Are substrate-mediated microbial community shifts the future of soilborne disease management?

The loss of methyl bromide as a soil fumigant, the limited efficacy of alternative fumigants, and the emergence of new diseases has necessitated fumigant-based crop production systems to radically restructure for continued productivity. In the coastal valleys of central California, the principal objective of soil fumigation has been to confine Verticillium dahliae population densities to levels below the threshold at which yield losses occur. The wide-spread adoption of alternative fumigants has coincided with the emergence of soilborne diseases caused by Fusarium oxysporum f. sp. fragariae and Macrophomina phaseolina. The ability to harness native soil microbiomes to manage plant pathogens remains a promising but relatively unexplored area. Our studies have focused on substrate-mediated changes in soil prokaryote communities with the goal to convert Verticillium wilt-conducive soils to Verticillium wilt-suppressive soils. The effect of broccoli residue and crustacean meal on soil microbiomes and suppression of Verticillium wilt were studied in soils with distinct land-use histories: intense agriculture, transition from pasture to agriculture, and native, undisturbed soil. Regardless of the soil type, the organic inputs significantly reduced V. dahliae microsclerotia and wilt incidence and severity on eggplants in the greenhouse, and these reductions were correlated with an increase in the proportion of known fungal antagonists. Prokaryote communities identified were distinct in the wilt-suppressive soils as compared to the wilt-conducive soils. Three cycles of inputs nearly eliminated the pathogen in all three soil types. This approach was validated in a 12.2 ha commercial lettuce field in Salinas Valley with a known history of severe Verticillium wilt. After an 18-month broccoli-Romaine lettuce-broccoli rotation including amending soil with crustacean meal before each crop, significant reductions in V. dahliae microsclerotia density were achieved. These studies demonstrated the potential for harnessing native soil microbiomes to manage plant pathogens using specific carbon sources that favor fungal antagonists. This approach worked in soils with various land use and disease incidence histories and was validated in a commercial lettuce field in Salinas Valley, California.