Recycling drainage solutions (DS) in closed-loop soilless culture systems reduces fertilizer and water consumption in greenhouse production while preventing environmental pollution caused by nitrogen and phosphorus emissions. However, recycling DS increases the risk of spreading root- infective pathogens through the irrigation system, making disinfection necessary prior to reuse. In this study, two oxygen-containing oxidizing agents, hydrogen peroxide (H₂O₂) and chlorine dioxide (ClO₂) were evaluated as nutrient solution (NS) disinfectants against Verticillium dahliae. The experiment was conducted in a closed-loop soilless pepper crop grown in a greenhouse during the spring–summer period. All treatments received nutrient solutions (NS) of identical composition. Three treatments were applied with three replicates each: (i) non-treated NS (control), (ii) NS supplemented with 2 ppm ClO₂, and (iii) NS supplemented with 2 ppm H₂O₂. Six-week-old pepper plants were inoculated with V. dahlia strain 402V. Both disinfectants significantly improved pepper fruit yield and quality compared with the non-disinfected control. ClO₂ resulted in the highest number of marketable fruits and total fruit yield, while both ClO₂ and H₂O₂ reduced unmarketable fruits and increased average fruit weight. Pathogen biomass quantification by qPCR demonstrated that ClO₂ significantly reduced pathogen presence in the hydroponic system, achieving approximately 63% lower biomass compared with the untreated control. In contrast, H₂O₂ showed limited efficacy and pathogen levels comparable to the control treatment. Application of H₂O₂ and ClO₂ significantly enhanced mineral accumulation in pepper tissues, increasing macronutrient (P, K, Mg, Ca) and micronutrient (Fe, Zn, Cu) concentrations compared with the control treatment.

Viral diseases pose a major threat to tomato cultivation, mainly due to the lack of effective antiviral control methods. Plant growth-promoting microorganisms (PGPMs) represent a promising and sustainable strategy for virus disease management, as, in addition to plant growth, they can promote resistance to pathogens. In this study, we examined the antiviral potential of selected PGPMs against three economically important and genetically distinct tomato viruses, tomato spotted wilt virus (TSWV, Orthotospovirus tomatomaculae), cucumber mosaic virus (CMV, Cucumovirus CMV), and tomato brown rugose fruit virus (ToBRFV, Tobamovirus fructirugosum) under controlled greenhouse conditions. The efficacy of each PGPM was assessed by monitoring disease development via visual scoring and DAS-ELISA. Our results indicate a significant TSWV symptom attenuation upon the application of Paraburkholderia eburnea EP3 and the yeast isolate SRL248, though, without a respective reduction in virus accumulation. However, no antiviral effect was observed by any PGPM tested against CMV or ToBRFV. A targeted gene expression analysis revealed a PGPM-specific induction of salicylic acid-dependent defense and RNA silencing markers, indicating priming of host immune responses. Overall, this work increases our knowledge on the antiviral potential of PGPMs showing a strain- and virus-specific effect primarily associated with enhanced symptom tolerance.

The extensive use of chemical fungicides for the management of Botrytis cinerea and Pseudomonas syringae pv. tomato (Pst) in tomato crops has contributed to the emergence of resistant pathogen populations, potentially limiting the long-term effectiveness of conventional control strategies. Consequently, alternative and sustainable disease management approaches are being actively explored. In this study, we evaluated the efficacy of the biological control agents (BCAs) Bacillus velezensis K165 and Rhodotorula glutinis Y44 against B. cinerea and Pst in tomato plants. The BCAs were applied individually and in combination as root and foliar treatments, respectively. Application of K165 and Y44 reduced disease severity caused by B. cinerea compared with untreated controls, with levels of protection comparable to those achieved with a commercial fungicide (active ingredients: cyprodinil and fludioxonil). Similarly, treatments with K165 and Y44 were associated with reductions in disease severity and bacterial populations of Pst on tomato leaves relative to the untreated control, with effects that were comparable to or, in certain cases, lower than those observed with a copper-based fungicide. Notably, the combined application of K165 as a root treatment and Y44 as a foliar spray resulted in more consistent and, in several cases, enhanced disease suppression compared with the individual BCA applications against both pathogens. Molecular analyses further indicated that both BCAs were associated with the induction of the defense-related genes PR1 and PIN2 following pathogen challenge, suggesting activation of plant defense responses.

