The role of AI-enhanced microscopy in soil biodiversity assessment: Advancing soil security, connectivity and governance with implications for the European Directive on Soil Monitoring and Resilience, and global agendas

There is a renewed awareness of the finite nature of the world’s soil resources, growing concern about soil security and significant uncertainties about the carrying capacity of the planet. Regular assessments of soil conditions from local through to global scales are requested, and there is a clear demand for accurate, up-to-date and spatially referenced soil information by the modelling scientific community, farmers and land users, and policy- and decision-makers. Soil and imaging spectroscopy, based on visible–near-infrared and shortwave infrared (400–2500 nm) spectral reflectance, has been shown to be a proven method for the quantitative prediction of key soil surface properties. With the upcoming launch of the next generation of hyperspectral satellite sensors in the next years, a high potential to meet the demand for global soil mapping and monitoring is appearing. In this paper, we briefly review the basic concepts of soil spectroscopy with a special attention to the effects of soil roughness on reflectance and then provide a review of state of the art, achievements and perspectives in soil mapping and monitoring based on imaging spectroscopy from air- and spaceborne sensors. Selected application cases are presented for the modelling of soil organic carbon, mineralogical composition, topsoil water content and characterization of soil crust, soil erosion and soil degradation stages based on airborne and simulated spaceborne imaging spectroscopy data. Further, current challenges, gaps and new directions toward enhanced soil properties modelling are presented. Overall, this paper highlights the potential and limitations of multiscale imaging spectroscopy nowadays for soil mapping and monitoring, and capabilities and requirements of upcoming spaceborne sensors as support for a more informed and sustainable use of our world’s soil resources.

Soil is the most important natural resource for life on Earth after water. Given its fundamental role in sustaining the human population, both the availability and quality of soil must be managed sustainably and protected. To ensure sustainable management we need to understand the intrinsic functional capacity of different soils across Europe and how it changes over time. Soil monitoring is needed to support evidence-based policies to incentivise sustainable soil management. To this aim, we assessed which soil attributes can be used as potential indicators of five soil functions; (1) primary production, (2) water purification and regulation, (3) carbon sequestration and climate regulation, (4) soil biodiversity and habitat provisioning and (5) recycling of nutrients. We compared this list of attributes to existing national (regional) and EU-wide soil monitoring networks. The overall picture highlighted a clearly unbalanced dataset, in which predominantly chemical soil parameters were included, and soil biological and physical attributes were severely under represented. Methods applied across countries for indicators also varied. At a European scale, the LUCAS-soil survey was evaluated and again confirmed a lack of important soil biological parameters, such as C mineralisation rate, microbial biomass and earthworm community, and soil physical measures such as bulk density. In summary, no current national or European monitoring system exists which has the capacity to quantify the five soil functions and therefore evaluate multi-functional capacity of a soil and in many countries no data exists at all. This paper calls for the addition of soil biological and some physical parameters within the LUCAS-soil survey at European scale and for further development of national soil monitoring schemes.

Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function

Soil Security includes dimensions, soil capability, soil condition, soil capital, soil connectivity and soil codification (the “five C's”). This article provides a short review on how soil mapping, digital soil mapping and soil monitoring systems (SM, DSM and SMS) over large areas contribute to these five C's at scales ranging from country to globe. Changes and the evolution in aims of SM, DSM and SMS were driven both by main issues related to policy priorities and associated advances in science and technology. This review shows that SM, DSM and SMS can provide the basis for assessing soil capability and condition over large areas, especially if we assume that capability mainly depends on rather stable soil attributes. Repeated DSM or SMS are appropriated tool to monitor changes in soil condition at these scales. They may even allow mapping changes in soil capability. However, broad-scale SM, DSM and SMS have not yet fully achieved the provision of information concerning the delivery of some soil functions and soil-based ecosystem services. Although significant progress in estimating the capital dimension of soil security has been achieved, there is need to progress monitoring changes in soil capital. Broad-scale SM, DSM and SMS has great potential to increase soil connectivity. The main challenge is adapting our language and our communication to the target audience. There are encouraging initiatives to enhance soil codification. Codification issues are largely driven by the political agenda, there is still an urgent need to increase soil connectivity, especially towards citizens, NGOs and policy-makers.

