The HoloGrain initiative mobilises several INRAE teams whose work targets a particular stage in the production chain (pre- or post-harvest) or a specific issue. This network will make it possible to integrate the various stages and to follow a wheat grain holobiont throughout the agri-food chain.

The HOLOBROM project study the acquisition and transmission of microbial endophytes (i.e. living inside a plant) in the development and growth of plants. Works on cultivated species have suggested maternal effects, but they remain relatively unknown in natural ecosystems which are subject to marked environmental gradients.

The HOUSE project will try to answer evolutionary science questions by mobilising microbial ecology and plant biology methods. It aims to analyse the pertinence of the holobiont concept using artificial selection of the plant, the rhizosphere microbiota, or both at the same time, in order to determine the importance of plant-microbiota interactions in the response to selection.

The INT-BXL project deals with the bioremediation of polluted river sediments and agricultural soils. In agroecosystems, the contamination of soils by xenobiotic compounds, such as pesticides used in conventional agriculture and antibiotics used to treat livestock or supplied via organic soil fertilisation, can lead to the transfer of these compounds, and/or their degradation intermediaries, towards surface and ground water, thus contaminating all water resources.

The µFlyAdapt project aims to highlight the selective recruitment and role of rhizosphere microorganisms in the adaptation of a phytophagous root insect (the cabbage maggot Delia radicum) to its host plant (Brassica napus).

Although agrifood systems are heavily reliant on nitrogen inputs, most crops (and especially cereals) have low nitrogen utilization efficiency (30–50%). This means that much of the nitrogen applied in agroecosystems ends up in the atmosphere or terrestrial and aquatic ecosystems, which then causes the nitrogen cycle to spiral out of control, in turn leading to various problems such as eutrophication and higher nitrous oxide emissions. This nitrogen cycle is largely governed by soil microorganisms. Recent research, supported by the European Commission, has explored new strategies for more sustainable soil nitrogen management (e.g. improving nitrogen retention in agricultural systems), with the development of solutions and levers for action based on microbiota management (Theme 3 of the HOLOFLUX metaprogramme). The current scientific approach to microbial management is basically to inoculate microbial strains or consortia to make limiting nutrients bioavailable, or to implement biological control. But many questions remain about the sustainable deployment of these inoculants, and specifically their persistence, their non-target effects and the proliferation of potential invasive microorganisms.