Many countries, particularly in Europe, are implementing various directives to reduce the use of pesticides in agriculture through the introduction of integrated pest management (IPM) strategies. IPM comprises the use of suppressive organic amendments, beneficial microbes and their products (e.g. metabolites) as alternatives to synthetic chemicals. In order to achieve the necessary reduction of chemical inputs, synergistic combinations of well-characterized organic amendments used together with highly effective microbial biocontrol agents can address the increasing problem of plant pathogen control.

Plant microbiomes include beneficial microbes that can protect the plant from biotic and abiotic stresses, and improve crop growth and productivity. Beneficial microbes are a heterogeneous group of organisms that include: 1) beneficial fungi (i.e. Trichoderma spp.); 2) mycorrhiza (i.e. Glomus spp.; 3) symbiotic nitrogen-fixing bacteria (i.e. rhizobia); 4) endophytes that promote plant growth. Interactions of the microbial community in the rhizosphere contribute significantly to the plant health, improving the fitness in diverse environments. These microbes can have: i) a direct effect on phytopathogens by the production of metabolites with antibiotic activity, or by competition for space and nutrients; iii) an indirect beneficial effect on the plant by enhancing defense responses or promoting plant growth. Many compounds are involved in this interaction such as secondary and primary metabolites, proteins, small peptides, low molecular weight carbohydrates (from cell wall).

The future challenge is related to the possibility to create specific formulations, also associated with specific compounds, with a beneficial effect and useful for agricultural applications under different environmental stresses. Management of plant microbiome, production of bioformulations and technologies to improve these microorganisms and/or their metabolites are an important part of the strategies to positively affect plant health reducing the use of chemicals (pesticides and/or fertilizers).

This Research Topic welcomes the submission of Review, Technology Report, Methods, Opinion and Original Research articles aiming to address the recent advances and challenges on soil microbiome engineering for plant protection and growth promotion, falling under, but not limited to:
- Ecology of the plant-soil microbial community
- Biochemistry and molecular biology of microbiomes
- Metabolomics of complex interactions
- Proteomics of multiple interactions
- Formulation of synthetic microbial communities
- Application strategies
- Plant protection products
- Functionality of the plant-microbiome interaction

Studies on biochars, composts and any other products that can interact positively with beneficial microbiomes to improve the environmental sustainability of agroecosystems are also considered.

Keywords: Microbiomes, Metabolites, Disease Resistance, Plant Growth Promotion, Immunity, Organic Amendments

Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.