Characterization, comparative genomics, and metabolome analysis of Streptomyces tuberiscabiei sp. nov., a novel actinomycete causing potato scab disease in Long Khot, Chiang Mai Province, Thailand

Abstract

Three actinomycete strains, WSLK1–3T, WSLK1–4, and WSLK1–5, associated with scabby potato tuber, were characterized using polyphasic and genome-based taxonomy. All strains were found to be Gram-stain-positive, filamentous bacteria, including LL-diaminopimelic acid in cell-wall peptidoglycan. Whole-cell sugars were glucose, mannose, rhamnose, and ribose. MK-9(H6) and MK-9(H10) were major menaquinones; C16:0, isoC16:0, ante iso-C15:0, and anteiso -C17:0 were major cellular fatty acids; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol mannoside were major phospholipids; and DNA G + C contents were 71.5 mol%. Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that strains WSLK1–3T, WSLK1–4, and WSLK1–5 are closely related to Streptomyces canus DSM 40017T (=JCM 4212T), and S. pseudovenezuelae DSM 40212T (=JCM 11516T), respectively. The 16S rRNA gene sequences, average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm), and digital DNA-DNA hybridization (dDDH) values among the three strains were 100%, 99.12%, 99.33%, and 94.3%, respectively, indicating that these strains belong to the same species. Strains WSLK1–3T, WSLK1–4, and WSLK1–5 showed 88.54–90.62% ANIb, 90.99–92.27% ANIm, and 40.4–45.1% to their closely related type strains: S. canus JCM 4212T, and S. pseudovenezuelae JCM 11516T. All novel strains were pathogenic, causing necrosis on potato tuber slices, inhibiting plant seedlings, and inducing superficial to raised scab lesions on potato tubers. Based on the phenotypic, chemotaxonomic, pathogenic, and genomic data, strains WSLK1–3T, WSLK1–4, and WSLK1–5 could be assigned to the novel species within the genus Streptomyces for which the name Streptomyces tuberiscabiei sp. nov. is proposed. The type strain is WSLK1–3T (=TBRC 19150T = LMG 33893T).