Metagenomics of plant—microbe interactions

The complex world of interactive patterns between microorganisms and plants includes relationships that span from soil, to rhizosphere, to phyllosphere and culminate inside the plant tissues in the endophytic condition. The nature of these interactions can be beneficial, neutral or pathogenic with a number of subtle differences and some overlaps between these conditions. The availability of metagenomics and NGS technologies has opened new perspectives and powerful ways to investigate this scenario. The questions that are central to such field involve: the identity and diversity of microorganisms relating with plants, the array of genes that are functional to this lifestyle, the relative effects of host genotype vs. environment of source in determining which taxa can become established as plant-associated microbiota; which genes are expressed when on or inside plants and which proteins are abundant in the different stages of the process. Metagenomics can in this respect be efficiently coupled to other—omics to provide a multiphasic picture of the ongoing phenomena that exploits the growing potentialities of high throughput investigations. The practical applications of these studies, besides the clearer insight into environmental biodiversity and ecology of microorganisms, can also involve valuable strategies for the improvement of crop productivity and their defense against plant pathogens.