The characterisation and detection of plant Pathogenic streptomycetes in the natural environment

Streptomyces scabies has been attributed to be the causal agent of common scab, a superficial disease of the potato. Confusion over the taxonomic position of the organism arose as a result of the erroneous designation of a type strain that did not match the original description. This confusion was compounded by the deposition of many taxonomically distinct pathogenic strains in culture collections under the name of Streptomyces scabies. These studies attempted to clarify the taxonomic position of this organism. Common scab strains were characterised on the basis of phenotypic variation and hybridization to 16S rRNA probes. Pathogenic strains appeared to conform to three centres of variation similar to the S.albidoflavus, S.rochei and S.diastaticus Streptomyces spp. groups. The pathogenicity of putative pathogens was investigated and the pathogenic basis to the taxonomically heterogeneous group confirmed. Further studies focused on the development and application of approaches to the monitoring and detection of these strains in soil. Strain, ISP5078 has been well characterised and was selected as a model strain to pursue these objectives. Monitoring and detection strategies evaluated included: screening ISP5078 for selective phenotypic markers (such as antibiotic resistance) to assist in its selective recovery from soil and attempting to insert the marker genes xylE (novel to the Streptomyces) and nptll (a kanamycin resistance determinant) into the chromosome of strain ISP5078. Studies were also initiated to apply 16S rRNA targeted oligonucleotide probes to the monitoring of streptomycete inoculants in the natural environment. Studies focused on the development and evaluation of a method for the extraction and recovery of 16S ribosomal RNA from soil and the application of 16S rRNA probes to in situ hybridizations in the analysis of the lifecycle of scab-causing Streptomyces strains in situ. The influence of the potato rhizosphere on common scab strain populations was assessed by applying specific strategies to follow the fate of ISPS078 in sterile soil with and without potato plants. The lifecycle and activity of scab-causing streptomycetes in association with potatoes and soil was investigated using scanning electron microscopy and in situ hybridization