Bioinoculant-induced plant resistance is modulated by interactions with resident soil microbes

Abstract

Background: Entomopathogenic fungi are increasingly used as bio-inoculants to enhance crop growth and resistance. When applied to rhizosphere soil, they interact with resident soil microbes, which can affect their ability to colonize and induce resistance in plants as well as modify the structure of the resident soil microbiome, either directly through interactions in the rhizosphere or indirectly, mediated by the plant. The extent to which such direct versus indirect interactions between bio-inoculants and soil microbes impact microbe-induced resistance in crops remains unclear. This study uses a split-root system to examine the effects of direct versus indirect (plant-mediated) interactions between an entomopathogenic fungus, Metarhizium brunneum, and resident soil microbes on induced resistance in tomato against two-spotted spider mites. Additionally, the study explores how these interactions influence the composition and diversity of soil fungal and bacterial communities.

Results: Resident soil microbes reduced the efficacy of M. brunneum to induce resistance against spider mites. This reduction occurred not only when resident microbes directly interacted with the bio-inoculant but also when they were spatially separated within the root system, indicating plant-mediated effects. M. brunneum inoculation did not affect rhizosphere microbial diversity but led to changes in fungal and bacterial community composition, even when these communities were not in direct contact with the inoculant.

Conclusions: This research highlights the impact of both direct and plant-mediated interactions between bio-inoculants and resident soil microbes on bio-inoculant-induced pest resistance in crop plants and underscores the importance of assessing potential adverse effects of fungal bio-inoculants on native soil communities.

Keywords: Arthropod pests; Entomopathogenic fungi; Soil microbial communities; Spider mites; Tomato.

Fig. 1

Experimental setup with a split-root system to discriminate between effects of direct versus indirect interactions between a bio-inoculum (Metarhizium brunneum, Mb) and the native microbial community (NMC) on two-spotted spider mite (Tetranychus urticae) resistance in tomato. Three weeks old tomato seedlings were transferred to two adjacent pots with half of their roots in each of the pots. Direct interactions were enabled by putting the native microbial community and M. brunneum in the same pot (NMC + Mb), indirect (plant-mediated) interactions were enabled by putting the native microbial community and M. brunneum in different pots (NMC-Mb), no interactions were enabled with only M. brunneum (Mb) and only the native microbial community (NMC) treatments. A sterile soil treatment served as a control. Plants were either infested with spider mites or not

Fig. 2

Impact of direct versus indirect interactions between Metarhizium brunneum and native microbial community on population growth of two-spotted spider mites (Tetranychus urticae) on tomato plants. Each box in the plot corresponds to a specific treatment in the split-root setup, i.e., control with 0.01% Triton X-100 (C), only-native microbial community (NMC), only-M. brunneum bio-inoculum (Mb), native microbial community and M. brunneum in different pots (NMC-Mb) and native microbial community and M. brunneum in the same pot (NMC + Mb). Boxes not sharing a common letter are significantly different from each other (Tukey post-hoc test, α = 0.05 following generalized mixed model). The median value for each treatment is represented by a thick horizontal line within its respective box

Fig. 3

Impact of direct versus indirect interactions between Metarhizium brunneum and native microbial community on total dry biomass of tomato plants in the absence (grey boxes) and presence (brown boxes) of two-spotted spider mites. Each box in the plot corresponds to a specific treatment in the split-root setup, i.e., control with 0.01% Triton X-100 (C), only-native microbial community (NMC), only-M. brunneum bio-inoculum (Mb), native microbial community and M. brunneum in different pots (NMC-Mb) and native microbial community and M. brunneum in the same pot (NMC + Mb). Boxes not sharing a common letter are significantly different from each other (Tukey post-hoc test, α = 0.05 following linear mixed model). The median value for each treatment is represented by a thick horizontal line within its respective box

Fig. 4

Impact of direct versus indirect interactions between Metarhizium brunneum and the native microbial community on the concentration of chlorogenic acid, rutin, glucose and C:N ratio of local leaves in the absence (grey boxes) and presence (brown boxes) of two-spotted spider mites. Each box in the plot corresponds to a specific treatment in the split-root setup, i.e., control with 0.01% Triton X-100 (C), only-native microbial community (NMC), only-M. brunneum bio-inoculum (Mb), native microbial community and M. brunneum in different pots (NMC-Mb) and native microbial community and M. brunneum in the same pot (NMC + Mb). Boxes not sharing a common letter are significantly different from each other (Tukey post-hoc test, α = 0.05 following linear mixed model). The median value for each treatment is represented by a thick horizontal line within its respective box

Fig. 5

Impact of direct versus indirect interactions between Metarhizium brunneum (Mb) and native microbial community (NMC) on resident fungal communities. Non-metric multidimensional scaling (NMDS) plots (using Bray–Curtis dissimilarity) showing the impact of three inoculation treatments on fungal communities: (i) only NMC when not inoculated with Mb (purple symbols), (ii) when NMC inoculated with Mb in a separate root compartment (blue symbols), or (iii) when NMC inoculated with Mb in the same root compartment (green symbols) in the absence (circles) and presence (triangles) of two-spotted spider mites. Plot a shows the fungal communities including Metarhizium ASVs and plot b shows the fungal communities excluding Metarhizium ASVs

Fig. 6

Impact of direct versus indirect interactions between Metarhizium brunneum and the native microbial community on top 20 most abundant fungal and bacterial genera in the rhizosphere for the treatments with only-native microbial community (NMC), native microbial community and M. brunneum in different pots (NMC-Mb) and native microbial community and M. brunneum in the same pot (NMC + Mb) when the spider mites were present or not present on the plants. a Heat map comparing the relative abundance of the top 20 fungal genera among treatments, b relative abundance graph of the top 20 fungal genera, c heat map comparing the relative abundance of the top 20 bacterial genera among treatments, and d relative abundance graph of the top 20 bacterial genera

Fig. 7

Impact of direct versus indirect interactions between Metarhizium brunneum (Mb) and native microbial community (NMC) on resident bacterial communities. Non-metric multidimensional scaling (NMDS) plots (using Bray–Curtis dissimilarity) showing the impact of three inoculation treatments on bacterial communities: (i) only NMC when not inoculated with Mb (purple symbols), (ii) when NMC inoculated with Mb in a separate root compartment (blue symbols), or (iii) when NMC inoculated with Mb in the same root compartment (green symbols) in the absence (circles) and presence (triangles) of two-spotted spider mites