Date of Award


Document Type


Degree Name

Master of Science (MS)


Plant and Soil Science

First Advisor

Deborah Neher


Compost can suppress soilborne plant pathogens that cause significant damage on globally important food crops. However, reports of plant pathogen suppression are inconsistent likely because there are no established standards for feedstock material, application rate, and maturity age upon application. Excellent results can be achieved in greenhouse trials, but field applications are much less reliable. Disease suppression occurs through the activity of biocontrol organisms (direct antagonism), and general microbial competition. Biocontrol species are hypothesized to colonize the pile during the curing phase, but single species may not be as important as microbial consortia. Substrate composition during maturation may give rise to a suppressive microbial community. More research is needed to understand the relationships between feedstock, maturity, and production process on compost microbial ecology. The thesis had two main objectives: 1) identify biological indicators in compost that could (a) characterize maturity, process, and feedstock, and (b) predict disease suppression against R. solani, and 2) identify bacterial and fungal community composition and/or structure that is associated with suppression of soilborne disease.

Rhizoctonia solani is a facultative saprophytic fungus and soilborne plant pathogen that attacks many globally important food crops and turfgrass. Prior research suggests that managing carbon quality and compost maturity will alter relative competition between biological control microbes and the R. solani pathogen. The pathogen is responsible for economic losses to organic vegetable production in Vermont and there are no available methods to manage the disease that meet organic certification. R. solani on radish was chosen as a model system given its global importance, competitiveness affected by carbon quality, and lack of disease management options for organic production.

Compost samples were most abundant in the bacterial phyla Proteobacteria and Bacteroidetes, and known biocontrol species were not detected in abundance. Compost samples did not differ significantly in fungal community composition, suggesting a dominance effect from the native soil fungal community.

Overall, anaerobic digestate and vermicompost were most suppressive against R. solani. Thermophilic composts were not very suppressive overall, though a specially made hardwood bark compost was comparable to the suppressiveness of vermicompost application. Ecoenzyme analysis was able to integrate information on environmental substrate composition, microbial nutrient acquisition, and microbial community metabolism, offering the best view of current ecological conditions in compost. Ecoenzyme analysis showed that the most suppressive composts, anaerobic digestate and vermicompost, were most nutrient limited. All compost samples were severely nitrogen (N) limited, and anaerobic digestate and vermicompost were severely limited in both N and phosphorus (P). The additional P limitation may support non-pathogenic species to outcompete R. solani. The key to disease suppression may lie in matching up the ecology of the plant pathogen with the ecology of biocontrol, which may be engineered in compost.



Number of Pages

151 p.