Evaluating environmental DNA (eDNA) metabarcoding as a method for monitoring biodiversity in marine ecosystems.
Halting current global biodiversity loss is important to maintain ecosystem functioning. To succeed in halting biodiversity loss, information is needed on community composition, abundance of species, and changes in these patterns over time. However, such comprehensive assessments, traditionally based on visual species detection, are often challenging in the marine biome. Ecologists are, therefore, driven to implement innovative monitoring techniques. One approach gaining increasing traction is environmental DNA (eDNA) metabarcoding, a process referring to the simultaneous identification of a multitude of species from environmental samples. While circumventing the need for taxonomic expertise to identify species and invasive sampling, the indirect manner of species detection requires extensive validation to demonstrate the utility of aquatic eDNA metabarcoding. This thesis describes three experiments intended to provide evidence for the capabilities of eDNA metabarcoding as a method for monitoring biodiversity in marine environments. 1) I developed an optimal and easy-to-use eDNA metabarcoding protocol: filtration through cellulose-nitrate filters and extraction with Qiagen’s DNeasy Blood & Tissue Kit. Subsequently, I showed that the use of optimized protocols leads to a significant increase in OTU and species richness for targeted metabarcoding assays detecting fish and crustacean species. Finally, I developed user-friendly bioinformatic pipelines allowing data processing and analysis on a home computer to facilitate the implementation of this technique. 2) I investigated the accuracy of eDNA metabarcoding as a method for monitoring biodiversity in the marine environment. Possible eDNA signal dispersal through water movement is one of the main sources of skepticism halting the integration of eDNA metabarcoding surveys into existing monitoring programs. However, by distinguishing localized eDNA signals from a coastal region harboring different habitats and distinct community assemblages on a small spatial scale, I provide evidence that eDNA metabarcoding surveys can be successfully used to detect a broad range of taxa. 3) I determined the influence of water column stratification on the ability of eDNA metabarcoding surveys to uncover subtidal biodiversity patterns in marine systems. Comparing eDNA signals between non-mixing water layers showed highly distinct patterns, while similar eDNA signals were obtained in areas subject to vertical water displacement. Based on these results, I advocate to take into consideration the oceanographic processes within an area when designing eDNA sampling strategies in marine ecosystems. This study recommends the implementation of eDNA metabarcoding surveys into established monitoring programs in marine environments, by highlighting the advantages of eDNA metabarcoding over traditional monitoring techniques. In particular, the increased sensitivity, DNA-based species identification, and non-invasive sampling strategies have the ability to aid marine ecosystem conservation. My results also point out certain key limitations in eDNA metabarcoding as a monitoring method, with regards to the present-day inability to obtain abundance and life-history data. The findings promote the suggestion that eDNA metabarcoding to be implemented in tandem with traditional monitoring methods. Visual observations will provide more detailed information on commercially important or key indicator species, while eDNA metabarcoding provides a more complete overview of the species-composition of the community.
Advisor: Gemmell, Neil; Spencer, Hamish; Lamare, Miles; Knapp, Michael
Degree Name: Doctor of Philosophy
Degree Discipline: Anatomy
Publisher: University of Otago
Keywords: Environmental; eDNA; Genetics; Metabarcoding; Biodiversity; Marine; Monitoring
Research Type: Thesis