Luethi, T. | Search bioRxiv

bioRxiv2026

A scalable screening approach reveals phylogenetic patterns of bacterial antagonism against potato pathogens

Microbial biological control agents (mBCAs) offer a promising alternative to conventional disease management, but identifying effective strains requires screening large microbial collections against many pathogens. Here, we developed a scalable screening approach to characterize the antagonistic activity of potato-associated bacteria against multiple pathogens and investigated how bacterial origin and phylogeny relate to antagonistic phenotypes. A collection of 600 bacterial strains isolated from two potato cultivars, three plant compartments using four cultivation media was screened against six major potato pathogens: the bacteria Dickeya solani and Pectobacterium carotovorum, the fungi Alternaria solani and Rhizoctonia solani, and the oomycetes Phytophthora infestans and Pythium ultimum. A scalable confrontation method was developed for non-filamentous bacteria, while complementary lower-throughput assays were used for filamentous strains. This approach enabled successful assessment of 92% of non-filamentous and 97% of filamentous strain-pathogen combinations. Isolation cultivar, plant compartment and cultivation medium had only limited effects on the proportion of antagonistic strains. In contrast, pathogen sensitivity varied markedly: P. infestans was the most susceptible pathogen, whereas D. solani and P. carotovorum were generally resistant to bacterial antagonism. Antagonistic activity clustered phylogenetically, with Bacillus and Streptomyces containing many broad-spectrum inhibitors. In addition, several taxa showed preferential activity against the oomycetes, including P. infestans-specific antagonists from the Pseudomonas genus and P. ultimum-specific antagonists from the Frigoribacterium, Curtobacterium, Pedobacter and Phyllobacterium genera. Overall, multi-pathogen screening revealed distinct generalist and specialist antagonistic profiles and identified candidate strains and taxa for further evaluation as mBCAs.

microbiology↗

bioRxiv2026

The plant immune receptor LORE binds agonistic and antagonistic 3-hydroxy fatty acid ligands via a dynamic loop in its G-type lectin domain

The Arabidopsis thaliana S-domain receptor kinase LORE senses bacterial medium-chain 3-hydroxy fatty acids (mc-3-OH-FAs) as microbe-associated molecular patterns to activate pattern-triggered immunity. How LORE recognises these fatty acid ligands at the molecular level remains unknown. Here, we combined protein structure prediction, protein-ligand interaction modelling and molecular dynamics (MD) simulations with ligand-binding assays using chimeric and mutant receptor ectodomains, and functional analysis of receptor activation to characterise the mc-3-OH-FA binding mechanism. Domain-swap experiments between LORE and its non-binding paralog AtSD1-23 identify the lectin 2 (L2) domain as the ligand-binding domain. Mutational analysis and reverse engineering confirm a hydrophobic pocket in the L2 core as the primary ligand-binding site. Multiple walker Supervised MD (mwSuMD) simulations reveal that the acyl tail enters the pocket first, whilst polar interactions between the headgroup and a flexible L2 loop guide and stabilise the bound state. In support of this model, 3-OH-C10:0 analogues with bulky headgroup modifications dock into the pocket but act as antagonists, presumably by preventing the loop from adopting the conformation required for signalling. Together, these data suggest that the flexible L2 loop has multiple functions: it acts as a dynamic gate regulating pocket access, provides essential anchoring points once the ligand is bound, and contributes to receptor activation. These findings provide a mechanistic framework for immunogenic mc-3-OH-FA sensing by LORE.

plant biology↗