Rhizobia isolated from root nodules of tropical leguminous trees characterized using DNA-DNA dot-blot hybridisation and rep-PCR genomic fingerprinting

Fifty-one fast growing rhizobial strains isolated from root nodules of Acac ia senegal and Prosopis chilensis in Sudan and Kenya were divided into DNA homology groups using non-radioactive DNA-DNA dot-blot hybridisation. Rhizo bium leguminosarum, R. galegae, R. tropici, Mesorhizobium loti, Sinorhizobi um fredii, S. meliloti used in numerical taxonomy were included in the hybr idisation experiments as reference strains and, at a later stage S. saheli and S. terangae. Scores given to the intensities of dots detected in the hy bridisation experiments were used in principal component analysis, which cl ustered the majority of the tree rhizobia in two separate DNA-homology grou ps. The 51 strains were also analysed by genomic fingerprinting using the r epetitive sequence-based polymerase chain reaction (rep-PCR) method with RE P, ERIC, BOX and GTG5 primers. The resulting genomic fingerprints were comp ared with strains representing 15 rhizobial species. The relationship of 17 Sudanese strains to established sinorhizobial species was examined using t he optical renaturation rates method and the G+C content of nine strains wa s determined. Results from dot-blot hybridisation and rep-PCR experiments w ere found to be in close agreement with each other and with the results obt ained from spectrophotometric reassociation analysis. We suggest that rep-P CR fingerprinting can be used as a first and dot-blot hy bridisation as a s econd rapid and dependable genomic screening method to classify new rhizobi al isolates of unknown taxonomic status and to choose the representative st rains for the more laborious DNA-DNA reassociation experiments.