Taxonomic Utility of Restriction Endonuclease Fingerprinting of Large DNA Fragments from Streptomyces Strains

Using a method known as low-frequency restriction fragment analysis (LFRFA) (M. L. Beyazova and M. P. Lechevalier, Int. J. Syst. Bacteriol. 42:422-433, 1992), we determined the molecular weights of Ase I restriction fragments of Streptomyces DNAs by pulsed-field gel electrophoresis. The levels of similarity of fragment patterns among strains were determined by using the simple matching coefficient, and clustering was performed by using the unweighted pair group with mathematical average algorithm. A total of 59 strains representing eight species and the numerically classified taxon Streptomyces cyaneus group A18 (S. T. Williams, M. Goodfellow, G. Alderson, E. M. H. Wellington, P. H. A. Sneath, and M. J. Sackin, J. Gen. Microbiol. 129:1743-1813, 1983) were studied. Forty-two strains (six species) formed eight clusters at levels of similarity of more than 80%; 17 strains (including the entire S. cyaneus group) were unclustered. Cluster 1 contained all of the Streptomyces albus strains studied plus two strains of Streptomyces somaliensis and two strains of Streptomyces lavendulae. Cluster 2 contained 8 of the 12 Streptomyces fradiae strains examined plus one strain each of S. somaliensis and S. lavendulae. Cluster 3 was heterogeneous in terms of species. Cluster 4 contained two S. somaliensis strains; cluster 5 contained three S. fradiae strains; cluster 6 contained three Streptomyces rimosus strains; and clusters 7 and 8 contained seven and three Streptomyces ipomoea strains, respectively. The S. cyaneus group strains exhibited no clustering among themselves or with the other species examined. Some Streptomyces species which exhibited high levels of similarity (85 to 95%) in physiological tests (e.g., S. albus and the S. fradiae strains in cluster 2) exhibited high levels of similarity in the LFRFA (84 and 81%, respectively). Other taxa (S. cyaneus group) which exhibited equally high levels of physiological similarity (90%) appeared to be unrelated as determined by the LFRFA. Species with lower levels of physiological similarity (e.g., S. somaliensis[75%], S. lavendulae[63%], and S. rimosus[68%]) exhibited low levels of LFRFA similarity (75, 64, and 54%, respectively). High levels of DNA-DNA relatedness (≫90%) (S. ipomoea) were reflected in high levels of similarity as determined by the LFRFA (75 to 100%); lower levels of DNA-DNA relatedness (ca. 70%) (S. cyaneus group) were reflected in low levels of LFRFA similarity (strains not clustered). We concluded that the presently used physiological tests reflect too small a portion of the genome to be universally useful in streptomycete species characterization. In contrast, high levels of DNA-DNA relatedness (≫90%) and high LFRFA similarity values will probably both be valuable in species delineation in actinomycetes.