Unravelling the microbial world in European soils

Soil biodiversity assessments are necessary for its better protection and monitoring. Here, we present the first Europe-wide assessment and show that a higher microbial diversity can also mean more potential pathogens. We propose guidelines for environmental policy actions.
Published in Ecology & Evolution
Unravelling the microbial world in European soils

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For many of us, the experience of lying in the grass of an urban park and being surrounded by a multitude of insects hidden amongst the leaves and flowers is a familiar one. However, this experience now serves as a reminder of how rare it has become in our modern world. The decline of biodiversity that we have witnessed over the past few decades has made it increasingly difficult to find such natural havens, highlighting the pressing need to take action to protect and preserve our planet's rich array of species. It's hard to ignore the fact that we are currently facing the sixth mass extinction, and that 70% of insects have disappeared. Yet, at the same time, people are becoming increasingly aware of the importance of these tiny creatures, such as bees and their role in pollination. 

But while we're witnessing the loss of above-ground biodiversity, there's another type of biodiversity that has been ignored for far too long. Soil biodiversity has been the left-behind of many initiatives, however, it's now gaining more recognition as we begin to understand its importance.

When we think of soil biodiversity, we usually imagine moles and earthworms carving burrows in the ground, but soil biodiversity is much more than that. It's a myriad of individuals, ranging from microorganisms like archaea, bacteria, and fungi (Fig. 1), to “larger” animals like mites and springtails. What's even more fascinating is that, just like bees and pollination, soil biodiversity provides several ecosystem services that humans rely on and benefit from, directly and indirectly. For example, soil inhabitants play a critical part in food production, climate regulation, and drug discovery in medicine. Depending on the carried-out activities, soil organisms can be organised into functional groups, such as plant symbionts of pathogens.

Fig. 1. Soil bacteria (a) and fungi (b) are part of soil microorganisms that ensure crucial ecosystem services in soils (Global Soil Biodiversity Atlas, Orgiazzi et al. 2016).

The scientific community is actively working together to unravel the mysteries of the above-below ground dynamics. However, limited surveys conducted at a continental scale pose challenges in assessing the factors influencing soil community diversity across large areas. To overcome this, comprehensive field studies and standardized datasets considering spatial microbial diversity, as well as soil properties and climate, are necessary. These efforts will enhance our understanding of microbial community distribution under various environmental and human-induced conditions. While previous studies have focused on individual driving factors, there is a need to explore their combined effects on soil communities. Furthermore, the interaction between different drivers and functional groups involved in specific ecosystem services requires more attention.

Novel approaches for monitoring the impact of human activity and the environment on soil communities are needed to better understand their drivers and enforce monitoring and preservation plans in Europe. As a result, a biodiversity module (LUCAS Soil Biodiversity) has been added to the largest European soil survey, the Land Use/Cover Area frame Survey (LUCAS), coordinated by the European Commission.

Using this unique dataset, our study focuses on soil microbes, particularly bacterial and fungal communities and several functional groups, such as nitrogen-fixing bacteria and fungal pathogens. Microbial communities were assessed in over 700 sites covering a wide range of soil and climatic conditions across Europe (Fig. 2a). Sampling sites belonged to six vegetation cover types ordered along a gradient of increasing land-use perturbation, from forests to extensive and intensive grasslands, up to croplands (Fig. 2b).

Fig. 2. Sampling design. a Sampling points distribution coloured by vegetation cover type. The number of sites is indicated between brackets. b Vegetation cover types ordered along a gradient of increasing land-use perturbation (Labouyrie et al. 2023) © European Union, 2023.

We observed an incredible diversity beneath our feet. We detected more than 25’000 fungal and 79’000 bacterial taxa. Our findings demonstrate that microbial richness and diversity are highest in more disturbed areas, such as croplands and grasslands, but potential plant pathogens are more abundant in these areas as well (Fig. 3). In addition, croplands and grasslands host distinct microbial communities from less-perturbed areas like woodlands. We conclude that accurate estimates of the impact of land-use intensification and environmental factors on below-ground diversity would require considering both taxonomic and functional diversity in monitoring and preservation schemes. Relying solely on taxonomic diversity may lead to a misleading assumption that increased biodiversity improves ecosystem functioning.

Fig. 3. a Boxplots of the values taken by the fungal observed richness among vegetation cover types and b barplots of the mean relative proportion in percentages (± SE) of fungal OTUs (weighted by their read counts) identified as potential fungal plant pathogens, for each vegetation cover type. Different letters correspond to a significant difference in compared vegetation cover types, and p-value corresponds to the one obtained with a Kruskal-Wallis test testing the vegetation cover effect. Adjusted R-squares are expressed in percentages and colours represent the different vegetation cover types. Here, n = 715 total sites, with 160 belonging to coniferous woods, 99 to broadleaved woods, 128 to extensive grasslands, 18 to intensive grasslands, 46 to permanent crops and 264 to non-permanent crops sites (adapted from Labouyrie et al. 2023) © European Union, 2023.

Also, our analyses confirm long-known observations that were based on more scattered information. For instance, based on the 700 sites investigated, we observe that arbuscular mycorrhizal fungi, beneficial plant symbionts that associate with many plants, are most abundant in grasslands. Also, not surprisingly, ectomycorrhizal fungi, fungal symbionts of many trees, are the dominant fungal group in most forests, confirming many other studies. The study also highlights that soil microorganisms are driven by different factors; bacterial diversity is mainly shaped by soil conditions, while fungal diversity is influenced by vegetation cover. Additionally, the same soil and climatic conditions can have contradictory impacts on functional group patterns, promoting or hindering their presence.

Altogether, these observations highlight thevariety of soil biodiversity and its responses to both human activity and environmental factors. When implementing conservation measures, it is crucial to consider the various impacts on communities and different functional groups. Thus, future studies should investigate both taxonomic and functional assemblages, and include as many soil properties as possible, along with information on vegetation cover and climatic conditions, to deepen our knowledge of soil microbial drivers. And this may not be enough, as an important portion of the drivers still remain unknown.

Although studying the impact of environmental drivers as independent factors provides a suitable understanding of microbial patterns at a continental scale, exploring their interactions may offer new insights into soil diversity monitoring and preservation. Large areas could be divided into multiple patches of environmental features known to affect microorganisms through their interactions. This method could help identify clusters of action, or areas of priority, where appropriate monitoring tools and preservation measures can have the most significant impact.

Finally, I am grateful to have had the opportunity to contribute to this challenging yet fascinating project as a PhD student, and to work alongside motivated individuals who share a passion for understanding and protecting soil biodiversity. It is my hope that our current and future collective efforts will make a positive impact in the pursuit of a more sustainable outlook for our soils and, thus, planet.


Orgiazzi, A. et al. Global Soil Biodiversity Atlas. European Commission, Publications Office of the European Union, Luxembourg. 176 pp (2016)

Labouyrie, M. et al. Patterns in soil microbial diversity across Europe. Nature Communications. 14, 3311. (2023) https://doi.org/10.1038/s41467-023-37937-4

Poster image by © Matthias Zomer, pexels.com

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