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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

12 páginas.- 6 figuras.- referencias.- Supplementary data to this article can be found online at https://doi. org/10.1016/j.geoderma.2023.116474, Elucidating contents and drivers of soil bacterial and fungal biomass in contrasting land uses and climates at European scale is useful to define appropriate policies for the conservation of the ecosystem services that soil microorganisms provide. Here, we aimed to (i) quantify and compare bacterial and fungal biomass in 513 European soils collected from three different land uses (forests, grasslands, and croplands) and climates (arid, temperate, and cold) through analysis of fatty acid methyl esters; (ii) model the factors controlling soil bacterial and fungal biomass; and (iii) investigating levels of bacterial and fungal biomass in cropland soils cultivated with three important crop types in Europe: cereals, oil-producing crops, and orchards. Bacterial biomass decreased with land use in the following order: grasslands > croplands > forests and was found to be the highest in temperate environments. Similar patterns were found for biomass of Gram-positive and Gram-negative bacteria and Actinobacteria. Soil fungal biomass was greater in forests than in croplands and grasslands and was favoured by colder environments. The fungi to bacteria ratio (F/B) decreased as follows: forests > croplands > grasslands, with soils in colder climates showing greater F/B ratios in croplands and forests. Soil texture, soil organic carbon, and nitrogen were shown to directly drive bacterial and fungal biomass. The biomass of the different microbial groups was not influenced by the crop type when only croplands were considered. Fungi appear to be more susceptible to agricultural soil use than bacteria. Moreover, agricultural use of soil seems to buffer the effect of harsh climatic conditions on soil bacterial biomass. The present study improves our understanding of the combined effects of land use and climate on soil bacterial and fungal biomass across Europe., This publication is part of the I + D + I project PID2020-114942RB-I00 funded by MCIN/ AEI/ /10.13039/501100011033. J.A.S. acknowledges the support of the program “Juan de la Cierva Incorporación” of the “Ministerio de Ciencia, Innovación y Universidades” (agreement no. IJC2018-034997-I). N.E. gratefully acknowledges the support of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig funded by the German Research Foundation (FZT 118, 202548816). The LUCAS Survey is coordinated by Unit E4 of the Statistical Office of the European Union (EUROSTAT). The LUCAS Soil sample collection is supported by the Directorate‐General Environment (DG‐ENV), Directorate‐General Agriculture and Rural Development (DG‐AGRI) and Directorate‐General Climate Action (DG‐CLIMA) of the European Commission.

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.

Dryland soils provide different societal and environmental services, such as food supply and biodiversity support. In Europe, most of the dryland areas are devoted to agriculture. In the next decades, both European and worldwide drylands are expected to suffer with increased intensity due to the expected climate change-derived rise in aridity. Many studies have focussed on aridity-induced changes in major nutrients in drylands, but little is known of the impact of environmental and biogeochemical factors on micronutrients with critical roles in life, and as inorganic contaminants with ecotoxicological implications. We analysed and explored drivers of total and available concentrations of micronutrients (Co, Cu, Fe, Mo, Mn, Ni and Zn) and contaminants (As, Cd and Pb) in 148 soil samples collected from European drylands covering a wide range of aridity and of other geochemical parameters. The availability of micronutrients increased with their total content, decreased with pH and was enhanced by organic C content. Aridity decreased the availability of Fe, a key element in human diet. Our findings also highlight the scarcity of this micronutrient in European drylands, as well as of some other important micronutrients like Zn and Mo in agricultural soils. Total content was the main driver of the availability of Cd and Pb, and organic matter exerted synergistic effects on contaminant release. Our data show the need for precise management practices to be incentivised by agricultural and environmental policies in order to ensure micronutrient supply and avoid contamination, thus maintaining adequate levels of agricultural productivity and simultaneously preserving dryland ecosystems. Highlights: Drylands are important for food production in Europe and sensitive to climate change. The occurrence of metals in European Union dry soils and the drivers influencing them were studied. Some micronutrients (Fe, Mo and Zn) were scarce while contaminants were abundant. SOC, pH and clays were the main drivers of element availability; aridity reduced Fe. Agricultural practises are needed to ensure nutrient supply and prevent contamination., This work was funded by a 2018 Leonardo Grant for Researchers and Cultural Creators of the Fundación BBVA (Spain).

