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

Abstract

Compost is a valuable amendment for soil and potting substrate when it comes to sup-pressing soilborne pathogens. However, the effectiveness of different composts varies and can not yet be predicted. Microbial communities in compost play a key role in disease suppression, and therefore their composition or specific taxa may serve as indicators of suppressive composts. In this study, we investigated 37 composts from seven commercial compost producers to analyze the association of their bacterial and fungal communi-ties with suppressive activity in three plant-pathogen systems: cress-Globisporangium ultimum, cucumber-Globisporangium ultimum and cucumber-Rhizoctonia solani. Our results underscore that compost suppressiveness is primarily pathogen-specific and, to a lesser extent, host-plant-specific. Suppressiveness was not correlated with physico-chemical properties, microbial activity, or the alpha-and beta-diversity of composts bac-terial and fungal communities. Instead, microbial composition was largely shaped by producer-specific composting conditions and maturation processes, which were not nec-essarily linked to suppressive activity. A more nuanced comparison between the most and least suppressive composts revealed bacterial and few fungal taxa as potential indicators of suppressiveness for each plant-pathogen system. Notably, for G. ultimum-suppression, bacteria from the genera Luteimonas, Sphingopyxis, and Algoriphagus and for R. solani bacteria belonging to the phylum Actinomycetota emerged as promising candidates. ImportanceSoilborne diseases are a major yield-limiting factor in agricultural crop production world-wide, particularly in seedling cultivation. Their control remains a significant challenge and still largely relies on chemical fumigation of soils and steam sterilization of pot-ting substrates. While chemical fumigants are increasingly criticized for their negative environmental impact, sterilization practices in general disrupt beneficial microbial com-munities, making substrates more susceptible to pathogen (re)-infestation. Amending soil or potting substrate with disease-suppressive compost offers a promising alternative. However, the targeted use of compost for plant protection is hindered by variable effec-tiveness and the lack of reliable tools to identify effective composts. This study provides a comprehensive abiotic and biotic characterization of compost, enabling a detailed anal-ysis of the properties associated with suppressiveness. The identification of bacterial and fungal taxa indicative of disease-suppressive composts lays the groundwork for targeted isolation of microorganisms and functional studies, with the ultimate aim of predicting and optimizing compost-mediated disease suppression.