Date of Award

August 2018

Degree Type


Degree Name

Doctor of Philosophy


Freshwater Sciences

First Advisor

Ryan J Newton

Committee Members

Sandra L McLellan, Jin Li, Matthew C Smith, Mark J McBride


aquaculture, aquaponics, bioinformatics, microbial ecology, process design, urban agriculture


Intensive cultivation of fish is necessary to meet future global market demands. Recirculating aquaculture systems (RAS) enable dense growth of fish, while occupying less space than traditional aquaculture farms. However, RAS often experience complications and high fish mortalities due to disease and improper waste management. In properly functioning systems, the microorganisms associated with fish (gut, scales) as well as those found in the system environment (water, component surfaces) remove waste and maintain fish health by discouraging growth of opportunistic pathogens. Previous RAS microbiome studies are small in scope, utilize coarse methods, and contain limited long-term spatial or temporal data. With advances in computation, microbial ecology, and RAS technology it is possible to test the relationship between RAS operational management practices and microbial community composition. Using the RAS at the UW-Milwaukee School of Freshwater Sciences, I used massively parallel DNA sequencing platforms, cutting-edge fluorescent microscopy, and classical molecular and microbiological methods to rigorously examine microbial community structures. Results from this dissertation advance our knowledge of aquaculture by analyzing RAS microbiota throughout the system over time; evaluate waste removal function, and track system condition correlations to pathogen blooms. These analyses will provide insight as to how environmental changes during rearing cycles affect system function and fish health. To investigate the connection of waste componentry failure to pathogen blooms, this dissertation uses Flavobacterium columnare as a model organism, since F. columnare infects fish across a myriad of freshwater systems. Genome sequencing of pathogenic F. columnare strains gives insight into the metabolic connections between fish waste and persistence of opportunistic pathogens. By better understanding the role of the microbiome in RAS, we can improve fish health, optimize waste removal, and increase yields and profits for aquaculturalists.