The application of DNA-based methods to the diet of Antarctic krill (Euphausia superba)

Studying the diet of Antarctic krill (Euphausia superba Dana) is important for modelling the flow of energy and nutrients through the Southern Ocean food web. Previous studies have demonstrated that krill consume a diverse range of prey, but, have failed to detect or quantify the contribution of important prey groups. The aim of this thesis was to examine whether new DNA based methods can contribute to the analysis of krill diet. Initial work developed methods for preserving, extracting and analysing prey DNA derived from krill stomachs. These methods were shown to be capable of preserving large amounts of intact prey DNA and generating reproducible diet data. However, two problems with the method were identified. The first problem was the presence of a large amount of predator DNA in diet samples that competed with prey DNA during PCR amplification. Further work developed methods that removed predator DNA prior to PCR, or, blocked predator DNA amplification during PCR. These methods were successful when applied to a simplified test system but failed when applied to real field samples. The second problem was a discrepancy between the results obtained with DNA and concurrent results obtained with microscopy. This suggested the initial method suffered from bias that skewed results for some prey groups. Subsequent work attempted to resolve this problem by changing the approach from quantifying various prey within individual krill stomachs to quantifying the presence or absence of various prey groups in a large number of krill. When applied to field samples this approach correctly identified the same prey groups as microscopy, and, suggested that gastropods are a more important component of krill diet than previously recognised. However, there were still issues regarding the quantification of prey. The remaining work focused on fundamental issues related to the longevity and quantification of prey DNA in krill stomachs. In krill stomachs, prey DNA was found to: be stable for several hours after ingestion, vary in quantity over six orders of magnitude; and, exit the stomach faster when krill continued to engage in feeding activity. Overall the results were promising and the application of DNA methods to krill diet warrants further investigation.