Denmark must regularly monitor protected species across its Habitat sites to meet EU reporting obligations. With conventional methods, that is costly, labour-intensive and squeezed into a short season.

The Danish Agency for Green Transition and Aquatic Environment worked with NatureMetrics to test whether eDNA could make national monitoring of protected and vulnerable species faster, cheaper and more consistent. Samples from more than 230 locations revealed 398 invertebrate and 21 vertebrate taxa. eDNA results for great crested newts closely matched conventional surveys. The project could support Denmark’s national monitoring programme, NOVANA, and has started work on technical guidance for using eDNA nationwide.

Under NOVANA, Denmark’s national programme for monitoring aquatic and land ecosystems, the agency divides the country into ten-by-ten squares and monitors four ponds per square for amphibians and other species.

With conventional methods, this work:

• Relies on specialist field staff and is time-consuming
• Depends on the weather, with summer especially overloaded
• Has to fit into the short window when amphibians are most visible
• Can produce false negatives

Biologist Jens Erik Lindgaard Hansen summed it up: “We need more efficient methods to collect this data.”

The agency wanted more complete data, a longer sampling season, a more even workload, standardised results regardless of who collected the samples, and lower costs. It needed to test whether eDNA could deliver all of this at national scale before building it into government protocols.

• Kits and lab services at scale: NatureMetrics supplied eDNA sampling kits and lab analysis for more than 230 locations, keeping collection consistent across Denmark.
• Two methods: we used targeted qPCR for great crested newts and metabarcoding for a broader view of species.
• Fast turnaround: standard operating procedures and results were delivered within eight weeks.
• Quality control: we supported field hygiene, daily negative controls and equipment sterilisation, alongside lab procedures that minimise contamination and false positives.
• Expert support: our technical team ran consultation sessions on CT values, interpretation thresholds and quality controls.

• Strong match with conventional surveys: qPCR results for great crested newts correlated very highly with conventional methods.
• Rich invertebrate data: metabarcoding found 398 invertebrate taxa across 21 samples, an average of nearly 60 per sample. Two vulnerable diving beetles, Dytiscus latissimus and Graphoderus bilineatus, were targeted.
• Amphibians and other vertebrates: 21 vertebrate species were detected across 13 samples. These included moor frog, common frog, European tree frog and great crested newt.
• A longer sampling window: great crested newt detections differed between May and June samples, suggesting the season could be extended.
• Complementary results: eDNA sometimes detected species that conventional methods missed, and the reverse.
• Reliable results: 100% of invertebrate samples amplified successfully, and all but three vertebrate samples did.
• Consistent across teams: results stayed consistent across several field teams. Katrine Hansen Lemming, project manager and biologist, explained: “One of our goals was to put the field method to a test on a large scale with several different samplers”.

Katrine also stressed that expert biological knowledge is still needed to choose where samples are taken.

A route to national guidance
The project has fed into potential technical guidance and a standardised, flexible framework for using eDNA in national monitoring, if the method proves cost-efficient.

Potential benefits for national monitoring

• Higher detection sensitivity
• Simpler, more standardised processes
• A longer monitoring window, less dependent on the weather
• More efficient use of time, staff and budget

Ready for the Nature Restoration Regulation
Under the EU Nature Restoration Regulation, monitoring will expand from Habitat sites to the whole country. The agency is considering eDNA either as the main monitoring tool or as a screening tool to target traditional surveys.

Building skills and a long-term dataset
The project built eDNA knowledge within the agency. An ongoing eDNA monitoring platform could build a long-term national dataset. As Jens Erik put it, if colleagues in the field accept the method, “we have already had a little success.”

A model for other countries
The project offers a blueprint for other governments looking to monitor vulnerable species nationwide.