title: Impact of plant domestication on rhizosphere microbiome assembly and functions.
abstract: The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.
authors.affiliation: Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands.|Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
authors.forename: Juan E
authors.initials: JE
authors.lastname: Pérez-Jaramillo
authors.affiliation: Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000, Brazil.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Mendes
authors.affiliation: Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands. j.raaijmakers@nioo.knaw.nl.|Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands. j.raaijmakers@nioo.knaw.nl.
authors.forename: Jos M
authors.initials: JM
authors.lastname: Raaijmakers
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics / Q000382:microbiology*; D005838:Genotype; D064307:Microbiota; D018517:Plant Roots / Q000382:microbiology* / Q000502:physiology; D010944:Plants / Q000235:genetics / Q000382:microbiology*; D058441:Rhizosphere
keywords: Plant domestication; Plant–microbe interactions; Rhizosphere microbiome; Wild relatives