Soil immune responses: Soil microbiomes may be harnessed for plant health

Authors: RAAIJMAKERS, JOS - Netherlands Institute Of Ecology; Mazzola, Mark

Submitted to: Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/11/2016
Publication Date: 6/17/2016
Citation: Raaijmakers, J.M., Mazzola, M. 2016. Soil immune responses: Soil microbiomes may be harnessed for plant health. Science. 352:1392-1393.

Interpretive Summary: Soil ecosystems possess a wealth of biological resources that can be harnessed for use in control of plant diseases. Soils that naturally have low incidence of disease are commonly referred to as suppressive soils. Studies have been conducted to determine the properties of these soils that are important in this natural disease suppression, the goal being to identify those soil components of the soil microbiome (microbial community) function to limit plant disease development and the means these organisms utilize to limit pathogen activity. Study of these systems have led to the identification of many microorganisms that can provide disease control, but their application has exhibited limited success and practicality. A major barrier to biological disease control is the well adapted indigenous soil microbiome which limits survival, and thus effectiveness, of introduced biological control agents. The complexity of soil-microbiome-plant interactions argues for the biological disease control strategies that augment indigenous disease suppressive microorganisms for sustainable disease management. Directing assembly of such a microbiome may be achieved though using the plant host as a driving force or the application of specific organic amendments that actively select for disease suppressive microorganisms. A more comprehensive understanding of how the disease suppressive microbiome evolves are needed for successful implementation of such a management strategy.

Technical Abstract: The best examples of microbiome-mediated protection of plants against root pathogens are disease suppressive soils. The characteristics of general and specific disease suppressiveness of soils are strikingly comparable to innate and adaptive immunity in animals. Innate immunity and general soil suppressiveness both operate via basal mechanisms such as competition while specific suppressiveness requires activation of select microbial groups and traits much like specialized cell types are required in function of adaptive immunity in animals. While first identified in the late 19th century, only a limited number of suppressive soils and mechanisms have been elucidated. Although mechanistic studies have yielded a variety of microbial agents subsequently implemented in biological control, such an approach has exhibited limited success in large-scale agriculture. Much like artificially acquired passive immunity in animals, inundative release of microbial inoculants is unlikely to provide long-term disease suppression. The complexity of soil-microbiome-plant interactions argues for strategies that augment indigenous disease suppressive microorganisms for sustainable disease management. Directing assembly of a pathogen resistant microbiome rather than introduction of microbial products may yield a more persistent system with a durable capacity to resist pathogen infestations. Practical means to attain this outcome include selection of the appropriate plant host genotypes which direct microbiome assembly by recruiting species or even genotypes of a pathogen-suppressive microbial population. Alternatively, organic soil amendments (e.g. chitin, Brassica seed meal), can also be utilized to selectively drive the microbiome to a state that limits proliferation of soil-borne pathogens.