Metagenomic Approaches for Studying Plant–Microbe Interactions

Abstract

AbstractPlant microbiome from environmental samples, including soil rhizosphere, consists of all microbial genomes and plays an essential role in maintaining plant growth and health in addition to tolerating biotic and abiotic stresses and climate change. Plant microbiome is beneficial to the plant in many ways, such as nitrogen metabolism and enhancing plant growth-promoting (PGP) effects. It is also believed that plant growth-promoting microbes (PGPM) enhance plant growth by a variety of mechanisms such as enhancing soil nutrient bioavailability, disease resistance, damage due to herbivores, and improving water acquisition. However, the microbial composition is mostly influenced by soil factors, plant genotype, and exudates from the plants as well.Moreover, the plant microbiome depends on the plant–microbe interactions and cultivation practices as well. Recently, more emphasis is on the study of underlying genes affecting plant–microbe interaction by high-throughput methodologies, including 16S rRNA marker gene sequencing and metagenome approaches for studying plant-microbiome interaction and microbial community in the plant surroundings. The metagenomic studies offer the possibility to explore the taxonomic composition of plant microbiome and its functional properties as well. Taxonomic analysis for amplicon sequencing is carried out using bioinformatics tools such as QIAMI and Greengenes database to identify operational taxonomic units (OTUs); however, in the case of whole-genome shotgun (WGS) sequencing, taxonomic classification is achieved using tools such as “Kraken.” Recent advances in metatranscriptomics characterize members of the microbial community that are responsible for specific functions and identify the genes playing an essential role in plant–microbe interaction. Therefore, the present chapter focuses on reviewing the above molecular methodologies in detail for studying plant microbial community.KeywordsMetagenomeMicrobiomePlant–microbe interactionSequencing