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Land use is a key factor driving changes in soil carbon (C) cycle and contents worldwide. The priming effect (PE)-CO

Despite that all above-ground life depends on that below-ground, the knowledge on soil biodiversity is still very limited. Conservation activities have been often postponed due to missing data. For example, this was the case in previous EU Common Agricultural Policy agreements, when environmental indicators for soil biodiversity were meant to be integrated comparable to biodiversity indicators in place. While massive sequencing of soil biodiversity contributes significantly to shredding light on below-ground life, sampling methods are not adequately harmonised, preventing the establishment of reliable quantifiable conservation targets. In addition, broad-scale studies are often biased towards microorganisms and hence, in the majority of the published literature, eukaryotes, and more specifically, animals and protists, are neglected. Therefore, in a first EU-wide study of 885 sites, we investigated the response of environmental factors (i.e., soil properties, biogeographical location and climate) and land cover (cropland, grassland and woodland) on soil eukaryotic diversity. The LUCAS survey and previously published studies provided soil, climate and land cover data. DNA metabarcoding of the 18S genes allowed us to assess the diversity of animals, protists and fungi, but due to their high variability in body size, we grouped them into micro-, meso- and macrofauna. For the bioinformatics analyses, we clustered sequence reads into amplicon sequence variants using DADA2 and thereafter, we assessed alpha and beta diversity and the relationships between eukaryotic diversity and environmental drivers using regression, ordination, and variance partitioning analyses. Our results allowed us to identify potential indicator species for EU soils, representing the effect of different drivers on eukaryotic diversity. These findings will help to understand the links between soil abiotic and biotic patterns at large scale, pathing the way for quantifiable goals to be included in conservation activities and policies.

Lately, there has been a lot of discussion on soil terminology, perhaps because policymakers have recognized the need to use soil as an ally tackling future climate demands, but mostly because this recognition will likely be translated from the EU Soil Strategy into a new soil health law for the EU. Such an initiative for soil is tightly connected to the EU Biodiversity Strategy for 2030, the Climate Adaptation Strategy, the UN 15.3 Goal for Land Degradation Neutrality, and other environmentally-related policy initiatives (Figure 1) stemming from the European Green Deal and from the UN Sustainable Development Goals. Figure 1. Links between EU Soil Strategy and other EU initiatives. Source: European Commission, 2021. At the end of 2021 the European Commission launched the EU soil strategy for 2030, giving the first step towards a consolidated understanding of what a healthy soil means, “(…) when they are in good chemical, biological and physical condition, and thus able to continuously provide as many of the following ecosystem services as possible (…)”. This definition is therefore expected to be translated into a collection and combination of various soil parameters and associated dynamic thresholds (in time and space). Allowing thus the determination of the spatial extent of healthy - and unhealthy - soils, being likely used to assess the EU progress towards the objectives set.On top of the importance of such initiatives for our future, this is also a great opportunity for researchers and policymakers to understand i) where we stand in terms of major soil threats, ii) what the major current knowledge gaps for EU soils are, iii) and which are the areas at higher risk for land degradation that then require further restoration actions. The problem seems complex from a diversified European perspective, due to the policy landscape, [the lack of] harmonized data availability, as well as local and regional differences. Nevertheless, the EU needs to start building on the current environmental acquis.The aim of this work is to present the current status of the EU soils making extensive use of the latest LUCAS soil monitoring campaigns and to identify and discuss with the scientific community the identification of key-thresholds for identified parameters, which will likely determine future land and soil management actions towards a healthy soil.

