Advancing eDNA Sampling for Biodiversity Monitoring

Abstract

Environmental DNA (eDNA) is an important tool used in marine biodiversity monitoring. eDNA samplers offer a more cost effective and efficient means of the collection and concentration stages in the eDNA pipeline. A review of existing devices was done to compare their performance and features. This thesis describes the theory that determine the eDNA Sampler's effective flow rate, as well as using optics as a feedback mechanisms in eDNA sampling. The relationships between the dimensions of the fluid channel, the pressure source and flow rate were examined, and the physical limitations of flow through a membrane and filter cake buildup were also explored. This theory was supported by bench testing whose experimental results aligned with theoretical calculations. A submersible sampler was designed with this information, and was tested in the Bedford Basin in Halifax, Nova Scotia, Canada. The device captured samples at relatively high flow rates, which were successfully sequenced. The sequencing data from this instrument is presented and compared to samples captured by manual sampling and a previously tested instrument. The use of optics as a feedback mechanism during sampling was explored and showed favorable results. The results from this thesis will hopefully prove informative to the developers of eDNA samplers to refine instrument designs.