Soil biodiversity and related ecosystem functions are neglected in most biodiversity assessments and nature conservation actions. We examined how society, and particularly policy makers, have addressed these factors worldwide with a focus on Europe and explored the role of soils in nature conservation in Germany as an example. We reviewed past and current global and European policies, compared soil ecosystem functioning in- and outside protected areas, and examined the role of soils in nature conservation management via text analyses. Protection and conservation of soil biodiversity and soil ecosystem functioning have been insufficient. Soil-related policies are unenforceable and lack soil biodiversity conservation goals, focusing instead on other environmental objectives. We found no evidence of positive effects of current nature conservation measures in multiple soil ecosystem functions in Europe. In German conservation management, soils are considered only from a limited perspective (e.g., as physicochemical part of the environment and as habitat for aboveground organisms). By exploring policy, evidence, and management as it relates to soil ecosystems, we suggest an integrative perspective to move nature conservation toward targeting soil ecosystems directly (e.g., by setting baselines, monitoring soil threats, and establishing a soil indicator system).La biodiversidad del suelo y las funciones ambientales relacionadas se dejan de lado en la mayoría de las evaluaciones de la biodiversidad y de las acciones de conservación de la naturaleza. Analizamos cómo la sociedad, y particularmente los formuladores de políticas, han abordado estos factores a nivel mundial con un enfoque en Europa y exploramos como ejemplo el papel de los suelos en la conservación de la naturaleza en Alemania. Revisamos las políticas mundiales y europeas en el pasado y en la actualidad, comparamos el funcionamiento ambiental del suelo dentro y fuera de las áreas protegidas y examinamos el papel de los suelos en la gestión de la conservación por medio del análisis de textos. La protección y la conservación de la biodiversidad y el funcionamiento ambiental del suelo han sido insuficientes. Las políticas relacionadas con el suelo son inaplicables y carecen de objetivos de conservación para su biodiversidad, pues se enfocan más bien en otros objetivos ambientales. No descubrimos evidencias de los efectos positivos de las medidas actuales de conservación en múltiples funciones ambientales del suelo en Europa. En la gestión alemana de la conservación, los suelos sólo se consideran desde una perspectiva limitada (p. ej.: como una parte físico química del ambiente y como hábitat para los organismos que habitan por encima de él). Mediante la exploración de la política, evidencias y gestión conforme se relaciona con los ecosistemas del suelo, sugerimos una perspectiva integrada para dirigir a la conservación hacia el enfoque directo sobre los ecosistemas del suelo (p. ej.: al establecer líneas base, monitorear las amenazas para el suelo y establecer un sistema indicador del suelo).【摘要】 大多数生物多样性评估和自然保护行动都忽视了土壤生物多样性及相关生态系统功能。我们研究了社会, 特别是政策制定者, 如何在以欧洲为重点的全世界范围内应对这些问题, 并以德国为例探讨了土壤在自然保护中的作用。本研究综述了过去与现在全球及欧洲的政策, 比较了保护区内外的土壤生态系统功能, 并通过文本分析研究了土壤在自然保护管理中的作用。我们发现, 对土壤生物多样性和土壤生态系统功能的保护仍有欠缺。与土壤有关的政策难以实施, 且缺少土壤生物多样性保护目标, 已有的保护目标更多地集中在其他环境目标上。我们没有发现欧洲目前的自然保护措施对多种土壤生态系统功能产生积极影响的证据。德国的保护管理仅从有限的角度考虑土壤因素(如作为环境的物理化学部分和地上生物的栖息地)。通过探讨与土壤生态系统有关的政策、证据和管理, 我们提出了一个综合性观点, 以促进自然保护朝着直接针对土壤生态系统的方向发展, 如通过设定基线、监测土壤威胁, 以及建立土壤指标体系。【翻译:胡怡思;审校:聂永刚】.

Animals, such as termites, have largely been overlooked as global-scale drivers of biogeochemical cycles1,2, despite site-specific findings3,4. Deadwood turnover, an important component of the carbon cycle, is driven by multiple decay agents. Studies have focused on temperate systems5,6, where microbes dominate decay7. Microbial decay is sensitive to temperature, typically doubling per 10°C increase (decay effective Q10 = ~2)8–10. Termites are important decayers in tropical systems3,11–13 and differ from microbes in their population dynamics, dispersal, and substrate discovery14–16, meaning their climate sensitivities also differ. Using a network of 133 sites spanning 6 continents, we report the first global field-based quantification of temperature and precipitation sensitivities for termites and microbes, providing novel understandings of their response to changing climates. Temperature sensitivity of microbial decay was within previous estimates. Termite discovery and consumption were both much more sensitive to temperature (decay effective Q10 = 6.53), leading to striking differences in deadwood turnover in areas with and without termites. Termite impacts were greatest in tropical seasonal forests and savannas and subtropical deserts. With tropicalization17 (i.e., warming shifts to a tropical climate), the termite contribution to global wood decay will increase as more of the earth’s surface becomes accessible to termites. Acknowledgements. For materials, field, and lab assistance, we thank the Australian Landscape Trust Team, Juan Martínez de Aragón, Eric Roy, Hugh Wilson, Kylie Brice, Bethanie Coleman, Brendan Delroy, Coline Deveautour, Suzanne Donn, Generci Assis Neves, Ricardo Marques Barreiros, Ricardo Marques Barreiros, Generci Assis Neves from Resineves Agroflorestal company, Alfred Lochner, Pousada Vale do Céu, Humberto Robles, María M. Rivera, and Grant Kirker. Steve Allison and Tom Crowther provided comments on the manuscript and Abbey Yatsko helped with figure and manuscript formatting. Funding for this work was provided by US National Science Foundation (DEB-1655759, 2149151, 1713502, 1713435, 1647502, 1546686, 1831952), George Washington University, USDA Forest Service, Centre College Faculty Development Funds, Australia Terrestrial Ecosystem Research Network (TERN) National Collaborative Research Infrastructure Strategy (NCRIS), Royal Society-FCDO Africa Capacity Building Initiative, New Phytologist Foundation, Fondecyt grant:1160329, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brasil (CAPES), Department of Ecology and Conservation of the Federal University of Lavras, CNPq, FAPEMIG, Australian Academy of Science 2017 Thomas Davies Research Grant, Australian Research Council (DP160103765), UK National Environment Research Council (NE/L000016/1), Fundação de Amparo à Pesquisa do Estado de São Paulo, Brazil (NERC - FAPESP)19/07773-1, Environment Research and Technology Development Fund (ERTDF; JPMEERF15S11420) of the Environmental Restoration and Conservation Agency (ERCA) of Japan, COLCIENCIAS (No. FP44842-046-2017), Spanish Government (grant PID2019-110521GB-I00), Catalan Government (grant SGR 2017-1005), Fundación Ramón Areces (grant ELEMENTAL-CLIMATE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) PICT 2019- 2472, National Agency for the Promotion of Research, Technological Development and Innovation, Scientific and Technological Research Project 2018-01561 (PICT 2018- 01561), iDiv German Research Foundation (DFG– FZT 118, 202548816), European Research Council (ERC), European Union's Horizon 2020 research and innovation program (grant agreement no. 677232).

