Monitoring Fish Communities in Six Waikato Lakes Using Environmental DNA

Abstract

Environmental DNA (eDNA) describes the DNA from organisms that is discarded into the environment. It has a variety of sources such as loose skin cells, hair and faeces. Molecular methodologies are available to isolate this DNA from an environmental sample. Depending on the purpose of the sampling, techniques are available to either identify a range of species whose DNA is present or to target a particular species or taxa to determine whether it is present or absent. For the latter, it is even possible to estimate tax on biomass from the amount of DNA in a sample. These eDNA detection techniques are of interest to support biosecurity and conservation efforts because they can detect rare, endangered or invasive species, and are potentially less time consuming and more affordable compared with traditional surveying methods. In the Waikato region of New Zealand, koi carp (Cyprinus carpio varkoi) is an invasive fish and is classified as an unwanted organism. eDNA techniques could potentially identify lakes invaded by koi carp, estimate carp biomass and their impact on fish communities. This study attempts to quantify koi carp biomass in six lakes in the Waikato region and to describe the composition of fish communities in these lakes to see whether greater koi carp biomass has an impact on number of species present (and which species are present) in each of these lakes. After rarefaction, generic fish primers were able to detect 27 OTUs across eight family or genus based groups of fish, including three native genera. These showed that community composition was different between the sampled lakes. However, primers targeting koi carp DNA were not specific, limiting inferences that can be made on the biomass and impact of koi carp. This study indicates that eDNA methodologies can be effective for fish surveying in New Zealand.