Streptomyces songxianensis sp. nov. SX92T: biocontrol of tobacco black shank and modulation of the rhizosphere microbiome

Abstract

Streptomyces species are well-known for their potential in biocontrol and plant growth promotion, with the rhizosphere serving a rich reservoir for novel isolates. In this study, a Streptomyces strain (SX92T) was isolated from the rhizosphere of healthy tobacco plants. In dual-culture assays, SX92T displayed broad-spectrum antagonistic activity against six major fungal pathogens of tobacco, with the highest inhibition (59.22%) against Phytophthora nicotianae, the causal agent of tobacco black shank. Polyphasic taxonomic characterization, combining 16S rRNA gene phylogeny, distinctive physiological traits, chemotaxonomic markers (LL-diaminopimelic acid, major menaquinones MK-10(H₄) and MK-9(H₈), and predominant fatty acids anteiso-C₁₅:₀ and C₁₆:₀), and genome-based metrics (ANI and dDDH), clearly distinguished SX92T from its closest relatives. Accordingly, strain SX92T is proposed as the type strain of a novel species, Streptomyces songxianensis sp. nov. The genome of SX92T is 9.69 Mb in size with a G + C content of 71% and contains 26 biosynthetic gene clusters, including one showing 100% similarity to the albaflavenone cluster. In field trials, application of SX92T fermentation broth significantly improved tobacco agronomic traits and reduced black shank incidence by 44.97%. Furthermore, SX92T treatment reshaped the rhizosphere microbiome by enriching beneficial bacteria such as Flavobacterium and altering the relative abundance of specific fungi, including a reduction in the arbuscular mycorrhizal fungus Rhizophagus irregularis. It also shifted soil enzyme activities, with increased cellulase and decreased catalase levels. These findings establish Streptomyces songxianensis SX92T as a promising multifunctional biocontrol agent for sustainable tobacco production.