Genotypic characteristics of therrnoperon and genome of indigenous soybeanBradyrhizobiain cropping zones of China

2006 ◽  
Vol 52 (10) ◽  
pp. 968-976 ◽  
Author(s):  
Jiang Ke Yang ◽  
Wei Tao Zhang ◽  
Tian Ying Yuan ◽  
Jun Chu Zhou
Keyword(s):  
16S Rrna ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
23S Rrna ◽  
Group Iii ◽  
The North ◽  
Group I ◽  
Genotypic Characteristics ◽  
Reference Strains

Four genetic assays, 16S rRNA restriction fragment length polymorphism (RFLP), 16S rRNA sequencing, 16S–23S rRNA intergenetic spacer (IGS) RFLP, and amplified fragment length polymorphism (AFLP), were conducted to determine the genotypic characteristics of 44 indigenous strains of Bradyrhizobium from soybean (Glycine max L.) cropping zones of China. The results generated from different assays showed that soybean bradyrhizobial isolates comprised four genomic groups. Group I was composed of strains mainly isolated from the North and Northeast plains of China. All four assays confirmed this group as phylogenetically divergent from all the reference strains. Strains of the group may represent a new species. Strains in Group II isolated from a variety of geographic regions were ascribed to B. liaoningense. Strains in Group III, mainly isolated from Central and East China, were closely related to the reference strains of B. japonicum. Strains in Group IV belonged to B. elkanii.Key words: soybean bradyrhizobia, 16S rRNA RFLP, 16S–23S IGS RFLP, AFLP.

scholarly journals Rapid Identification and Differentiation of the Soft Rot Erwinias by 16S-23S Intergenic Transcribed Spacer-PCR and Restriction Fragment Length Polymorphism Analyses

2001 ◽  
Vol 67 (9) ◽  
pp. 4070-4076 ◽  
Author(s):  
I. K. Toth ◽  
A. O. Avrova ◽  
L. J. Hyman
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Soft Rot ◽  
Group Iii ◽  
Group I ◽  
Its Pcr ◽  
Restriction Fragment Length

ABSTRACT Current identification methods for the soft rot erwinias are both imprecise and time-consuming. We have used the 16S-23S rRNA intergenic transcribed spacer (ITS) to aid in their identification. Analysis by ITS-PCR and ITS-restriction fragment length polymorphism was found to be a simple, precise, and rapid method compared to current molecular and phenotypic techniques. The ITS was amplified fromErwinia and other genera using universal PCR primers. After PCR, the banding patterns generated allowed the soft rot erwinias to be differentiated from all other Erwinia and non-Erwinia species and placed into one of three groups (I to III). Group I comprised all Erwinia carotovorasubsp. atroseptica and subsp.betavasculorum isolates. Group II comprised allE. carotovora subsp. carotovora,subsp. odorifera, and subsp. wasabiae andE. cacticida isolates, and group III comprised allE. chrysanthemi isolates. To increase the level of discrimination further, the ITS-PCR products were digested with one of two restriction enzymes. Digestion with CfoI identified E. carotovora subsp.atroseptica and subsp. betavasculorum(group I) and E. chrysanthemi (group III) isolates, while digestion with RsaI identified E. carotovora subsp. wasabiae, subsp. carotovora, and subsp.odorifera/carotovora and E. cacticida isolates (group II). In the latter case, it was necessary to distinguishE. carotovora subsp. odorifera and subsp. carotovora using the α-methyl glucoside test. Sixty suspected soft rot erwinia isolates from Australia were identified as E. carotovora subsp.atroseptica, E. chrysanthemi,E. carotovora subsp. carotovora, and non-soft rot species. Ten “atypical” E. carotovora subsp. atroseptica isolates were identified as E. carotovora subsp.atroseptica, subsp. carotovora, and subsp. betavasculorum and non-soft rot species, and two “atypical” E. carotovora subsp.carotovora isolates were identified as E. carotovora subsp. carotovora and subsp.atroseptica.

