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.

Mobile genetic elements (MGEs), including plasmids, transposons, integrative and conjugative elements, and phage-derived sequences, are central drivers of bacterial evolution in agroecosystems. By enabling horizontal gene transfer, MGEs allow soil- and plant-associated bacteria to rapidly acquire complex functional traits, facilitating adaptation to fluctuating environmental conditions and different agricultural management practices. In agricultural soils, MGEs underpin key microbial functions such as nutrient acquisition and cycling, stress tolerance, rhizosphere competence, and interactions with plant hosts, thereby influencing soil fertility and crop performance. Selective pressures in agroecosystems extend beyond antimicrobial exposure and include fertilizers, pesticides, plant defense compounds, recurrent biotic and abiotic stress, as well as high-yielding crop varieties. These pressures generate co-selection dynamics that shape mobilome composition and activity, linking traits such as resistance, pathogenicity, and biocontrol to broader ecological functions relevant to plant health. Rather than acting as exceptional genetic entities, MGEs form a dynamic and environmentally responsive genetic network that enables rapid ecological tuning while preserving core genome stability. Comparative genomics has revealed that major lifestyle transitions in agroecosystem-associated bacteria, from free-living to commensal, mutualistic, or pathogenic states, are frequently mediated by the gain and loss of genomic islands and other MGEs. This review synthesizes the latest research on the ecological functions and evolutionary dynamics of MGEs in agroecosystems and explores how mobilome-informed approaches can support microbial-based strategies for sustainable agriculture.

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.

Beneficial microbial consortia provide an eco-friendly alternative to conventional inorganic fertilizers and can serve as a complementary management tool for enhancing soil fertility and crop productivity. This study aimed to assess the impact of microbial consortia application on the indigenous maize rhizosphere microbiome under different fertilization regimes in organically managed fields in Germany. Three experimental microbial consortia (MC_B, MC_C, MC_C_AMF) and one commercial product (Micosat F) were tested in combination with three fertilization levels (unfertilized, 110 kg nitrogen ha- 1, and 200 kg nitrogen ha- 1) in a split plot design. The diversity, composition and functional potential of the maize rhizosphere microbiome were analyzed at different maize growth stages. Fertilization levels exerted a stronger influence than microbial consortia, significantly shaping community composition and functional traits of the indigenous soil microbiome. Increasing fertilization intensity altered the abundance of specific plant growth-promoting (PGP)-determinants, either stimulating or suppressing potential PGP bacteria. In contrast, microbial consortia application did not impact PGP-associated abundance profiles. Overall, the results indicate that multifunctional microbial consortia can act as effective biofertilizers in sustainable maize cultivation without compromising resident microbiome diversity, thereby reducing long-term ecological risks on natural biodiversity.

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.

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.

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.

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.

Soil health is crucial for global food production in the context of an ever-growing global population. Microbiomes, a combination of microorganisms and their activities, play a pivotal role by biodegrading contaminants, maintaining soil structure, controlling nutrients’ cycles, and regulating the plant responses to biotic and abiotic stresses. Microbiome-based solutions along the soil-plant continuum, and their scaling up from laboratory experiments to field applications, hold promise for enhancing agricultural sustainability by harnessing the power of microbial consortia. Synthetic microbial communities, i.e., selected microbial consortia, are designed to perform specific functions. In contrast, natural communities leverage indigenous microbial populations that are adapted to local soil conditions, promoting ecosystem resilience, and reducing reliance on external inputs. The identification of microbial indicators requires a holistic approach. It is fundamental for current understanding the soil health status and for providing a comprehensive assessment of sustainable land management practices and conservation efforts. Recent advancements in molecular technologies, such as high-throughput sequencing, revealed the incredible diversity of soil microbiomes. On one hand, metagenomic sequencing allows the characterization of the entire genetic composition of soil microbiomes, and the examination of their functional potential and ecological roles; on the other hand, culturomics-based approaches and metabolic fingerprinting offer complementary information by providing snapshots of microbial diversity and metabolic activities both in and ex-situ. Long-term storage and cryopreservation of mixed culture and whole microbiome are crucial to maintain the originality of the sample in microbiome biobanking and for the development and application of microbiome-based innovation. This review aims to elucidate the available approaches to characterize diversity, function, and resilience of soil microbial communities and to develop microbiome-based solutions that can pave the way for harnessing nature’s untapped resources to cultivate crops in healthy soils, to enhance plant resilience to abiotic and biotic stresses, and to shape thriving ecosystems unlocking the potential of soil microbiomes is key to sustainable agriculture. Improving management practices by incorporating beneficial microbial consortia, and promoting resilience to climate change by facilitating adaptive strategies with respect to environmental conditions are the global challenges of the future to address the issues of climate change, land degradation and food security.

