rRNA based identification and detection systems for rhizobia and other bacteria

Ribosomal ribonucleic acids are excellent marker molecules for the elucidat ion of bacterial phylogeny; they also provide useful target sites for ident ification and detection with nucleic acid probes. Based on the currently av ailable 16S rRNA sequence data, bacteria of the rhizobial phenotype (plant nodulation, nitrogen fixation) are members of three moderately related phyl ogenetic sub-groups of the alpha-subclass of the Proteobacteria : i.e. the rhizobia group, the bradyrhizobia group, and the azorhizobia group. Ail rhi zobia, azo-, brady-, meso- and sinorhizobia are closely related to and in s ome cases phylogenetically intermixed with, non-symbiotic and/or non-nitrog en-fixing bacteria. Especially in the case of Bradyrhizobium japonicum stra ins, the 16S rRNA sequence data indicate substantial heterogeneity. Specifi c probe design and evaluation are discussed. A multiprobe concept for resol ving specificity problems with group specific probes is presented. In situ identification with group specific probes of rhizobia in cultures as well a s rhizobia and cyanobacteria within plant material is shown.