Document Type


Degree Name

Master of Science (MSc)



Program Name/Specialization

Integrative Biology


Faculty of Science

First Advisor

Dr. Robin M. Slawson

Advisor Role



The growing worldwide demand for fish production has prompted research towards intensive aquaculture. Innovative system designs, such as recirculating and flow-through aquaculture systems, have been developed to improve the efficiency and sustainability of intensive aquaculture practices. These LBAS systems exhibit a wide range of spatial and temporal heterogeneity. Although such heterogeneity suggests the potential for culture water to support a diverse and spatially complex assortment of microorganisms, there is a lack of information regarding the overall diversity and composition of microbial communities (including pathogens) in the different compartments of these systems. To better understand the diversity and functionality of microbial communities within different aquaculture systems, a field-based approach was taken to gain perspective on the spatial and temporal variation of microbial communities in aquaculture systems of varying design, including: two pilot-scale recirculating systems, each utilizing a different wastewater treatment technology; and two field-scale flow-through aquaculture systems. Of particular interest was gaining a better understanding of microbial community balance on the retention of organisms with pathogenic potential, including the fecal indicator bacteria E. coli and Enterococcus spp., as well as the fish pathogens Yersinia spp. and Aeromonas spp. An integrative approach to phenotypic (culture-based) and genotypic (molecular-based) analysis was taken to profile test microorganisms at multiple levels. Specifically, a media-based plate count approach was used to enumerate the heterotrophic and pathogenic bacterial levels, as well as removals, from the aquaculture environment. Additionally, ABR analysis was conducted for resistance profiling of select pathogens isolated from a local FTS against a panel of 12 antibiotics. The functional and structural fingerprints of the communities were investigated by community-level physiological profiling (CLPP) and denaturing gradient gel electrophoresis (DGGE), respectively. Cultivation results indicated the presence of Yersinia spp. and Aeromonas spp. within all system designs, with abundances of Yersinia spp. typically detected more frequently within the respective systems compared to Aeromonas spp. Pathogen levels in recirculating systems were observed to be sensitive to various wastewater treatment approaches, including NMB and UF technologies. Field-scale FTS results indicated spatial variation of microbial communities and pathogens, with a greater frequency of heterotrophic and pathogenic bacteria observed within effluent waters compared to influent. Functional and structural profiling of communities within recirculating and flow-through systems revealed distinct profiles for the different systems, each harbouring genetically and metabolically diverse communities, including communities demonstrating high metabolic versatility but low genetic diversity. Comparatively, the recirculating systems appeared to support more functionally and structurally stable communities than the flow-through systems, based on CLPP and DGGE results. Collectively, these findings suggest that microbial communities within different exhibit distinct responses to varying environmental parameters. Moreover, the use of NMB and UF wastewater treatment approaches may allow for the enhanced ability to manage pathogen loads within these systems. This information presents new knowledge on bacterial community composition and functionality in various parts of recirculating and flow-through systems, which constitute essential tools for overall aquaculture system management.

Convocation Year


Convocation Season