Diversity of PKS and NRPS gene clusters between Streptomyces abyssomicinicus sp. nov. and its taxonomic neighbor.

Streptomyces sp. CHI39, isolated from a rock soil sample, is a producer of abyssomicin I. The taxonomic status was clarified by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was closely related to Streptomyces fragilis, with similarity of 99.9%. Strain CHI39 comprised LL-diaminopimelic acid, glutamic acid, glycine, and alanine in its peptidoglycan. The predominant menaquinones were MK-9(H), and major fatty acids were anteiso-C, anteiso-C, and iso-C. The chemotaxonomic features matched those described for the genus Streptomyces. Genome sequencing was conducted for strain CHI39 and S. fragilis NBRC 12862. The results of digital DNA-DNA hybridization along with differences in phenotypic characteristics between the strains suggested strain CHI39 to be a novel species, for which Streptomyces abyssomicinicus sp. nov. is proposed; the type strain is CHI39 (=NBRC 110469). Next, we surveyed polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters in genomes of S. abyssomicinicus CHI39 and S. fragilis NBRC 12862. These strains encoded 9 and 12 clusters, respectively, among which only four clusters were shared between them while the others are specific in each strain. This suggests that strains classified to distinct species each harbor many specific secondary metabolite-biosynthetic pathways even if the strains are taxonomically close.