Deciphering the biocontrol mechanisms of Lysobacter capsici AZ78 against plant pathogenic oomycetes using omics-based approaches

Plants are susceptible to numerous biotic and abiotic factors that negatively affect their performance in the field and ultimately reduce crop yield. Among the biotic factors, oomycetes are responsible for several devastating plant diseases that lead to substantial agricultural losses worldwide. Oomycetes are a group of eukaryotic microorganisms known for causing economically important plant diseases across diverse cropping systems. These diseases contribute significantly to global agricultural losses, resulting in reduced productivity and potential food shortages. Among the well-known oomycete genera, Plasmopara, Peronospora, and Pythium are prominent plant pathogens responsible for foliar and soil-borne diseases in a wide range of host plants. Plasmopara viticola and Peronospora belbahrii are the causal agents of downy mildew diseases in different hosts. In this study, we focused on grapevine and basil downy mildews caused by P. viticola and P. belbahrii, respectively. In addition to these foliar pathogens, Pythium ultimum, a soil-borne oomycete pathogen, poses a serious threat to various crops by causing pre-emergence and post-emergence damping-off diseases. Current control strategies for oomycete plant pathogens largely rely on the application of fungicides to plants or soil. However, complete eradication of these pathogens from infected fields is nearly impossible. Although breeding programs aimed at developing resistant plant varieties are ongoing, this process is laborious and often challenged by the rapid evolution of pathogen resistance to both host resistance traits and chemical fungicides. Furthermore, extensive use of chemical control measures has raised concerns due to their negative impacts on human health and the environment. Consequently, farmers, scientists, and consumers are increasingly shifting toward sustainable pest management strategies. Modern disease management therefore emphasizes integrated approaches combining physical, chemical, and biological methods rather than relying on a single control strategy. Within this framework, biological control agents (BCAs) have gained considerable attention because of their ability to suppress a broad range of pathogens through direct mechanisms such as antagonism, nutrient and space competition, and mycoparasitism, as well as indirect mechanisms including activation of plant defense responses that enhance plant resistance against pathogens. The bacterial genus Lysobacter has emerged as a promising BCA and has been extensively studied for its antimicrobial activity against plant pathogenic fungi, oomycetes, nematodes, and both Gram-positive and Gram-negative bacteria. Several species, including Lysobacter enzymogenes, L. antibioticus, L. gummosus, and L. capsici, have demonstrated strong antimicrobial properties. These bacteria exert their effects through the secretion of lytic enzymes and a diverse array of secondary metabolites. Among them, L. capsici AZ78, isolated from the tobacco rhizosphere, has been widely investigated for its antimicrobial potential. Previous studies have demonstrated strong antagonistic activity of this strain against the foliar oomycete P. viticola, with efficacy comparable to commercially used copper-based fungicides in vineyards. Regarding soil-borne pathogens, volatile organic compounds (VOCs) emitted by L. capsici AZ78 have shown inhibitory effects on P. ultimum in in vitro split Petri dish assays. Despite multiple studies confirming the effectiveness of L. capsici AZ78 against both foliar and soil-borne oomycete plant pathogens, important knowledge gaps remain. In particular, the effects of L. capsici AZ78 and its antimicrobial secondary metabolites on host plants and the precise mechanisms of action against oomycete plant pathogens have not been fully elucidated. Moreover, studies involving soil-borne pathogens have largely been limited to laboratory conditions, with limited evaluation under realistic soil environments. To address these knowledge gaps, this study investigated the effects of L. capsici AZ78 cells and their metabolites against two major foliar oomycete pathogens, P. viticola and P. belbahrii. We examined the direct effects of bacterial cells and their secondary metabolites, particularly thermostable polycyclic tetramate macrolactams (PTMs), on pathogen development while also evaluating how plant protection responses were mediated in the host. Callose deposition and reactive oxygen species (ROS) accumulation were analysed in host plants treated with both bacterial cells and thermostable PTMs. To further understand grapevine responses to L. capsici AZ78 applications, gene expression analyses were performed on plants treated with a self-digestive solution (SDS) derived from the autolysis of L. capsici AZ78 cells grown in liquid culture for extended periods, allowing the accumulation of bioactive secondary metabolites in the growth medium. These analyses provided insights into the expression patterns of grapevine genes associated with defense-related functions against P. viticola. Simultaneously, phytoalexin accumulation was evaluated to determine whether L. capsici AZ78 and its metabolites could induce the production of antimicrobial compounds toxic to P. viticola. The second part of the study focused on the soil-borne oomycete plant pathogen P. ultimum. Experiments evaluated the effects of L. capsici AZ78 cells and their VOCs on damping-off disease development in tomato plants. To gain deeper insight into the interactions among host plants, pathogens, and the BCA, metagenomic analyses were conducted to assess how L. capsici AZ78 and the VOCs influenced soil microbial communities and contributed to the establishment of disease-suppressive soil conditions that limit P. ultimum growth. The effects of these interactions were further enhanced through the addition of organic amendments, which served as nutrient-rich substrates supporting bacterial growth and promoting the emission of antimicrobial volatiles. The combined application of organic amendments and L. capsici AZ78 improved both plant growth promotion and disease protection under soil conditions. Collectively, this study provides a comprehensive understanding of the mechanisms underlying the anti-oomycete activity of L. capsici AZ78. The results demonstrate that this bacterium employs multiple direct and indirect mechanisms to protect plants against pathogens. These include direct antagonism, production of secondary metabolites such as thermostable PTMs, emission of antimicrobial VOCs, activation of plant immune responses, induction of phytoalexin accumulation toxic to pathogens, and modification of the soil microbiome to establish disease-suppressive environments. By integrating multiple experimental approaches, this work advances our understanding of this BCA and supports its application under practical agricultural conditions. Furthermore, this study represents the first evaluation of the plant protection efficacy of L. capsici AZ78 against P. belbahrii. Currently, only a limited number of BCAs are available for controlling this pathogen, and they are typically applied in combination with chemical fungicides. Our results demonstrate that L. capsici AZ78 alone can provide more than 90% disease protection under semi-realistic greenhouse conditions. Additionally, this work expands upon previous in vitro studies on P. ultimum by validating the efficacy of L. capsici AZ78 under realistic soil conditions, thereby strengthening its potential for practical agricultural application.