WGS of Two Novel Streptomyces Isolates with Interesting Secondary Metabolite Gene Clusters

Streptomyces sp. bear antibiotics, antifungal and antitumor compounds. Anthracyclines and angucyclines are antitumor drugs with cytotoxic effects. During an artichoke cover cropping experiment at Rodale Organic Institute in Camarillo, actinomycetes were quantified and isolated. The purpose was to identify microbes with antibiotic qualities land unusual spore pigmentation in soil. Two Streptomyces sp. isolates, 37-AD-D4 and 42-E-JU, were from plots treated with polyethylene covers. The 16S rRNAs from the cultures were Sanger sequenced and analyzed on the DNA Subway Blue Line; there was low % similarity of partial 16S sequences. Strains were sent to Innomics for Whole genome sequencing (WGS) on BGI DNBseq. WGS reads were analyzed for quality and taxonomic classification using MiGA. WGS reads were assembled using SPAdes. Putative secondary metabolite gene clusters were identified with antiSMASH. Ketosynthase gene predictions were generated with NaPDoS2. The percentage of actinomycetes in the plots was between 6.2 and 6.45% in PLFA analysis; the Total Living Microbial Biomass was 2134.66-2258.31 ng/g. 16S microbial metabarcoding analysis was performed on soil. MiGA classification results from WGS indicated the closest relative to 37-AD-D4 was Streptomyces viridodiastaticus (88.68% AAI, p=0.39); 42-E-JU was most closely related to Streptomyces nigrum (84.16% AAI, p=0.549). Streptomyces sp. 37-AD-D4 contained an anthracycline domain 87% similar to mithramicin, an aromatic spore pigment domain 80% similar to the Streptomyces collinus reference, and a PK spore pigment gene cluster 83% ID to the known Streptomyces avermitilis cluster. WGS of 42-E-JU contained a spore pigment polyketide 75% similar to S. avermitilis and kinamycin, an angucycline (73% ID). The 16S Illumina metabarcoding output from soil sample 42-JU contained 256 rarified reads of Streptomyces that were unassigned to a species. The output from sample 37-AD contained 34 rarified reads assigned to unclassified species of Streptomyces. The secondary metabolite biochemical analysis should be explored. Volatiles should be analyzed and potential antitumor effects tested.