Prospects for biological soil-borne disease control: application of indigenous versus synthetic microbiomes

Authors: Mazzola, Mark; FREILICH, SHIRI - Agricultural Research Organization, Volcani Center

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/18/2016
Publication Date: 1/27/2017
Citation: Mazzola, M., Freilich, S. 2017. Prospects for biological soil-borne disease control: application of indigenous versus synthetic microbiomes. Phytopathology. 107:256-263. doi: 10.1094/PHYTO-09-16-0330-RVW.
DOI: https://doi.org/10.1094/PHYTO-09-16-0330-RVW

Interpretive Summary: In general, biological disease control has been employed in agricultural systems through the introduction of single or multi-strain inoculations of organisms not indigenous to the soil system. While this approach has had value in contained or controlled systems, it generally has not been a widely used or successful disease management approach for field-level production systems. Regardless, application of biological controls can be option in certain production systems, organic soils, where alternative options are limited. An alternative option is the management of the microbial resource native to a soil system in a manner that leads to the recruitment of a soil microbial community (microbiome) that possess properties that can limit progression of plant diseases. Microbes require substrate in order to persist and multiply, and the introduction of specific types of organic resources will result in selective microbial growth. New technologies allow us to garner a more complete understanding of the soil microbial community that can suppress plant diseases as well as the identification of substrates that foster the growth and activity of these communities. This information can be utilized to devise systems based on substrate inputs to selectively recruit an indigenous microbiome capable of yielding soil-borne plant disease control.

Technical Abstract: Biological disease control of soil-borne plant diseases has traditionally employed the biopesticide approach whereby single strains or strain mixtures are introduced into production systems through inundative/inoculative release. The approach has significant barriers that have long been recognized, including narrow markets and limited persistence, which can plague progress in the utilization of this resource in commercial field-based crop production systems. Thus, although potential exists, this model has continued to lag in its application. New omics’ tools have enabled more rapid screening of microbial populations allowing for the identification of strains with multiple functional attributes that may contribute to pathogen suppression. Similarly, these technologies also enable the characterization of consortia in natural systems which provide the framework for the construction of synthetic microbiomes for disease control. Harnessing the potential of the microbiome indigenous to agricultural soils for disease suppression through application of specific management strategies has long been a goal of plant pathologists. Although this tactic also possesses limitation, our enhanced understanding of functional attributes of suppressive soil systems through application of community and metagenomic analysis methods provide opportunity to devise effective resource management schemes. As these microbial communities in large part are fostered by the resources endemic to soil and the rhizosphere, substrate mediated recruitment of disease suppressive microbiomes constitutes a practical means to foster their establishment in crop production systems.