Analyses of 37 composts revealed microbial taxa associated with disease suppressiveness.

Abstract

Compost is a valuable amendment for soil and potting substrate when it comes to suppressing soilborne pathogens. However, the effectiveness of different composts varies and cannot 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 7 commercial compost producers to analyze the association of their bacterial and fungal communities with suppressive activity in three plant-pathogen systems: cress-Globisporangium ultimum, cucumber-G. 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 physicochemical properties, microbial activity, or the alpha- and beta-diversity of composts' bacterial and fungal communities. Instead, microbial composition was largely shaped by producer-specific composting conditions and maturation processes, which were not necessarily linked to suppressive activity. A more nuanced comparison between the most and least suppressive composts revealed bacterial and a 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.

Importance: Soilborne diseases are a major yield-limiting factor in agricultural crop production worldwide, particularly in seedling cultivation. Their control remains a significant challenge and still largely relies on chemical fumigation of soils and steam sterilization of potting substrates. While chemical fumigants are increasingly criticized for their negative environmental impact, sterilization practices, in general, disrupt beneficial microbial communities, 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 effectiveness and the lack of reliable tools to identify effective composts. This study provides a comprehensive abiotic and biotic characterization of compost, enabling a detailed analysis 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.