The global area of cultivated land has increased considerably over the past five decades. Despite the many ecosystem services provided by soil, at large-scale, it is still poorly understood whether land-use intensification influences soil life and the services that rely upon it. Here we used an extensive soil metabarcoding database, derived from the European Union’s (EU) Land Use/Cover Area frame statistical Survey (LUCAS), to assess how vegetation (land) cover, biogeographic factors (i.e., climate) and soil properties influence the structure and potential functions of bacterial and fungal communities at a continental scale. We selected 715 LUCAS sampling locations, classified according to an increasing land-use intensification: from woodland (less disturbed), to grassland, and cropland (more disturbed). We found that croplands and grasslands had a higher microbial richness than woodlands. We observed that bacteria and fungi were not driven by the same environmental variables. While soil properties (e.g. pH, C:N ratio, potassium, phosphorus and carbonate contents) drove bacterial community composition, vegetation cover was the main driver for the fungal community. We found that vegetation cover, biogeographic factors and soil properties differently determined the distribution of main functional groups; for example, cropland soils with a higher pH and a lower C:N ratio hosted more nitrogen fixing bacteria whereas woodlands were dominated by ectomycorrhizal fungi, especially in non-compacted clay soils, with lower C:N ratio and potassium content. We observed that increasing aridity may inhibit functions beneficial for the plant communities (i.e. bacterial chemoheterotrophy and nitrogen fixation, arbuscular mycorrhizal symbiosis) and favour the spread of fungal pathogens. In addition, a high diversity was not always a positive aspect for ecosystem functioning, as for example, croplands were characterized by a higher presence of fungal pathogens. Maps of microbial functional groups for the EU were also generated. In conclusion, our results represent a step forward to a more comprehensive assessment of soil microbial diversity and associated functions across the European Union. Beside possible ecological implications, our findings can contribute to the development of indicators and implementation of soil management policies.

The European Soil Observatory (EUSO) was launched in December 2020 to generate and disseminate policy-relevant and harmonized EU–wide soil data and indicators in support of the soil perspectives of the European Green Deal, in particular the new Soil Strategy and the Mission on Soil Health and Food. Among the activities of the Observatory, paramount importance is placed on the development of an EU-wide soil monitoring system, to assess progress towards soil-related targets, to support research & innovation and provide a European Soil Forum dedicated to a broad user base (citizens, farmers, land planners, scientists). These features will be an important step in providing access to a huge range of soil-related data through dedicated data-streams, from biodiversity to heavy metal concentrations.The EUSO will establish a comprehensive dashboard containing indicators that present data on soil-related issues within and, in some cases, outside of the EU. Examples of indicators i include soil erosion, soil carbon, pollutants and soil nutrients (phosphorus, nitrogen, potassium) with relevance to the new EU Soil Strategy, the Common Agricultural Policy (CAP), Zero Pollution Action Plan and Sustainable Development Goals (SDGs).Indicators will be fed through models and operational soil monitoring systems ensuring seamless and harmonised data flows, where the LUCAS Soil programme will be fully integrated with national soil monitoring systems. s In addition to supporting the development of oil health indicators, an integrated monitoring system should also support the assessment of soil-related ecosystem services. .Operational policy support for the policy makers and other stakeholders will be a key issue for the development of accurate soil properties assessment and specific soil management strategies and tailored suggestion to member states targeted to their farming systems. The EUSO forum was a great debate where five working groups were launched addressing key aspects in the implementation or the underpinning knowledge base of the EUSO. These included: i) soil monitoring, ii) soil biodiversity, iii) soil data sharing, iv) soil erosion and v) soil pollution. A strong emphasis will be given to data harmonization, a specific section on data is proposed to coordinate MS efforts in providing data that need to be harmonized and out of that comprehensive statistics and maps will be delivered to the stakeholders.The EUSO will work with EU countries to identify and present relevant national soil data, possibly using advanced web service technologies. The EUSO builds on the achievements of the European Soil Data Centre (ESDAC), which has been the thematic node for soil-related data in Europe since 2006. The EUSO aims to incorporate the legacy data stemming from EU-funded soil-related projects in order not to lose valuable, useful and usable results for the future. The EUSO will contribute to collaborate with the European Soil Partnership a regional partnership of European countries under the United Nations FAO’ Global Soil Partnership (GSP). from the EUSO aims to bring a European perspective to the many activities of the GSP in the areas of sustainable soil management, raising soil awareness, soil research and soil data collection and handling.

