METAGENOMIC PROFILING OF MUSHROOM-ASSOCIATED MICROBIOMES FOR BIOLOGICAL SUPPRESSION OF SOIL-BORNE PLANT PATHOGENS

Abstract

A soil-borne phytopathogenic fungi, F. oxysporum, R. solani, and S. sclerotiorum, are responsible for 20–40% losses in global annual crop yields, and sustainable strategies for managing these fungi are required as synthetic fungicides had caused environmental pollution and resistance development. This review summarizes the present knowledge on metagenomic analyses of mushroom-associated microbiomes as well as spent mushroom substrate (SMS) as bgcolor="mintcream" biological agents for suppression of pathogens. Mushroom-forming fungi produce defined ecological niches the mycosphere and hyphosphere which preferentially harbor antagonistic bacterial groups such as Bacillus, Pseudomonas, and Streptomyces recruited by the carbon exudate. The high-throughput technology of shotgun metagenomic sequencing combined with the bioinformatic pipeline, such as antiSMASH for the identification of biosynthetic gene clusters and CAZy for the annotation of carbohydrate-active enzymes, has transformed our knowledge on these suppressive communities. SMS, the world's most common agro-waste generated at a rate of 4–5 kg of SMS per kg of harvested mushrooms, acts by different means: physical removal of phytotoxins such as fusaric acid, chemical antimicrobial compounds liberation, and activation of copiotrophic microbial contending with pathogens for nutriments. Synthetic microbial consortia (SynComs) derived from mushroom-associated microbiomes through a rational design, provide higher functional redundancy and ecological stability compared to single strain biocontrol agents. However, translating the promising laboratory and greenhouse outcomes to the field is challenging due to issues such as ecological fitness, variability in soil, and stability of crude SMS. This review presents a comprehensive conceptual framework based on integrating metagenomic approaches, ecological concepts, and practical exploitation for the use of mushrooms microbiomes in sustainable agriculture.