Botrytis cinerea, the causal agent of grey mold, poses a significant threat to tomato production and other crops globally. With rising resistance to chemical fungicides, there is increasing interest in sustainable alternatives such as biological control agents (BCAs). In this study, we evaluated the biocontrol potential of Paraburkholderia oxyphila strain EP4, isolated from the rhizosphere of eggplants, against B. cinerea in tomato and cucumber. EP4 significantly reduced disease severity in both hosts, particularly in cucumber where foliar application decreased lesion size by 93

Epigenetics refers to dynamic chemical modifications to the genome that can perpetuate gene activity without changes in the DNA sequence. Epigenetic mechanisms play important roles in growth and development. They may also drive plant adaptation to adverse environmental conditions by buffering environmental variation. Grapevine is an important perennial fruit crop cultivated worldwide, but mostly in temperate zones with hot and dry summers. The decrease in rainfall and the rise in temperature due to climate change, along with the expansion of pests and diseases, constitute serious threats to the sustainability of winegrowing. Ongoing research shows that epigenetic modifications are key regulators of important grapevine developmental processes, including berry growth and ripening. Variations in epigenetic modifications driven by genotype–environment interplay may also lead to novel phenotypes in response to environmental cues, a phenomenon called phenotypic plasticity. Here, we summarize the recent advances in the emerging field of grapevine epigenetics. We primarily highlight the impact of epigenetics to grapevine stress responses and acquisition of stress tolerance. We further discuss how epigenetics may affect winegrowing and also shape the quality of wine.

Botrytis cinerea poses a recurring threat to viticulture, causing significant yield losses each year. The study explored the biocontrol capabilities of commercially used winemaking yeasts as a strategy to manage B. cinerea in grape berries. The winemaking yeast strains-Saccharomyces cerevisiae ES181, Saccharomyces pastorianus KBG6, S. cerevisiae BCS103, Lachancea thermotolerans Omega, and Torulaspora delbrueckii TD291-reduced B. cinerea growth and conidiation in vitro. Furthermore, they demonstrated a decreased disease severity and number of conidia in grape berries. Among these strains, S. cerevisiae BCS103 was the most effective, inducing the expression of the defense-related gene PR4 in berries. Its diffusible compounds and volatile organic compounds also reduced the expression of BcLTF2, a positive regulator of B. cinerea conidiogenesis. The examined winemaking yeast strains, especially S. cerevisiae BCS103, demonstrated effective inhibition of B. cinerea in vitro and in grape berries, influencing key defense genes and reducing BcLTF2 expression, offering potential solutions for disease management in viticulture. The study underscores the promise of commercially available winemaking yeast strains as eco-friendly tools against B. cinerea in viticulture. Leveraging their safety and existing use in winemaking offers a potential avenue for sustainable disease management.

Aims This study aimed to assess the impact of rocket (Eruca sativa) extract on Verticillium wilt in eggplants, explore rhizospheric microorganisms for disease biocontrol, and evaluate selected strains' induced systemic resistance (ISR) potential while characterizing their genomic and biosynthetic profiles.Methods and results Rocket extract application led to a significant reduction in Verticillium wilt symptoms in eggplants compared to controls. Isolated microorganisms from treated soil, including Paraburkholderia oxyphila EP1, Pseudomonas citronellolis EP2, Paraburkholderia eburnea EP3, and P. oxyphila EP4 and EP5, displayed efficacy against Verticillium dahliae, decreasing disease severity and incidence in planta. Notably, strains EP3 and EP4 triggered ISR in eggplants against V. dahliae. Genomic analysis unveiled shared biosynthetic gene clusters, such as ranthipeptide and non-ribosomal peptide synthetase-metallophore types, among the isolated strains. Additionally, metabolomic profiling of EP2 revealed the production of metabolites associated with amino acid metabolism, putative antibiotics, and phytohormones.Conclusions The application of rocket extract resulted in a significant reduction in Verticillium wilt symptoms in eggplants, while the isolated microorganisms displayed efficacy against V. dahliae, inducing systemic resistance and revealing shared biosynthetic gene clusters, with metabolomic profiling highlighting potential disease-suppressing metabolites.