CONTEXT: In the European Union (EU-27) and UK, animal farming generated annually more than 1.4 billion tonnes of manure during the period 2016–2019. Of this, more than 90% is directly re-applied to soils as organic fertiliser. Manure promotes plant growth, provides nutritious food to soil organisms, adds genetic and functional diversity to soils and improves the chemical and physical soil properties. However, it can also cause pollution by introducing toxic elements (i.e., heavy metals, antibiotics, pathogens) and contribute to nutrient losses. Soil organisms play an essential role in manure transformation into the soil and the degradation of any potential toxic constitutes; however, manure management practices often neglect soil biodiversity. OBJECTIVE: In this review, we explored the impact of manure from farmed animals on soil biodiversity by considering factors that determine the effects of manure and vice versa. By evaluating manure's potential to enhance soil biodiversity, but also its environmental risks, we assessed current and future EU policy and legislations with the ultimate aim of providing recommendations that can enable a more sustainable management of farm manures. METHODS: This review explored the relationship between manure and soil biodiversity by considering 407 published papers and relevant legislative provisions. In addition, we evaluated whether benefits and risks on soil biodiversity are considered in manure management. Thereafter, we analysed the current legislation in the European Union relevant to manure, an important driver for its treatment, application and storage. RESULTS AND CONCLUSIONS: This review found that coupling manure management with soil biodiversity can mitigate present and future environmental risks. Our analyses showed that manure quality is more important to soil biodiversity than manure quantity and therefore, agricultural practices that protect and promote soil biodiversity with the application of appropriate, high-quality manure or biostimulant preparations based on manure, could accelerate the move towards more sustainable food production systems. Soil biodiversity needs to be appropriately factored in when assessing manure amendments to provide better guidelines on the use of manure and to reduce costs and environmental risks. However, radical changes in current philosophies and practices are needed so that soil biodiversity can be enhanced by manure management. SIGNIFICANCE: Manure quality in the EU requires greater attention, calling for more targeted policies. Our proposed approach could be applied by European Union Member States to include soil protection measures in national legislation, and at the EU level, can enable the implementation of strategic goals. Financiado para publicación en acceso aberto: Universidade de Vigo/CISUG

[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).

Soil fungi strongly influence ecosystem structure and functioning, playing a key role in many ecological services as decomposers, plant mutualists and pathogens. Arbuscular mycorrhizal fungi (AMF) establish mutualistic symbiotic associations with plant roots and act as biofertilizers by enhancing plant nutrients and water uptake. Information about the AMF association with Crocus sativus L. (saffron) and their impact on crop performances and spice quality has been increasing in recent years. Instead, there is still little data on the biodiversity of soil microbial communities associated with this crop in the Alpine environments. The aims of this study were to investigate the fungal communities of two Alpine experimental sites cultivated with saffron, and to rank the relative impact of two AMF inocula, applied to soil as single species (R = Rhizophagus intraradices, C. Walker &amp, A. Sch&uuml, &szlig, ler) or a mixture of two species (M = R. intraradices and Funneliformis mosseae, C. Walker &amp, ler), on the resident fungal communities which might be influenced in their diversity and composition. We used Illumina MiSeq metabarcoding on nuclear ribosomal ITS2 region to characterize the fungal communities associated to Crocus sativus cultivation in two fields, located in the municipalities of Saint Christophe (SC) and Morgex (MG), (Aosta Valley, Italy), treated or not with AMF inocula and sampled for two consecutive years (Y1, Y2). Data analyses consistently indicated that Basidiomycota were particularly abundant in both sites and sampling years (Y1 and Y2). Significant differences in the distribution of fungal taxa assemblages at phylum and class levels between the two sites were also found. The main compositional differences consisted in significant abundance changes of OTUs belonging to Dothideomycetes and Leotiomycetes (Ascomycota), Agaricomycetes and Tremellomycetes (Basidiomycota), Mortierellomycetes and Mucoromycetes. Further differences concerned OTUs, of other classes, significantly represented only in the first or second year of sampling. Concerning Glomeromycota, the most represented genus was Claroideoglomus always detected in both sites and years. Other AMF genera such as Funneliformis, Septoglomus and Microdominikia, were retrieved only in MG site. Results highlighted that neither sites nor inoculation significantly impacted Alpine saffron-field fungal communities, instead, the year of sampling had the most appreciable influence on the resident communities.

