Research Topic: Pathogen Suppression by Plant-Associated Microbiota

Ariel Herrera-Vásquez ¹ Rudolf Schlechter ² Grace Armijo ^3* Mariela I Monteoliva ^4,5*

• ¹ Centro de Biotecnología Vegetal, Universidad Andres Bello, Santiago, Santiago Metropolitan Region (RM), Chile
• ² Institute of Microbiology and Dahlem Centre of Plant Sciences, Department of Biology, Chemistry, Pharmacy, Freie Universität, Berlin, Germany
• ³ Agriaquaculture Nutritional Genomic Center, Temuco, Chile
• ⁴ Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (INTA)., Cordoba, Argentina
• ⁵ Unidad de Estudios Agropecuarios (UDEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Cordoba, Argentina

Microbial pathogen suppression operates through two primary mechanisms. The first involves direct antagonism, where beneficial microbes parasitize or compete with pathogens for resources, produce antimicrobials, or disrupt quorum sensing. The second mechanism involves the indirect suppression of pathogens via priming or Induced Systemic Resistance (ISR) in the host plant. During ISR, non-pathogenic microbes trigger plant immune responses, modulating hormonal signaling and enhancing pathogen resistance. These mechanisms are highly interconnected and influenced by external conditions such as soil composition, microbial activity, and community structure. Microbial consortia may interact synergistically to suppress plant diseases through collective effects within the plant-microbiomeenvironment system (Maciag et al., 2023).Microbiome manipulation to suppress pathogens is an under-explored strategy to improve crop health and yield. There is an urgent need for sustainable disease management solutions, intensified by pathogen-resistance acceleration and even more by climate change. This Research Topic compiles studies examining the ecological, physiological, molecular, and functional aspects of pathogen suppression by plant microbiota, with a focus on symbiotic interactions.The six articles provide valuable methodological approaches and insights into how the plant microbiota contributes to pathogen suppression (Figure 1). Comparative microbiome analyses reveal how microbial diversity and composition influence pathogen suppression, while biocontrol studies that focus on one species demonstrate the efficacy of microbial inoculants in suppressing phytopathogens, enhancing plant defenses, and influencing the host microbiome. Additionally, an in-depth review highlights the role of ISR, linking microbiome dynamics to plant immune responses.Tran et al. contribute to this issue by analyzing the microbiomes of soybean roots, rhizosphere, and bulk soil, as well as community shifts in response to cyst nematode (Heterodera glycines) infections. Using 16S rRNA gene amplicon sequencing, this study illustrated how resistant and susceptible host genotypes differentially recruited microbes during nematode infection. Flavisolibacter and Sphingomonas genera were enriched in the rhizosphere, while Dyella was enriched in the roots of the resistant genotype. These findings shed light on beneficial microbial communities that may contribute to nematode suppression in crops.Oeum et al. compared microbial communities of healthy rice leaves and those affected by bacterial leaf blight (Xanthomonas oryzae pv. oryzae). They identified Methylobacterium species as indicators of healthy leaves and demonstrated their biocontrol potential to reduce disease severity. These findings provide a framework for leveraging microbiome signatures as an effective disease monitoring and suppression strategy.From microbiome studies, particular species could be isolated and identified to be used as biocontrol agents. Biocontrol microbes offer a promising and eco-friendly alternative to traditional chemical treatments, which can harm beneficial microbes and contribute to pathogen resistance and soil degradation.Elmeihy et al. explored the combined biocontrol effect of Trichoderma viride and Azospirillum brasilense against Harpophora maydis, the causal agent of late wilt disease in maize. Their study highlights the antagonistic activity of these microbes through metabolite production and the improvement of physiological and agronomical traits.Teng et al. investigated the role of the yeast Pichia sp. and the bacterium Klebsiella oxytoca in promoting tobacco growth, as well as suppressing bacterial wilt (Ralstonia solanacearum) and black shank (Phytophthora nicotianae) diseases. Their findings proved that composite microbial fertilizers can modulate soil microbial communities and enhance plant health.De Troyer et al. assessed the effectiveness of Streptomyces rimosus in mitigating Fusarium head blight caused by Fusarium graminearum in wheat ears. Their study demonstrated the ability of S. rimosus to reduce disease severity and stabilize the wheat ear microbiome, shifting its composition closer to a healthy microbiome.Lastly, Jung et al. reviewed the systemic plant defense signaling induced by beneficial microbes as an alternative approach for pathogen suppression instead of direct microbemicrobe interactions. The authors describe how rhizospheric microbes can stimulate plant defenses while environmental stressors (biotic and abiotic agents) trigger changes in the root exudates that recruit and reshape the microbiome, further reinforcing plant defenses. They highlight the role of phytohormones and other signaling molecules in coordinating microbial recruitment and plant immune responses. Those interconnected effects underscore the dynamic relationship between plant and microbial communities, positioning ISR as a key process in microbiome-driven plant protection strategies.