In this article, we explore models predicting soil bacterial diversity to: spectral indices derived from optical satellite remote sensing; and meteorological variables. We computed alpha and beta diversity indices using metabarcoding data generated from 214 cropland soil samples collected in the context of Eurostat's 2018 pan-European LUCAS Soil module. Subsequently, we derived 12 spectral indices from sentinel-2 images and monthly meteorological variables from the TerraClimate dataset. We then built models of bacterial diversity using the earth observation and climatic variables, experimenting with different algorithms and predictor time lags from the soil sampling date. Random-forest and Cubist regressors yielded MAE <= 7% of the observed range and R-2 = 0.87 for beta diversity indices, while alpha diversity models reached MAE approximate to 10% and R-2 approximate to 0.15. Feature importance pointed to winter moisture variability as the chief control on richness/evenness, whereas growing-season thermal extremes governed community turnover, with Sentinel-2 indices contributing secondary signals. Overall, our results indicate that freely-available satellite multispectral and meteorological data, can predict dimensions of cropland soil bacterial diversity and with particularly strong skill for principal coordinates analysis and canonical analysis of principal based beta diversity axes.

Soils host a significant proportion of biodiversity on Earth providing ecosystem functions vital to human well-being, making it imperative to include them and their ecological features when addressing sustainability goals. We performed a comprehensive assessment of soil health across Europe by explicitly integrating biotic and abiotic indicators alongside soil degradation processes. We further identified areas with high restoration potential, quantifying the potential positive changes achievable when mitigating degradation processes. Our results show that 93% of soils in Europe are either degraded (62%) or in a moderate state (31%), with only 7% having a good (6.5%) or high (0.5%) health status. We found Southeast Europe to have the highest restoration potential, particularly for forests and annual crops. By providing spatially explicit indicators of soil health and restoration potential, our approach offers valuable guidance to support sustainable soil management and inform policies aimed at enhancing soil health across Europe.

Soil biodiversity and functioning are the foundation of ecosystem sustainability, but we do not know whether current nature conservation areas are efficiently protecting soils. Here, we investigated the contribution of terrestrial nature conservation areas to protect soil biodiversity and functioning across scales. We found no general positive effect on diversity of bacteria, fungi, protists, invertebrates, and nematodes, captured as richness, Shannon diversity and dissimilarity, and 5 soil functions (pathogen control, nutrient provision, soil carbon, soil organic matter decomposition, and soil aggregate stability). Our findings suggest that nature conservation areas show an inconsistent role in protecting soil biodiversity and functioning, as we found mostly non-significant and otherwise mixed effects across scales. Despite few positive and negative effects of protection status, our work highlights the urgent need to directly target soils in nature conservation.

The role of soil health in regulating primary productivity at large scale across different land-use types remains poorly understood. This hinders our ability to predict the impact of soil degradation on essential ecosystem services such as food provision and climate regulation. To address this gap, we conducted a pan-European observational field study using data from 588 sites and 27 countries to investigate the link between soil health (a composite index based on soil properties, biodiversity, and plant disease control) and primary productivity across three major land-use types: woodlands, grasslands, and croplands. We found that soil health in woodlands was 31.4% higher than in grasslands, and 76.1% higher than in croplands. We further observed that soil health was positively linked to cropland and grassland productivity at the continental scale. Woodland productivity was linked to climate conditions rather than to soil health status. We observed that soil organic carbon and the richness of Acidobacteria, Firmicutes, and Proteobacteria had a positive effect on primary productivity. Among microbial functional groups, we found that nitrogen-fixing bacteria and mycorrhizal fungi positively related to primary productivity in croplands and grasslands, while plant pathogens showed a negative relationship. Together, our results point to the importance of soil biodiversity and soil health for maintaining primary productivity across contrasting land-use types.

