From microbiome to biostimulants: unlocking the potential of tomato root endophytes

Background: Microbe-based biostimulants offer a sustainable and promising alternative to synthetic inputs, potentially reducing or replacing conventional inputs in crop management. Studying the native microbiota, particularly endophytic microbes, helps in selecting those that are naturally adapted to persist and to enhance plant growth under specific environmental conditions. This study aims to define the endophytic microbiota adapted to tomato crops by selecting discriminant amplicon sequence variant (ASVs) that are enriched during key plant growth stages and found in the core microbiota. Results: This study presents a large-scale analysis of tomato root endophytic prokaryotic microbiota using 16 S sequencing across the most common and widespread conditions used for tomato cultivation, offering comprehensive insight into its structure and dynamics. The results revealed a predominance of the Actinobacteriota and Proteobacteria phyla; less abundant groups included Bacteroidota, Verrucomicrobiota, Patescibacteria, and Firmicutes. Core microbiota analysis and discriminant ASV identification across different plant growth stages enabled the selection of the most abundant and persistent taxa adapted to the tomato endorhizosphere. Streptomyces, Shinella, Devosia, and Pseudoxanthomonas, as well as the lesser known genera Variovorax, Pseudarthrobacter, and Lechevalieria, represented the key genera identified, suggesting long-term host‒microbe associations. Conclusions: The description of the representative framework of the tomato-associated microbiota and the identification of its most important components provide a basis for developing tailored microbial formulations that can increase crop resilience and reduce dependence on synthetic agricultural inputs, aimed at developing more sustainable environmental management strategies.