Genomics of root-microbe interactions

Roots are exposed to a multitude of soil organisms and often form intimate associations with bacteria, fungi, and nematodes. Microbes influence roots by producing signals, toxins, altering nutrient cycling, and by invading roots as endosymbionts or endoparasites. Genomic tools have helped to elucidate the molecular changes induced in roots by microbes. Two mutualistic symbioses of roots, those with nitrogen-fixing rhizobia rhizobia and with mycorrhizal fungi mycorrhizal fungi, and the parasitic relationship between roots and endoparasitic nematodes endoparasitic nematodes have been at the center of research efforts to unravel molecular communication between roots and microbes. This had led to new insights into intracellular accommodation of symbionts, the balancing of defense responses, nutrient exchange, alteration of plant development, and feedback regulation of root organ numbers. This chapter highlights some of the recent advances gained by genomic and postgenomic studies focused on root-microbe interactions.