Functional Metagenomics for Rhizospheric Soil in Agricultural Systems

The study of plant microbiota has been stimulated by recognizing the fundamental role that the genetic capacity of the associated microbial communities has to modulate the phenotypic expression of plants, which is crucial for its health, physiology, and productivity. All genes in a metagenome can be described by whole-metagenome shotgun sequencing, but it is time-consuming, and a high level of experience is required. Alternatively, the amplification and high-throughput sequencing of the16S-rRNA gene allow describing themicrobial composition. Then functional activities can be inferred by listing the abundance of each gene. Also, the identification and the quantification of microbiome transcripts are now accessible to determine the profile and changes in gene expression occurring in a microbial community in response to environmental or experimental variations. Considering the beneficial role of microbial communities in soil environments, it is important increasing the understanding of plant-microbe relationships to provide biotechnological information for control and management with sustainable practices.