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.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide., 677232 to N.E.). K.S.R. and W.H.v.d.P. were supported by ERC-ADV grant 323020 to W.H.v.d.P. Also supported by iDiv (DFG FZT118) Flexpool proposal 34600850 (C.A.G. and N.E.); the Academy of Finland (285882) and the Natural Sciences and Engineering Research Council of Canada (postdoctoral fellowship and RGPIN-2019-05758) (E.K.C.); DOB Ecology (T.W.C., J.v.d.H., and D.R.); ERC-AdG 694368 (M.R.); and the TULIP Laboratory of Excellence (ANR-10-LABX-41) (M.L.). In addition, data collection was funded by the Russian Foundation for Basic Research (12-04-01538-a, 12-04-01734-a, 14-44-03666-r_center_a, 15-29-02724-ofi_m, 16-04-01878-a 19-05-00245); Tarbiat Modares University; Aurora Organic Dairy; UGC(NERO) (F. 1-6/Acctt./NERO/2007-08/1485); Natural Sciences and Engineering Research Council (RGPIN-2017-05391); Slovak Research and Development Agency (APVV-0098-12); Science for Global Development through Wageningen University; Norman Borlaug LEAP Programme and International Atomic Energy Agency (IAEA); São Paulo Research Foundation - FAPESP (12/22510-8); Oklahoma Agricultural Experiment Station; INIA - Spanish Agency (SUM 2006-00012-00-0); Royal Canadian Geographical Society; Environmental Protection Agency (Ireland) (2005-S-LS-8); University of Hawai‘i at Mānoa (HAW01127H; HAW01123M); European Union FP7 (FunDivEurope, 265171); U.S. Department of the Navy, Commander Pacific Fleet (W9126G-13-2-0047); Science and Engineering Research Board (SB/SO/AS-030/2013) Department of Science and Technology, New Delhi, India; Strategic Environmental Research and Development Program (SERDP) of the U.S. Department of Defense (RC-1542); Maranhão State Research Foundation (FAPEMA); Coordination for the Improvement of Higher Education Personnel (CAPES); Ministry of Education, Youth and Sports of the Czech Republic (LTT17033); Colorado Wheat Research Foundation; Zone Atelier Alpes, French National Research Agency (ANR-11-BSV7-020-01, ANR-09-STRA-02-01, ANR 06 BIODIV 009-01); Austrian Science Fund (P16027, T441); Landwirtschaftliche Rentenbank Frankfurt am Main; Welsh Government and the European Agricultural Fund for Rural Development (Project Ref. A AAB 62 03 qA731606); SÉPAQ; Ministry of Agriculture and Forestry of Finland; Science Foundation Ireland (EEB0061); University of Toronto (Faculty of Forestry); National Science and Engineering Research Council of Canada; Haliburton Forest and Wildlife Reserve; NKU College of Arts and Sciences Grant; Österreichische Forschungsförderungsgesellschaft (837393 and 837426); Mountain Agriculture Research Unit of the University of Innsbruck; Higher Education Commission of Pakistan; Kerala Forest Research Institute, Peechi, Kerala; UNEP/GEF/TSBF-CIAT Project on Conservation and Sustainable Management of Belowground Biodiversity; Ministry of Agriculture and Forestry of Finland; Complutense University of Madrid/European Union FP7 project BioBio (FPU UCM 613520); GRDC; AWI; LWRRDC; DRDC; CONICET (National Scientific and Technical Research Council) and FONCyT (National Agency of Scientific and Technological Promotion) (PICT, PAE, PIP), Universidad Nacional de Luján y FONCyT [PICT 2293 (2006)], Fonds de recherche sur la nature et les technologies du Québec (131894), Deutsche Forschungsgemeinschaft [SCHR1000/3-1, SCHR1000/6-1, 6-2 (FOR 1598), WO 670/7-1, WO 670/7-2, and SCHA 1719/1-2], CONACYT (FONDOS MIXTOS TABASCO/PROYECTO11316); NSF (DGE-0549245, DGE-0549245, DEB-BE-0909452, NSF1241932); Institute for Environmental Science and Policy at the University of Illinois at Chicago; Dean’s Scholar Program at UIC; Garden Club of America Zone VI Fellowship in Urban Forestry from the Casey Tree Endowment Fund; J. E. Weaver Competitive Grant from the Nebraska Chapter of The Nature Conservancy; the College of Liberal Arts and Sciences at DePaul University; Elmore Hadley Award for Research in Ecology and Evolution from the UIC Dept. of Biological Sciences; Spanish CICYT (AMB96-1161; REN2000-0783/GLO; REN2003-05553/GLO; REN2003-03989/GLO; CGL2007-60661/BOS); Yokohama National University; MEXT KAKENHI (25220104); Japan Society for the Promotion of Science KAKENHI (25281053, 17KT0074, 25252026); ADEME (0775C0035); Ministry of Science, Innovation and Universities of Spain (CGL2017-86926-P); Syngenta Philippines; UPSTREAM; LTSER (Val Mazia/Matschertal); Marie Sklodowska Curie Postdoctoral Fellowship (747607); National Science and Technology Base Resource Survey Project of China (2018FY100306); McKnight Foundation (14-168); Program of Fundamental Researches of Presidium of Russian Academy of Sciences (AAAA-A18-118021490070-5); Brazilian National Council of Research CNPq; and French Ministry of Foreign and European Affairs. Author contributions: H.R.P.P. led the analysis, data curation, and writing of the original manuscript draft. C.A.G. assisted in analyses and writing of the original manuscript draft. E.K.C. and N.E. revised subsequent manuscript drafts. J.v.d.H., D.R., and T.W.C. provided additional analyses. E.K.C., N.E., and M.P.T. acquired funding for the project. J.K., K.B.G., B.S., M.L.C.B., M.J.I.B., and G.B. contributed to data curation. H.R.P.P., C.A.G., M.L.C.B., M.J.I.B., G.B., O.F., A.O., E.M.B., J.B., U.B., T.D., F.T.d.V., B.K.-R., M.L., J.M., C.M., W.H.v.d.P., K.S.R., M.C.R., D.R., M.R., M.P.T., D.H.W., D.A.W., E.K.C., and N.E. contributed to the project conceptualization. All authors reviewed and edited the final draft manuscript. The majority of the authors provided data for the analyses. Competing interests: The authors declare no competing interests. Data and materials availability: Data and analysis code are available on the iDiv Data repository (DOI: 10.25829/idiv.1804-5-2593) and GitHub (https://github.com/helenphillips/GlobalEWDiversity; DOI: 10.5281/zenodo.3386456).

