DNA as a detective: how metabarcoding reveals hidden biodiversity

Anyone who has ever watched a crime series knows how forensic experts use DNA to identify suspects. In nature, researchers can do something very similar – but instead of tracking criminals, they identify plants. Every plant species has a unique genetic code. By analysing a small fragment of that DNA – essentially a genetic barcode – scientists can determine exactly which species are or were present.

The remarkable part is that they do not need an entire plant to do this. A handful of soil, a water sample, or even the air contains enough tiny DNA fragments to read those barcodes. That makes metabarcoding a revolutionary method for studying biodiversity.

How metabarcoding works

Researchers collect samples from soil, water, air, or even animal remains. Each sample contains countless DNA traces from plants in the surrounding area. In the lab, this environmental DNA (eDNA) is isolated: a mixture of genetic material from many species mixed together.

Using specialised techniques, a small DNA fragment is copied and sequenced. This fragment acts as a barcode: slightly different for every plant species. Software then compares the detected barcodes with large reference databases that link each barcode to a known species. This reveals which plants are or were present in the locality sampled.

In rare cases, species share the same barcode, especially if they are closely related. In such cases, information about their geographic distribution helps: if one species occurs only in Norway and the close relative only in France, the correct match can easily be made. That is why interoperable species lists from across Europe are essential for researchers.

Metabarcoding in practice

Metabarcoding provides an unprecedentedly detailed picture of the flora in an area. Even species that are normally hard to spot, such as seedlings or deciduous plants, suddenly become visible. This makes the technique extremely valuable to scientists and conservationists who want to understand biodiversity and its changes over time.

Researchers from Hortus botanicus Leiden, Naturalis Biodiversity Center and the University of Oslo are applying this method in the Natura 2000 reserve De Bruuk. Every two months, they collect soil samples. By tracking the read DNA barcodes over time, the researchers are investigating how reliably metabarcoding can detect plant species at times when many species die off above ground, such as in winter, when it is difficult to recognize plants with the naked eye. This allows for a valuable, standardized measurement method for monitoring biodiversity using eDNA.

European collaboration for biodiversity conservation

This research is part of the EU Biodiversa+ project MetaPlantCode, which focuses on testing, improving, and harmonising plant metabarcoding methods. The project brings together botanists and bioinformaticians from across Europe to develop a shared, reliable approach for DNA-based monitoring of plant biodiversity.

A key component is making European species lists interoperable. These lists serve as reference frameworks for metabarcoding analyses, enabling researchers to identify species more efficiently and accurately, even when DNA sequences of different species are very similar.

A look into the future

Metabarcoding generates enormous amounts of data. Processing all this information requires advanced software and smart analytical methods. The technique offers a wealth of possibilities and is already used in countless studies. To make the most of this richness, it is crucial that studies can be compared properly. That is only possible when data is open access and accompanied by complete background information (metadata) on locality, collection date and local habitat.

eDNA metabarcoding is transforming the way we look at biodiversity. It makes the invisible visible and helps us better understand how ecosystems function. And that is exactly the kind of knowledge we need to protect and restore Europe’s biodiversity.

Text: Lycka Kamoen, Hortus botanicus Leiden
Photos: Lycka Kamoen; Barbara Gravendeel