Freshwater Environmental DNA Sampling

Genetic clues left behind by the organisms that swim through, splash in, and make their homes in streams, rivers, and lakes.

Last month, our freshwater Ecologist, Nicola Pyper, went out to assess an underground stream, searching for any signs of aquatic life within the caves! Enspire were asked to assist with a large-scale project that was faced with the challenge of  assessing the value of an underground stream, which could not be safely accessed due to low oxygen levels.

Enspire was able to suggest the use of an emergent sampling method called environmental DNA (eDNA).  eDNA sampling involves the filtering of a water sample downstream of the reach of interest.  The filter collects DNA fragments left behind by anything that moves through or comes into contact with the water (e.g., skin cells, mucus, hair/fur, faeces).  As such, the method did not require access to the underground section of the waterway.  Rather, we found the stream was best sampled at the cave entrance where the stream submerged, and again at the sites where the stream daylighted.  This was a welcome opportunity for Nicola to sample some beautiful springs and investigate some interesting cave entrances!

Following the field sampling, the samples were sent to Wilderlab, Wellington, who used a multi-species assay to determine what species may be using and living in the stream.  Finally, some exciting results showed that our endemic long-fin eels, who are very good climbers in their elver stage, were able to traverse one of the cave systems.  However, no fish DNA was detected in the other cave system, which suggested a significant fish barrier existed, such as a large waterfall, which can prevent fish traversing underground topography. 

The results of the eDNA samples assisted our client and their project to understand the significance of the underground stream.  This provided them with valuable data, allowing them to make better decisions going forward.  Enspire can assist with ongoing monitoring, as well as one-off ecological assessments.  We can provide robust recommendations and advice and we understand that many of our client’s projects are unique.  We assist clients to make better informed decisions for their environment management practices.

This article is intended only to provide a summary of the subject covered. It does not claim to be comprehensive or to provide advice. No person should act in reliance on any statement contained in the article without first obtaining specific professional advice. If you require any advice or further information on the subject matter, please contact us.

Contributed by: Nicola Pyper
Published on: 23 November 2021