Genomics and the Rhizosphere

The rhizosphere is a nutrient-rich area surrounding roots with increased microbial number and activity compared with bulk soil. Plant–microbe interactions in the rhizosphere are an essential determinant of plant health and productivity, as well as biogeochemical cycling. Traditionally, genomics has focussed on the small proportion of cultivable microbes, but recent advances in culture-independent molecular tools, high-throughput deoxyribonucleic acid (DNA) sequencing, and bioinformatics are revolutionising our understanding of plant–microbe interactions. Identification of total DNA (metagenomics), ribonucleic acid (RNA) (metatranscriptomics) and expressed proteins (metaproteomics) and metabolites (metabolomics) are now applicable to complex microbial communities such as those in the rhizosphere. Combining these genomic technologies will enable us to analyse the rhizosphere at the systems level. Key Concepts: Soil microbial diversity is vast and plant interfaces are a focus of microbial activity. Plant–microbial interactions are an essential determinant of plant health and productivity. Microbes in the rhizosphere play a key role in biogeochemical cycling. Genomic technologies enable the investigation of the genetic and functional diversity of noncultivable microbes. Next generation sequencing technologies are revolutionising the study of microbial community analysis. Keywords: Genomics; rhizosphere; soil; plant–microbe interaction; microbial community; roots; metagenomics; metatranscriptomics; metaproteomics; metabolomics