Growth promotion and biological control of fungal diseases in tomato by a versatile rhizobacterium, Pseudomonas chlororaphis subsp. aureofaciens SPS-41

Pseudomonas chlororaphis subsp. aureofaciens SPS-41, a beneficial bacterium isolated from rhizosphere of sweet potato, has been explored as a biological control agent for the management of soil-borne diseases. In this study, its plant growth-promoting and antifungal properties against two major tomato fungal pathogens (Fusarium oxysporum and Botrytis cinerea) were evaluated using in vitro and in vivo experiments. Strain SPS-41 produced indole-3-acetic acid (IAA), siderophore, biofilm, protease, amylase, chitinase, and could solubilize phosphate. It also inhibited fungal mycelial growth, with an inhibition rate of more than 80% in dual culture assays. Volatile organic compounds (VOCs) produced by SPS-41 also exhibited strong antifungal activity. In addition, SPS-41 promoted the growth of tomato seedlings in greenhouse conditions, and the severity of wilt disease and grey mold decreased significantly with rhizospheric inoculation of cell suspension and VOC fumigation comparing to untreated controls. The composition of VOCs emitted by SPS-41 was analyzed, and 57 volatiles were identified by SPME/GC-MS. Of these, 2-tridecanone, 2-undecanone, 2-nonanone, 2-acetylthiazole, 9-decenyl acetate, 2-hexadecanol, α-farnesene, and nonanal were the major volatiles. Nonanal, 2-nonanone and 2-acetylthiazole were confirmed to inhibit the growth of all three pathogens. The complete genome of strain SPS-41 was sequenced and annotated. We identified a series of gene clusters responsible for the synthesis of active secondary metabolites with antimicrobial and biocontrol functions. Moreover, several genes related to plant growth promotion, such as nitrogen fixation and indole-3-acetic acid and siderophore biosynthesis were also identified. This research indicates that strain SPS-41 is a plant growth promoting bacterium with the potential for development as a new biocontrol agent for tomato fungal pathogens.