[Aim] Quantify direct and indirect relationships between soil microbial community properties (potential basal respiration, microbial biomass) and abiotic factors (soil, climate) in three major land-cover types., [Location] Europe., [Time period] 2018., [Major taxa studied] Microbial community (fungi and bacteria)., [Methods] We collected 881 soil samples from across Europe in the framework of the Land Use/Land Cover Area Frame Survey (LUCAS). We measured potential soil basal respiration at 20 ºC and microbial biomass (substrate-induced respiration) using an O2-microcompensation apparatus. Soil and climate data were obtained from the same LUCAS survey and online databases. Structural equation models (SEMs) were used to quantify relationships between variables, and equations extracted from SEMs were used to create predictive maps. Fatty acid methyl esters were measured in a subset of samples to distinguish fungal from bacterial biomass., [Results] Soil microbial properties in croplands were more heavily affected by climate variables than those in forests. Potential soil basal respiration and microbial biomass were correlated in forests but decoupled in grasslands and croplands, where microbial biomass depended on soil carbon. Forests had a higher ratio of fungi to bacteria than grasslands or croplands., [Main conclusions] Soil microbial communities in grasslands and croplands are likely carbon-limited in comparison with those in forests, and forests have a higher dominance of fungi indicating differences in microbial community composition. Notably, the often already-degraded soils of croplands could be more vulnerable to climate change than more natural soils. The provided maps show potentially vulnerable areas that should be explicitly accounted for in future management plans to protect soil carbon and slow the increasing vulnerability of European soils to climate change., The LUCAS Soil sample collection is supported by the Directorate-General Environment (DG-ENV), Directorate-General Agriculture and Rural Development (DG-AGRI), Directorate-General Climate Action (DG-CLIMA) and Directorate-General Eurostat (DG-ESTAT) of the European Commission. F. Bastida thanks the Spanish Ministry and European Regional Development Fund (FEDER) funds for the project AGL2017–85755-R (AEI/FEDER, UE), the i-LINK+ 2018 (LINKA20069) from CSIC, and funds from ‘Fundación Séneca’ from Murcia Province (19896/GERM/15). M.C.R. acknowledges support from an European Research Commission (ERC) Advanced Grant (694368). This project was funded by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig of the German Research Foundation (FZT 118-202548816).

Arbuscular mycorrhizal fungi (AMF) are obligate symbionts of most land plants. They have great ecological and economic impacts as they support plant nutrition and water supply, soil structure, and plant resistance to pathogens. Investigating AMF presence and distribution at small and large scales is critical. Therefore, research requires standard protocols to be easily implemented. In this chapter, we describe a workflow for AMF identification by high-throughput sequencing through Illumina MiSeq platform of two DNA target regions: small subunit (SSU) and internal transcribed spacer (ITS). The protocol can apply to both soil and root AMF communities.

