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.

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One of the motivating reasons for the development of hydroponics was avoidance of root pathogens. Hydroponics involves growing crops in relatively sterile media, isolated from the underlying soil which may have disease pressure. However, even when hydroponics is coupled with controlled environments such as high tunnels and climate-controlled greenhouses, soil-borne pathogens can enter the growing area and proliferate due to optimal environmental conditions for pathogen growth. Control of root pathogens is difficult and usually achieved through synthetic fungicides since few biocontrol options are available. Compost water extracts (CWE) have recently been gaining the attention of greenhouse growers because they may be a low-cost, environmentally friendly approach to control root disease. CWE are mixtures of compost and water incubated for a defined period of time, either with or without aeration, and with or without additives intended to increase microbial populations, which in turn suppress disease. Much anecdotal, but very little scientific, evidence exists describing CWE effect on suppressing soil-borne pathogens. The present study 1) examined the effect of an aerated CWE on disease suppression at the laboratory scale and in container studies using different soilless substrates, 2) investigated a phenotypic change at the root level caused by CWE that may be associated with disease suppression, and 3) isolated some factors in the production of CWE that affect the ability of a CWE to suppress disease. The common model pathogen-host system of Fusarium solani f.sp. pisi and pea was used to examine CWE-induced disease suppression, with information then being translatable to similar patho-systems involved in greenhouse crop production. In the first study, laboratory-based root growth and infection assays resulted in 100% suppression of F. solani when roots were drenched in CWE. These protected seedlings were then taken to a greenhouse and transplanted into fine coconut coir, watered with hydroponic nutrient solution, and grown for five weeks. At the end of the experiment, 23% of the shoots of the pathogen-inoculated, CWE-drenched seedlings remained healthy while only 2% of the inoculated seedlings without CWE drench remained healthy. All of the roots of the inoculated seedlings developed lesions, even those drenched in CWE. However, 29% of the CWE drenched roots were able to recover from disease, growing white healthy roots past the lesion, while only 2% recovered naturally. A shorter-term container study was conducted in the laboratory to determine the effects of CWE-induced suppression when peas were grown in different substrates and to determine if the hydroponic nutrient solution had an effect on the suppression. Peas were grown in sterilized fine and coarse coconut coir fiber and sand irrigated with water, with a second set of fine coir irrigated with hydroponic nutrient solution. Pea seeds with 20-25mm radicles were inoculated with pathogen and sown directly into CWE-drenched substrate and grown for three weeks. At the end of the experiment, 80%, 60%, 90%, and 50% of the shoots of the inoculated, CWE-drenched seedlings remained healthy when grown in fine coir, coarse coir, sand, and fine coir irrigated with hydroponic nutrient solution, respectively. Nearly 100% of the roots grown in coconut coir substrates again developed necrotic lesions but 83%, 87%, 100%, and 87% grew healthy roots beyond the disease region. The hydroponic nutrient solution had a negative effect on suppression, with a reduction of at least 30 percentage points. Sand demonstrated a natural ability to suppress F. solani. Only 23% of inoculated seedlings had dead or dying shoots by the end of the experiment (compared to 77-80% in coir substrates) and although all but one of the roots developed lesions, all were able to recover on their own with CWE. CWE further increased shoot health and also prevented 57% of the roots from developing lesions. In a second study, two different CWE were used to examine the effect on root border cell dispersion and dynamics in pea, maize, cotton, and cucumber and its relation to disease suppression. Dispersal of border cells after immersion of roots into water or CWE was measured by direct observation over time using a compound microscope and stereoscope. Pictures were taken and the number of border cells released into suspension were enumerated by counting the total number of cells in aliquots taken from the suspension. Border cells formed a mass surrounding root tips within seconds after exposure to water, and most cells dispersed into suspension spontaneously. In CWE, >90% of the border cell population instead remained appressed to the root surface, even after vigorous agitation. This altered border cell phenomena was consistent for pea, maize, and cotton and for both CWE tested. For most cucumber roots (n=86/95), inhibition of border cell dispersal in both CWE was similar to that observed in pea, maize, and cotton. However, some individual cucumber roots (8±5%) exhibited a distinct phenotype. For example, border cells of one root immersed into CWE remained tightly adhered to the root tip even after 30 minutes while border cells of another root immersed at the same time in the same sample of CWE expanded significantly within 5 minutes and continued to expand over time. In a previous study, sheath development over time in growth pouches also was distinct in cucumber compared with pea, with detachment of the sheaths over time, and root infection was reduced by only 38% in cucumber compared with 100% protection in pea (Curlango-Rivera et al. 2013). Further research is needed to evaluate whether this difference in retention of border cell sheaths plays a role in the observed difference in inhibition of root infection. In the third study, a series of investigations were conducted to isolate different factors that contribute to the suppression ability of a CWE by changing incrementally changing some aspect of the CWE production process. The basic aerated CWE recipe (with molasses, kelp, humic acid, rock phosphate, and silica) provided 100% protection of pea from root disease while the non-aerated basic recipe CWE provided 72% protection. Aerated CWE made of only compost and water resulted in 58% protection. It was found that molasses did not contribute to the suppression ability of the ACWE, while kelp contributed strongly. When soluble kelp was added by itself to the compost and water, the CWE provided 80% suppression. However, when all additives were included except molasses and kelp, suppression remained high (93%) indicating that humic acids, rock phosphate, and/or silica were also major contributors toward the suppression effect. Optimal fermentation time for ACWE was 24 hr to achieve 100% suppression, with increased time resulting in inconsistent suppression results. Optimal fermentation time for NCWE was 3 days or 8 days. These studies are important contributions to understanding the differences that might be expected in CWE suppression when growing in different substrates, some of the factors in the production of CWE that affects the ability of a CWE to suppress disease, and the phenotypic effect CWE has on the root zone of plants and the possible relationship between that effect and disease suppression.