Metabolomics as an emerging tool to study plant–microbe interactions

Abstract

In natural environments, interaction between plant roots and microorganisms are common. These interactions between microbial species and plants inhabited by them are being studied using various techniques. Metabolomics research based on mass spectrometric techniques is one of the crucial approaches that underpins system biology and relies on precision instrument analysis. In the last decade, this emerging field has received extensive attention. It provides a qualitative and quantitative approach for determining the mechanisms of symbiosis of bacteria and fungi with plants and also helps to elucidate the tolerance mechanisms of host plants against various abiotic stresses. However, this -omics application and its tools in plant–microbe interaction studies is still underutilized compared with genomic and transcriptomic methods. Therefore, it is crucial to bring this field forward to bear on the study of plant resistance and susceptibility. This review describes the current status of methods and progress in metabolomics applications for plant–microbe interaction studies discussing current challenges and future prospects.

Current Techniques to Study Beneficial Plant-Microbe Interactions

“…Moreover, the sizes of public databases containing metabolite references are limited, so it can quite often be difficult to correctly assign a detected metabolite to a specific organism. However, metabolomics represents a powerful tool to detect and quantify small molecules and identify specific metabolic pathways involved in plant–microbe interactions thus obtaining a comprehensive view of the complexity of interrelationship occurring among the members of the microbiota and between the microbiota and its host plant [ 72 , 88 ].…”

The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont

“…Currently, mass spectrometry-based metabolomics is one of the key technologies used to characterize these diverse complex chemical inventories [ 119 ]. In the past decade, the improved accessibility and knowledge obtained from metabolomics has been crucial to understanding how plant metabolites shape their microbial communities and how microbially derived molecules affect plant hosts and ecosystems [ 120 , 121 , 122 ]. In general, metabolomics is frequently applied to (i) characterize plant root exudation and its impact on microbes in the surrounding environment and (ii) the effect of associated microbes on host metabolism.…”

Metabolomics of plant root exudates: From sample preparation to data analysis

“…Albeit the progress that has been recently made in plant metabolomics, comprehensive analysis of a metabolome in the rhizosphere is still challenging. Despite the growing number of reviews demonstrating potential plant-microbiome interaction ( Jacoby and Kopriva, 2019 ; Trivedi et al., 2020 ; Pang et al., 2021 ; Gupta et al., 2022 ; Trivedi et al., 2022 ), sampling root exudates ( Oburger and Jones, 2018 ; Pantigoso et al., 2021 ), and analysis of exudates ( Van Dam and Bouwmeester, 2016 ; Canarini et al., 2019 ; Escolà Casas and Matamoros, 2021 ), relatively few reviews have attempted to integrate the strategies for metabolomics analysis of plant root exudates from sample preparation to data analysis.…”