Luciana Di Gregorio

Preserving ex situ soil microbial communities is essential for bacterial biodiversity conservation in microbiome biobanking, accurate microbiome research, and future biotechnological applications in sustainable agriculture. The effect of three soil preservation methods—cryopreservation at −80 °C, refrigeration at 4 °C, and lyophilization—on the viability, diversity and metabolic functionality of the soil microbiome was evaluated using soil from untreated and solarized strawberry fields stored at 0, 6 and 12 months. Microbial viability, ecological strategies, functionality, and diversity were assessed using plate counts, r/K strategist profiling, BIOLOG EcoPlates, and 16S rRNA/ITS gene amplicon-based sequencing, respectively. Cryopreservation outperformed the other preservation strategies by generally maintaining total bacterial counts, especially in control soil, preserving the balance between oligotrophic and copiotrophic communities, and sustaining high alpha diversity indices over 12 months. Refrigeration provided moderate preservation, though microbial viability and community stability declined over time. In contrast, lyophilization significantly reduced microbial abundance, altered community composition, and diminished metabolic diversity and substrate utilization. Beta diversity analyses confirmed that cryopreserved samples remained similar in microbial structure to the initial timepoint, while lyophilized samples diverged substantially. Functional analyses also revealed reduced metabolic activity in lyophilized soils, underscoring the negative impact on the microbiome’s ecological roles. Overall, the results of this study identify cryopreservation as the most effective storage method for maintaining soil microbiome integrity, providing critical guidance for preserving soil samples in microbiome research and sustainable agricultural biotechnology.

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

The role of soil microbial communities in soil organic matter (OM) decomposition, transformation, and the global nitrogen (N) and carbon (C) cycles has been widely investigated. However, a comprehensive understanding of how specific agricultural practices and OM inputs shape microbial-driven processes across different European pedoclimatic conditions is still lacking, particularly regarding their effectiveness in mitigating greenhouse gas (GHG) emissions. This systematic review synthesizes current knowledge on the biotic mechanisms underlying soil C sequestration and GHG reduction, emphasizing key microbial processes influenced by land management practices. A rigorous selection was applied, resulting in 16 eligible articles that addressed the targeted outcomes: soil microorganism biodiversity, including microbiome composition and other common Biodiversity Indexes, C sequestration and non-CO₂ GHG emissions (namely N₂O and CH₄ emissions), and N leaching. The review highlights that, despite some variations across studies, the application of OM enhances soil microbial biomass (MB) and activity, boosts soil organic carbon (SOC), and potentially reduces emissions. Notably, plant richness and diversity emerged as critical factors in reducing N₂O emissions and promoting carbon storage. However, the lack of methodological standardization across studies hinders meaningful comparison of outcomes—a key challenge identified in this review. The analysis reveals that studies examining the simultaneous effects of agricultural management practices and OM inputs on soil microorganisms, non-CO₂ GHG emissions, and SOC are scarce. Standardized studies across Europe’s diverse pedoclimatic regions would be valuable for assessing the benefits of OM inputs in agricultural soils. This would enable the identification of region-specific solutions that enhance soil health, prevent degradation, and support sustainable and productive farming systems.

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.

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.

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.

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.

Effective antimicrobial and biofilm control strategies require an understanding of the differential effects of antimicrobial agents on the viability and culturability of microbial cells. A viable but non-culturable (VBNC) state, a survival strategy of non-spore-forming bacteria in response to adverse conditions, poses a significant challenge for public health and food safety. In the present study, we investigated the antimicrobial and antibiofilm effects of nisin and gallium (III) nitrate hydrate against the Gram-positive strain Lactiplantibacillus plantarum subsp. plantarum DSM 20174 and the Gram-negative strain Pseudomonas fluorescens ATCC 13525, respectively. Both strains were chosen as model systems for their relevance to food and clinical settings. Culture-based methods and flow cytometry (FCM) were used to evaluate the culturability and viability of both planktonic and sessile cells, providing insights into their physiological response to antimicrobial treatment-induced stress at different concentrations (100, 250, 350, and 500 ppm). The findings highlight the strain-specific action of nisin on L. plantarum and the promising antibiofilm effects of Ga (III) against P. fluorescens. This study underscores the promising potential of FCM as a powerful tool for high-throughput analyses of antimicrobial efficacy, providing valuable insights into developing targeted biofilm control strategies for food safety and clinical applications.

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.

Mixed tree plantations containing nitrogen (N₂)-fixing species have the potential to enhance C sequestration, soil biodiversity and forest productivity. Here, we investigated the impact of Acacia mangium and Eucalyptus urophilla x E. grandis mixed plantations in the Congolese coastal plains on soil mycobiota community structure and diversity by ITS metabarcoding sequencing and bioinformatic analysis. Higher Faith’s phylogenetic diversity and Evenness’ was found in Eucalyptus monoculture relative to stands containing Acacia. Differences in beta diversity were found among Eucalyptus and Acacia monoculture, and mixed-species stands highlight the effects of plant species on fungal community structure. Ascomycota, Basidiomycota and Rozellomycota phyla were predominant in all stands, with both Dikarya (Ascomycota and Basidiomycota) accounting for more than 70% in all stands. Correlation analysis revealed that sulfur (S) was the most correlated soil attribute with the three predominant phyla but also with Mucoromycota and Calcarisporiellomycota phyla, although mostly negatively correlated (4 out of 5). Phosphorus was mostly positively correlated to soil attributes (3 out of 4) and nitrogen was correlated twice, positively and negatively. Distance-based redundancy analysis revealed a positive correlation of nitrogen (p-value = 0.0019, contribution = 22%) and phosphorus (p-value = 0.0017, contribution = 19%) with soil mycobiota. A high prevalence of generalists (28% to 38%) than specialists (9% to 24%) were found among the different sites. In stands containing Acacia (pure and mixed species) the soil mycobiota harbor the prevalence of generalist strategies with the potential to withstand environmental stresses and utilize a higher number of resources against specialists in Eucalyptus stands. Stronger positive correlation between soil attributes and main fungal taxa, higher generalists’ strategies and lower Faith’s phylogenetic diversity and Evenness were reported in stands containing Acacia. This highlights the potential of mixed-species in preserving community stability following environmental disturbances and increasing the number of resources confirming their important ecological role in boosting the resilience of the forest ecosystems to climate and land-use (plant species as shown by PCA analysis) changes.