Aims This study explores the biocontrol potential of Pseudomonas putida Z13 against Botrytis cinerea in tomato plants, addressing challenges posed by the pathogen's fungicide resistance. The aims of the study were to investigate the in vitro and in silico biocontrol traits of Z13, identify its plant-colonizing efficacy, evaluate the efficacy of different application strategies against B. cinerea in planta, and assess the capacity of Z13 to trigger induced systemic resistance (ISR) in plants.Methods and results The in vitro experiments revealed that Z13 inhibits the growth of B. cinerea, produces siderophores, and exhibits swimming and swarming activity. Additionally, the Z13 genome harbors genes that encode compounds triggering ISR, such as pyoverdine and pyrroloquinoline quinone. The in planta experiments demonstrated Z13's efficacy in effectively colonizing the rhizosphere and leaves of tomato plants. Therefore, three application strategies of Z13 were evaluated against B. cinerea: root drenching, foliar spray, and the combination of root drenching and foliar spray. It was demonstrated that the most effective treatment of Z13 against B. cinerea was the combination of root drenching and foliar spray. Transcriptomic analysis showed that Z13 upregulates the expression of the plant defense-related genes PR1 and PIN2 upon B. cinerea inoculation.Conclusion The results of the study demonstrated that Z13 possesses significant biocontrol traits, such as the production of siderophores, resulting in significant plant protection against B. cinerea when applied as a single treatment to the rhizosphere or in combination with leaf spraying. Additionally, it was shown that Z13 root colonization primes plant defenses against the pathogen.

Phytopathogenic strains of Fusarium oxysporum cause destructive vascular wilt disease limiting the yield of many economically important crops. Because of the pathogen's vascular lifestyle, the use of resistant cultivars is an effective, environmentally friendly and sustainable strategy for disease management. Our study showed that the disruption of β-amylase 3 gene (BAM3) led to increased resistance to F. oxysporum f. sp. raphani, since the Arabidopsis thaliana bam3 mutant exhibited significantly reduced susceptibility to the pathogen. Additionally, cell wall pectin modification by methylesterification is important for bam3 defense responses against F. oxysporum.

The biology and biotechnology of bacteriophages have been extensively studied in recent years to explore new and environmentally friendly methods of controlling phytopathogenic bacteria. Pseudomonas syringae pv. tomato (Pst) is responsible for bacterial speck disease in tomato plants, leading to decreased yield. Disease management strategies rely on the use of copper-based pesticides. The biological control of Pst with the use of bacteriophages could be an alternative environmentally friendly approach to diminish the detrimental effects of Pst in tomato cultivations. The lytic efficacy of bacteriophages can be used in biocontrol-based disease management strategies. Here, we report the isolation and complete characterization of a bacteriophage, named Medea1, which was also tested in planta against Pst, under greenhouse conditions. The application of Medea1 as a root drenching inoculum or foliar spraying reduced 2.5- and fourfold on average, respectively, Pst symptoms in tomato plants, compared to a control group. In addition, it was observed that defense-related genes PR1b and Pin2 were upregulated in the phage-treated plants. Our research explores a new genus of Pseudomonas phages and explores its biocontrol potential against Pst, by utilizing its lytic nature and ability to trigger the immune response of plants. KEY POINTS: • Medea1 is a newly reported bacteriophage against Pseudomonas syringae pv. tomato having genomic similarities with the phiPSA1 bacteriophage • Two application strategies were reported, one by root drenching the plants with a phage-based solution and one by foliar spraying, showing up to 60- and 6-fold reduction of Pst population and disease severity in some cases, respectively, compared to control • Bacteriophage Medea1 induced the expression of the plant defense-related genes Pin2 and PR1b.

Several studies have described the potential use of volatile organic compounds (VOCs) emitted by soil microorganisms, specifically of the genus Bacillus, as a sustainable solution for disease management in plants. The Bacillus species have been extensively studied as biocontrol agents (BCAs) due to their ability to inhibit pathogens, trigger induced systemic resistance (ISR) in plants, and enhance plant growth. The ability of the Bacillus species to produce long-lasting resting structures, such as endospores, makes them particularly appealing as BCAs. In recent years, there has been a growing body of research on the effects of Bacillus-emitted VOCs on plant pathogen growth and the triggering of ISR. This review aims to highlight recent advances in the understanding of the biological activities of Bacillus-emitted VOCs, identify new subjects for VOCs research, and stimulate interest in the academic and agri-business sectors for developing pre- and post-harvest application methods.

The wilt-inducing strains of Fusarium oxysporum are responsible for severe damage to many economically important plant species. The most cost-effective and environmentally safe method for the management of Fusarium wilt is the use of resistant cultivars when they are available. In the present study, the Arabidopsis genotype with disruptions in the β-amylase 3 (BAM3) gene, which encodes the major hydrolytic enzyme that degrades starch to maltose, had significantly lower susceptibility to Fusarium oxysporum f. sp. raphani (For) compared to wild-type (wt) plants. It showed the lowest disease severity and contained reduced quantities of fungal DNA in the plant vascular tissues when analyzed with real-time PCR. Through metabolomic analysis using gas chromatography (GC)–mass spectrometry (MS) and gene-expression analysis by reverse-transcription quantitative PCR (RT-qPCR), we observed that defense responses of Arabidopsis bam3 mutants are associated with starch-degradation enzymes, the corresponding modification of the carbohydrate balance, and alterations in sugar (glucose, sucrose, trehalose, and myo-inositol) and auxin metabolism.

