A tool for ecological monitoring and management
As organisms move through their environment they shed genetic material, environmental DNA (eDNA), which can be extracted from natural substrates including soil, water, permafrost or sediment. eDNA can persist in the environment for very long time periods – such as plant DNA extracted from a 400,000-year-old permafrost sample in Siberia and Moa DNA from a 600-year-old cave sediment sample in Aotearoa New Zealand.
eDNA can be used as a very sensitive measure of species presence. It has been used to study single-cellular species diversity since the 1980’s and multi-cellular species diversity since the 2000’s. Technological advances in DNA sequencing and reduction in cost has enabled more widespread use of eDNA as a monitoring tool over the last decade. It is used in a range of ecological applications such as monitoring biodiversity, detecting the presence and spread of an invasive species or detecting the presence of a rare species over time. Morphum started using eDNA as a tool in the freshwater space in 2020 and was one of the first consultancies to start using eDNA for monitoring purposes in Aotearoa.
Biodiversity wheel for an eDNA sample
In 2021 we used eDNA to complement observations of freshwater biodiversity in our Kopurererua catchment Watercourse Assessment for Tauranga city council. We detected eight native fish species - longfin and shortfin tuna, kōaro, banded kōkopu, shortjaw kōkopu, redfin bully, torrentfish and common smelt - two exotic fish species, a range of bird species, livestock, native plants and confirmed the presence of four mammalian pest species - possums, norwegian rat, black rat, and red deer. Species detection through eDNA analysis supplemented observational findings and led to advice to prioritise protection and habitat enhancement of these areas, the exclusion of stock access to waterways and the need for pest management.
Collection & Detection
Collection of eDNA samples from a stream
DNA encodes instructions for organisms to develop and function and is made up of sequences of nucleotides. These sequences vary between species and allow species identification from short segments of DNA.
In order to find this DNA, water samples are collected from a waterbody with a syringe and passed through a filter, with a membrane that binds eDNA. Barcoding is then performed for single-species detection or metabarcoding for multi-species detection.
Once the sample collection is complete, the sample is sent to the laboratory, where the team can identify the unique segments of DNA that allow us to identify the species that are present.
The laboratory workflow starts with eDNA extraction from the membrane followed by amplifying short segments of eDNA by Polymerase Chain Reaction (PCR). PCR requires the use of short segments of manufactured single-stranded DNA, or primers, to bind to and define the perimeter of a short DNA segment to be analysed. Universal primers are used, which will bind to the DNA of a range of species, and define a DNA segment that varies between species.
High-throughput sequencing is then performed where the nucleotide sequence of the amplified segment, a read, is identified and analysed by aligning the sequencing reads to a database of species’ nucleotide sequences, a barcode library. This workflow enables detection of eDNA sourced from up to 10km upstream (but usually much less) of the sampling site and can identify aquatic and terrestrial animals, plants, insects, fungi & bacteria.
The applications of eDNA in ecological monitoring and management are broad. We use eDNA to support stream ecological valuations (SEVs) and the effectiveness of fish passage barrier removal. Remediation work in or around streams requires relocating fish before works begin and we use eDNA to identify which fish are present so appropriate fishing techniques can be employed.
Kākahi on a streambed
eDNA monitoring offers a sampling technique that has less impact on flora, fauna and the environment than other traditional methods, and does not require extensive specialist knowledge and experience to collect data, while offering high sensitivity and specificity.
Habitat location and species distribution can make monitoring using traditional techniques time consuming, while eDNA monitoring offers a faster and cheaper alternative with less opportunities for human error. Rare species such as Kākahi can be logistically difficult to monitor because of their low biomass, and to the potential risk that physical searches pose for their wellbeing, and eDNA offers a potential means to overcome these risks. We are collaborating across the industry to develop standard community guidance for Kākahi monitoring and exploring the role eDNA sampling may play in this endeavour.
As with any new technology, there is ample space for exploration to tailor this powerful tool to the question at hand. We are currently performing state of the environment (SOE) monitoring for Auckland Council where we are building an essential dataset which will enable comparison of physical fish monitoring against eDNA sampling. This plans to address how eDNA monitoring quantitatively compares to the standard protocol and explore if eDNA may be an appropriate alternative tool to current standard techniques for fish monitoring.
Limitations and Outlook
eDNA is a very exciting space for ecological monitoring and management. It offers an alternative monitoring tool that is faster, cheaper, more sensitive and limits the impact on organisms & the environment over standard monitoring techniques. However, as with many technologies, there are limitations which need to be considered when interpreting results. The origin of eDNA is still not fully understood but is commonly from shed or expelled biological material such as skin, exoskeletons, larvae, or faecal matter. Another potential bias to account for is that larger organisms will likely shed higher quantities of eDNA, and therefore be more easily detected than smaller organisms. eDNA sampling is a snapshot and so time of year can have a large impact, especially in larvae dispersal (inside/outside of breeding season) or invertebrates who shed their exoskeleton periodically with growth. These species may evade detection due to reduced eDNA levels at the time of sampling, depending on when the sample is taken.
Environmental factors also need to be accounted for, with factors such as temperature and the substrate in which eDNA is stored, both impacting the rate of eDNA breakdown, making it unclear to what extent the catchment is being sampled. Recent weather can impact eDNA collection – for example, rain can dilute eDNA concentrations in the waterbody. Heavy rainfall can cause sediment loading to water and generate turbidity, which clogs collection filters, limiting the amount of water and so eDNA which is collected. Low flows can reduce the upstream catchment area eDNA collection represents, and variable flow regimes impact which portions of the catchment are included. Contaminants can cloud interpretation and the number of sample replicates can impact the number of detected species. This means sample timing, location, and rigor are aspects that need careful planning and consideration in results interpretation.
Further, variation in primer efficiency between species may skew metabarcoding results and may limit detection of some species to single-species assays. eDNA is currently used for species presence but further investigations are required to understand if accurate species abundance can be determined from eDNA signal intensity.
The Future of eDNA
eDNA is a powerful tool to supplement standard monitoring techniques. The development of bioinformatic pipelines and investigation of current limitations will expand the application breadth of eDNA in ecological monitoring and management in the coming years. We’re very excited to see where the future takes this relatively new means of data collection, and the positive impacts this pursuit could lead to.