Genome Sequence Resources for Verticillium dahliae-Inhibiting Streptomyces spp. Isolated from Agricultural Soil

Abstract

Gram-positive Streptomyces bacteria are common in soil, where they can inhibit soilborne plant pathogens by producing antimicrobial secondary metabolites. This study generated genome assemblies of Streptomyces isolates from soil that inhibit the soilborne plant pathogen Verticillium dahliae. Five bacterial isolates were cultured from soil collected from the Salinas Valley region of California. In vitro tests showed that three bacterial isolates inhibited V. dahliae growth when applied at low and high spore concentrations, whereas two isolates only inhibited V. dahliae when applied at high spore concentrations. Generation of hybrid Illumina-Nanopore assemblies showed that isolate genomes ranged from 7.45 to 8.95 Mbs. The contig number per assembly ranged from 1 to 54. All assemblies had 100% completeness values based on a standard set of conserved orthologs found in all bacteria. The number of predicted genes ranged from 6,594 to 8,098. Over 25 putative secondary metabolite biosynthetic clusters were identified in each assembly. Calculation of digital DNA:DNA hybridization and average nucleotide identity values using additional genome assemblies from type specimens of Streptomyces showed that the five isolates are likely novel Streptomyces spp. The results and data generated from this study will provide a basis for future research on the use of Streptomyces for managing common soilborne pathogens such as V. dahliae. [Figure: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.

Keywords

• biological control
• microbiome
• secondary metabolism
• soilborne disease