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A growing population coupled with a higher demand for food is putting pressure on agriculture. The use of synthetic pesticides and chemical fertilizers allowed us to boost agricultural productions, but at a great environmental cost. Exploitation of beneficial microorganism (BM)-plant interactions has been proposed as an eco-friendly solution to improve plant resistance to stresses and to increase productivity sustainably. We provide an overview of scientific evidence that this positive interaction is often mediated also by the release of microbial Volatile Organic Compounds (mVOCs). A few mVOCs are reported to have a double, not mutually exclusive, positive effect on plants, as plant growth promoters, and/or inducers of resistance against biotic and abiotic stress factors. They may also alter plant VOCs indirectly improving plant performances. However, mechanisms and functions of mVOCs need deeper investigation. By understanding mVOC modes of action on plants, further tools for sustainably improving plant productivity in agro-ecosystems may become soon available.

Plant cells secrete membrane-enclosed micrometer- and nanometer-sized vesicles that, similarly to the extracellular vesicles (EVs) released by mammalian or bacterial cells, carry a complex molecular cargo of proteins, nucleic acids, lipids, and primary and secondary metabolites. While it is technically complicated to isolate EVs from whole plants or their tissues, in vitro plant cell cultures provide excellent model systems for their study. Plant EVs have been isolated from the conditioned culture media of plant cell, pollen, hairy root, and protoplast cultures, and recent studies have gathered important structural and biological data that provide a framework to decipher their physiological roles and unveil previously unacknowledged links to their diverse biological functions. The primary function of plant EVs seems to be in the secretion that underlies cell growth and morphogenesis, cell wall composition, and cell–cell communication processes. Besides their physiological functions, plant EVs may participate in defence mechanisms against different plant pathogens, including fungi, viruses, and bacteria. Whereas edible and medicinal-plant-derived nanovesicles isolated from homogenised plant materials ex vivo are widely studied and exploited, today, plant EV research is still in its infancy. This review, for the first time, highlights the different in vitro sources that have been used to isolate plant EVs, together with the structural and biological studies that investigate the molecular cargo, and pinpoints the possible role of plant EVs as mediators in plant–pathogen interactions, which may contribute to opening up new scenarios for agricultural applications, biotechnology, and innovative strategies for plant disease management.

Background Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results. Results The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD -type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene. Conclusions The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea . The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control.

Background Drought is a major abiotic stress that significantly limits potato productivity and tuber quality. Microbial biostimulants have emerged as promising tools to improve crop resilience and promote sustainable agriculture. This study aimed to investigate the transcriptomic response to severe drought stress in three potato cultivars (Camelia, Cicero, and Agata) characterized by differing polyphenol content. In addition, the potential mitigating effects of a microorganism-based biostimulant mixture composed by two Trichoderma species, were evaluated. Results Severe drought stress led to a significant reduction in tuber yield in Camelia and Agata, whereas Cicero exhibited greater tolerance. Application of the microbial biostimulant slightly alleviated yield loss in Camelia but was associated with an increased proportion of non-commercial tubers. Polyphenol content varied according to genotype and treatment, Cicero displayed elevated polyphenol levels in the skin under drought, while Camelia showed increased levels in both skin and pulp when drought was combined with biostimulant application. Transcriptomic analysis revealed genotype-specific drought response strategies. Camelia exhibited enhanced proteostasis and osmoprotection via anthocyanin accumulation, while Cicero maintained photosynthetic activity, redox homeostasis, and genome stability. Trichoderma -based biostimulant treatment modulated these responses by enhancing endoplasmic reticulum protein quality control in Camelia, and promoting photosynthesis and sugar metabolism in Cicero. Conclusions Potato responses to drought are highly genotype-dependent and involve complex trade-offs among growth, stress defense, and metabolic reprogramming. Microbial biostimulants offer a promising approach to enhance drought resilience and tuber nutraceutical quality. However, their efficacy is genotype-specific and requires targeted application strategies for optimal results.

Soil is a depletable and non-renewable resource essential for food production, crop growth, and supporting ecosystem services, such as the retaining and cycling of various elements, including water. Therefore characterization and preservation of soil biological health is a key point for the development of sustainable agriculture. We conducted a comprehensive review of the use of Artificial Intelligence (AI) techniques to develop forecasting models based on soil microbiota data able to monitor and predict soil health. We also investigated the potentiality of AI-based Decision Support Systems (DSSs) for improving the use of microorganisms to enhance soil health and fertility. While available studies are limited, potential applications of AI seem relevant to develop predictive models for soil fertility, based on its biological properties and activities, and implement sustainable precision agriculture, safeguarding ecosystems, bolstering soil resilience, and ensuring the production of high-quality food.Article HighlightsMaintaining healthy soil is crucial for sustainable agriculture to ensure long-term food production and environmental protection.Soil microbiota plays a main role in preserving soil health, therefore a correct analysis of soil microorganisms will help farmers understand and improve soil quality.Although research is limited, integrating AI technologies to monitor soil health holds great promise for sustainable precision agriculture.