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...

This paper presents the second part of the mapping of topsoil properties based on the Land Use and Cover Area frame Survey (LUCAS). The first part described the physical properties (Ballabio et al., 2016) while this second part includes the following chemical properties: pH, Cation Exchange Capacity (CEC), calcium carbonates (CaCO3), C:N ratio, nitrogen (N), phosphorus (P) and potassium (K). The LUCAS survey collected harmonised data on changes in land cover and the state of land use for the European Union (EU). Among the 270,000 land use and cover observations selected for field visit, approximately 20,000 soil samples were collected in 24 EU Member States in 2009 together with more than 2000 samples from Bulgaria and Romania in 2012. The chemical properties maps for the European Union were produced using Gaussian process regression (GPR) models. GPR was selected for its capacity to assess model uncertainty and the possibility of adding prior knowledge in the form of covariance functions to the model. The derived maps will establish baselines that will help monitor soil quality and provide guidance to agro-environmental research and policy developments in the European Union., Highlights • The LUCAS harmonised soil survey comprising 20,000 observations was used in this study. • Soil chemical properties were mapped over the extent of Europe using Gaussian process regression (GPR). • GPR with Matérn kernel modelled soil properties with high accuracy. • GPR allows the production of uncertainty maps as it allows the estimation of prediction variance. • These maps complete the series of topsoil properties for Europe based on LUCAS.

Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity. Published version M.P.T. acknowledges funding from the GermanResearch Foundation (DFG, TH 2307/1-1). H.R.P.P.was supported by the sDiv (DFG FZT 118). M.L.was supported by the TULIP Laboratory of Excellence(ANR-10-LABX-41). M.C.R. and W.H.V.d.P. acknowledgesupport from ERC Advanced Grants [grant number:ERC-ADV 694368 and ERC-ADV 323020 (SPECIALS),respectively]. F.T.D.V. is supported by a BBSRC DavidPhillips Fellowship (BB/L02456X/1). N.E. and O.F.acknowledge funding by the European Research Council(ERC Starting Grant 677232, ECOWORM). C.A.G. issupported by the European Union’s Horizon 2020 researchand innovation programme under grant agreement No641762-ECOPOTENTIAL. E.K.C. acknowledges fundingfrom the Academy of Finland (285882) and the NaturalSciences and Engineering Research Council of Canada(postdoctoral fellowship 471903 and RGPIN-2019-05758).

