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 effectiveness of public policies and management practices. In this context, reducing biological and ecological soil complexity to this single component carries a risk related to interpretation difficulties.
However, the EU directive stipulates that member states may supplement mandatory indicators with other biological indicators in their national monitoring arrangements, thus opening up the possibility of more integrated approaches.
A support tool for policymaking
Environmental monitoring has two distinct and complementary objectives: detecting changes in the state of ecosystems and attributing these changes to environmental pressures, land uses or management practices. These two dimensions are closely linked by the biological and ecological processes that structure how ecosystems function.
Beyond their scientific scope, the indicators used for monitoring soil biodiversity are instrumental in public decision-making. It is not only a question of identifying the dynamics within biological communities, but also understanding their causes. Therefore, this primarily concerns policymakers. The aim is to guide planning and sustainable management practices, identify situations presenting degradation, implement policies to remedy them, and be able to assess their effectiveness.
A monitoring system that would be limited to detecting changes in soil biodiversity without taking into account interpretation and attribution related to environmental pressures would provide a limited basis for evaluating public policies and the implementation of suitable management strategies.
Biodiversity is not just about the number of taxa
Ecological soil functions – such as regulating water and contaminants, providing nutrients, storing carbon, maintaining structure, or supporting biodiversity itself are not static states, but dynamic processes. They are based on the activity of living organisms, their biomass and their functional characteristics (physiology, behaviour), as well as their interactions (competition, symbiosis, parasitism). They are expressed through renewal flows and speeds rather than mere stocks.
In this context, molecular approaches provide valuable information on the presence of organisms, but by themselves do not allow us to assess these dynamic processes or their actual intensity. A correct interpretation of soil functioning therefore requires additional measures as well as interpretation references linking biological indicators to different land use contexts and environmental conditions.
eDNA data is increasingly used for developing new approaches, such as those based on interaction networks, which show how biological soil communities are organised. When these networks are built only on presence or co-occurrence data, they mainly reflect how ecological conditions or environmental niches are shared by different species.
This only provides indirect information on the biological activities at work and on matter and energy flows, which also determine soil functioning. Ecological interpretation requires additional information, particularly on the abundance or biomass of organisms. This is how biological communities can be linked to the ecological processes supporting soil functions.
A graduated and complementary approach
In order to reconcile operational efficiency and ecological relevance, soil biodiversity monitoring benefits from combining several types of approaches, each providing specific information on the condition and functioning of biological communities.
eDNA-based approaches enable broad and standardised detection of microbial biodiversity, and could be extended to other organisms, such as invertebrates.
Other methods are based on direct observation of soil fauna organisms, estimation of their abundance or biomass, or analysis of their functional characteristics. They provide essential information on the biological structure and ecological role of soil communities.
These approaches should not be seen as mutually exclusive, but as complementary tools. They allow us to link the composition of biological communities (taxonomic and functional structure) to the ecological processes that support soil functions. Their combination is, as such, particularly interesting for building a monitoring strategy with different levels of information.
This logic of complementary is already implemented in some existing monitoring tools as it the case in the framework of France’s national soil monitoring network (RMQS) or in the mountain biodiversity observatory Orchamp. These approaches are not meant to be deployed everywhere, but their combination is essential for correctly interpreting the condition and evolution of soil biodiversity.
Suggested guidelines for national implementation of the EU directive
Preserving our ability to understand, explain and take action requires us to recognise that the biological complexity of soils calls for a controlled diversity of monitoring approaches.
With the support of GIS Sol, France is among the nations at the forefront of soil biodiversity monitoring. It has been experimenting with this approach, combining several protocols within RMQS for several years. This experience, which is rare on a European scale, should be the basis for building the country’s future national soil monitoring network.
In addition to the mandatory indicators, the directive enables member states to supplement their own systems with optional indicators. This flexibility gives them the opportunity to set up a monitoring system that’s not only capable of detecting trends in changing soil biodiversity, but interpreting the causes and possibilities for remediation. This finally allows us to assess the implications for public policy.
With this in mind, several principles should be taken into consideration when implementing the EU directive at national level:
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Do not restrict national soil biodiversity monitoring to a single eDNA-derived measure, which limits our ability to interpret observed changes.
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Implement a combination of complementary measures in order to link the detection of biodiversity to community structure and ecological processes that support soil functions, with the support of protocols and measures developed across Priority Research Programmes and Equipments (PEPR) Dynabiod and SolsVivants in France, for example.
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Develop open interpretation frameworks and analytical frameworks to assess whether the observed variations are significant, in order to link biological indicators to land uses and environmental pressures.
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Take advantage of existing analysis mechanisms, in particular France’s soil quality measurement network supported by GIS Sol, to ensure consistency, comparability and the scientific robustness of any given future national monitoring system.
This article was a collaborative effort by RMQS Biodiversité, several PEPR by SolsVivants, Dynabiod and RNEST and their respective co-authors. Other contributers included: Apolline Auclerc, Nolwenn Bougon, Miriam Buitrago, Philippe Hinsinger, Claudy Jolivet, Antoine Lévêque, Gwenaël Magne, Florence Maunoury-Danger, Jérôme Mathieu, Christian Mougin, Laurent Palka, Benjamin Pauget, Guénola Pérès, Sophie Pouzenc, Sophie Raous, Claire Salomon, Marie-Françoise Slak, Wilfried Thuiller, Cécile Villenave, Quentin Vincent.
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