Fungi emit a broad spectrum of volatile organic compounds (VOCs), sometimes producing species-specific volatile profiles. Volatilomes have received over the last decade increasing attention in ecological, environmental and agricultural studies due to their potential to be used in the biocontrol of plant pathogens and pests and as plant growth-promoting factors. In the present study, we characterised and compared the volatilomes from four different Trichoderma species: T. asperellum B6; T. atroviride P1; T. afroharzianum T22; and T. longibrachiatum MK1. VOCs were collected from each strain grown both on PDA and in soil and analysed using proton transfer reaction quadrupole interface time-of-flight mass spectrometry (PTR-Qi-TOF-MS). Analysis of the detected volatiles highlighted a clear separation of the volatilomes of all the four species grown on PDA whereas the volatilomes of the soil-grown fungi could be only partially separated. Moreover, a limited number of species-specific peaks were found and putatively identified. In particular, each of the four Trichoderma species over-emitted somevolatiles involved in resistance induction, promotion of plant seed germination and seedling development and antimicrobial activity, as 2-pentyl-furan, 6PP, acetophenone and p-cymene by T. asperellum B6, T. atroviride P1, T. afroharzianum T22 and T. longibrachiatum MK1, respectively. Their potential role in interspecific interactions from the perspective of biological control is briefly discussed.

Extracellular Vesicles (EVs) play pivotal roles in cell-to-cell and inter-kingdom communication. Despite their relevant biological implications, the existence and role of plant EVs released into the environment has been unexplored. Herein, we purified round-shaped small vesicles (EVs) by differential ultracentrifugation of a sampling solution containing root exudates of hydroponically grown tomato plants. Biophysical analyses, by means of dynamic light scattering, microfluidic resistive pulse sensing and scanning electron microscopy, showed that the size of root-released EVs range in the nanometric scale (50–100 nm). Shot-gun proteomics of tomato EVs identified 179 unique proteins, several of which are known to be involved in plant-microbe interactions. In addition, the application of root-released EVs induced a significant inhibition of spore germination and of germination tube development of the plant pathogens Fusarium oxysporum, Botrytis cinerea and Alternaria alternata. Interestingly, these EVs contain several proteins involved in plant defense, suggesting that they could be new components of the plant innate immune system.

Early and accurate detection of lemon disease is necessary for effective citrus crop management. Traditional approaches often lack refined diagnosis, necessitating more powerful solutions. The article introduces adaptive PSO-LemonNetX, a novel framework integrating a novel deep learning model, adaptive Particle Swarm Optimization (PSO)-based feature selection, and explainable AI (XAI) using LIME. The approach improves the accuracy of classification while also enhancing the explainability of the model. Our end-to-end model obtained 97.01% testing and 98.55% validation accuracy. Performance was enhanced further with adaptive PSO and conventional classifiers—100% validation accuracy using Naive Bayes and 98.8% testing accuracy using Naive Bayes and an SVM. The suggested PSO-based feature selection performed better than ReliefF, Kruskal–Wallis, and Chi-squared approaches. Due to its lightweight design and good performance, this approach can be adapted for edge devices in IoT-enabled smart farms, contributing to sustainable and automated disease detection systems. These results show the potential of integrating deep learning, PSO, grid search, and XAI into smart agriculture workflows for enhancing agricultural disease detection and decision-making.

Background ATP-binding cassette proteins have been recognized as playing a crucial role in the regulation of growth and resistance processes in all kingdoms of life. They have been deeply studied in vertebrates because of their role in drug resistance, but much less is known about ABC superfamily functions in plants. Results Recently released plant genome sequences allowed us to identify 803 ABC transporters in four vascular plants ( Oryza. sativa, Solanum lycopersicum, Solanum tuberosum and Vitis vinifera ) and 76 transporters in the green alga Volvox carteri , by comparing them with those reannotated in Arabidopsis thaliana and the yeast Saccharomyces cerevisiae . Retrieved proteins have been phylogenetically analysed to infer orthologous relationships. Most orthologous relationships in the A, D, E and F subfamilies were found, and interesting expansions within the ABCG subfamily were observed and discussed. A high level of purifying selection is acting in the five ABC subfamilies A, B, C, D and E. However, evolutionary rates of recent duplicate genes could influence vascular plant genome diversification. The transcription profiles of ABC genes within tomato organs revealed a broad functional role for some transporters and a more specific activity for others, suggesting the presence of key ABC regulators in tomato. Conclusions The findings achieved in this work could contribute to address several biological questions concerning the evolution of the relationship between genomes of different species. Plant ABC protein inventories obtained could be a valuable tool both for basic and applied studies. Indeed, interpolation of the putative role of gene functions can accelerate the discovering of new ABC superfamily members.

Plants are central to complex networks of multitrophic interactions. Increasing evidence suggests that beneficial microorganisms (BMs) may be used as plant biostimulants and pest biocontrol agents. We investigated whether tomato ( Solanum lycopersicum ) plants are thoroughly colonized by the endophytic and entomopathogenic fungus Beauveria bassiana , and how such colonization affects physiological parameters and the phenotype of plants grown under unstressed conditions or exposed to the pathogenic fungus Botrytis cinerea . As a positive control, a strain of the well-known biocontrol agent and growth inducer Trichoderma afroharzianum was used. As multitrophic interactions are often driven by (or have consequences on) volatile organic compounds (VOCs) released by plants constitutively or after induction by abiotic or biotic stresses, VOC emissions were also studied. Both B. bassiana and T. afroharzianum induced a significant but transient (one to two-day-long) reduction of stomatal conductance, which may indicate rapid activation of defensive (rejection) responses, but also limited photosynthesis. At later stages, our results demonstrated a successful and complete plant colonization by B. bassiana , which induced higher photosynthesis and lower respiration rates, improved growth of roots, stems, leaves, earlier flowering, higher number of fruits and yield in tomato plants. Beauveria bassiana also helped tomato plants fight B. cinerea , whose symptoms in leaves were almost entirely relieved with respect to control plants. Less VOCs were emitted when plants were colonized by B. bassiana or infected by B. cinerea , alone or in combination, suggesting no activation of VOC-dependent defensive mechanisms in response to both fungi.