Structuring of communities around symbioses

In the context of agro-ecological transition going from conventional management using massive amounts of synthetic inputs to sustainable management limiting the use of these inputs, it is necessary to understand and promote the beneficial microorganisms of soil, key players in guaranteeing the productivity and quality of agricultural products with a low ecological footprint. In beneficial plant-microorganism interactions, the improvement of services (e.g. plant health, nutrition, qualitative and quantitative production) has mainly been studied at the plant scale. Currently, we are changing the paradigm and are moving towards an integrative scale that places the beneficial soil microbiota at the heart of the functioning of the plant holobiont.

Beneficial interactions represent only part of the interactions that coexist within the holobiont comprising the plant and associated microorganisms, but also between microorganisms (e.g. competition, facilitation). Like the first green revolution which laid down the guidelines for fertilization, research must now define the main lines of symbiotic efficacy. Academic research on plant-symbiont interactions has largely been carried out at the species level. However, there is considerable genetic variability within each species of the holobiont (plants and microorganisms) that can strongly affect symbiotic efficiency at several scales: survival of microorganisms in the soil, ability of microorganisms to colonize their hosts, diversity of associated functions to the reservoir of microorganisms. The establishment (e.g. cellular reprogramming), as well as the functioning (e.g. transfer of resources to symbionts) of these beneficial mutualistic interactions, involves fine regulation in the selection of partners which conditions the effectiveness of symbioses. Efficacy is complex to measure because it (i) depends on the scale of the study (e.g. cell, tissue, individual, population, ecosystem), (ii) can evolve during the plant’s development cycle, and (iii) may depend on multiple factors (eg history of farming practices, pedoclimate, technical itineraries).

Several knowledge gaps can be identified:
– understanding of beneficial plant-microorganism interactions at different scales within a holobiont (e.g. culturomics, metabarcoding, metagenomics),
– defining markers of this efficiency to predict the emerging properties of symbiotic communities,
– defining levers to maximize or optimize the effectiveness of these plant-microorganism interactions (e.g. technical itineraries, inoculation),
– producing operational microbiological indicators in connection with stakeholders.

• How can we evaluate symbiotic effectiveness of AMFs at the interspecies level in the laboratory and in the field?
• Which strategies for the co-selection of complex symbiotic inoculum (Rhizobium, PGPR and AMF) in different plant varieties? How can we take into account the competitiveness of plant-microorganism associations to form symbiotic structures in these strategies, their efficiencies and the possible interactions between symbioses (including between symbiotic plants)?
• What is the role of soil microbiota that indirectly facilitate AMF symbiosis? How can we take them into account?
• What is exchanged through mycelial networks? How can we characterize and quantify these exchanges? What are the mechanisms and genetic factors? Do these factors constitute a target for the improvement of synergies between plants, between symbioses, at the level of cover, or in the case of associated crops (legumes-cereals for example)?
• How can stakeholders take AMFs and associated symbiotic communities into account in the selection of plant genotypes/varieties/ideotypes?
• Is it possible to define synthetic communities of AMFs or symbiotic microorganisms?