Streptomyces lycopersici sp. nov. and Streptomyces cucumeris sp. nov., two novel actinobacteria isolated from rhizosphere soil with broad-spectrum antifungal activity.

Abstract

Two actinobacterial strains, designated NEAU-383^T and NEAU-Y11^T, exhibiting antifungal activity, were isolated from the rhizosphere soil of plants in Harbin, Heilongjiang Province, and Guangzhou, Guangdong Province, respectively. Both strains formed short, wrinkled, spiral spore chains on aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains NEAU-383^T and NEAU-Y11^T were most closely related to Streptomyces iranensis HM 35^T, Streptomyces rapamycinicus NRRL B-5491^T and Streptomyces coffeae CA1R205^T. However, digital DNA-DNA hybridization values between the two strains and their close relatives (27.1% between the two strains; 27.5-59.0% for NEAU-383^T; 27.0-39.8% for NEAU-Y11^T) fell below the 70% species delineation threshold. The genomic G+C contents were 71.0 mol% for NEAU-383^T and 70.5 mol% for NEAU-Y11^T. Both strains contained glucose and ribose as whole-cell sugars. The predominant menaquinones were MK-9(H₆) and MK-9(H₈), with NEAU-Y11^T additionally containing MK-9(H₄). The major fatty acids (>10%) in both strains included iso-C_15 : 0, anteiso-C_15 : 0, iso-C_16 : 0 and C_16 : 0, whilst iso-C_17 : 0 was also a major component in NEAU-383^T. Both strains contained phosphatidylethanolamine and hydroxy-phosphatidylethanolamine as polar lipids. Additionally, NEAU-383^T also possessed diphosphatidylglycerol, phosphatidylinositol, an unidentified ninhydride-positive lipid and five unidentified lipids, whereas NEAU-Y11^T additionally contained two unidentified ninhydride-positive lipids and five unidentified lipids. Genomic analysis revealed that both strains possess abundant secondary metabolite biosynthesis gene clusters, including those for antibiotics, siderophores, polyketides and terpenoids, along with metabolic pathways associated with environmental adaptation. These findings provide insight into the potent antimicrobial activity exhibited by both strains. Based on genotypic, phenotypic and chemotaxonomic analyses, strains NEAU-383^T and NEAU-Y11^T represent two novel species within the genus Streptomyces, for which the names Streptomyces lycopersici (type strain NEAU-383^T=JCM 36736^T=MCCC 1K08878^T) and Streptomyces cucumeris (type strain NEAU-Y11^T=JCM 36418^T=MCCC 1K08681^T) are proposed.