The impact of microbial inoculation on resilience towards biotic stresses in plants under greenhouse cultivation

There is a lack of understanding on the collateral effects of microbial inoculations on culturable plants. The purpose of this study was to investigate if, and to which extent eventual changes in secondary metabolome and/ or microbiome compositions would correlate with increased resilience to biotic stressors, i.e. to Fusarium oxysporum for tomato and lettuce, and western flower thrips (WFT) for chrysanthemum plants. Tomato plants were individually treated with ten different microbial strains. Furthermore, four selected strains were also applied to lettuce and chrysanthemum plants. Inoculated plants of all three species were co-inoculated with the corresponding biotic stressor or remained mock inoculated. Plant colonization by applied microbial strains was established by cultivation or molecular detection from surface-sterilized roots and stems. Tomato and lettuce plant growth reduction, as a result of F. oxysporum colonization, was established by dry weight measurements. Damage in chrysanthemum plants was established by counting silver spots on leaves, as a result of WFT infestation. Secondary metabolome analysis was performed on leaves, and bacterial and fungal community analyses on roots of plants of the three species. Measured parameters in plants were compared between individual microbial treatments and the corresponding untreated control, separate for biotic stressor and mock-inoculated plants. In addition, measured parameters of biotic stressor and mock-inoculated plants, within each individual microbial and control treatment, were compared. All four selected strains colonized the three plant species while showing different prevalences for location in the plant and species type. Two strains, i.e. Trichoderma viride TV02 and Pseudomonas putida P9, evoked mitigating effects on damage caused by, respectively, F. oxysporum in lettuce, and WFT in chrysanthemum plants. Treatment with Bacillus mycoides strain 2003/84 in F. oxysporum-infected tomato plants tended to aggravate biotic stress caused by the pathogen. Impact of microbial inoculations on the secondary metabolomes of the three plant species was found for strain P9 in tomato and lettuce plants in the absence of the biotic stressor and for strains TV02 and Isaria javanica FE9901 in tomato plants inoculated with F. oxysporum. With the exception of strain P9, all applied strains impacted the tomato plant microbiome, either with or without F. oxysporum. The four selected strains also impacted the microbiomes of lettuce and chrysanthemum plants, with or without biotic stressor. In conclusion, microbial inoculations overall have strong effects on plant microbiome composition and modulations in leaf secondary metabolome and in root microbiome compositions are shown to be independent processes.