Human activities are accelerating global biodiversity change and have resulted in severely threatened ecosystem services. A large proportion of terrestrial biodiversity is harbored by soil, but soil biodiversity has been omitted from many global biodiversity assessments and conservation actions, and understanding of global patterns of soil biodiversity remains limited. In particular, the extent to which hotspots and coldspots of aboveground and soil biodiversity overlap is not clear. We examined global patterns of these overlaps by mapping indices of aboveground (mammals, birds, amphibians, vascular plants) and soil (bacteria, fungi, macrofauna) biodiversity that we created using previously published data on species richness. Areas of mismatch between aboveground and soil biodiversity covered 27% of Earth's terrestrial surface. The temperate broadleaf and mixed forests biome had the highest proportion of grid cells with high aboveground biodiversity but low soil biodiversity, whereas the boreal and tundra biomes had intermediate soil biodiversity but low aboveground biodiversity. While more data on soil biodiversity are needed, both to cover geographic gaps and to include additional taxa, our results suggest that protecting aboveground biodiversity may not sufficiently reduce threats to soil biodiversity. Given the functional importance of soil biodiversity and the role of soils in human well-being, soil biodiversity should be considered further in policy agendas and conservation actions by adapting management practices to sustain soil biodiversity and considering soil biodiversity when designing protected areas.Disparidades Mundiales entre la Biodiversidad Sobre y Bajo el Suelo Resumen Las actividades humanas están acelerando el cambio en la biodiversidad mundial y han tenido como resultado unos servicios ambientales severamente amenazados. Una gran proporción de la biodiversidad terrestre está albergada en el suelo, pero la biodiversidad de este ha sido omitida de varias evaluaciones mundiales de biodiversidad y de las acciones de conservación, además de que el entendimiento de los patrones mundiales de la biodiversidad del suelo permanece limitado; particularmente, la extensión del traslape entre los puntos fríos y calientes de biodiversidad sobre y bajo suelo no está clara. Examinamos los patrones mundiales de estos traslapes mapeando los índices de biodiversidad sobre el suelo (mamíferos, aves, anfibios y plantas vasculares) y bajo el suelo (bacterias, hongos y macrofauna) que creamos con datos previamente publicados de la riqueza de especies. Las áreas de disparidad entre la biodiversidad sobre y bajo el suelo cubrieron el 27% de la superficie terrestre del planeta. El bioma de los bosques templados de plantas frondosas y mixtas tuvo la proporción más alta de celdas de cuadrícula con una biodiversidad alta sobre el suelo, pero baja para en el subsuelo, mientras que los biomas boreales y de la tundra tuvieron una biodiversidad intermedia bajo el suelo, pero baja para el sobre suelo. Aunque se requieren más datos sobre la biodiversidad del suelo, tanto para cubrir los vacíos geográficos como para incluir a taxones adiciones, nuestros resultados sugieren que la protección a la biodiversidad sobre el suelo puede no reducir suficientemente las amenazas para la biodiversidad del suelo. Dada la importancia funcional de la biodiversidad del suelo y el papel de los suelos en el bienestar humano, se debería considerar a la biodiversidad del suelo mucho más en las agendas políticas y en las acciones de conservación, adaptando a las prácticas de manejo para que mantengan a la biodiversidad del suelo y la consideren cuando designen áreas protegidas.人类活动正在导致全球生物多样性的快速变化, 并已严重影响到生态系统服务功能。陆地生物多样性中很大一部分存在于土壤之中, 然而, 许多全球生物多样性评估和保护行动都没有考虑土壤生物多样性, 人们对全球土壤生物多样性格局的认识也十分有限, 特别是对地表生物多样性和土壤生物多样性的热点地区及贫瘠地区的重叠程度知之甚少。为了研究全球地表生物多样性和土壤生物多样性的重叠情况, 我们利用已发表的物种丰富度数据设计了地表生物多样性 (哺乳动物、鸟类、两栖类、维管植物) 及土壤生物多样性 (细菌、真菌、大型动物群) 指标, 用于绘制相应的地图。结果显示, 地表和土壤生物多样性不匹配的地区占地球陆地面积的 27% 。在温带阔叶林和混交林生物群中, 地表生物多样性高而土壤生物多样性低的栅格占比最高, 而寒带和苔原生物群则是土壤生物多样性中等而地表生物多样性低。虽然还有待增加土壤生物多样性的数据以囊括更多地理区域和生物类群, 但我们的结果已经表明, 保护地表生物多样性可能不足以减少对土壤生物多样性的威胁。鉴于土壤生物多样性的重要功能以及土壤对人类福祉的作用, 应在政策议程和保护行动中更多地考虑土壤生物多样性, 如调整管理实践以保护土壤生物多样性、在保护区设计中纳入土壤生物多样性等等。【翻译: 胡怡思; 审校: 聂永刚】.

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.

In the European Union (EU), copper concentration in agricultural soil stems from anthropogenic activities and natural sources (soil and geology). This manuscript reports a statistical comparison of copper concentrations at different levels of administrative units, with a focus on agricultural areas. Anthropogenic sources of diffuse copper contamination include fungicidal treatments, liquid manure (mainly from pigs), sewage sludge, atmospheric deposition, mining activities, local industrial contamination and particles from car brakes. Sales of fungicides in the EU are around 158,000 tonnes annually, a large proportion of which are copper based and used extensively in vineyards and orchards. Around 10 million tonnes of sewage sludge is treated annually in the EU, and 40% of this (which has a high copper content) is used as fertilizer in agriculture. In the EU, 150 million pigs consume more than 6.2 million tonnes of copper through additives in their feed, and most of their liquid manure ends up in agricultural soil. These three sources (sales of fungicides, sewage sludge and copper consumption for pigs feed) depend much on local traditional farming practices. Recent research towards replacing copper spraying in vineyards and policy developments on applying sewage and controlling the feed given to pigs are expected to reduce copper accumulation in agricultural soil.