The soil-borne fungus Verticillium dahliae is causing a devastating vascular disease in more than 200 species of dicotyledonous plants. The pathogen attacks susceptible plants through the roots, colonizes the plant vascular system, and causes the death of aerial tissues. In this study, we used Arabidopsis and eggplants to examine the plant protective and immunization effects of autoclaved V. dahliae spores against V. dahliae. We observed that the application of V. dahliae autoclaved spores in eggplants and Arabidopsis resulted in enhanced protection against V. dahliae, since the disease severity and pathogen colonization were lower in the plants treated with V. dahliae autoclaved spores when compared to controls. In addition, upregulation of the defense related genes PR1 and PDF1.2 in the Arabidopsis plants treated with the V. dahliae autoclaved spores was revealed. Furthermore, pathogenicity experiments in the Arabidopsis mutant cerk1, defective in chitin perception, revealed a loss of protection against V. dahliae in the cerk1 treated with the V. dahliae autoclaved spores. The participation of the chitin receptor CERK1 is evident in Arabidopsis immunization against V. dahliae using autoclaved spores of the pathogen.

Verticillium dahliae is one of the most devastating soilborne pathogens for horticulture production. The pathogen has a broad host range and currently there is no effective chemical disease management, therefore, novel sustainable integrated disease management strategies should be considered. In this respect, we questioned whether the soil application of common microbiological growth media can influence the plant-microbe interactions and, subsequently, offer protection against V. dahliae. Indeed, the addition of Nutrient Broth (NB) and Potato Dextrose (PD) in non-sterilized soil reduced Verticillium wilt symptoms in eggplants. The addition of NB in sterilized soil did not reduce the disease symptoms compared to controls, however the addition of PD enhanced plant protection against V. dahliae. Following the results of a split root bioassay in eggplants, the possibility that NB and PD triggered the plant defense mechanisms against V. dahliae was excluded, since NB and PD did not reduce wilt symptom. Therefore, PD may be used as an easy food source for V. dahliae, detouring the pathogen from the root system of plants, while NB may affect the soil microbiome by enhancing antagonism in rhizosphere, or antagonistic interaction between V. dahliae and rhizospheric microbiome. Subsequently, several bacterial strains were isolated from the NB-treated rhizosphere and examined for their biocontrol activity against V. dahliae. Among the examined strains, a Pseudomonas putida strain, Z13, significantly reduced Veticillium severity and incidence under greenhouse conditions.

Grapevine bunch rot, caused by Botrytis cinerea and Aspergillus carbonarius, causes important economic losses every year in grape production. In the present study, we examined the plant protective activity of the biological control agents, Paenibacillus alvei K165, Blastobotrys sp. FP12 and Arthrobacter sp. FP15 against B. cinerea and A. carbonarius on grapes. The in vitro experiments showed that strain K165 significantly reduced the growth of both fungi, while FP15 restricted the growth of A. carbonarius and FP12 was ineffective. Following the in vitro experiments, we conducted in planta experiments on grape berries. It was shown that K165, FP12 and FP15 reduced A. carbonarius rot severity by 81%, 57% and 37%, respectively, compared to the control, whereas, in the case of B. cinerea, the only protective treatment was that with K165, which reduced rot by 75%. The transcriptomic analysis of the genes encoding the pathogenesis-related proteins PR2, PR3, PR4 and PR5 indicates the activation of multiple defense responses involved in the biocontrol activity of the examined biocontrol agents.

The biocontrol agent Paenibacillus alvei K165 was previously shown to protect Arabidopsis thaliana plants against Verticillium dahliae. Here we show that K165 also confers inherited immune resistance to V. dahliae. By performing a histone acetyltransferases mutant screen, ChIP assays, and transcriptomic experiments, we were able to show that histone acetylation significantly contributes to the K165 biocontrol activity and establishment of inheritable resistance to V. dahliae. K165 treatment primed the expression of immune-related marker genes and the cinnamyl alcohol dehydrogenase gene CAD3 through the function of histone acetyltransferases. Our results reveal that offspring of plants treated with K165 have primed immunity and enhanced lignification, both contributing towards the K165-mediated inherited immune resistance. Thus, our study paves the way for the use of biocontrol agents for the establishment of inheritable resistance to agronomically important pathogens.

