Genome sequence resources for Verticillium dahliae-inhibiting Streptomyces spp. isolated from agricultural soil

Authors: Leblanc, Nicholas; Salgado-Salazar, Catalina

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2022
Publication Date: 3/25/2023
Citation: LeBlanc, N.R., Salgado-Salazar, C. 2023. Genome sequence resources for Verticillium dahliae-inhibiting Streptomyces spp. isolated from agricultural soil. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-10-22-0116-A.
DOI: https://doi.org/10.1094/PHYTOFR-10-22-0116-A

Interpretive Summary: Bacteria called Streptomyces that live in soil can be used to control soilborne diseases and reduce use of chemical pesticides on crops like lettuce and strawberry. This project generated genomic data for five Streptomyces bacteria from soil that inhibit the common soilborne plant pathogen Verticillium dahliae. Laboratory tests showed all bacterial isolates prevented growth of V. dahliae when applied at a high concentration, while three isolates also inhibited the pathogen at a reduced concentration. Use of two different genome sequencing techniques demonstrated the five bacteria had different genome sizes and number of genes that may be involved in production of compounds that prevent growth of the pathogen V. dahliae. Additional comparison of the five bacteria to known bacteria suggested they are novel species previously unknown to science. This research will be an important resource for future studies focused on using Streptomyces bacteria to manage common soilborne plant pathogens.

Technical 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 three bacterial isolates inhibited V. dahliae growth when applied at low and high spore concentrations, while two isolates only inhibited V. dahliae when applied at high spore concentrations. Generation of hybrid Illumina-Nanopore assemblies showed isolate genomes ranged from 7.45 to 8.95 Mbs. Contig number per assembly ranging 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 6594 to 8098. Over 25 putative secondary metabolite biosynthetic clusters were identified in each assembly. Calculation of digital DNA:DNA hybridization (dDDH) and average nucleotide identity (ANI) values using additional genome assemblies from type specimens of Streptomyces showed the five isolates are likely novel Streptomyces spp. Results and data generated from this study will provide a basis for future research on the use of Streptomyces for managing common soilborne pathogens like Verticillium dahliae.