Copper (Cu) distribution in soil is influenced by climatic, geological and pedological factors. Apart from geological sources and industrial pollution, other anthropogenic sources, related to the agricultural activity, may increase copper levels in soils, especially in permanent crops such as olive groves and vineyards. This study uses 21,682 soil samples from the LUCAS topsoil survey to investigate copper distribution in the soils of 25 European Union (EU) Member States. Generalized Linear Models (GLM) were used to investigate the factors driving copper distribution in EU soils. Regression analysis shows the importance of topsoil properties, land cover and climate in estimating Cu concentration. Meanwhile, a copper regression model confirms our hypothesis that different agricultural management practices have a relevant influence on Cu concentration. Besides the traditional use of copper as a fungicide for treatments in several permanent crops, the combined effect of soil properties such as high pH, soil organic carbon and clay, with humid and wet climatic conditions favours copper accumulation in soils of vineyards and tree crops. Compared to the overall average Cu concentration of 16.85 mg kg−1, vineyards have the highest mean soil Cu concentration (49.26 mg kg−1) of all land use categories, followed by olive groves and orchards. Gaussian Process Regression (GPR) combined with kriging were used to map copper concentration in topsoils and to evidence the presence of outliers. GPR proved to be performant in predicting Cu concentration, especially in combination with kriging, accounting for 66% of Cu deviance. The derived maps are novel as they include information about the importance of topsoil properties in the copper mapping process, thus improving its accuracy. Both models highlight the influence of land management practices in copper concentration and the strong correlation between topsoil copper and vineyards.

Will the rain wash away our soil organic carbon under future climate change?, Understanding of the processes governing soil organic carbon turnover is confounded by the fact that C feedbacks driven by soil erosion have not yet been fully explored at large scale. However, in a changing climate, variation in rainfall erosivity (and hence soil erosion) may change the amount of C displacement, hence inducing feedbacks onto the land C cycle. Using a consistent biogeochemistry-erosion model framework to quantify the impact of future climate on the C cycle, we show that C input increases were offset by higher heterotrophic respiration under climate change. Taking into account all the additional feedbacks and C fluxes due to displacement by erosion, we estimated a net source of 0.92 to 10.1 Tg C year−1 from agricultural soils in the European Union to the atmosphere over the period 2016–2100. These ranges represented a weaker and stronger C source compared to a simulation without erosion (1.8 Tg C year−1), respectively, and were dependent on the erosion-driven C loss parameterization, which is still very uncertain. However, when setting a baseline with current erosion rates, the accelerated erosion scenario resulted in 35% more eroded C, but its feedback on the C cycle was marginal. Our results challenge the idea that higher erosion driven by climate will lead to a C sink in the near future.

The establishment of the range of soil biodiversity found within European soils is needed to guide EU policy development regarding the protection of soil. Such a base-line should be collated from a wide-ranging sampling campaign to ensure that soil biodiversity from the majority of soil types, land-use or management systems, and European climatic (bio-geographical zones) were included. This paper reports the design and testing of a method to achieve the large scale sampling associated with the establishment of such a baseline, carried out within the remit of the EcoFINDERS project, and outlines points to consider when such a task is undertaken.Applying a GIS spatial selection process, a sampling campaign was undertaken by 13 EcoFINDERS partners across 11 countries providing data on the range of indicators of biodiversity and ecosystem functions including; micro and meso fauna biodiversity, extracellular enzyme activity, PLEA and community level physiological profiling (MicroResp (TM) and Biolog (TM)). Physical, chemical and bio-geographical parameters of the 81 sites sampled were used to determine whether the model predicted a wide enough range of sites to allow assessment of the biodiversity indicators tested.Discrimination between the major bio-geographical zones of Atlantic and Continental was possible for all land-use types. Boreal and Alpine zones only allowed discrimination in the most common land-use type for that area e.g. forestry and grassland sites, respectively, while the Mediterranean zone did not have enough sites sampled to draw conclusions across all land-use types. The method used allowed the inclusion of a range of land-uses in both the model prediction stage and the final sites sampled. The establishment of the range of soil biodiversity across Europe is possible, though a larger targeted campaign is recommended. The techniques applied within the EcoFINDERS sampling would be applicable to a larger campaign. (C) 2015 Elsevier B.V. All rights reserved.

Existing data sets on earthworm communities in Europe were collected, harmonized, modelled and depicted on a soil biodiversity map of Europe. Digital Soil Mapping was applied using multiple regressions relating relatively low density earthworm community data to soil characteristics, land use, vegetation and climate factors (covariables) with a greater spatial resolution. Statistically significant relationships were used to build habitat-response models for constructing earthworm maps with abundance, species richness, and diversity data. While a good number of environmental predictors were significant in our multiple regressions, geographical factors alone seem to be less relevant than climatic factors. Despite differing sampling protocols, land use and geological history were the most relevant factors determining the demography and diversity of the earthworms across Europe. Case studies from country-specific data sets (France, Germany, Ireland and The Netherlands) demonstrated the importance and efficiency of large databases for the detection of large spatial patterns that could be subsequently applied at smaller (local) scales. After the first set of maps, additional datasets were used to improve the regressions and maps and to extent the area depicting earthworm predictions (e.g. Portugal, Italy, England, Finland, Austria and some countries from Eastern Europe). The improved maps will be submitted for publication in the Global Soil Biodiversity Atlas.