The importance of soil biodiversity is increasingly recognized in agriculture and natural resource research and development. Yet, traditional soil biodiversity assessments are costly and time‐consuming, limiting the extent and frequency of sampling and analysis in space and time. Flow cytometry (FCM) is a powerful technique to characterize cell communities due to its high robustness and accuracy, requiring only a short time for the characterization. Therefore, FCM could expand soil research capabilities by allowing the characterization of different aspects of bacterial biodiversity. However, this implementation of FCM requires the previous dispersion, separation and purification of bacteria from complex soil matrices. Moreover, soil monitoring programs or evaluation of soil management practices require high‐throughput analysis. In this context, soil processing protocols need to consider not only an adequate recovery of undamaged, representative and pure soil bacteria, but also short‐time processing requirements. Although soil processing protocols have been reported over time, to our knowledge, there is no recommended soil extraction protocol for high‐throughput analysis of bacterial biodiversity by FCM. We reviewed the state‐of‐art of the use of flow cytometry in scientific research and the protocols used for the extraction of bacteria from soil. We analysed the literature to take stock of the diversity of methodologies for soil processing and applications of flow cytometry in bacterial characterization considering abundance, diversity, community structure and functional properties. This review provides several lines of evidence of the use of flow cytometry for soil bacterial biodiversity (SBB) characterization, highlighting its potential for soil monitoring and studies on soil bacterial community dynamics. The review also highlights and discusses the most relevant constraints and research gaps that need to be considered for high‐throughput analysis of SBB by FCM, such as evaluation of scale‐down, new reagents for and methods of purification, threshold of bacterial recovery efficiency and selection of a standardized and validated protocol. We proposed a protocol for soil bacterial extraction for high‐throughput analysis of SBB by FCM and we provided detailed databases of systematized information that would be useful to the scientific community.

Living soils are fundamental for human life as we know it. The top layer of Earth’s crust, essentially composed of minerals, water and air, harbours an immense variety of organisms, from plants to microorganisms, which qualifies it as a living system. Soil biodiversity is the main actor underlying the provision of services that are essential for regulating, providing and supporting human life. The increasing level of human activity has been subjecting soil to multiple pressures, resulting in soil degradation and biodiversity decline, hence deterioration in the system’s capability to render those ecosystem services. Growing concern on this resource’s misuse has led to a series of conventions and strategies targeting its conservation (such as the Thematic Strategy for Soil Protection in the European Union (EC) 2006) and advocating for specific protection measures that can ensure a sustainable use of soil. These measures mainly focus on extending our knowledge on how soil functions but also on developing monitoring programmes that can detect trends and changes in soil biodiversity. This demand boosted research on soil ecology over the last decades, with significant increases of scientific knowledge on its structural and functioning complexity. However, there are still some gaps and needs to be addressed in order to design adequate measures for soil protection. In this chapter we review the main advances in soil ecological research and monitoring and further discuss the status of current strategies towards soil protection and sustainability. Moreover, we present here a strategy, consisting of three action lines, for effectively contributing to soil protection. It is based on monitoring and mapping, experimentation and raising awareness towards soil issues, which hopefully can change the way we perceive and use soil, this very dynamic but non-renewable resource at the human life time scale.

Monitoring biodiversity in the Anthropocene using remote sensing in species distribution models

The groundwater contribution to surface water contamination in a region with intensive agricultural land use (Noord-Brabant, The Netherlands)

The monitoring of soil natural capital and ecosystem services (ES) is a vital tool for the sustainable use of soils. Without knowing the status and trajectory of the “health” of our soil ecosystems we are unable to make informed decisions about soil and land management. Long-term and large-scale monitoring programs provide a useful source of data for such purpose. This chapter presents a background to early developments of the National Resources Inventory (NRI) soil monitoring network in the United States and the established Countryside Survey (CS) monitoring program from the United Kingdom. It frames findings from these and several other international monitoring programs in the context of “measuring,” describing how the link between soil variables and ES indicators can be made, and how they can be upscaled; “monitoring,” discussing trends which have been recorded in long-term surveys under the broad groupings of soil organic carbon, physicochemical indicators, soil biodiversity and, contaminants and pollutants; and “modelling,” covering several beneficial uses of monitoring data including integrated analysis and trade-offs. Finally, the benefits and challenges of utilizing data from long-term soil monitoring programs, and the scope for future developments, are briefly summarized.

<p>The European Soil Observatory (<strong>EUSO</strong>) 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.</p><p>The EUSO will establish a comprehensive <strong>dashboard</strong> 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).</p><p><strong>Indicators </strong>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. .</p><p><strong>Operational policy support</strong> 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.</p><p><strong>The EUSO</strong> will work with EU countries <strong>to identify and present</strong> 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.</p>

