The circular bioeconomy, centred on the principles of “Reduce, Reuse, and Recycle”, is central to achieving the goals of the European Green Deal and the “Farm to Fork” strategy. The key approach, within this framework, is the valorisation of food processing side-streams through various processing technologies to produce fertilisers that, when applied to the soil, act as potential “soil improvers”. When applied to soil, these materials affect not only the physical, chemical, and biological properties of soil but also impact greenhouse gas emissions, nutrient leaching, and the levels of contaminants or pathogens. A systematic review of field studies conducted in European soils between 2014 and 2024 was performed with stringent inclusion and exclusion criteria, which allowed the identification of suitable articles in three independent steps. The main soil improvers derived from various agri-food side-streams were biochar, compost, and digestate. Their effects, along with the potential risks associated with their use in agricultural fields, were carefully evaluated and discussed. This review forms part of the DeliSoil project “Delivering safe, sustainable, tailored & societally accepted soil improvers from circular food production for boosting soil health” funded under the European Union “A Soil Deal for Europe”. This systematic review showed that soil improvers enhance soil health by improving microbial diversity, organic matter, and water retention, and by boosting plant growth. However, potential risks require careful management, and long-term studies are needed to fully assess their environmental and agronomic impacts. Graphical Abstract

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

European policies on climate change (CC), food security (FS), and biodiversity (BD) represent the EU’s commitment to a sustainable agri-food system, highlighting the interdependence between environmental health and food security. By analyzing key drivers and indicators, the present study evaluates the effectiveness of existing measures and identifies gaps in the policy framework. A Scoping Group activity facilitated dialogue between policymakers, industry, and farmer representatives to gather feedback and strengthen the data–policy link. The results highlight progress in areas such as promoting sustainable agriculture and biodiversity, while pointing out unresolved issues like the challenges faced by smallholder farmers. The study emphasizes the need for real-time monitoring tools and tailored solutions to address the complexities of the agri-food system. It also encourages the integration of emerging technologies, such as IoT and AI, to enhance the sustainability of agricultural practices. Ultimately, the findings call for a landscape-specific approach to maximize biodiversity gains, mitigate climate impacts, and ensure food security within the broader context of the EU’s ecological and socio-economic challenges.

Soil health is crucial for the sustainability of agricultural practices and ecosystem resilience. Using a data mining approach, this study aims to explore emerging themes related to the impact of soil improvers on soil health by analyzing results from various EU-funded agricultural projects, with the final goal of identifying the key factors driving the effectiveness of soil amendments. By integrating data mining and text analysis, the study extracts, aggregates, and visualizes insights, providing a comprehensive overview of innovative strategies to enhance soil fertility and promote ecological balance. This integrated analytical framework offers a nuanced understanding of the conceptual landscape surrounding soil health in EU projects, highlighting the multifaceted roles of organic amendments and microbial solutions. Our findings underscore the critical link between organic amendments and soil health, highlighting their potential as strategic tools for achieving more sustainable agricultural systems. These findings provide a basis for refining soil management strategies in agriculture and support the development of evidence-based policies aimed at improving soil health and fostering ecological balance across Europe.

Mobile genetic elements such as integrons are key drivers of microbial evolution, enabling rapid adaptation to environmental pressures through the acquisition and rearrangement of gene cassettes. In this study, we explored the structural diversity and synteny of class 1 integrons (intI1) across a set of agroecosystem-related environments, including digestate, compost, and rhizosphere soils from wheat crops (Triticum durum and T. aestivum). Our results reveal distinct gene cassette architectures shaped by the origin of the samples: digestate harbored the most diverse and complex arrays, while compost displayed streamlined structures. Rhizosphere soils exhibited intermediate configurations, reflecting a dynamic balance between environmental exposure and host influence. Genes associated with resistance to antibiotics and heavy metals, such as qacEΔ1 and ebrA, were differentially distributed, suggesting site-specific selective pressures. The observed patterns of cassette organization and diversity underscore the role of integron synteny as a molecular fingerprint of microbial adaptation. These findings position class 1 integrons as promising bioindicators of soil health and functional resilience, supporting a One Health approach to sustainable agriculture and microbial risk monitoring.

Drought stress poses a significant threat to olive cultivation in Mediterranean regions. This study investigated the resilience and functional adaptation of root-associated and rhizosphere soil microorganisms of four olive cultivars under contrasting water regimes (irrigated vs. drought) across seasons. Using a combination of amplicon-targeted metagenomics, phylogenetic analysis, and text mining of the scientific literature, we identified a conserved core microbiome and revealed that drought stress significantly alters the structure of root-associated—but not rhizosphere soil—bacterial communities. Potential functional profiling indicated that drought conditions enriched for genes involved in stress response pathways, including branched-chain amino acid transport, glutathione S-transferase activity, thioredoxin reductase, and chemotaxis. Text mining co-occurrence networks highlighted strong associations between some key bacterial genera and plant growth-promoting functions like phytohormone production and biocontrol. Furthermore, we identified Solirubrobacter, Microvirga, and Pseudonocardia as the primary contributors to these drought-resilience functions. The stability of the soil microbiome suggests functional redundancy, whereas the restructuring of the root endophytic compartment indicates active plant selection for beneficial microbes. Our findings provide a foundation for developing tailored microbial consortia (SynComs) to enhance drought tolerance in olive trees and support sustainable agriculture in water-limited environments.