Disease Suppressive Soils: New Insights from the Soil Microbiome

Abstract

Soils suppressive to soilborne pathogens have been identified worldwide for almost 60 years and attributed mainly to suppressive or antagonistic microorganisms. Rather than identifying, testing and applying potential biocontrol agents in an inundative fashion, research into suppressive soils has attempted to understand how indigenous microbiomes can reduce disease, even in the presence of the pathogen, susceptible host, and favorable environment. Recent advances in next-generation sequencing of microbiomes have provided new tools to reexamine and further characterize the nature of these soils. Two general types of suppression have been described: specific and general suppression, and theories have been developed around these two models. In this review, we will present three examples of currently-studied model systems with features representative of specific and general suppressiveness: suppression to take-all (Gaeumannomyces graminis var. tritici), Rhizoctonia bare patch of wheat (Rhizoctonia solani AG-8), and Streptomyces. To compare and contrast the two models of general versus specific suppression, we propose a number of hypotheses about the nature and ecology of microbial populations and communities of suppressive soils. We outline the potential and limitations of new molecular techniques that can provide novel ways of testing these hypotheses. Finally, we consider how this greater understanding of the phytobiome can facilitate sustainable disease management in agriculture by harnessing the potential of indigenous soil microbes.

Crop rotational diversity increases disease suppressive capacity of soil microbiomes

“…, Schlatter et al. ). Plants can also facilitate recruitment of specific biocontrol microorganisms in some cases.…”

“…, Schlatter et al. ). For example, soils harbor a diverse collection of microorganisms that affect the evolution and ecology of plant populations (Lau and Lennon , van der Putten et al.…”

Linking ecology and plant pathology to unravel the importance of soil-borne fungal pathogens in species-rich grasslands

“…In general, it is thought that a larger plant diversity creates more 'niches' for soil microbes and/or promotes multiple microbial activities due to chemically more diverse exudates, thereby increasing soil suppressiveness (Gómez Expósito et al 2017;Mendes et al 2011;Schlatter et al 2017;Steinauer et al 2016). A higher microbial diversity is expected to reduce invasion of pathogens and increase antagonism in soils, thereby reducing the impact of plant pathogenic fungi (Larkin 2015;Mallon et al 2015).…”

Transcript accumulation in a trifold interaction gives insight into mechanisms of biocontrol

“…An alternative possibility to control diseases caused by soil‐borne pathogens has emerged from the study of ‘suppressive soils’ in which biotic agents suppress disease despite the presence of a pathogen (Schlatter et al ., ). This phenomenon was termed biocontrol, and has now been demonstrated in a wide variety of crops (De Vrieze et al ., ; Newitt et al ., ).…”