Performance of different wheat varieties and their associated microbiome under contrasting tillage and fertilization intensities: Insights from a Swiss long-term field experiment

Winter wheat is an important global cereal crop. However, conventional farming practices, characterised by intensive tillage and high fertilizer inputs, pose significant threats to the environment. In response, more conservative management practices are being applied aiming to maintain wheat production while promoting a beneficial microbiome. Here, we evaluated the suitability of three different wheat varieties for less intensive agricultural systems, focusing on reduced tillage and fertilizer intensity. The study was conducted over two consecutive years in a Swiss long-term field experiment comparing conventional versus reduced tillage and full fertilization versus half fertilization. In addition, we investigated the composition of plant-associated microbial communities using amplicon sequencing of phylogenetic marker genes, specifically targeting bacteria and fungi in rhizosphere samples and fungi in root samples. Our results revealed that in our study wheat variety most strongly predicted grain yield and quality, independent of tillage and fertilization intensity. Specifically, wheat varieties demonstrated higher yields and N uptake in plots subjected to conventional ploughing and full fertilization compared to those under reduced tillage and half fertilization. We found no significant effect of wheat variety on the composition of microbial communities. However, tillage emerged as the primary factor influencing microbial community composition in the rhizosphere, while fertilization intensity significantly impacted fungal communities in the root system. These findings underscore the complex interplay between agronomic practices, plant genetics, and microbial dynamics in agroecosystems, emphasizing the need for holistic and adaptive approaches and their further development to ensure sustainable crop production. • Wheat variety but not tillage nor fertilization predicted grain yield and quality. • Differential effect of management on microbial communities in roots and rhizosphere. • Tillage shaped bacterial and fungal communities in the rhizosphere. • Fertilization but not tillage shaped fungal communities in wheat roots.