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Fungal Biology Reviews
Vol. 28 (4), 2015; Pages: 97–125

Fungal proteins and genes associated with biocontrol mechanisms of soil-borne pathogens: a review

Yohann Daguerre, Katarzyna Siegel, Véronique Edel-Hermann, Christian Steinberg

INRA, UMR1347 Agroécologie, 17 Rue Sully, BP 86510, F-21000 Dijon, France.

Abstract

Soil suppressiveness to soil-borne diseases relies mainly on microbial interactions. Some of them, e.g. antibiosis and mycoparasitism, are directly deleterious to pathogenic fungi; others indirectly affect microbial populations, pathogens included, when quite active non pathogenic microorganisms intensively exploit trophic or spatial resources. The mechanisms that govern the suppressive nature of the various known suppressive soils are often hypothetical. The objective of this article is to review the fungal proteins and corresponding genes directly or indirectly involved in antagonistic relationships between pathogens and non-pathogens and associated with biocontrol of soil-borne pathogens. The current hypothesis is that they contribute to soil suppressiveness. We assigned the proteins encoded by these genes to five function-based groups. The first group contains the proteins involved in host recognition and signaling pathways and the transcription factors involved in biocontrol activities. Proteins that protect antagonistic fungi against their own toxins and against other microorganisms are also included in this first group. The second group lists enzymes and proteins involved in the biosynthesis pathway of secondary metabolites, such as peptaibols, terpenes, polyketides, and gliotoxins that have antifungal activity towards soil-borne plant pathogens. The third group deals with proteins and molecules involved in competition for nutrients and root colonization. The fourth one contains the fungal cell wall-degrading enzymes secreted by antagonistic fungi during mycoparasitism. They are mainly chitin-degrading enzymes, glucanases and proteases. Finally, the last group gathers fungal proteins and molecules that induce plant defense reactions and prevent infection by plant pathogens. We conclude that the proteins involved or simply associated with the specific suppression of pathogens are not all known yet, but genes encoding a number of them or facilitating their expression are identified. Selecting candidate genes among them may help to understand the underlying mechanisms of soil suppressiveness when using metatranscriptomic analyses to identify functional groups.

Keywords: Fungi; Microbial antagonism; Pathogen suppression; Plant-microorganisms interactions; Soil suppressiveness; Transcriptomics.

 
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