From compost microbiomes to potentially disease suppressive bacterial isolates

Summary

Composting helps closing nutrient cycles, and applying composts improves soil structure. Even more, composts application can suppress soilborne diseases, most likely driven by microorganisms present in the compost. A disease-suppressing effect has been demonstrated for many microorganisms (MO) isolated from composts, or effective biocontrol strains isolated from other environments can also be found in composts. In practice, composts are often more effective than individual biocontrol strains when applied to pathogen-infested soils. Yet, the disease-suppressive activity varies among different composts, and cannot yet be predicted or reliably reproduced, even though this would be crucial for optimizing compost use in disease control.
In a study, we analyzed 37 composts from 7 large-scale compost producers to determine whether suppressiveness in three different plant-pathogen systems (cress - Globisporangium ultimum, cucumber - G. ultimum, cucumber - Rhizoctonia solani) is associated with certain bacterial or fungal communities, and whether these could be used as indicators of suppressiveness. We were able to confirm that the suppressiveness of composts is strongly pathogen- and, to a lesser extent, host-plant specific. Suppressiveness did neither correlate with physicochemical parameters of the composts nor with microbial parameters such as microbial activity, alpha- and beta-diversity. However, specific bacterial and a few fungal sequences could be identified that were associated with the most suppressive composts in the respective plant-pathogen system. Bacteria of the genera Luteimonas, Sphingopyxis and Algoriphagus were promising candidates for G. ultimum suppressiveness. We isolated bacteria belonging to the last two and to 14 additional genera from compost, and selected those which matched an indicative sequence. They are now being analyzed for their function (e.g. in vitro inhibitory effect against G. ultimum, in vivo effect of single strains/consortia of selected strains).
Our findings emphasize the need for more nuanced approaches to identify compost traits that promote disease suppression, particularly by investigating specific microbial taxa that may serve as indicators of disease-suppressive composts.