Chapter 9 - Functional genomics tools for studying microbe-mediated stress tolerance in plants

Abstract

Microbial communities associated with plants are highly diverse and complex and are an excellent model for understanding biological interaction and evolution. These microbes are essential for the survival of the host and interaction with the host, and other associated microbes of the entire microbiome in the complex and interconnected networks that affect the physiology, biochemistry, and functional dynamics of each other in a multidynamic way. Understanding signal communication, interaction, and genetic-relatedness using genome-based and other high throughput methodologies is the current and most advanced topic in plant-microbiome research. Advancement in functional genomics tools such as high-throughput sequencing analysis, proteomics, metabolomics, and their interpretation with bioinformatics tools, latest computational algorithms, system biology approaches have provided additional platforms to better understand the functional and dynamical aspects of the microbial communities and their interaction with the host, and therefore provided a new direction to the plant-microbiome research. In addition, such studies are also useful in exploring the structure, composition, diversity, and dynamics of the microbial communities, their functional interaction, ecological sustainability in a functional plant microbiome, and further impact of different environmental variables, in the presence and absence of the microbial diversity in such microbiome, to better understand the stress tolerance and/or mitigation capabilities by these microbes. Nevertheless, plant microbiome research is challenged by regular updates from the latest genome and transcriptome sequencing projects. Advancements in the latest RNA sequencing technologies have identified putative genes, protein products, and other complex interaction networks that are actively involved in mediating the host–microbe interactions. Further, CRISPR/Cas9 genome editing system provides a novel tool to efficiently introduce target-specific modifications into the genome. Genome editing and its further validation using functional genomics approaches have helped a lot in the comprehensive assessment of the functional aspects, competency, and flexibility of the microbial system and their products (genes, proteins, and metabolites) for their further application in stress tolerance and crop improvement programs.