Native soil fungal symbionts substantially contribute to crop yields in commercial-scale farming

The supporting functions of soil organisms are receiving increasing interest as means to improve agricultural sustainability. Arbuscular mycorrhizal (AM) fungi are widespread plant symbionts that can benefit plants' performance, including important crops. However, knowledge about their benefits has been mostly generated under controlled greenhouse conditions. It remains unclear to what extent AM fungi contribute to crop performance in real-world agricultural operations, and to what extent agricultural practices like rotations affect AM fungal effects. We used a tomato model system, consisting of a non-mycorrhizal tomato mutant and its wildtype progenitor, to study the contribution of native AM fungi to crop yields in a commercial-scale long-term farming systems trial. A genetic modification hinders the tomato mutant from establishing regular AM-fungal relationships in roots. We assessed AM fungal abundance and community composition across farming systems by sequencing plant roots and quantified the AM fungal contribution to tomato yields by comparing wildtype tomato yields to those of the tomato mutant. Native AM fungi contributed up to 33% of tomato yields. A rotation including a three-year period of continuous alfalfa growth showed the most distinctive AM fungal communities compared to other systems and the highest contribution of AM fungi to tomato yields. AM diversity did not differ across farming systems. Our study implies that native AM fungal communities can substantially support crop production. It highlights the potential for farming system management to increase soil-derived ecosystem services and reduce dependence on agrochemical inputs.