Omics technologies for understanding the plant–fungal endophyte interactions: crop improvement for future security

Abstract

Fungi are a unique group of microbes that exist in all of the world’s niches having different habitats and environments. They are known to interact with various species present on the earth, including plants. Fungi interact with different niches of plants such as roots (rhizosphere), tissue, and internal spaces (endophytic) and surfaces (epiphytic). The fungi that inhabit the plants are specifically known as endophytic fungi. These plant–fungal interactions play a significant role for the host, such as protecting the plants from biotic and abiotic factors known as major growth constraints. Fungal endophytes also supply several nutrients and plant growth hormones, which help in plant growth enhancement. Additionally, nitrogen fixation, solubilization of minerals, production of phytohormones, antibiotics, secondary metabolites, hydrogen cyanide proteolytic enzymes, and activation of plant responses to stresses are the various mechanisms of endophytic fungi. Endophytic fungi have been known for various biotechnological applications that were unraveled through exploring biodiversity and understanding the interaction of plant–fungal endophyte. There are many unexplored species and interaction studies that need to be explored, and for the study, omics tools are recognized as the finest approach. In the present review, different omics tools that could be used for a deeper understanding of plant–fungal endophyte interactions and endophytic fungi biodiversity have been detailed.