Transcriptomic and Metabolomic Approaches Deepen Our Knowledge of Plant–Endophyte Interactions

Abstract

In natural systems, plant–symbiont–pathogen interactions play important roles in mitigating abiotic and biotic stresses in plants. Symbionts have their own special recognition ways, but they may share some similar characteristics with pathogens based on studies of model microbes and plants. Multi-omics technologies could be applied to study plant–microbe interactions, especially plant–endophyte interactions. Endophytes are naturally occurring microbes that inhabit plants, but do not cause apparent symptoms in them, and arise as an advantageous source of novel metabolites, agriculturally important promoters, and stress resisters in their host plants. Although biochemical, physiological, and molecular investigations have demonstrated that endophytes confer benefits to their hosts, especially in terms of promoting plant growth, increasing metabolic capabilities, and enhancing stress resistance, plant–endophyte interactions consist of complex mechanisms between the two symbionts. Further knowledge of these mechanisms may be gained by adopting a multi-omics approach. The involved interaction, which can range from colonization to protection against adverse conditions, has been investigated by transcriptomics and metabolomics. This review aims to provide effective means and ways of applying multi-omics studies to solve the current problems in the characterization of plant–microbe interactions, involving recognition and colonization. The obtained results should be useful for identifying the key determinants in such interactions and would also provide a timely theoretical and material basis for the study of interaction mechanisms and their applications.

Piriformospora indica and Azotobacter chroococcum Consortium Facilitates Higher Acquisition of N, P with Improved Carbon Allocation and Enhanced Plant Growth in Oryza sativa

“…Presence of inoculants in the soil also upregulate the expression of genes that in turn increases the root hair formation, resulting in enhanced absorption by the roots. These changes are brought by accelerating the production of hormones and metabolites [ 71 ], which are responsible for higher growth and biomass production. Thus, besides improving the nutritional uptake in plants, A. chroococcum also plays an important role in stabilizing the plant and endophyte association by solubilizing nutrients and promoting growth of endophytic fungi, leading to improved plant growth.…”

The Multifunctions and Future Prospects of Endophytes and Their Metabolites in Plant Disease Management

“…Metabolomics, widely used in bioanalytical procedures, enables the identification and quantification of the metabolites in a sample. It can complement transcriptomic and proteomic data, thus facilitating a better understanding of host phenotypic features and unveiling the mechanisms of plant–microbe interactions [ 151 ]. Metabolomics are often classified into two groups: untargeted metabolomics, a comprehensive analysis of numerous known/unknown metabolites in the sample, and targeted metabolomics, the measurement of the specific metabolites in the sample [ 152 ].…”

Endophytes and their potential in biotic stress management and crop production

“…Metabolomic analysis is a popular technique for quantifying metabolites. It can be used to complement transcriptomic and proteomic data, allowing for a well understanding of host phenotypical structures and elucidating plant–microbe interaction and mechanism ( Chen et al, 2022 ). During various stages of plant development, endophytes synthesize a variety of secondary metabolites and mediate an increase in metabolites biosynthesis in particular species and organs ( Zhai et al, 2017 ).…”