Microbial Community Assessment Via Environmental DNA: A Supplemental Method For Monitoring Finfish Aquaculture Impacts

Abstract

With the increasing demand for fish consumption and the plateauing production of capture fisheries, aquaculture has become the primary supplier of fish for global consumption. However, the rapid growth and expansion of aquaculture have raised concerns about its environmental impacts, particularly those associated with organic effluents. With the accumulation of uneaten feed and feces under the fish pens, the benthic environment can quickly turn from oxic to anoxic, leading to the production of hydrogen sulfide, a toxic compound to the local ecosystems. To mitigate the impact of organic loading, various monitoring approaches have been applied and tested globally, mainly consisting of direct measurement of sulfide or employing biological indices, although each has noticeable limitations. As a result of the advancement of sequencing technologies, environmental DNA (eDNA) metabarcoding has become a promising tool for environmental monitoring. This thesis uses eDNA metabarcoding and metagenomics to characterize patterns in benthic microbial community composition associated with aquaculture activities, with the goal of supplementing the current monitoring practices. The results demonstrated that aquaculture is one of the factors that shape the microbial community. Chapter 2 developed and tested a supervised machine learning model using microbial eDNA amplicon sequence variants (ASVs) as a taxonomic-free environmental assessment tool. Although the model’s performance was hindered by extreme class imbalance, its integration with statistical indicator species analysis resulted in several indicator ASVs for aquaculture monitoring. Chapter 3 showed that organic effluent introduces fish-associated bacteria into the sediment communities and documented the first metagenome-assembled genome (MAG) of cable bacteria on the East Coast of Canada, possibly functioning as a sulfur oxidizer to remediate the aquaculture impact. Overall, this thesis demonstrated that microbial communities are sensitive to the aquaculture activities and have a strong potential to serve as a supplementary tool to the current aquaculture environmental monitoring practice.