A Metabarcoding Approach Measuring Four Complementary eDNA Marker Genes From Prokaryotes To Cetaceans Reveals Ecosystem Structure In The Coastal Northwest Atlantic Ocean

Abstract

This thesis investigates biodiversity and seasonal dynamics of the marine ecosystem on the Canadian Atlantic Scotian Shelf using environmental DNA (eDNA) metabarcoding of four marker genes. It addresses two primary questions: (1) How does eDNA multi-marker metabarcoding detect ecosystem structure in Scotian Shelf marine environments? (2) How does quantitative eDNA analyses contribute to improve the resolution of metabarcoding on seasonal biodiversity patterns in a coastal ocean ecosystem? Chapter 2 presents the first assessment of biodiversity made in the Gully Marine Protected Area (MPA) using eDNA metabarcoding from the Atlantic Zone Monitoring Program (AZMP). A multi-marker gene approach (12S rRNA, 16S rRNA, 18S rRNA, and COI) revealed biodiversity patterns structured primarily by depth and seasons, with 115 phyla, 566 families, and 631 species detected. Methodological factors, such as membrane filter pore size and reference database, influenced community detection and taxonomic resolution. The presentation of these pilot findings concludes with recommendations for the refinement of biomonitoring using eDNA in seawater. Chapter 3 examines eDNA-based seasonal ecosystem dynamics across Inuktpikjuik (Halifax Harbour and Bedford Basin) through a quantitative metabarcoding approach that combines qPCR quantification of the marker genes and amplicon sequencing. Monthly river-to-ocean transects of eDNA sampling and metabarcoding revealed distinct seasonal shifts in community composition and richness. From the same samples of eDNA, qPCR assays measured independently distinct seasonal fluctuations in concentrations of marker genes in seawater. Combining the two approaches, these seasonal eDNA signals were analyzed in parallel with field-filtered blanks and internal standards spiked in samples to better quantify potential biases. My findings demonstrate that eDNA metabarcoding captures fine-scale ecological heterogeneity in the marine environment, while qPCR quantification of the same genes complements ecological interpretation. Further, my results provide an eDNA biodiversity baseline for long-term biomonitoring of the Scotian Shelf at different scales. In the conclusion chapter, I provide insights and suggestions on how to further develop a quantitative eDNA metabarcoding for future ecosystem management and multi-trophic ecology modelling based on eDNA metabarcoding.