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Societal Impact Statement Summary Agricultural intensification is a major driver of biodiversity decline in agrosystems. For instance, it has been shown that conventional farming leads to a decline in soil microbial diversity and triggers a strong selection process, altering the functioning of the whole ecosystem. The present study shows that organic farming increases diversity and affects composition of crop plant microbiota, mostly as a response to field management and soil characteristics. Furthermore, crop plant microbiota influences crop production and resistance to pathogens. Therefore, agricultural practices affect plant performance through microorganism‐mediated changes, which may be important pillars of future sustainable crop production. Agricultural intensification threatens biodiversity, but the effects of intensification on microorganisms are still overlooked despite their role in ecosystem functioning. Microorganisms associated with plants provide many services that affect plant growth and health. Organic farming is expected to strongly affect species composition, richness, and their interactions. We analyzed the effect of the farming system on endophytic microbial assemblages associated with winter wheat plants and plant performance in the field. We collected environmental data through farmer interviews, soil analyses, and plant inventories and analyzed root microbiota at vegetative and flowering stages. Organic farming increased fungal and bacterial diversity associated to wheat plants and affected species composition in most phyla. This effect was mostly due to soil characteristics and field management and a little to plant diversity in the field. Microbial responses were more pronounced at the late developmental stage, likely as a result of accumulative effect of management actions during plant development. Seed production and resistance to pathogens were related to specific phyla that are important for seed production and/or wheat resistance to septoriose. This work advances our understanding of how agricultural practices affect plant performance through microorganism‐mediated changes and supports the use of microorganisms as pillars of sustainable crop production. [ABSTRACT FROM AUTHOR]

Agricultural intensification reduces not only biodiversity in agroecosystems but also key ecosystem functions such as soil fertility. By reintroducing biological diversity in fields, weeds may enhance soil biological fertility through their influence on crop microbiota. However, letting weeds grow in crop fields will depend on weed competitiveness, farmers' perception and acceptance, and on crop management, which influences the occurrence and the abundance of weeds in the field. This study assessed the use of eight weed species to modify wheat plant root endospheric mycobiota, and the applicability of using these plants for mycobiota enrichment in the field. By combining controlled lab experiments and field studies, we demonstrated that weeds act either as a refuge for a high diversity of fungi or as a vector for transferring fungi to the crop, particularly symbionts. Weeds differed in their competitive effect on wheat growth and only three species significantly reduced wheat growth. Interviews with farmers' revealed that weed species were better known and more appreciated in crop fields by organic farmers than by conventional farmers. Floristic surveys confirmed that both weed occurrence and cover were higher in organic fields than in conventional fields. A multicriteria analysis showed that Trifolium repens and V. persica had the highest potential for promoting wheat plant mycobiota. Among the weed species tested, these two are worth considering as auxiliaries to improve soil biological fertility in crop fields. Their use with the goal of selecting appropriate crop mycobiota should be relatively easier in organic farms where weeds are better accepted, whereas their use in conventional farms would require raising farmers' awareness of the benefits of weeds for soil fertility. • Weeds influence wheat root endospheric mycobiota. • Weeds harbour diverse fungi (refuge effect) and transfer numerous fungi to wheat (vector effect). • Weeds occur more in organic fields and are more positively perceived by organic farmers. • Wheat growth depletion differs among weed treatments • Some weed species could be effective auxiliaries for improving soil fertility. [ABSTRACT FROM AUTHOR]

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Agricultural intensification has been demonstrated to induce a loss of biodiversity. Despite the key role of symbiotic microorganisms in plant nutrition and protection, the impact of agricultural intensification on these microorganisms is not fully understood. Organic farming and field edges (as semi-natural elements) may promote a higher microbial diversity thanks to lower anthropic disturbance and higher plant diversity. We sampled wheat individuals in pairs of wheat fields (one organic and one conventional) along a distance gradient to the edges (hedgerow vs. grassy), in 20 landscape windows selected along an uncorrelated gradient of organic farming and hedgerow density. We demonstrated that organic farming shaped microbial composition and increased fungal and bacterial richness, while hedgerows had a neutral or negative effect on richness depending on the microbial phyla considered. In contrast to bacteria, fungal communities were heterogeneously distributed within fields, having a higher diversity for some phyla close to field edges. Overall we highlighted that fungi responded more to the field scale while bacteria were more affected by landscape scale. The effect of agricultural intensification on plant microbiota and therefore on the functions provided by microorganisms to the plants has to be considered at a multiple spatial scale—from field to landscape. [ABSTRACT FROM AUTHOR]

Finding more sustainable ways to produce food is a major challenge for humanity in the face of biodiversity extinction and climate change. Consequently, research on the ability of agroecosystems to provide multiple functions is growing. In this regard, the relative importance of organic farming and landscape‐scale measures for improving multifunctionality has recently been debated. We investigated the effects of farming system (conventional vs. organic) at field scale, total length of hedgerows in the landscape and their interaction on the multifunctionality of 40 winter cereal fields in Brittany (France). Our multifunctionality assessment integrated 21 indicators of five agroecosystem goods: biodiversity conservation, nutrient cycling and soil structure, pest and disease regulation, food production and socio‐economic performance. Many indicators of biodiversity conservation, pest and disease regulation, and socio‐economic performance were higher in organic than in conventional systems. However, indicators of nutrient cycling and soil structure did not improve and food production was much lower in organic systems. Total hedgerow length in the landscape had less influence than organic farming on indicators, although we observed positive interactions. Granivorous carabid abundance and semi‐net margin were highest in organic fields located in well‐preserved hedgerow landscapes. Synthesis and applications. Our study suggests that field‐scale organic farming is necessary to promote biodiversity conservation and associated ecological functioning in crop fields, whereas landscape‐scale preservation of semi‐natural habitats alone is likely insufficient. Preservation of hedgerows in the landscape brings additional ecological and socio‐economic benefits for organic systems without compromising agricultural production. More broadly, our results call for more ambitious research into the myriad possible combinations of farming practices and agri‐environmental measures at both field and landscape scales, to improve both below‐ground and above‐ground functioning. [ABSTRACT FROM AUTHOR]