Linking microbiome structure to functional analysis identifies resilient Pseudarthrobacter, Pseudomonas, and Streptomyces antagonists of Phytophthora infestans in tomato

Introduction Late blight, caused by Phytophthora infestans , remains one of the most destructive tomato diseases, driving the need for sustainable measures to reduce intensive fungicide use. Plant-associated microbial communities offer a promising but still underexplored source of biological control agents. Moreover, links between community-level microbiome patterns and functionally effective antagonists remain poorly resolved. Methods In this study, we combine culture-dependent isolation, functional profiling of lytic enzymes and siderophores, with 16S rRNA Illumina-based microbiome analysis to identify ecologically relevant bacterial antagonists of P. infestans in tomato. Healthy and P. infestans -challenged tomato plants cultivated in soils from two organic tomato farms in the Rhine-Main region of Germany were analyzed. Results Of the 594 bacterial isolates from tomato rhizosphere and phyllosphere, 84 inhibited P. infestans , and 63 of these suppressed Alternaria solani in vitro . Functional screening identified 28 isolates with broad-spectrum antagonistic potential, predominantly affiliated with the genera Pseudomonas, Bacillus, Streptomyces, Paenibacillus , and Pseudarthrobacter , characterized by broad siderophore and taxon-specific lytic enzyme activities. In planta assays identified Pseudarthrobacter sp._Pb177 as a novel and most effective antagonist of P. infestans , alongside effective Streptomyces and Pseudomonas isolates. Amplicon-based microbiome analyses of different tomato compartments under both healthy and P. infestans -challenged conditions revealed soil origin as the primary driver of bacterial community assembly, particularly in the rhizosphere and phyllosphere. Disease-associated shifts were limited to specific soil-compartment combinations (rhizosphere soil B). Key rhizosphere bacterial taxa ( Acinetobacter and Chryseobacterium ) remained largely stable across plant health states. Instead, disease effects are confined to shifts among rare or conditionally detected ASVs. Mapping cultured isolates to amplicon sequence variants demonstrated that most antagonists corresponded to low-abundance members of the tomato microbiome (including Bacillus, Chryseobacterium, Paenibacillus, Pseudomonas, Streptomyces , etc.), with their distribution shaped primarily by soil and plant compartment rather than disease. Discussion These findings indicate that effective biocontrol candidates are defined less by abundance than by their resilience and function within plant-associated microbial communities. By linking microbial community profiling with functional screening and in planta assays, this study outlines a microbiome-informed approach for identifying bacterial antagonists of P. infestans and supports an ecologically grounded framework for managing tomato late blight.