Document of bibliographic reference 405804

BibliographicReference record

Type

Bibliographic resource

Type of document

Book/Monograph

Type of document

Dissertation

BibLvlCode

M

Title

Towards a DNA-based monitoring approach for nearshore benthic invertebrates

Abstract

This thesis explores the utility and challenges of DNA-based methods, including DNA barcoding and environmental DNA (eDNA) metabarcoding, for monitoring biodiversity in marine ecosystems. Comprised of four data chapters, it investigates gaps in DNA barcoding coverage, addresses methodological concerns in metabarcoding, and optimizes protocols for specific environmental conditions. The first of these chapters highlights significant gaps in Canadian DNA barcoding efforts, particularly in marine ecozones where a low percentage of species are represented in the Barcode of Life Data System (BOLD) database. These gaps limit the effectiveness of DNA barcoding for marine biodiversity assessments by constraining the accurate taxonomic assignment of many sequences. The second chapter considers the potential impact of pseudogenes on results obtained through eDNA metabarcoding, specifically the impacts linked to the amplification of non-functional gene copies that can inflate biodiversity estimates. Using the cytochrome c oxidase subunit I (COI) gene as a model, my work demonstrates that pseudogenes are present but can be effectively mitigated through appropriate bioinformatic filtering, ensuring the utility of COI in marine biodiversity studies. My third chapter describes efforts to optimize eDNA metabarcoding protocols for organically enriched marine sediments impacted by log handling and storage activities. The results show that sampling strategy and DNA extraction protocols significantly influence biodiversity estimates, and that four sediment subsamples per grab can effectively capture infaunal diversity in this study system. This work further emphasizes the importance of adapting protocols to specific environmental conditions. My final chapter compares the consistency of ecological patterns detected by different taxonomic assignment methods applied to eDNA data. Despite variability in taxonomic resolution and composition, all methods consistently detected broad ecological patterns such as the effect of grain size on benthic communities while none detected effects linked to acid volatile sulfides (AVS). This study underscores the robustness of eDNA-based methods for detecting large-scale ecological patterns but highlights limitations in detecting finer-scale environmental impacts. Collectively, these studies help advance the use of eDNA and DNA barcoding for marine biodiversity monitoring and underscore the need for continued methodological refinement and expansion of reference libraries.

Bibliographic citation

Schultz, J.A. (2025). Towards a DNA-based monitoring approach for nearshore benthic invertebrates. PhD Thesis. University of Guelph: Guelph. 190 pp.

Topic

Marine

Access rights

open access

Is accessible for free

true