Understanding the microbiome shift and bacterial VOC-based control-mechanism in the Meloidogyne disease complex in Ugandan tomatoes

Background: Root-knot nematodes (RKNs, Meloidogyne spp.) are plant pests that cause severe crop losses worldwide, especially in tropical climates. When establishing a feeding site in the root endosphere, they change the physiological state of the root cells, which also increases the severity of secondary fungal and bacterial infections. Bacterial microbiome changes due to RKN infections in the root endosphere of Ugandan tomato (Solanum lycopersicum) were investigated using 16S rRNA gene amplicon analysis. Furthermore, we screened for autochthonic bacteria that may be suitable for biocontrol RKNs by the production of nematicidal volatile organic compounds (nVOCs). RKNs were identified using morphological and molecular techniques as M. javanica and M. incognita. Bacterial strains were isolated from the rhizosphere, as well as from the healthy and diseased endosphere of 20 different tomato plants.Results: Bacterial alpha diversity of galls differed both qualitatively and quantitatively from healthy roots, while composition of the bacteriome of the rhizosphere and healthy endosphere only differed in abundances. Pasteuriaceae and Rhizobiaceae were more abundant in diseased roots, whereas Enterobacteriaceae and Burkholderiaceae were less abundant. A set of 260 bacterial isolates were tested for nVOC production. By using SPME GC-MS analysis, sulfuric compounds (dimethyl disulfide, methanethiol), alkenes (mainly 1-undecene) and one pyrazine (3-methoxy-2,5-dimethylpyrazine) were found amongst others. Present alkenes and pyrazines were further tested as single compounds for their nematicidal activity. Accordingly, six nVOC-producing strains were identified as members of the genera Pseudomonas, Comamonas and Variovorax. Their relative abundance was highest in rhizosphere (Pseudomonas spp. and Comamonas spp.) or diseased root endosphere (Variovorax spp.). Additionally, all bacterial strains were tested in dual cultures for antagonistic activity towards Botrytis cinerea, Fusarium verticilloides, F. oxysporum, Sclerotium rolfsii and Verticillium dahliae. Five fungal antagonists were identified as Bacillus amyloliquefaciens, B. methylotrophicus and B. velezensis. Bacillus spp. mainly found in healthy root parts. Bacterial antagonists of V. dahliae were only found in rhizosphere isolates; they were less efficient against the other fungal pathogens and vice versa.