Inoculation of beneficial microorganisms: a practice aiming at improving the performance and sustainability of agricultural and horticultural systems. Plants host a diverse community of tightly associated microbes – their microbiome – which increases their access to nutrients and enhances their growth, facilitates tolerance of stress such as drought, and increases disease resistance [1-3]. Manipulation of plant-associated microorganisms has thus considerable potential to improve the performance of cropping and horticultural systems [4, 5]. The plant-associated microorganisms inducing beneficial effects are often called ‘plant probiotics’ by private sector actors working on fruits and horticultural crops as inoculation can improve food nutritional quality [6]. More precisely, inoculation of plant-beneficial microorganisms to soil can allow phytostimulation through several microbial processes including stimulation of root growth [7], biological N₂ fixation [8], phosphate solubilization [7] and protection against plant pathogens [9]. For instance, Partner #1 of this proposal has participated in the ANR project AZODURE (2013-2017) analysing how inoculation of maize by an Azospirillum strain influences the soil microbiota and functioning [10] and the economic and environmental performance of this crop [11]. Although not yet fully explored, microbial inoculation can also improve other ecosystem services delivered by soils such as mitigation of greenhouse gas (GHG) emissions [12]. For instance, inoculating bacteria with N₂O-reducing capacity to pasture [13] or crop soils [14] can mitigate N₂O emissions under greenhouse conditions, and this potential is particularly high for non-denitrifying N₂O-reducing strains as shown by IMMINENT Partner #2. Such N₂O sink capacity may be invaluable microbiological property to develop inoculants delivering new ecosystem services.

To overcome the challenge of increasing food production with a significant reduction of agrochemical use and environmental pollution, many private companies are actively exploiting the potential of microbial inoculants and associated formulations that support inoculant survival. It is predicted that the global market for biofertilizers could reach USD 1.66 billion by 2022 [15]. For example, the private Partner #3 of IMMINENT (PT GHA) sells mixtures of Bacillus strains and substrates as inoculants that allow better growth of crop and horticultural plants. Given the demand for more sustainable agricultural and horticultural systems and mistrust of genetically modified organisms in Europe, improving the efficiency of inoculation approaches using microorganisms naturally occurring in soil is thus of major importance.

The need to study biotic interactions for understanding inoculum ability to maintain itself in soil and improving the efficiency and reliability of inoculation. A common difficulty when using microbial inoculants is the inconsistency of their beneficial effects in field conditions and large variability of inoculation outcome [16]. Meta-analyses have shown that this variability is partly due to abiotic conditions (in particular water regime, organic matter, pH and nutrient availability) [5]. However, a large part of the variability in the observed inoculation effects on the performance of agricultural/horticultural systems remains poorly identified. A major assumption of the IMMININENT project is that the role of biotic interactions, i.e. interactions between the inoculum and the native soil microbiota, for inocula survival has been largely overlooked. Actually, many studies have reported that most biostimulants poorly survive in soil upon inoculation because the inoculated microbes are often outcompeted by the native community. For instance, following sowing of inoculated maize seeds, Azospirillum lipoferum CRT1 is not detected by quantitative PCR already after the 6-leaves stage [10]. Private companies in this sector generally invest a great deal in the development of matrices supporting their inoculants in order to extend their survival in soil and efficacy, as it represents a major factor restricting the efficiency of biostimulants on soil functioning and plant performance. In contrast, guiding inoculation approaches based on a better knowledge of biotic interactions requires development of synergies between research capacities of private and public actors.