Flow cytometry (FCM) provides unique information on bacterial viability and physiology, allowing a real-time early warning antimicrobial and antibiofilm monitoring system for preventing the spread risk of foodborne disease. The present work used a combined culture-based and FCM approach to assess the in vitro efficacy of essential oils (EOs) from condiment plants commonly used in Mediterranean Europe (i.e., thyme EO, oregano EO, basil EO, and lemon EO) against planktonic and sessile cells of food-pathogenic Listeria monocytogenes 56 LY, and contaminant and alterative species Escherichia coli ATCC 25922 and Pseudomonas fluorescens ATCC 13525. Evaluation of the bacterial response to the increasing concentrations of natural compounds posed FCM as a crucial technique for the quantification of the live/dead, and viable but non-culturable (VBNC) cells when antimicrobial agents exert no real bactericidal action. Furthermore, the FCM results displayed higher numbers of viable bacteria expressed as Active Fluorescent Units (AFUs) with a greater level of repeatability compared with outcomes of the plate-count method. Overall, accurate counting of viable microbial cells is a critically important parameter in food microbiology, and flow cytometry provides an innovative approach with high-throughput potential for applications in the food industry as “flow microbiology”.

The prevalence of biofilm-associated microorganisms and the increasing use of ready-to-eat fresh products represent the current duality the food industry must address. Innovative and eco-friendly antibiofilm solutions and appropriate microbiological food control systems are urgently needed to improve food quality and safety. This study aimed to investigate the in vitro combined efficacy of carvacrol with a pre-formed biofilm monolayer of the probiotic Lactiplantibacillus plantarum DSM 20174. The antimicrobial activity of carvacrol against both planktonic and sessile cells of foodborne pathogens and spoilage microorganisms, alone or in the presence of the pre-formed biofilm of L. plantarum, was investigated by culture-based methods along with flow cytometry (FCM) to monitor cells' cultivability and viability. The synergistic action of carvacrol and the pre-formed biofilm of L. plantarum was evaluated in the 96-well plates. The results showed that L. plantarum pre-formed biofilm monolayer enhanced the antimicrobial effect of carvacrol determining a bactericidal action while the treatment alone induced the viable but not culturable (VBNC) cell state only. Furthermore, the great efficacy of the combined treatment allowed the application of a lower concentration of carvacrol (100 ppm) to achieve significant damage in cell viability. In conclusion, the incorporation of carvacrol into the L. plantarum pre-formed biofilm represents a promising alternative for an antimicrobial functionalized ready-to-eat packaging.

The strengthening effect of a mild temperature treatment on the antimicrobial efficacy of essential oils has been widely reported, often leading to an underestimation or a misinterpretation of the product’s microbial status. In the present study, both a traditional culture-based method and Flow Cytometry (FCM) were applied to monitor the individual or combined effect of Origanum vulgare essential oil (OEO) and mild heat treatment on the culturability and viability of Escherichia coli in a conventional culture medium and in a fruit juice challenge test. The results obtained in the culture medium showed bacterial inactivation with an increasing treatment temperature (55 °C, 60 °C, 65 °C), highlighting an overestimation of the dead population using the culture-based method; in fact, when the FCM method was applied, the prevalence of injured bacterial cells in a viable but non-culturable (VBNC) state was observed. When commercial fruit juice with a pH of 3.8 and buffered at pH 7.0 was inoculated with E. coli ATCC 25922, a bactericidal action of OEO and a higher efficiency of the mild heat at 65 °C for 5′ combined with OEO were found. Overall, the combination of mild heat and OEO treatment represents a promising antimicrobial alternative to improve the safety of fruit juice.