Antibiotic resistance (AR) is recognized by the World Health Organization as a major threat to human health, and recent studies highlight the role of microplastics (MPs) in its spread. MPs in the environment may act as vectors for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Bacterial communities on the plastisphere, the surface of MPs, are influenced by plastic properties, allowing ARB to colonize and form biofilms. These biofilms facilitate the transfer of ARGs within microbial communities. This study analyzed data from the LUCAS soil dataset (885 soil samples across EU countries) using the Emu tool to characterize microbial communities at the genus/species level. Functional annotation via PICRUSt2, supported by a custom tool for Emu output formatting, revealed significant correlations between the genera Solirubrobacter, Bradyrhizobium, Nocardioides, and Bacillus with pathways linked to microplastic degradation and antibiotic resistance. These genera were consistently present in various soil types (woodland, grassland, and cropland), suggesting their potential as bioindicators of soil health in relation to MP pollution. The findings underscore MPs as hotspots for ARB and ARGs, offering new insights into the identification of bioindicators for monitoring soil health and the ecological impacts related to MP contamination.

Comparability of soil data derived from different sources is crucial to obtain consistent results when evaluating the soil health status. Discrepancies may arise due to various factors, including uncertainties resulting from different sampling methods. In this study, we compared various soil Physicochemical properties (ST)-pH, organic carbon, texture, cation exchange capacity, nutrients, heavy metals-and microbial diversity (BIO) of samples collected following both the LUCAS Soil (performed by the European Commission Joint Research Centre, JRC) and the Italian (performed by two regional agencies) procedures. The aim was to evaluate the effect of applying different soil sampling protocols on ST and BIO data. Soil samples from 58 LUCAS Soil 2022 sampling sites located in northern Italy were collected following both sampling protocols. Data obtained from ST analyses highlighted that the LUCAS and Italian protocols are comparable for most of the soil properties. Nevertheless, results can differ significantly depending on the parameter being considered, as evidenced by the concordance index varying from 0.37 to 1. Concerning BIO analyses, although the investigation of the microbial diversity indicators did not show a good concordance between the two sampling strategies, an analysis of the community structure highlighted a good correlation (Pearson's R > 0.6). An effect of the different land cover was observed for both ST and BIO analyses, suggesting that this could be a parameter to be considered when combining soil data obtained by different sampling protocols. Also, fungal communities showed lower concordance between LUCAS and Italian samples, highlighting a higher heterogeneity and a minor replicability with respect to bacteria and ST soil properties. In conclusion, this comparison generally showed consistency among the two sampling methods, suggesting that an integration of data from different sources is indeed possible for most of the parameters being analysed. However, further research is needed to obtain a sufficient level of harmonisation between LUCAS Soil and Italian sampling procedures for those soil properties for which a significant discordance was found.

Ecosystem functioning is potentially dependent on the relationships between soil microbial diversity and biomass. Yet, it remains unclear how land use and climate influence these relationships. Here, we (i) analysed relationships and ratios between richness and biomass of bacteria and fungi in ~500 soils across Europe, including three land-use types (woodlands, grasslands and croplands) and climates (cold, temperate and arid) and (ii) identified the driving factors of changes in richness:biomass (R:B) ratios. Richness and biomass of soil bacteria and fungi followed a unimodal pattern, with a peak in mid-levels of biomass. This pattern was more evident in bacteria and more clearly exerted by land use than by climate. Bacterial R:B ratios decreased with land use in the following order: croplands > woodlands > grasslands. Fungal R:B ratios decreased as follows: grasslands > croplands > woodlands. Climate was found to interact with land use. In this way, arid climate tended to increase bacterial R:B ratios in the different land uses; however, the agricultural practices associated with croplands seem to buffer this effect. In fungi, the interactive effect of land use and climate was less straightforward than for bacteria. According to our models, soil organic carbon (SOC) and total nitrogen (N) in bacteria and SOC in fungi were identified as the primary predictors of R:B ratios. Therefore, factors related to climate and land-use change with impact on SOC and N contents are potential disruptors of soil microbial R:B ratios. This study clarifies the diversity:biomass relationships across different land uses and climates.

