This just in - eDNA metabarcoding proves more sensitive than electrofishing for fish surveys!

When it comes to detecting fish species the general methods used are netting, trapping and electrofishing. Environmental DNA (eDNA) is the newest innovation for wildlife detection tools. This molecular based method can detect traces of DNA left behind in aquatic environments by fish species. Fish don’t need to be captured or seen and the identification is based on a DNA sequence match rather than morphological identification. A growing number of environmental practitioners are adding eDNA to their survey toolkit.

As research continues to develop, so does our understanding of the increased sensitivity that eDNA demonstrates against traditional survey techniques. As this latest research proves, it can now be the go-to detection tool for fish surveys! Functioning either as a standalone tool for fish biodiversity detection or to help target traditional survey efforts when other population information is needed, such as juvenile recruitment, health and abundance.

Latest Research

Our Research Director, Dr. Andrew Weeks and Molecular Scientist, Dr. Sue Song, collaborated with colleagues from Melbourne Water, Monash University, The University of Melbourne, and the Arthur Rylah Institute in Victoria to investigate the sensitivity of eDNA metabarcoding for detecting entire fish communities in freshwater streams.

The findings of this study were recently published in the international science journal Molecular Ecology. This paper is at the forefront of comparative research into the sensitivity of multi-species eDNA metabarcoding by comparing the results with backpack electrofishing, the current gold standard for detecting fish species in small rivers and waterways. The findings were significant and captured the true value of eDNA metabarcoding as this method successfully delivered greater sensitivity for determining freshwater fish community composition.

Study Approach

• 24 sites were selected across Melbourne’s 5 catchments and assessed by eDNA and backpack electrofishing
• Each site consisted of a 100 m stretch of river netted off at either end (to stop fish moving into or out of the study area). First, 5 eDNA water samples (~300 mL / sample filtered through a Sterivex filter) were taken along the length of the 100 m (moving from downstream to upstream). Then double pass electrofishing was undertaken (where the electrofisher moves from downstream to upstream collecting all fish that are stunned in a bucket, waits 30 mins, and then repeats). All fish collected are morphologically identified and counted.
• Back in the lab, DNA was then extracted from the filters and eDNA metabarcoding undertaken using an assay targeting fish and another assay targeting all vertebrates (which included fish, as well as a bunch of other species – in this study only the fish data was analysed).
• Analyses focused on comparing the sensitivity of the two methods using species occupancy detection models (SODMs)

Results

The results illustrate that eDNA metabarcoding can provide an effective and more sensitive alternative to backpack electrofishing for sampling freshwater fish communities. The sensitivity of eDNA metabarcoding varied among species and sites, but the community-level effect of the method was always in favour of eDNA. Key findings included:

• Species richness estimates were higher using eDNA metabarcoding compared to electrofishing.
• eDNA metabarcoding can provide additional data that cannot be collected with electrofishing. This is evident from the results of using the vertebrate primers, in which 25 fish species and 69 non-target species were detected. Electrofishing detected 19 target species and eight non-target species.
• Logistical constraints were experienced when using electrofishing. For example, some sites could not be surveyed with electrofishing due to high salinity levels, but eDNA samples could still be taken at these sites. 
• Electrofishing is site-specific and gives estimates of fish occupancy only within the traversed reach. In contrast, eDNA sampling can include detections from fish upstream of the sampling site.

This research is highly valuable in proving the effectiveness of eDNA and plays a vital role in supporting its transition as a widely adopted technique by industry.

This research was led by PhD student Emily McColl-Gausden at The University of Melbourne.

By Jacquie Murphy, EnviroDNA 

Want to use eDNA for your next fish survey? 
Please get in touch. We love discussing new project ideas for eDNA and can help you determine if this is a valuable option for you! 

Find out more:
Discover how organisations in Australia are adopting eDNA as an innovative wildlife detection tool by viewing our 
case studies.