Comprehensive analysis of 37 composts: microbial indicators for soilborne disease suppression in three plant-pathogen systems

Soilborne diseases pose a significant threat to crop production and their control remains a major challenge. Compost is a valuable soil amendment when it comes to suppressing soilborne pathogens, but the effectiveness of different composts varies and cannot yet be predicted. Microbial communities in compost play a key role in disease suppression, and therefore microbial taxa may serve as indicators for suppressive composts. In this study, we investigated 37 composts from seven commercial compost producers to analyze the association of their bacterial and fungal communities with disease-suppressive activity across three plant-pathogen systems: cress-Globisporanigum ultimum, cucumber-Globisporanigum ultimumand cucumber-Rhizoctonia solani. Our results underscore that compost suppressiveness is primarily pathogen-specific and, to a smaller extent, hostplant-specific. Suppressiveness was not found to be correlated to physicochemical properties or microbial activity, alpha- and beta-diversity of the composts. However, specific bacterial and a few fungal taxa were identified as potential indicators of suppression for each plant-pathogen system. Notably, forG. ultimum-suppression, bacteria from the generaLuteimonas,Sphingopyxis, andAlgoriphagusemerged as promising candidates. These findings provide a foundation for targeted microbial isolation, aiming to elucidate the role of microorganisms in compost-mediated disease suppression, and to predict and optimize suppressive activity.