Genetic diversity amongBradyrhizobiumisolates that effectively nodulate peanut (Arachis hypogaea)

1996 ◽  
Vol 42 (11) ◽  
pp. 1121-1130 ◽  
Author(s):  
Bruce E. Urtz ◽  
Gerald H. Elkan
Keyword(s):  
Genetic Diversity ◽  
Restriction Fragment Length Polymorphism ◽  
16S Rrna ◽  
Arachis Hypogaea ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Dna Homology ◽  
Symbiotic Gene ◽  
Restriction Fragment Length

Symbiotic gene diversity and other measures of genetic diversity were examined in Bradyrhizobium isolates that form an effective symbiosis with peanut (Arachis hypogaea). Initially, restriction fragment length polymorphism (RFLP) analysis using a nitrogenase (nif) gene probe was performed on 33 isolates along with one Bradyrhizobium elkanii and two Bradyrhizobium japonicum strains. Considerable diversity was observed among the RFLP patterns of many of the isolates, especially those from South America. Some isolates, however, were found to have similar nif and subsequent nod (nodulation) gene RFLP patterns, indicating symbiotic gene relatedness. With some noted exceptions, symbiotic gene relatedness correlated with relatedness based on total DNA homology and ribotyping analyses. Symbiotic gene relatedness also correlated with symbiotic effectiveness. The RFLP and DNA homology analyses indicate that bradyrhizobia effective with peanut are genetically diverse and consist of at least three different species. This diversity, however, was not particularly evident with partial 16S rRNA gene sequencing. Sequences obtained from the isolates were very similar to each other as well as to sequences previously reported for other Bradyrhizobium strains.Key words: Bradyrhizobium, nif, peanut, restriction fragment length polymorphism, 16S rRNA.

scholarly journals Analysis of the Endophytic Actinobacterial Population in the Roots of Wheat (Triticum aestivum L.) by Terminal Restriction Fragment Length Polymorphism and Sequencing of 16S rRNA Clones

2004 ◽  
Vol 70 (3) ◽  
pp. 1787-1794 ◽  
Author(s):  
Vanessa M. Conn ◽  
Christopher M. M. Franco
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
16S Rrna ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Restriction Fragment Length

ABSTRACT The endophytic actinobacterial population in the roots of wheat grown in three different soils obtained from the southeast part of South Australia was investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of the amplified 16S rRNA genes. A new, validated approach was applied to the T-RFLP analysis in order to estimate, to the genus level, the actinobacterial population that was identified. Actinobacterium-biased primers were used together with three restriction enzymes to obtain terminal restriction fragments (TRFs). The TRFs were matched to bacterial genera by the T-RFLP Analysis Program, and the data were analyzed to validate and semiquantify the genera present within the plant roots. The highest diversity and level of endophytic colonization were found in the roots of wheat grown in a dark loam from Swedes Flat, and the lowest were found in water-repellent sand from Western Flat. This molecular approach detected a greater diversity of actinobacteria than did previous culture-dependent methods, with the predominant genera being Mycobacterium (21.02%) in Swedes Flat, Streptomyces (14.35%) in Red Loam, and Kitasatospora (15.02%) in Western Flat. This study indicates that the soil that supported a higher number of indigenous organisms resulted in wheat roots with higher actinobacterial diversity and levels of colonization within the plant tissue. Sequencing of 16S rRNA clones, obtained using the same actinobacterium-biased PCR primers that were used in the T-RFLP analysis, confirmed the presence of the actinobacterial diversity and identified a number of Mycobacterium and Streptomyces species.

scholarly journals Detection and Characterization of a Dehalogenating Microorganism by Terminal Restriction Fragment Length Polymorphism Fingerprinting of 16S rRNA in a Sulfidogenic, 2-Bromophenol-Utilizing Enrichment