1. Isolation and Culture of Arbuscular Mycorrhizal Fungi from Field Samples Dora Trejo-Aguilar and Jacob Banuelos 2. The Mycorrhizal Donor Plant (MDP) In Vitro Culture System for the Efficient Colonization of Whole Plants Ismahen Lalaymia and Stephane Declerck 3. A Whole-Plant Culture Method to Study Structural and Functional Traits of Extraradical Mycelium Cristiana Sbrana, Alessandra Pepe, Nuria Ferrol, and Manuela Giovannetti 4. Histochemical Staining and Quantification of Arbuscular Mycorrhizal Fungal Colonization Tania Ho-Plagaro, Maria Isabel Tamayo-Navarrete, and Jose Manuel Garcia-Garrido 5. Fluorescent Staining of Arbuscular Mycorrhizal Structures Using Wheat Germ Agglutinin (WGA) and Propidium Iodide Gennaro Carotenuto and Andrea Genre 6. Visualization of Arbuscular Mycorrhizal Fungal Extra-Radical Hyphae and Spores Vitality and Activity Pablo Cornejo and Humberto Aponte 7. Molecular Quantification of Arbuscular Mycorrhizal Fungal Root Colonization Martina Janouskova and Petra Caklova 8. Single-Spore-Extraction for Genetic Analyses of Arbuscular Mycorrhizal Fungi Dirk Redecker 9. High Throughput DNA Sequence-Based Analysis of AMF Communities Iris Marisa Maxaieie Victorino, Andrea Berruti, Alberto Orgiazzi, Samuele Voyron, Valeria Bianciotto, and Erica Lumini 10. Analysis of Arbuscular Mycorrhizal Fungal Communities by Terminal Restriction Fragment Length Polymorphism (TRFLP) Alvaro Lopez-Garcia 11. Bioinformatic Methods for the Analysis of High-Throughput RNA Sequencing in Arbuscular Mycorrhizal Fungi Francesco Venice, Alessandra Salvioli di Fossalunga, and Paola Bonfante 12. Arbuscular Mycorrhizal Fungal Gene Expression Analysis by Real-Time PCR Alessandro Silvestri, Jacob Perez-Tienda, and Juan Antonio Lopez-Raez 13. Laser Microdissection as a Useful Tool to Study Gene Expression in Plant and Fungal Partners in AM Symbiosis Raffaella Balestrini and Valentina Fiorilli 14. Detection of Arbuscular Mycorrhizal Fungal Gene Expression by In Situ Hybridization Bettina Hause and Natalia Requena 15. Functional Analyses of Arbuscular Mycorrhizal Fungal Genes in Yeast Elisabeth Tamayo, Tamara Gomez-Gallego, and Nuria Ferrol 16. Isotope Labelling to Study Phosphorus Uptake in the Arbuscular Mycorrhizal Symbiosis Carla Cruz-Paredes and Mayra E. Gavito 17. Recovery of Extra-Radical Fungal Peptides Amenable for Shotgun Protein Profiling in Arbuscular Mycorrhizae Ghislaine Recorbet, Pierre-Emmanuel Courty, and Daniel Wipf 18. Host-Induced Gene Silencing of Arbuscular Mycorrhizal Fungal Genes via Agrobacterium Rhizogenes-Mediated Root Transformation in Medicago truncatula Meike Hartmann, Stefanie Voss, and Natalia Requena 19. Application of Virus-Induced Gene Silencing to Arbuscular Mycorrhizal Fungi Tatsuhiro Ezawa, Hayato Maruyama, Yusuke Kikuchi, Kaede Yokoyama, and Chikara Masuta

Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research., Soil organism biodiversity contributes to ecosystem function, but biodiversity and function have not been equivalently studied across the globe. Here the authors identify locations, environment types, and taxonomic groups for which there is currently a lack of biodiversity and ecosystem function data in the existing literature.

Arbuscular mycorrhizal fungi (AMF) are obligate symbionts of most land plants. They have great ecological and economic impacts as they support plant nutrition and water supply, soil structure, and plant resistance to pathogens. Investigating AMF presence and distribution at small and large scales is critical. Therefore, research requires standard protocols to be easily implemented. In this chapter, we describe a workflow for AMF identification by high-throughput sequencing through Illumina MiSeq platform of two DNA target regions: small subunit (SSU) and internal transcribed spacer (ITS). The protocol can apply to both soil and root AMF communities.

