Co-managing soil and plant pathogens: effects of organic amendments on soil fertility and fungal pathogen survival

Abstract

This study examined presence and persistence of the gray mold pathogen Botrytis cinerea in organic field soils and the dual effect of different organic soil amendments on soil fertility and survival of Botrytis cinerea – one of the most important broad-host-range plant pathogens in the world. Field soil was collected and assayed for two consecutive years from an organic farm in Maryland to determine baseline levels of B. cinerea inoculum. Then a controlled environment study was conducted in triplicate, where laboratory-reared B. cinerea survival structures (sclerotia) were buried in potted mixtures of field soil containing compost and chitin amendments and assessed over time for viability, fragmentation, and colonization by microbes antagonistic to B. cinerea growth. A one-year in-situ field trial was also conducted to evaluate dual effects of different combinations of soil amendment and cover crop treatments on pathogen persistence and soil fertility as they would occur in an organic grower’s field, under winter and summer conditions. Surveys revealed that the selected organic farm sustained high levels of soil-borne B. cinerea inoculum, with up to 1200 B. cinerea propagules per gram of soil, and field studies demonstrated that the fungus could persist for both a five-month over-winter (2–24% of sclerotia viable) and a five-month over-summer period (0–1% of sclerotia viable) in-situ. In general, compost and cover crop treatments increased persistence of the fungus compared to fallow (control) treatments in both controlled environment and field trials. On the other hand, application of chitin (crushed crab shells) facilitated fragmentation and mortality of sclerotia. Compost and chitin applications resulted in a two- to three-fold increase in recovery of sclerotia-associated microbial antagonists, while the addition of dwarf essex rape (Brassica napus) significantly reduced recovery compared to the control. In both the winter and summer field studies, all compost treatments significantly increased soil N, P, and pH, but the combined treatment of compost, chitin, and cover crop had the greatest increase in soil fertility. Based on molecular analysis, putative bacterial antagonists recovered from non-viable sclerotia included species of Bacillus, Paenibacillus, Stenotrophomonas, and Lactobacillus – all of which have been previously described to inhibit B. cinerea growth. Overall, our studies indicate that organic strategies to co-manage B. cinerea and soil fertility can be optimized by adding chitin to composted amendments.