2004 ◽  
Vol 70 (2) ◽  
pp. 1169-1175 ◽  
Author(s):  
Donna E. Fennell ◽  
Sung-Keun Rhee ◽  
Young-Beom Ahn ◽  
Max M. Häggblom ◽  
Lee J. Kerkhof
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
16S Rrna ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Reductive Dehalogenation ◽  
Polymorphism Analysis ◽  
Sulfate Reducing ◽  
Restriction Fragment Length

ABSTRACT Terminal restriction fragment length polymorphism analysis of reverse-transcribed 16S rRNA during periods of community flux was used as a tool to delineate the roles of the members of a 2-bromophenol-degrading, sulfate-reducing consortium. Starved, washed cultures were amended with 2-bromophenol plus sulfate, 2-bromophenol plus hydrogen, phenol plus sulfate, or phenol with no electron acceptor and were monitored for substrate use. In the presence of sulfate, 2-bromophenol and phenol were completely degraded. In the absence of sulfate, 2-bromophenol was dehalogenated and phenol accumulated. Direct terminal restriction fragment length polymorphism fingerprinting of the 16S rRNA in the various subcultures indicated that phylotype 2BP-48 (a Desulfovibrio-like sequence) was responsible for the dehalogenation of 2-bromophenol. A stable coculture was established which contained predominantly 2BP-48 and a second Desulfovibrio-like bacterium (designated BP212 based on terminal restriction fragment length polymorphism fingerprinting) that was capable of dehalogenating 2-bromophenol to phenol. Strain 2BP-48 in the coculture could couple reductive dehalogenation to growth with 2-bromophenol, 2,6-dibromophenol, or 2-iodophenol and lactate or formate as the electron donor. In addition to halophenols, strain 2BP-48 appears to use sulfate, sulfite, and thiosulfate as electron acceptors and is capable of simultaneous sulfidogenesis and reductive dehalogenation in the presence of sulfate.

scholarly journals Genotypic Characterization of Bradyrhizobium Strains Nodulating Small Senegalese Legumes by 16S-23S rRNA Intergenic Gene Spacers and Amplified Fragment Length Polymorphism Fingerprint Analyses

2000 ◽  
Vol 66 (9) ◽  
pp. 3987-3997 ◽  
Author(s):  
Florence Doignon-Bourcier ◽  
Anne Willems ◽  
Renata Coopman ◽  
Gisele Laguerre ◽  
Monique Gillis ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Restriction Analysis ◽  
Intergenic Spacer ◽  
Amplified Fragment Length Polymorphism ◽  
Rrna Genes ◽  
Leguminous Plant ◽  
23S Rrna ◽  
Pcr Rflp

ABSTRACT We examined the genotypic diversity of 64Bradyrhizobium strains isolated from nodules from 27 native leguminous plant species in Senegal (West Africa) belonging to the genera Abrus, Alysicarpus,Bryaspis, Chamaecrista, Cassia,Crotalaria, Desmodium, Eriosema,Indigofera, Moghania, Rhynchosia,Sesbania, Tephrosia, and Zornia, which play an ecological role and have agronomic potential in arid regions. The strains were characterized by intergenic spacer (between 16S and 23S rRNA genes) PCR and restriction fragment length polymorphism (IGS PCR-RFLP) and amplified fragment length polymorphism (AFLP) fingerprinting analyses. Fifty-three reference strains of the different Bradyrhizobium species and described groups were included for comparison. The strains were diverse and formed 27 groups by AFLP and 16 groups by IGS PCR-RFLP. The sizes of the IGS PCR products from the Bradyrhizobium strains that were studied varied from 780 to 1,038 bp and were correlated with the IGS PCR-RFLP results. The grouping of strains was consistent by the three methods AFLP, IGS PCR-RFLP, and previously reported 16S amplified ribosomal DNA restriction analysis. For investigating the whole genome, AFLP was the most discriminative technique, thus being of particular interest for future taxonomic studies in Bradyrhizobium, for which DNA is difficult to obtain in quantity and quality to perform extensive DNA:DNA hybridizations.

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