werner Liesack, B M GoebelAbstract:In order to investigate the genetic diversity of streptomycetes in an acid forested soil sample from Mt. Coot-tha, Brisbane, Australia, cells were mechanically lysed within the soil matrix and genomic DNA was isolated and purified. 16S ribosomal (r)DNA was amplified by the polymerase chain reaction (PCR) method using one primer conserved for members of the domain Bacteria and a second designed specifically for streptomycetes and related taxa. PCR amplification products were cloned into phage vector M13 mp19 and the diversity of 16S rDNA genes was determined by sequence Analysis and oligonucleotide probing of the resultant clone library. Comparison of partial 16S rDNA sequences with published sequences revealed that few sequences originated from streptomycetes. The majority of sequences belonged to members of the alpha subclass of Proteobacteria. Other clones were related to planctomycetes, actinomycetes, or represented novel lines of descent. Bacteria that are customarily isolated from soil of pH 4-7 such...
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16s rDNA Analysis of spirochaeta thermophila its phylogenetic position and implications for the systematics of the order spirochaetales
Systematic and Applied Microbiology, 1992Co-Authors: Frederick A Rainey, Matthias Dorsch, Hugh W Morgan, Erko StackebrandtAbstract:Summary The 16S rRNA gene of Spirochaeta thermophila DSM 6578 was amplifed by the polymerase chain reaction and Analysis of a 1333 nucleotide long stretch performed. The sequence was aligned to the homologous region of 13 representatives from six spirochete genera, and the phylogenetic position of S. thermophila determined. This species constitutes a deep-branching member of a cluster that is defined by representatives of Spirochaeta and Treponema and by Borellia burgdorferi . The genera Serpulina, Leptonema and Leptospira are more ancient representatives of the spirochete line of descent. The branching pattern confirms earlier results of phylogenetic studies which showed the genus Spirochaeta to be heterogeneous, with S. zuelzerae and S. stenostrepta displaying a higher degree of relatedness to treponemas than to the main (authentic) Spirochaeta group.
Huynmyung Oh - One of the best experts on this subject based on the ideXlab platform.
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archaeal diversity in tidal flat sediment as revealed by 16s rDNA Analysis
Journal of Microbiology, 2005Co-Authors: Huynmyung Oh, Hojeong Kang, Jongsik ChunAbstract:: During the past ten years, Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages. More recently, the presence of novel archaeal phylogenetic lineages has been discovered in coastal marine environments, freshwater lakes, polar seas, and deep-sea hydrothermal vents. Therefore, we conducted an investigation into the archaeal community existing in tidal flat sediment collected from Ganghwa Island, Korea. Phylogenetic Analysis of archaeal 16S rDNA amplified directly from tidal flat sediment DNA revealed the presence of two major lineages, belonging to the Crenarchaeota (53.9%) and Euryarchaeota (46.1%) phyla. A total of 102 clones were then sequenced and analyzed by comprehensive phylogenetic Analysis. The sequences determined in our samples were found to be closely related to the sequences of clones which had been previously obtained from a variety of marine environments. Archaeal clones exhibited higher similarities (83.25-100%) to sequences from other environments in the public database than did those (75.22-98.46%) of previously reported bacterial clones obtained from tidal flat sediment. The results of our study suggest that the archaeal community in tidal flat sediment is remarkably diverse.
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remarkable bacterial diversity in the tidal flat sediment as revealed by 16s rDNA Analysis
Journal of Microbiology and Biotechnology, 2004Co-Authors: Huynmyung Oh, Hojeong Kang, Seok Soon Park, Jongsik ChunAbstract:A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community Analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.