Current advancements in molecular techniques for identifying multiple species from bulked soil samples have expanded our capacity for large-scale soil biodiversity assessments. However, these methods often lack validation and contextualization. Recent cross-European studies based on environmental DNA (eDNA) have reported unexpectedly high biodiversity in intensively managed agricultural soils compared to woodlands and grasslands, challenging previous findings based on morphological assessments. Here, we analyze these discrepancies by comparing standardized soil faunal diversity data from the LUCAS Soil 2018 survey (eDNA) with morphological assessments from the EU-funded projects EcoFINDERS (2012) and SOILSERVICE (2015). We found that molecular methods indicate higher soil biodiversity in croplands, whereas morphological methods suggest the opposite trend. A significant variability in diversity metrics across ecosystem types emphasizes the need to compare and validate molecular results with complementary morphological approaches. The increasing need for biodiversity indicators and thresholds in monitoring frameworks demands robust methods, yet widely used molecular techniques remain insufficiently standardized. We call for more systematic assessments to clarify the interpretation of eDNA signals (e.g., primer bias, relict DNA), and to enable a better integration of molecular and morphological data in conservation policies and large-scale monitoring efforts.

The role of soil microorganisms in supporting multiple ecosystem functions (multifunctionality) remains poorly understood across diverse environmental conditions. Here, we investigate 484 soils from 27 European countries spanning a range of climatic and edaphic contexts. We assess the contribution of climate, soil properties, and soil microbiome traits (i.e., the relative abundance of co-occurring taxa) to explain six key functional proxies related to soil structure, biochemical activity, and productivity. We find the highest multifunctionality values in grasslands, woodlands, loamy and acidic soils, and temperate humid regions, and the lowest in croplands, alkaline soils, and drier regions. Soil properties explain 12-31% of variation in multifunctionality, with microbial biomass and nitrogen content emerging as the strongest predictors. The soil microbiome accounts for 2-14% of unique variance in multifunctionality but explains more than 25% of variation in enzymatic activities and primary productivity in clay-rich soils and soils originating from temperate dry regions. Specific taxa, particularly within Actinobacteria, Acidobacteria, and the fungal genus Mortierella consistently emerge as strong predictors of ecosystem multifunctionality. Our findings highlight that ecosystem multifunctionality is jointly shaped by soil properties and microbial communities. We argue that specific taxa hold potential as context-dependent indicators for multifunctionality monitoring across environmental gradients.

Arbuscular mycorrhizal (AM) fungi form mutualistic associations with most land plants and are of pivotal importance for plant growth and nutrition. AM fungi include both the well-known phylum Glomeromycota (G-AMF) and the recently established clade of Endogonomycete fine root endophytes within the phylum Mucoromycota, often viewed as putative AMF (E-AMF). Yet, the global richness of these fungal groups, in particular of E-AMF, is poorly understood. To provide comprehensive global species of G-AMF and E-AMF, we analysed long-read sequencing data of the full-length ITS marker from 4,733 sampling sites across all continents and biomes. Our study provides the first combined estimate of global G-AMF and putative E-AMF richness, far exceeding the numbers and taxa reported so far. Specifically, we detected 8,517 OTUs of G-AMF, surpassing previous AMF richness estimates by a factor of five to fifteen. In addition, we identified 600 OTUs for putative E-AMF, providing the first global estimate for this group.

The European Union's strategic agenda for 2024-2029 prioritizes a prosperous and competitive Europe, with soil health potentially playing a role in achieving this goal. However, the current state of European soils is of concern, with over 60 % of soils not in healthy condition, as reported by the European Union's Soil Mission Board and the EU Soil Observatory. This results not only in environmental issues, but also economic ones, as the costs of soil degradation in the EU are estimated to be higher than 50 billion per year, underscoring the need for soil health to be placed more prominently on the political agenda. Soil-related business models, including biotechnology, remediation of contaminated sites, carbon removals and farming, regenerative agriculture, and agritech solutions, can contribute to EU competitiveness. These business models may help address most of the challenges posed by soil degradation, climate change, and biodiversity loss, while promoting sustainable agriculture practices and improving ecosystem functioning. The EU's soil remediation market is valued at 8.5 billion, with an annual growth rate of 5 %. The EU Carbon Removals and Carbon Farming Regulation provides a framework for certifying carbon removals, with potential revenue of 6 billion per year. Regenerative agriculture, which prioritises soil health and ecosystem services, can increase crop yields, reduce dependency on synthetic fertilisers and pesticides, and promote biodiversity. Agritech solutions, such as precision agriculture and artificial intelligence, can optimize farming practices, reduce costs, and improve environmental sustainability. Here we present the potential of soil-related business models to contribute to EU competitiveness, while addressing environmental and societal challenges. However, a number of challenges remain and need to be addressed as the need for acceleration, a clear policy framework, a closer collaboration of different actors in the food supply chain and a digital transformation are still needed.

