Date of Award

Winter 2020

Project Type


Program or Major

Plant Biology

Degree Name

Master of Science

First Advisor

Anissa Poleatewich

Second Advisor

Jessica Ernakovich

Third Advisor

Todd Guerdat


Holding advantages in efficiency and geographical flexibility, soilless Controlled Environmental Agriculture (CEA) systems have emerged as economically viable and ecologically sound alternatives to field agriculture, especially in high-value fruit and vegetable production. While commercial soilless operations typically use synthetic, mineral-based nutrient solutions for plant nutrition, there is interest in incorporating more ecologically sustainable naturally derived sources. Aquaponics - the linkage of aquaculture with soilless crop production - represents one such alternative. Aquacultural effluents can provide partial to complete plant nutrition following solids removal and nitrifying biofiltration, while the incorporation of solutes into crop biomass reduces the need to discharge culture water and provides a secondary source of revenue for producers. Bacteria that suppress common soilless root pathogens (e.g. Pythium spp., Fusarium spp., Rhizoctonia solani) have been isolated from aquaponic culture water, suggesting potential for in vivo suppression. Aquacultural effluent and other naturally derived nutrient solutions contain variable concentrations of dissolved organic carbon (DOC). In recirculating aquaculture system (RAS) biofilters, high DOC can stimulate a proliferation of opportunistic heterotrophs that outcompete nitrifiers for oxygen, reducing nitrification efficiency. The plant health and microbial community effects of DOC in the crop subsystem of aquaponics are less understood. The objectives of this research were a) to characterize the plant growth effects of synthetic and aquaponic nutrient solutions with and without added DOC, b) to evaluate Pythium root rot severity in plants irrigated with each nutrient solution, and c) to explore the compositions of solution, substrate, and rhizosphere microbial communities associated with each nutrient solution. Strawberries (Fragaria x ananassa Duch. cv. “Albion”) were grown in drip irrigated coco coir substrate culture using four nutrient solutions: a synthetic mineral solution (Synth), dilute culture water from three recirculating aquaponics systems at Kingman Farm (Aqua), and the same two solutions amended with sucrose to raise DOC concentrations (Synth C and Aqua C). Half of the bags in each nutrient solution treatment were inoculated with the root rot pathogen Pythium aphanidermatum. Five weeks after inoculation, plant above- and belowground health was evaluated; roots were rated for disease; and bulk substrate, solution, and rhizosphere samples were collected for 16S rRNA and ITS amplicon metabarcoding. P. aphanidermatum inoculation failed to produce significant symptoms, so suppression could not be evaluated. Plants irrigated with sucrose amended solutions were stunted, with smaller root balls and reduced aboveground biomass compared to unamended solutions. Irrigation with Synth produced plants with 40% greater aboveground dry mass than those irrigated with Aqua. Bacterial richness was significantly greater in coir substrate samples from the Synth C treatment than those from Synth. Substrate bacterial community compositions differed significantly between the Aqua and Aqua C treatments. Substrate fungal communities did not significantly differ across nutrient solution. Abundant bacterial and fungal taxa in substrate samples included saprotrophs of refractory organic carbon as well as strains with putative plant growth promoting and phytopathogen suppressive effects. This work affirmed the importance of keeping labile DOC low in nutrient solutions to maintain crop health. Microbial taxa with putative plant-beneficial activity were identified in coco coir substrate samples, informing future work to elucidate complex relationships among organic carbon, nutrient solutions, microbial communities, and soilless CEA system health.