Training soil microbiomes for sustainable agriculture

Abstract

Agriculture faces increasing pressure from climate change which significantly reduce crop yields. Simultaneously, conventional practices such as intensive use of fertilizers and pesticides escalate the environmental impact of food production. To meet the urgent need for sustainable yet productive agricultural systems, one promising approach is to leverage the natural functions of soil microbial communities. Beneficial microbes can improve plant performance conferring tolerance to (a)biotic stresses. However, exploiting these traits in field conditions remains a challenge due to the complexity and context-dependence of soil microbiomes. Our project addresses this challenge by developing a novel approach referred to as “training” — a strategy that applies selection pressures to steer microbial communities toward plant-beneficial functions. As a proof of concept, we applied microbial training to rhizosphere communities associated with tomato plants under saline conditions. The trained communities significantly enhanced plant tolerance to salt stress, as demonstrated by improved growth compared to untrained controls. These results show that microbiome training can effectively induce compositional and functional shifts in microbial communities, resulting in increased stress resilience in plants. This work highlights the potential of microbial community training as a sustainable strategy to improve crop health and resilience under environmental stress.