A multidisciplinary on-farm survey of maize-bean intercropping shows that revival of traditional agricultural systems requires careful consideration of partner varieties and agronomic practices.

Cereal-legume intercropping is emerging as a promising strategy for fostering more sustainable agroecosystems. The traditional farming system of maize-bean intercropping, originating from Central America, where both crops were domesticated, is experiencing a revival in modern agricultural settings. This is exemplified in southwestern France, where maize hybrids are intercropped with the recently commercialized Tarbais bean variety. Here, we combined on-farm investigations of agronomic practices, plant yield and nutrition measurements, characterization of soil and bacterial assemblages by metabarcoding, along with transcriptomic assays to compare the performance of sole cropped maize and beans to intercropped plants. Agronomic practices and soil-related variables differed among farms, with results suggesting that farmers adjust the former according to soil mineralization level. Despite this farm-specific effect, we detected a notable increase in bacterial diversity in intercropping, both in bulk and rhizosphere soil. Multivariate analyses unveiled a significant impact of cropping systems on agronomic traits in maize and beans, with frequent farm-by-cropping system interactions (11 of 22 traits in maize and 12 of 24 traits in bean). Competition dominated maize-bean intercropping, with 54 of 89 significant correlations between maize and bean traits being negative. Beans were notably impacted by this competition, yielding fewer seeds in intercropped conditions, albeit exhibiting higher seed size and weight, as well as nitrogen and carbon percentages. We set up a controlled field assay to quantify differentially expressed (DE) genes between cropping conditions for the two species. While competition between the two crops was much more severe than on-farm, we found that it primarily affected the bean and its transcriptome, with nearly 30% of DE genes vs none in maize. Overall, our findings suggest that synergies between the two crops are likely hindered, underscoring the importance of carefully considering partner varieties and agronomic practices in the revival of traditional agricultural systems.