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Microbe induced Resistance to Agricultural pests

Periodic Reporting for period 1 - MIRA (Microbe induced Resistance to Agricultural pests)

Reporting period: 2017-12-01 to 2019-11-30

Plants are intimately associated with beneficial microorganisms in their root zone, which can enhance their resistance against pests. Use of Microbe-induced Resistance (MIR) to reduce pest losses has therefore emerged as an option to improve resilience and reduce pesticide use in agriculture. However, MIR is often context dependent with reduced benefits under certain environmental conditions, and it is a challenge to deliver and ensure stable associations of microbes and plants, and to avoid negative effects on beneficial organisms. Improved understanding and skilled researchers are therefore needed.

In the training network MiRA: Microbe-induced Resistance to Agricultural pests, 15 early-stage researchers (ESRs) are trained in basic and applied aspects of MIR and its impacts, context dependency, mechanisms, impacts on biocontrol organisms, formulation of inoculants, and economic constraints. The ESRs are hosted by, and receive training from, a consortium of academic and private institutions across Europe.
The MiRA ESRs have been trained in specialized and transferable skills at three successful MiRA events, and from secondments with other MiRA hosts. At the events, they have interacted on scientific and practical issues within work packages (WPs), and on career development within mentor groups. Outside the joint events, the ESRs interact regularly through internet communication systems. Administrative procedures and systems have been developed and improved; e.g. ESRs submit biennial progress reports for evaluation both at individual and consortium level.

Several ESRs have participated in scientific conferences and public meetings to present projects and MiRA, and to build professional networks.

In WP1, four ESRs are focusing on context dependency of MIR. Different strains of arbuscular mycorrhizal fungi (AMF) and other plant-associated beneficial fungi were evaluated for induction of resistance in potato and tomato, with simultaneous exposure to water stress, different light and nutrient conditions, and biotic stress from plant pathogens. First results show varied effects of plant-associated microbes on plant resistance against caterpillars, depending on drought severity and nitrogen addition. Plant chemical defenses were moderated by beneficial fungi when exposed also to a necrotrophic fungus and herbivory. Accessions of wild tomato, representing its phylogenetic diversity, are evaluated for genotypic differences of MIR caused by climatic adaptation. The gut microbiome of caterpillars, which can promote caterpillar’s resistance to plant defenses, is evaluated for response to different plant-soil microbe associations.

WP2 focuses on the mechanisms and processes of MIR. Volatile compounds from certain consortia of beneficial soil microbes enhanced survival of tomato plants when also exposed to a plant pathogen, but not when exposed to an insect herbivore. Phosphate availability influences the strength of AMF-induced plant resistance against pathogens and insect herbivores, and optimal levels of phosphorous were determined for further experiments. Promising resistance-inducing rhizobacteria with effects against plant pathogens were identified and standard assays for evaluation of phytohormone regulation developed. Effects of beneficial fungi on plant defense against specialist and generalist herbivores is analyzed with untargeted metabolomics and transcriptomic approaches. Only few genes were upregulated by two beneficial fungi tested so far, whereas the metabolome clearly responds to herbivore exposure, illustrating dynamics of the plant response. Beneficial bacteria consistently affect plant carbohydrate and antioxidant metabolism and will be evaluated under drought stress for enzymatic activities in the rhizosphere and relevance in MIR.

Impact of MIR on other beneficial organisms is studied by two ESRs in WP3. Experiments tested AMF-effects on generalist insect herbivores (direct defense) and parasitoids (indirect defense) under different light regimes. MIR consistently reduced survival of herbivores, independent of light conditions but did not affect parasitoids, suggesting compatibility of AMF with other biocontrol agents. AMF modulated volatiles in different tomato varieties attacked by herbivores, including compounds known to attract generalist predators. Ability of tomato varieties to attract beneficial rhizosphere microbes was studied by metagenomics but revealed no overall association between variety and bacterial community.

The four ESRs in WP4 focus on methods, validation and economy. Inoculation methods with beneficial microbes alone and in consortia showed effective protection against necrotrophic leaf pathogens but no effect on tomato growth, confirming that MIR and growth promotion can be uncoupled. Some microbial treatments affected insect herbivore performance. Optimal methods for root inoculations with plant-associated insect-pathogenic fungi were developed, and compatibility with AMF in the rhizosphere established. These combinations did impact necrotic lesions on tomato leaves, indicating joint beneficial effects. Delivery of beneficial microbes to plant tissue is investigated and the potential of predatory insect larvae to transfer beneficial bacteria with their mouthparts from colonized plant material or artificial diets was verified. Methods for in-planta PCR detection of these bacteria were developed. In a survey on MIR technology, researchers highlighted the need for more research, especially on MIR under field conditions. Interviews with bio-tech companies in Spain revealed that residue free products and pesticide bans are important for uptake of MIR technologies, as well as their costs; increased use is dependent on information campaigns.
By the end of the project, we expect to have a collection of different microorganisms and consortia for enhancing MIR against arthropod pests, with characterized performance in different abiotic and biotic contexts, such as water and nutrient deficiency, increased salinity, and presence of other plant-associated microbes. Impact of the treatments on insect symbionts and soil microbiomes will be characterized.

The major signaling pathways involved in MIR will be identified, and we expect to be able to predict conditions and microbial treatments that may facilitate MIR. A large joint field experiment with selected microbes is planned in Spain at realistic production conditions, supervised by field experts. Several ESRs from different WPs will test MIR efficiency against key pests, effects on beneficial insects, and resulting fruit quality and market perspective. Selected genes, metabolites and enzymes will be tested to evaluate their potential as MIR indicators and feasibility for large-scale screenings.

The project will have broader social-economic and societal impact by training highly skilled and interdisciplinary researchers with expertise in the opportunities and challenges for using MIR to reduce crop losses and inputs of chemical pesticides. Major barriers for adopting MIR technologies in food production will be identified to recommend measures to take by politicians and food production associations.