Factors regulating the diversity and composition of soil microbial communities include soil properties, land cover and climate. How these factors interact at large scale remains poorly investigated. Here, we used an extensive dataset including 715 locations from 24 European countries to investigate the interactive effects of climatic region, land cover and pH on soil bacteria and fungi. We found that differences in microbial diversity and community composition between land cover types depended on the climatic region. In Atlantic, Boreal and Continental regions, microbial richness was higher in croplands and grasslands than woodlands while richness in Mediterranean areas did not vary significantly among land cover types. These differences were further related to soil pH, as a driver of bacterial and fungal richness in most climatic regions, but the interaction of pH with land cover depended on the region. Microbial community composition differed the most between croplands and woodlands in all regions, mainly due to differences in pH. In the Mediterranean region, bacterial communities in woodlands and grasslands were the most similar, whereas in other regions, grassland and cropland-associated bacteria showed more similarity. Overall, we showed that key factors interact in shaping soil microbial communities in a climate-dependent way at large scale.

Antibiotic resistance crisis dictates the need for resistance monitoring and the search for new antibiotics. The development of monitoring protocols is hindered by the great diversity of resistance factors, while the “streetlight effect” denies the possibility of discovering novel drugs based on existing databases. In this study, we address these challenges using high-throughput environmental screening viewed from a trait-based ecological perspective. Through an in-depth analysis of the metagenomes of 658 topsoil samples spanning Europe, we explored the distribution of 241 prokaryotic and fungal genes responsible for producing metabolites with antibiotic properties and 485 antibiotic resistance genes. We analyzed the diversity of these gene collections at different levels and modeled the distribution of each gene across environmental gradients. Our analyses revealed several nonparallel distribution patterns of the genes encoding sequential steps of enzymatic pathways synthesizing large antibiotic groups, pointing to gaps in existing databases and suggesting potential for discovering new analogues of known antibiotics. We show that agricultural activity caused a continental-scale homogenization of microbial antibiotic-related machinery, emphasizing the importance of maintaining indigenous ecosystems within the landscape mosaic. Based on the relationships between the proportion of the genes in the metagenomes with the main predictors (soil pH, land cover type, climate temperature and humidity), we illustrate how the properties of chemical structures dictate the distribution of the genes responsible for their synthesis across environments. With this understanding, we propose general principles to facilitate the discovery of antibiotics, including principally new ones, establish abundance baselines for antibiotic resistance genes, and predict their dissemination.

The 2018 LUCAS (Land Use and Coverage Area frame Survey) Soil Pesticides survey provides a European Union (EU)-scale assessment of 118 pesticide residues in more than 3473 soil sites. This study responds to the policy need to develop risk-based indicators for pesticides in the environment. Two mixture risk indicators are presented for soil based, respectively, on the lowest and the median of available No Observed Effect Concentration (NOECsoil,min and NOECsoil,50) from publicly available toxicity datasets. Two further indicators were developed based on the corresponding equilibrium concentration in the aqueous phase and aquatic toxicity data, which are available as species sensitivity distributions. Pesticides were quantified in 74.5% of the sites. The mixture risk indicator based on the NOECsoil,min exceeds 1 in 14% of the sites and 0.1 in 23%. The insecticides imidacloprid and chlorpyrifos and the fungicide epoxiconazole are the largest contributors to the overall risk. At each site, one or a few substances drive mixture risk. Modes of actions most likely associated with mixture effects include modulation of acetylcholine metabolism (neonicotinoids and organophosphate substances) and sterol biosynthesis inhibition (triazole fungicides). Several pesticides driving the risk have been phased out since 2018. Following LUCAS surveys will determine the effectiveness of substance-specific risk management and the overall progress toward risk reduction targets established by EU and UN policies. Newly generated data and knowledge will stimulate needed future research on pesticides, soil health, and biodiversity protection. Integr Environ Assess Manag 2024;20:1639-1653. © 2024 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Soil protists have vital roles as major microbiome predators in soil functioning and plant performance. Protists are also suggested to be the most responsive microbial group to external changes, such as anthropogenic land use types. While protists were long used as models for biogeography such as to investigate if 'everything is everywhere' among microbes, their biogeography at the taxonomic level has never been explored in depth at the continental scale and linked to anthropogenic drivers. Here we evaluated how land-use types affect the diversity and structure of soil protist communities across 885 locations in Europe based on the European Commission’s Land Use and Coverage Area frame Survey (LUCAS). We observed higher α-diversity of soil protists but lower community structure dissimilarity (β-diversity) in croplands compared with woodlands, with grasslands in an intermediate position. The diversity of protist groups with a broader spatial niche was higher in croplands, whereas taxa with a narrower niche increased in woodlands. The importance of climate factors on α-diversity variations reduced as land use intensity increased, but the opposite trend was observed for the effect of soil properties. Our study suggests that there is an interaction between land use type, environmental effects, and spatial niche attributes of soil protist groups, highlighting the importance of land-use type on the dynamics of protist communities.