AIM: The relationship between erosion and biodiversity is reciprocal. Soil organisms can both reduce soil loss, by improving porosity, and increase it, by diminishing soil stability as a result of their mixing activities. Simultaneously, soil runoff has ecological impacts on belowground communities. Despite clear research into interactions, soil erosion models do not consider biodiversity in their estimates and soil ecology has poorly investigated the effects of erosion. In order to start filling in these research gaps, we present a novel biological factor and introduce it into a well‐known soil erosion model (the revised universal soil loss equation). Furthermore, we propose insights to advance soil erosion ecology. LOCATION: Pan‐European. TIME PERIOD: Simulation of present‐day conditions. MAJOR TAXA STUDIED: Earthworms. METHODS: We present three pathways to fill in current knowledge gaps in soil biodiversity and erosion studies: (a) introducing a biological factor into soil erosion models; (b) developing plot‐scale experiments to clarify and quantify the positive/negative effects of soil organisms on erosion; (c) promoting ecological studies to assess both short‐ and long‐term effects of soil erosion on soil biota. RESULTS: We develop a biological factor to be included in soil erosion modelling. Thanks to available data on earthworm diversity (richness and abundance), we generate an “earthworm factor”, incorporate it into a model of soil erosion and produce the first pan‐European maps of it. MAIN CONCLUSIONS: New estimates of soil loss can be generated by including biological factors in soil erosion models. At the same time, the effects of soil loss on belowground diversity require further investigation. Available data and technologies make both processes possible. We think that it is time to commit to fostering the fundamental, although complex, relationship between soil biodiversity and erosion.

Summary Soil is a non-renewable resource that requires constant monitoring to prevent its degradation and promote its sustainable management. The ‘Land Use/Cover Area frame statistical Survey Soil’ (LUCAS Soil) is an extensive and regular topsoil survey that is carried out across the European Union to derive policy-relevant statistics on the effect of land management on soil characteristics. Approximately 45 000 soil samples have been collected from two time-periods, 2009–2012 and 2015. A new sampling series will be undertaken in 2018, with new measurements included. The organization for the 2018 sampling campaign represents an opportunity to summarize past LUCAS Soil achievements and present its future objectives. In 2009–2012 and 2015, LUCAS Soil surveys targeted physicochemical properties, including pH, organic carbon, nutrient concentrations and cation exchange capacity. Data from 2009–2012 (ca. 22 000 points) and derived output (more than 20 maps) are available freely from the European Soil Data Centre website. Analyses of samples collected during 2015 are ongoing and data will be available at the end of 2017. In the 2018 LUCAS Soil sampling campaign, additional properties, including bulk density, soil biodiversity, specific measurements for organic-rich soil and soil erosion will be measured. Here we present the current dataset (LUCAS Soil 2009–2012 and 2015), its potential for reuse and future development plans (LUCAS Soil 2018 and over). LUCAS Soil represents the largest harmonized open-access dataset of topsoil properties available for the European Union at the global scale. It was developed as an expandable resource, with the possibility to add new properties and sampling locations during successive sampling campaigns. Data are available to the scientific community and decision makers, thus contributing to both research and the development of the land-focused policy agenda. Highlights LUCAS Soil consists of soil physicochemical and biological properties data from Europe. Harmonized and open-access dataset allowing inclusion of soil in large-scale inter-disciplinary assessments. LUCAS Soil has a broad pool of users from scientists to policy makers, and applications from map validation to modelling. LUCAS Soil confirms the need for open-access and a large-scale dataset for soil properties.

The relationship between erosion and biodiversity is reciprocal. Soil organisms can both reduce soil loss, by improving porosity, and increase it, by diminishing soil stability as a result of their...

Because of the increasing pressures exerted on soil, below-ground life is under threat. Knowledge-based rankings of potential threats to different components of soil biodiversity were developed in order to assess the spatial distribution of threats on a European scale. A list of 13 potential threats to soil biodiversity was proposed to experts with different backgrounds in order to assess the potential for three major components of soil biodiversity: soil microorganisms, fauna, and biological functions. This approach allowed us to obtain knowledge-based rankings of threats. These classifications formed the basis for the development of indices through an additive aggregation model that, along with ad-hoc proxies for each pressure, allowed us to preliminarily assess the spatial patterns of potential threats. Intensive exploitation was identified as the highest pressure. In contrast, the use of genetically modified organisms in agriculture was considered as the threat with least potential. The potential impact of climate change showed the highest uncertainty. Fourteen out of the 27 considered countries have more than 40% of their soils with moderate-high to high potential risk for all three components of soil biodiversity. Arable soils are the most exposed to pressures. Soils within the boreal biogeographic region showed the lowest risk potential. The majority of soils at risk are outside the boundaries of protected areas. First maps of risks to three components of soil biodiversity based on the current scientific knowledge were developed. Despite the intrinsic limits of knowledge-based assessments, a remarkable potential risk to soil biodiversity was observed. Guidelines to preliminarily identify and circumscribe soils potentially at risk are provided. This approach may be used in future research to assess threat at both local and global scale and identify areas of possible risk and, subsequently, design appropriate strategies for monitoring and protection of soil biota.