Objectives and study Ulcerative colitis (UC) and Crohn's disease (CD) are complex chronic disorders commonly known as inflammatory bowel disease (IBD).It is known that chronic or unresolved inflammation can result in an activated epithelial mesenchymal transition (EMT) that may lead to tissue destruction and fibrosis, both representing a common and severe complication in IBD patients.Specific molecular processes are engaged to initiate EMT, including the activation of several transcription factors.Recently, the zinc finger transcription factor ZNF281 (also known as ZBP-99 or ZNP-99) has been involved in EMT and cancer promotion in colorectal cancer (CRC).The aims of the present study are to investigate: 1) in vitro and ex vivo the expression levels of ZNF281 in intestinal inflammation and 2) in vitro the role of ZNF281 in EMT induced by inflammation.Methods ZNF281 protein expression was analyzed by western blot in mucosal biopsies from inflamed and uninflamed colon of pediatric IBD patients (29 CD, 25 UC) and 16 healthy controls as well as in HT29 cells exposed to cytomix (TNF-alpha + INF-gamma) for 24 and 48 hours.ZNF281 mRNA was also analyzed in HT29 cells exposed to cytomix, by real-time PCR.Furthermore, ZNF281 was silenced and EMT (Snail, Timp1, ColA31, Slug) as well as inflammatory cytokine (IL8, IL17, IL23, IL1beta) genes were evaluated by real-time PCR.Results ZNF281 protein levels were significantly increased in inflamed colon of CD and UC patients as compared to uninflamed tissue of patients and controls (p<0.001).Similarly, ZNF281 protein and mRNA levels were significantly increased in HT29 cells exposed to cytomix compared to unexposed (p<0,05).Moreover, mRNA levels of Snail, Timp1, ColA31, Slug, IL8, IL17, IL23 and IL1beta were strongly decreased in ZNF281-silenced cells exposed to cytomix as compared to controls (cells treated with cytomix and scramble siRNA).Conclusions We show for the first time that zinc finger transcription factor ZNF281, previously known for its role in EMT, is importantly increased in gut inflammation and its deletion causes a fall in expression levels of EMT and inflammatory genes in inflamed cells.We suggest that ZNF281 may actively contribute to fibrosis development during IBD.

Current research into original therapies to treat intestinal inflammation is focusing on no-drug therapies. KLD is a mixture of krill oil (KO), probiotic Lactobacillus reuteri (LR), and vitamin D (VitD3). The aim of this study was to assess in vitro and in vivo the potential cooperative effects of KLD in reducing gut inflammation. Colorectal adenocarcinoma cell lines, CACO2 and HT29, and C57BL/6 mice were used for in vitro and in vivo analyses, respectively. Cells were exposed to cytomix (interferon gamma + tumour necrosis factor alpha (TNF-α)) to induce inflammation or co-exposed to cytomix and KO, LR and VitD3 alone or to cytomix and KLD. Animals were treated for 7 days with dextran sodium sulphate (DSS) to induce colitis or with DSS and KLD. In vitro assays: F-actin expression was analysed by immunofluorescence; scratch test and trans-epithelial electric resistance test were performed to measure wound healing; adhesion/invasion assays of adhesive and invasive Escherichia coli (AIEC) bacteria were made; mRNA expression of TNF-α, interleukin (IL)-8 and vitamin D receptor (VDR) was detected by quantitative PCR. In vivo assays: body weight, clinical score, histological score and large intestine weight and length were estimated; mRNA expression of TNF-α, IL-1β, IL-6, IL-10 by quantitative PCR; VDR expression was detected by quantitative PCR and immunohistochemistry. In vitro: KLD restores epithelial cell-cell adhesion and mucosal healing during inflammation, while decreases the adhesiveness and invasiveness of AIEC bacteria and TNF-α and IL-8 mRNA expression and increases VDR expression. In vivo: KLD significantly improves body weight, clinical score, histological score and large intestine length of mice with DSS-induced colitis and reduces TNF-α, IL-1β and IL-6 mRNA levels, while increases IL-10 mRNA and VDR levels. KLD has significant effects on the intestinal mucosa, strongly decreasing inflammation, increasing epithelial restitution and reducing pathogenicity of harmful commensal bacteria.