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

The expansion of exotic trees and particularly Eucalyptus globulus in the north of the Iberian Peninsula forests is known to greatly affect ecosystem properties. For instance, it promotes negative effects such as soil erosion, acidification or decreases in soil humidity, which reflect significant functional contrasts with their native counterparts. However, their impact on the communities of millions of organisms living below‐ground is much less understood, even though soil biodiversity, abundance and community structure are crucial for forest soil health. We evaluated the effects of native and exotic forests in the north of Portugal on the structure of soil communities through co‐occurrence networks and linear discriminant analysis effect size (LEfSe) tools. We aimed to understand the effects of forest type and location and identify community biomarkers or taxa that consistently define the differences between these forests. Although community composition was similar in exotic and native forests, we found that the network structure of these soil communities differed significantly depending on the edaphoclimatic region. Soil communities in native forests exhibited more similar interactions and stability compared to those in exotic forests in interior and coastal regions. Connectance and robustness were higher in native forests of the interior region. On the contrary, exotic forests from the central region showed more homogeneity, stability, connectance and robustness than their native counterparts. A small group of 52 biomarkers dominated by fungi consistently explained the community differences between native and exotic forests, with 30 and 22 taxa in native and exotic forests, respectively. They were also found to be keystone taxa of these soils, as their extraction resulted in significant changes in network structure. Policy implications : Our results point to the importance of taking management decisions for these forests considering regional conditions as well as forest type. The provided list of soil keystone taxa should be taken into account in future research and soil monitoring, which is essential for sustainable management of land.

The urgency of protecting ecosystems and their recovery from contamination has been highlighted in several recent European strategies because Europe's biodiversity and landscapes are declining rapidly due to different human pressures. Despite the existence of EU and national laws addressing environmental contamination, practical procedures are often missing. For example, competent authorities must deal promptly and effectively with environmental accidents, noncompliance, and criminal offenses but relevant tools that facilitate these processes are often lacking. For example, thorough planning is crucial for effective investigation and assessment to improve environmental damage assessments in line with the European Environmental Liability Directive (ELD, 2004/35/EC). With regard to soils, a specific European legislation for their protection, the European Soil Monitoring Law, is currently being developed. However, it is crucial that this law bridges the gaps between existing chemical regulations and that it aligns with current European strategies for environmental protection and sustainability. Continuous feedback of soil monitoring results to regulatory frameworks will be essential. This feedback loop ensures that chemical regulations are relevant and effective in protecting soil health. In this context, development and sharing of effective and practical procedures for recovering ecosystems from contamination are crucial. This was the case at the RemTech Europe meeting, which was held online and onsite in Ferrara, Italy, in September 2022. The discussion covered all aspects of environmental contaminants. It ranged from the basic understanding of these contaminants to the various types that pose a threat to organisms, studies of their environmental fate, detection methods, and sustainable practices for contaminant management. The special series dedicated to RemTech Europe 2022 is particularly relevant to these purposes and resulted in six articles that were selected from oral presentations. The articles emphasize the need for integrated approaches to risk management and remediation to address the problems of soil, sediment, and groundwater contamination. Integr Environ Assess Manag 2024;00:1-5. © 2024 The Author(s). Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

The article examines the European experience of agricultural policy aimed at increasing productivity and production in general, helping to maintain ecosystems and strengthen the industry's ability to adapt to climate change, extreme weather, drought, floods and other disasters while gradually improving land quality, resources and soils. It is substantiated that since the main means of agriculture is land resources, the main practices of sustainable development of the industry are related to the ability to improve soil quality. The main types of soil degradation, their consequences and costs in the EU countries are identified. It is established that the framework and specific measures for the protection and restoration of soils, as well as ensuring their rational use in the EU is determined by the new EU Soil Strategy for 2030, which replaced the Soil Thematic Strategy (STS) in 2006. The new Strategy is based on several goals of the Green Agreement and the Sustainable Development Goals by 2030 and sets medium-term (2030) and long-term (2050) goals. The implementation of the Strategy envisages framework actions and implementation of specific policies in nine areas: organic content in soil and climate change; test-soil-for-free initiative; closed-loop economy and soil; organic farming, soil health and climate change; soil biodiversity for ecosystems and human health; prevention of soil contamination; reclamation of disturbed and contaminated lands; soil and digital agenda; soil monitoring. The main activators (drivers) of the Strategy are financing, management, promotion and participation in global actions, which are systematized by funding for sustainable management and restoration of soils at the EU level, institutions of management and restoration of soils in the EU, areas of promotion and participation in global actions on soils in the EU.

A large number of biological indicators have been proposed over the years for assessing soil quality. Although many of those have been applied in monitoring schemes across Europe, no consensus exists on the extent to which these indicators might perform best and how monitoring schemes can be further optimized in terms of scientific and policy relevance. Over the past decade, developments in environmental monitoring and risk assessment converged toward the use of indicators and endpoints that are related to soil functioning and ecosystem services. In view of the proposed European Union (EU) Soil Framework Directive, there is an urgent need to identify and evaluate indicators for soil biodiversity and ecosystem services. The recently started integrated project, Ecological Function and Biodiversity Indicators in European Soils (EcoFINDERS), aims to address this specific issue within the EU Framework Program FP7. Here, we 1) discuss how to use the concept of ecosystem services in soil monitoring, 2) review former and ongoing monitoring schemes, and 3) present an analysis of metadata on biological indicators in some EU member states. Finally, we discuss our experiences in establishing a logical sieve approach to devise a monitoring scheme for a standardized and harmonized application at European scale.