In the last two decades grapevine trunk diseases (GTDs) have emerged as the most significant threat for grapevine sustainability worldwide. The tracheomycotic fungus Phaeomoniella chlamydospora (Pch) is the predominant GTD-associated species and cannot be controlled with available chemicals. In the present study, we evaluated the effectiveness of two microbial strains (Paenibacillus alvei K165 and Fusarium oxysporum F2) against Pch in grapevine. In vitro bioassays, performed in a growth culture medium simulating the xylem environment, indicated that F2 decreased Pch growth and sporulation, whereas K165 did not have any effect on Pch growth. In planta experiments revealed that root-drench and stem-puncture application of K165 and F2 reduced the endophytic relative DNA amount of Pch by 90% and 82%, respectively, compared to controls. However, wood discoloration, the typical symptom of Pch infection, was not reduced in the F2 treated grapevines. Nevertheless, the F2 treated grapevines harbored higher lignin levels compared to mocks, as it was also done by K165. Therefore, F2 and K165 have the potential to be used as biocontrol agents against Pch in grapevines.

The olive tree (Olea europaea L.) is the most important oil-producing crop of the Mediterranean basin. However, although plant protection measures are regularly applied, disease outbreaks represent an obstacle towards the further development of the sector. Therefore, there is an urge for the improvement of plant protection strategies based on information acquired by the implementation of advanced methodologies. Recently, heavy fungal infections of olive fruits have been recorded in major olive-producing areas of Greece causing devastating yield losses. Thus, initially, we have undertaken the task to identify their causal agent(s) and assess their pathogenicity and sensitivity to fungicides. The disease was identified as the olive anthracnose, and although Colletotrichum gloeosporioides and Colletotrichum acutatum species complexes are the two major causes, the obtained results confirmed that in Southern Greece the latter is the main causal agent. The obtained isolates were grouped into eight morphotypes based on their phenotypes, which differ in their sensitivities to fungicides and pathogenicity. The triazoles difenoconazole and tebuconazole were more toxic than the strobilurins being tested. Furthermore, a GC/EI/MS metabolomics model was developed for the robust chemotaxonomy of the isolates and the dissection of differences between their endo-metabolomes, which could explain the obtained phenotypes. The corresponding metabolites-biomarkers for the discrimination between morphotypes were discovered, with the most important ones being the amino acids L-tyrosine, L-phenylalanine, and L-proline, the disaccharide α,α-trehalose, and the phytotoxic pathogenesis-related metabolite hydroxyphenylacetate. These metabolites play important roles in fungal metabolism, pathogenesis, and stress responses. The study adds critical information that could be further exploited to combat olive anthracnose through its monitoring and the design of improved, customized plant protection strategies. Also, results suggest the necessity for the comprehensive mapping of the C. acutatum species complex morphotypes in order to avoid issues such as the development of fungicide-resistant genotypes.

Verticillium dahliae is one of the most destructive soilborne plant pathogens since it has a broad host range and there is no chemical disease management. Therefore, there is a need to unravel the molecular interaction between the pathogen and the host plant. For this purpose, we examined the role of 1-aminocyclopropane-1-carboxylic acid synthases (ACSs) of Arabidopsis thaliana upon V. dahliae infection. We observed that the acs2, acs6, and acs2/6 plants are partially resistant to V. dahliae, since the disease severity of the acs mutants was lower than the wild type (wt) Col-0 plants. Quantitative polymerase chain reaction analysis revealed that acs2, acs6, and acs2/6 plants had lower endophytic levels of V. dahliae than the wt. Therefore, the observed reduction of the disease severity in the acs mutants is rather associated with resistance than tolerance. It was also shown that ACS2 and ACS6 were upregulated upon V. dahliae infection in the root and the above ground tissues of the wt plants. Furthermore, the addition of 1-aminocyclopropane-1-carboxylic acid (ACC) and aminooxyacetic acid (AOA), the competitive inhibitor of ACS, in wt A. thaliana, before or after V. dahliae inoculation, revealed that both substances decreased Verticillium wilt symptoms compared to controls irrespectively of the application time. Therefore, our results suggest that the mechanism underpinning the partial resistance of acs2 and acs6 seem to be ethylene depended rather than ACC related, since the application of ACC in the wt led to decreased disease severity compared to control.