New genus-specific primers for the PCR identification of members of the genus Saccharomonospora and evaluation of the microbial diversity of wild-type isolates of Saccharomonospora detected from soil DNAs.

Members of the genus Saccharomonospora are isolated infrequently, probably due to the low occurrence of these actinomycetes in the environment. Although members of this genus can easily be identified by micromorphological criteria, the extensive chemotaxonomic characterization of each new isolate is a time-consuming task which cannot always be undertaken when handling large numbers of strains as is the case in natural products screening programmes. In this work, the design of one set of genus-specific oligonucleotides which allows rapid detection of members of the genus Saccharomonospora by means of PCR-specific amplification is presented. The genus specificity of these primers was validated on a wide range of collection and wild-type strains, and subsequently applied to evaluate the presence of representatives of this taxon directly from soil DNAs. Partial 16S rDNA sequencing of representative wild-type strains was used to validate their genus assignment. Further analyses of PCR fingerprinting patterns and 16S-23S internal transcribed spacer sequences were used to determine the diversity of wild-type isolates obtained from soils. This study shows the usefulness of the application of these primers for the direct identification of members of this genus and in assessment of its occurrence within natural microbial habitats.