Microbiome‐Wide Association Studies of Host Beneficial Microbes and Their Functional Mechanisms and Promising Applications in Sustainable Crops

Plant microbiome plays important roles in modulating host growth, production and stress resistance, exhibiting potential implications in sustainable agriculture and environmental improvement. Recent microbiome-wide association studies (MWAS) have established the relationships between host microbes and plant genotypes or phenotypes. However, the comprehensive discussion of their associations, mechanisms and applications remains elusive. This review systemically reveals plant traits-associated beneficial microbes and their functional mechanisms. First of all, this review proposes the systemic framework from microbiome diversity to association studies such as MWAS. Moreover, MWAS-based multi-omics studies reveal the complex interplay between microbial community and host genetics as well as traits, identifying multiple beneficial microbes in nutrient (nitrogen, phosphate and potassium) uptake, stress (drought, salinity and heavy metals) alleviation, disease control (microbial competition, microbial antagonism and host immune activation) and agronomic traits (yield and quality). In addition, this review highlights the potential applications of MWAS in the design of optimal synthetic microbial communities (SynComs) and precision microbiome-based crop breeding for sustainable agriculture, and provides new insights into multiple agricultural practices including domestication, heterosis, rotation, and so forth. Notably, this review discusses the current challenges and future perspectives in the field, thereby improving microbiome-based sustainable agricultural protection and important agronomic traits.