MOLECULAR ECOLOGY OF FRANKIA - ADVANTAGES AND DISADVANTAGES OF THE USE OF DNA PROBES

Ecological studies on the actinomycete Frankia are often influenced by the difficulty to isolate and identify this microorganism. The application of molecular biological techniques offers possibilities to detect microbes without isolation and cultivation. Nif genes or whole plasmids can serve as targets for the design of specific probes. Alternatively, ribosomal RNA (rRNA), commonly used in modern phylogenetic studies, can be used as a target molecule in ecological studies. This paper gives an overview of new developments on the use of 16S rRNA as a target molecule for oligonucleotide probes. Group-specific sequences in the 16S rRNA of Frankia can be used as targets for oligonucleotide probes that a) recognize ineffective Frankia strains on Alnus, b) recognize effective strains on Alnus, c) recognize all Frankia strains tested so far. The present paper summarizes the essential steps needed for the use of these probes for the detection of Frankia strains in soil without isolation and cultivation.