Apple replant disease is a significant barrier to organic orchard production systems. This disease is believed to arise from soil-borne pathogens and parasites that accumulate in the soil over the lifespan of an orchard. While apple replant disease does not affect existing orchard plantings, newly planted trees in these orchards often experience substantial reductions in yield and vigor, and in some cases, may even die. Due to these severe impacts, orchardists have removed land from organic certification and resorted to pre-plant fumigation to eliminate soil-borne pathogens before planting new apple trees. However, pre-plant fumigation negatively affects the health and diversity of soil biological communities.

As an alternative, orchardists can address apple replant disease by planting wheat. Our trial results indicate that planting wheat in orchard soils boosts populations of beneficial soil microbial communities, which are known for their ability to combat soil-borne pathogens. We observed a corresponding decrease in soil-borne pathogens and parasites, a reduction in apple root infections caused by these pathogens, and an increase in the vigor of apple seedlings following wheat cultivation. Additionally, our findings suggest that the selection of wheat varieties plays a role in enhancing beneficial microbial antagonists and suppressing soil-borne pathogens. Wheat varieties bred under organic conditions demonstrated the greatest potential to improve beneficial soil microbial communities and control pathogens and parasites in our trials.

Similar pathogen complexes also affect various crop plants, suggesting that the insights from our studies may be valuable across multiple agricultural systems. Furthermore, our trials provide evidence that plant breeders can select for beneficial relationships between plant roots and microbial communities.