Abstract
Soil biodiversity is fundamental to terrestrial ecosystem functions, and its preservation is crucial for sustaining life on Earth. A wide range of studies have shown that aboveground biodiversity loss accelerates rapidly due to environmental change and intensified human activities. However, the state of soil biodiversity remains insufficiently understood and it is still unclear how different factors impact soil biota. To set effective conservation targets and preserve soil biodiversity, it is essential to deepen our understanding of how soil organisms and their functional groups (e.g., symbionts) respond to disturbances. This PhD thesis assesses soil biodiversity across Europe using the Land Use/Cover Area Frame Survey Soil (LUCAS Soil), a soil monitoring program from the European Union. This PhD is part of a collaboration between the University of Zurich and the European Commission’s Joint Research Centre (EC-JRC) and aims to (i) understand the factors (vegetation, land-use, soil properties, and climate) driving patterns in soil biodiversity, especially for bacteria and fungi (Chapter 1), (ii) specifically examine climate impacts on key drivers of these belowground biodiversity patterns (Chapter 2), (iii) explore the effects of anthropogenic activities like pesticide use on soil biodiversity (Chapter 3), and (iv) produce the first maps of soil microbial diversity in Europe (Chapter 4). First, this thesis highlights the high biological diversity that can be found in soils. Over 79,000 bacterial and 25,000 fungal operational taxonomic units (OTUs) were detected in 715 sites across 24 European countries. Environmental properties had a significant impact on soil microbial diversity, as we found bacterial communities to be primarily shaped by changes in soil properties, while fungi were more influenced by vegetation cover (Chapter 1). We further found that climatic conditions interacted with other key factors (e.g., land cover, pH) to shape soil microbial diversity (Chapter 2), such that spatial patterns of soil microbes were best explained when considering interactions among multiple environmental determinants. Second, anthropogenic activities, particularly land-use intensification and pesticide use, significantly impacted soil biodiversity (Chapters 1 and 3). We found the lowest bacterial and fungal diversity in less-disturbed environments, like woodlands, compared to grasslands and highly-disturbed environments, such as croplands. Managed areas harbored distinct microbial biodiversity pools compared to less disturbed sites. Specifically, croplands contained significantly more bacterial chemoheterotrophs, a higher proportion of fungal plant pathogens and saprotrophs, and fewer beneficial fungal plant symbionts such as mycorrhizal fungi compared to woodlands and extensively-managed grasslands. Consequently, the increased taxonomic richness found in highly perturbed soils was coupled with a higher prevalence of potentially undesirable taxa (e.g., fungal plant pathogens), challenging the assumption that increased biodiversity always translates to beneficial outcomes for ecosystem functioning (Chapter 1). Importantly, we found that pesticides were major drivers of soil biodiversity patterns in Europe. Statistical models demonstrated that the impact of pesticides on belowground biodiversity was as strongly as soil characteristics and climate, not only in croplands but also in grassland and woodland areas. This is the first large-scale demonstration indicating that pesticides are such a major driver of soil biodiversity, similar to earlier observations made for bees, some insects, and birds. We observed that pesticides affected various soil organisms and functional groups differently, e.g., a higher presence of pesticides was positively associated with bacterial diversity while it negatively related to fungi. In addition, we found several non-target effects of pesticides and a complex interplay with the environmental background that warrant further investigations. (Chapter 3). Next, we developed maps of soil microbial diversity at continental scale in Europe (Chapter 4). This was the first assessment of predicted soil biodiversity across Europe at high resolution (100 meters), identifying key drivers of soil taxa at that scale, such as soil properties, climate, vegetation, and geography. Overall, these findings carry significant scientific and policy implications for soil biodiversity conservation. Among these, we advocate for systematic DNA-based assessments to accurately monitor soil community diversity and composition, alongside evaluating the functional profiles of detected organisms across various ecosystems, to capture a comprehensive picture of underground biodiversity (Chapters 1 and 3). Furthermore, we explore avenues for defining priority areas and developing ad-hoc conservation actions for soil biodiversity (Chapters 1, 2, and 4). This thesis also highlights that pesticides are a major factor influencing belowground biological communities. Consequently, potential improvements in pesticide risk assessment are proposed, including assessing a broader range of soil organisms and functional groups in various soil types, ecosystems – not limited to croplands, and climatic conditions (Chapter 3). In addition, we propose indicator taxa to be monitored to assess the impacts of land-use intensification and pesticide inputs on soil biodiversity (Chapters 3 and 4). Finally, we discuss how defining concrete spatial and temporal targets for soil life monitoring and conservation at the European Union scale remains challenging due to the varied responses of soil organisms and functional groups to environmental changes. Addressing these complexities requires tackling numerous unresolved questions and fostering collaboration among scientists, policymakers, and other stakeholders. Crucially, long-term studies are key to understanding the fate of soil biodiversity, making its preservation not just an ecological concern but a global mission essential for sustaining life. Overall, this thesis demonstrates that European soils harbour highly diverse communities and it shows that the environment, land use and pesticide use have a big impact on soil organisms.
Labouyrie, Maeva Patricia