Soils encompass a huge diversity of organisms which mostly remains to be characterized due to a number of methodological and logistical issues. Nonetheless, remarkable progress has been made in recent years toward developing strategies to characterize and describe soil biodiversity, especially thanks to the development of molecular approaches relying on direct DNA extraction from the soil matrix. Metabarcoding can be applied to DNA from any environment or organism, and is gaining increasing prominence in biodiversity studies. This approach is already commonly used to characterize soil microbial communities and its application is now being extended to other soil organisms, i.e. meso- and macro-fauna. These developments offer unprecedented scientific and operational opportunities in order to better understand soil biodiversity distribution and dynamics, and to propose tools and strategies for biodiversity diagnosis. However, these opportunities also come with challenges that the scientific community must face. Such challenges are related to i) clarification of terminology, (ii) standardisation of methods and further methodological development for additional taxonomic groups, (iii) development of a common database, and (iv) ways to avoid waste of information and data derived from metabarcoding. In order to facilitate common application of metabarcoding in soil biodiversity assessment, we discuss these opportunities and challenges and propose solutions towards a more homogeneous framework., JRC.H.5-Land Resources Management

Arbuscular Mycorrhizal Fungi (AMF) are a group of obligate biotrophs, to the extent that they must develop a close symbiotic association with the roots of a living host plant in order to grow and complete their life cycle [1]. The term “mycorrhiza” literally derives from the Greek mykes and rhiza, meaning fungus and root, respectively. AMF can symbiotically interact with almost all the plants that live on the Earth. They are found in the roots of about 80-90% of plant species (mainly grasses, agricultural crops and herbs) and exchange benefits with their partners, as is typical of all mutual symbiotic relationships [2]. They represent an interface between plants and soil, growing their mycelia both inside and outside the plant roots. AMF provide the plant with water, soil mineral nutrients (mainly phosphorus and nitrogen) and pathogen protection. In exchange, photosynthetic compounds are transferred to the fungus [3].

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.

International audience; Identifying a soil core microbiome is crucial to appreciate the established microbial consortium, which is not usually subjected to change and, hence, possibly resistant/resilient to disturbances and a varying soil context. Fungi are a major part of soil biodiversity, yet the mechanisms driving their large-scale ecological ranges and distribution are poorly understood. The degree of fungal community overlap among 16 soil samples from distinct ecosystems and distant geographic localities (truffle grounds, a Mediterranean agro-silvo-pastoral system, serpentine substrates and a contaminated industrial area) was assessed by examining the distribution of fungal ITS1 and ITS2 sequences in a dataset of 454 libraries. ITS1 and ITS2 sequences were assigned to 1,660 and 1,393 Operational Taxonomic Units (OTUs; as defined by 97% sequence similarity), respectively. Fungal beta-diversity was found to be spatially autocorrelated. At the level of individual OTUs, eight ITS1 and seven ITS2 OTUs were found in all soil sample groups. These ubiquitous taxa comprised generalist fungi with oligotrophic and chitinolytic abilities, suggesting that a stable core of fungi across the complex soil fungal assemblages is either endowed with the capacity of sustained development in the nutrient-poor soil conditions or with the ability to exploit organic resources (such as chitin) universally distributed in soils.

Background Fungi strongly influence ecosystem structure and functioning, playing a key role in many ecological services as decomposers, plant mutualists and pathogens. The Mediterranean area is a biodiversity hotspot that is increasingly threatened by intense land use. Therefore, to achieve a balance between conservation and human development, a better understanding of the impact of land use on the underlying fungal communities is needed. Methodology/Principal Findings We used parallel pyrosequencing of the nuclear ribosomal ITS regions to characterize the fungal communities in five soils subjected to different anthropogenic impact in a typical Mediterranean landscape: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards. Marked differences in the distribution of taxon assemblages among the different sites and communities were found. Data analyses consistently indicated a sharp distinction of the fungal community of the cork oak forest soil from those described in the other soils. Each soil showed features of the fungal assemblages retrieved which can be easily related to the above-ground settings: ectomycorrhizal phylotypes were numerous in natural sites covered by trees, but were nearly completely missing from the anthropogenic and grass-covered sites; similarly, coprophilous fungi were common in grazed sites. Conclusions/Significance Data suggest that investigation on the below-ground fungal community may provide useful elements on the above-ground features such as vegetation coverage and agronomic procedures, allowing to assess the cost of anthropogenic land use to hidden diversity in soil. Datasets provided in this study may contribute to future searches for fungal bio-indicators as biodiversity markers of a specific site or a land-use degree.

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.

A monitoring and indicator system can inform policy