The selection of biological indicators for monitoring progress towards policy goals for soil quality should be without bias and in line with individual scenarios of need. Here we describe the prescription of a suite of appropriate indicators for potential application in such monitoring schemes across Europe. We applied a structured framework of assessment and ranking (viz. a ‘logical sieve’), building upon published data and a new survey taken from a wide section of the global soil biodiversity research and policy community. The top ten indicators included four indicators of biodiversity (three microbial and one meso-faunal) by various methods of measurement, and three indicators of ecological function (Multiple enzyme assay, Multiple substrate-induced respiration profiling, and ‘Functional genes by molecular biological means’). Within the techniques assessed, seven out of the top ten indicators made use of molecular methods.

Arbuscular Mycorrhizal Fungi (AMF) are well known for their ecological importance and their positive influence on plants. The genetics and phylogeny of this group of fungi have long been debated. Nuclear markers are the main tools used for phylogenetic analyses, but they have sometimes proved difficult to use because of their extreme variability. Therefore, the attention of researchers has been moving towards other genomic markers, in particular those from the mitochondrial DNA. In this study, 46 sequences of different AMF isolates belonging to two main clades Gigasporaceae and Glomeraceae have been obtained from the mitochondrial gene coding for the Cytochrome c Oxidase I (COI), representing the largest dataset to date of AMF COI sequences. A very low level of divergence was recorded in the COI sequences from the Gigasporaceae, which could reflect either a slow rate of evolution or a more recent evolutionary divergence of this group. On the other hand, the COI sequence divergence between Gigasporaceae and Glomeraceae was high, with synonymous divergence reaching saturated levels. This work also showed the difficulty in developing valuable mitochondrial markers able to effectively distinguish all Glomeromycota species, especially those belonging to Gigasporaceae, yet it represents a first step towards the development of a full mtDNA-based dataset which can be used for further phylogenetic investigations of this fungal phylum.

The biodiversity of arbuscular mycorrhizal fungi (AMF) communities present in five Sardinian soils (Italy) subjected to different land-use (tilled vineyard, covered vineyard, pasture, managed meadow and cork-oak formation) was analysed using a pyrosequencing-based approach for the first time. Two regions of the 18S ribosomal RNA gene were considered as molecular target. The pyrosequencing produced a total of 10924 sequences: 6799 from the first and 4125 from the second target region. Among these sequences, 3189 and 1003 were selected to generate operational taxonomic units (OTUs) and to evaluate the AMF community richness and similarity: 117 (37 of which were singletons) and 28 (nine of which were singletons) unique AMF OTUs were detected respectively. Within the Glomeromycota OTUs, those belonging to the Glomerales order were dominant in all the soils. Diversisporales OTUs were always detected, even though less frequently, while Archaeosporales and Paraglomerales OTUs were exclusive of the pasture soil. Eleven OTUs were shared by all the soils, but each of the five AMF communities showed particular features, suggesting a meaningful dissimilarity among the Glomeromycota populations. The environments with low inputs (pasture and covered vineyard) showed a higher AMF biodiversity than those subjected to human input (managed meadow and tilled vineyard). A reduction in AMF was found in the cork-oak formation because other mycorrhizal fungal species, more likely associated to trees and shrubs, were detected. These findings reinforce the view that AMF biodiversity is influenced by both human input and ecological traits, illustrating a gradient of AMF communities which mirror the land-use gradient. The high number of sequences obtained by the pyrosequencing strategy has provided detailed information on the soil AMF assemblages, thus offering a source of light to shine on this crucial soil microbial group.