The European soil monitoring directive, adopted by the European Union at the end of 2025, aims to achieve healthy soils by 2050. Brussels’ directive is centred on an environmental DNA based approach. France’s experience in measuring soil quality could be used advantageously, particularly as the best monitoring tools are those that integrate several complementary approaches at the same time.

Since November 2025, the European Soil Monitoring and Resilience Directive requires member states to regularly assess soil biodiversity. It calls for soil microbial diversity analysis (bacteria and fungi) at six year intervals based on environmental DNA or “eDNA”.

Yet, while eDNA is a powerful tool for detecting biodiversity at scale, it is not enough on its own for interpreting observed changes and identifying their causes. This is because bacterial and fungal communities only represent part of the soil biodiversity, which also includes many organisms with crucial and varied ecological roles.

Abundance, biomass and the activity of living organisms – dimensions that cannot be assessed by molecular detection alone also determine how soils function. A graduated approach combining several complementary protocols is therefore required to produce robust and useful indicators for field work.

France’s track record via its soil quality measurement network (Réseau de Mesures de la Qualité des Sols (RMQS) and GIS Sol, constitutes, as such, a benchmark for interpreting results and an established operational framework for monitoring soil biodiversity. This could usefully complement the basis of the European legislation.

Environmental DNA: necessary but not sufficient

DNA works with a molecular approach and, as such, offers advantages in environmental monitoring in other words – broad and standardised biodiversity analysis, strong spatial and temporal comparability. Such methods provide a particularly effective tool for detecting changes in the composition of biological communities.

However, the molecular signatures derived from eDNA do not always allow us to correctly identify the taxa that is present in soil. They may show representativeness biases. They are often poorly correlated with other biological characteristics that are essential for characterising biodiversity and soil ecosystem functioning, such as the abundance of organisms, their biomass, their demographic structure or even their activities. They will thus offer an incomplete and sometimes distorted view of soil health.

However, beyond the simple detection of changes in diversity, monitoring devices must also make it possible to interpret these developments, that is to say, to understand what they imply for soil functionality in agriculture, for example, and to identify their causes. This is what will allow us to assess the........

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