Launched in December 2020, the EU Soil Observatory (EUSO) is the principal provider of reference data and knowledge at the EU level for all soil-related matters. Hosted at the Joint Research Centre of the European Commission, the EUSO is evolving to be a dynamic and inclusive platform that supports EU soil-related policymaking. EUSO has five main objectives: To support the development of an operational EU-wide soil monitoring system; To support research and innovation through the implementation of Horizon Europe’s Mission ‘A soil deal for Europe’; To further consolidate and enhance the capacity and functionality of the current European Soil Data Centre; To monitor the state of soil health and the policies in place through a Soil Health and Policy Dashboard; To provide an open and inclusive EUSO forum that supports the drive towards a societal change in the perception of soil. In this presentation, we will present the activities of EUSO that have taken place in 2023 under the five objectives outlined above. We will provide an overview of ongoing research and innovation projects, new datasets that were added to the European Soil Data Centre and the outcome of the third EUSO stakeholder forum. In 2023, the EUSO has been supporting the proposal for the Soil Monitoring Law and has contributed significantly to the Impact assessment. In addition, EUSO has contributed to Nature Restoration Law, the implementation of the Soil Mission: “A Soil Deal for Europe”, Carbon Removals and Clean Soil outlook. In 2023, the EUSO has launched the EU Soil Health Dashboard with 18 indicators which show that 62% of EU soils are not in Healthy condition. The EUSO dashboard is a dynamic tool providing evidence where hotspots exist and which are the main threats to soils. In November 2023, the 3rd EUSO Stakeholder Forum brought together 700 participants to attend three days of meeting with over 60 presentations. In relation to research, EUSO has published 40 papers and has supported the research agenda through the Soil Mission HORIZON programs. In addition, important research has been addressed within EUSO activities, such as the carbon losses in the EU, the novel assessments in soil biodiversity, and the nutrient budget. The European Soil Data Centre (ESDAC) has also grown with the inclusion of new datasets and the exponential number of users downloading almost 12,000 datasets from ESDAC within 2023.

Soil health is expected to be of key importance for plant growth and ecosystem functioning. However, whether soil health is linked to primary productivity across environmental gradients and land-use types remains poorly understood. To address this gap, we conducted a pan-European field study including 588 sites from 27 countries to investigate the link between soil health and primary productivity across three major land-use types: woodlands, grasslands and croplands. We found that mean soil health (a composite index based on soil properties, biodiversity and plant disease control) in woodlands was 31.4% higher than in grasslands and 76.1% higher than in croplands. Soil health was positively linked to cropland and grassland productivity at the continental scale, whereas climate best explained woodland productivity. Among microbial diversity indicators, we observed a positive association between the richness of Acidobacteria, Firmicutes and Proteobacteria and primary productivity. Among microbial functional groups, we found that primary productivity in croplands and grasslands was positively related to nitrogen-fixing bacteria and mycorrhizal fungi and negatively related to plant pathogens. Together, our results point to the importance of soil biodiversity and soil health for maintaining primary productivity across contrasting land-use types. Geographic patterns in plant growth are probably influenced by soil abiotic and biotic conditions. Here, the authors assess the relationship of a composite soil health index to primary productivity and the underlying environmental predictors across major land-use types in Europe.