title: Roots shaping their microbiome: global hotspots for microbial activity.
abstract: Land plants interact with microbes primarily at roots. Despite the importance of root microbial communities for health and nutrient uptake, the current understanding of the complex plant-microbe interactions in the rhizosphere is still in its infancy. Roots provide different microhabitats at the soil-root interface: rhizosphere soil, rhizoplane, and endorhizosphere. We discuss technical aspects of their differentiation that are relevant for the functional analysis of their different microbiomes, and we assess PCR (polymerase chain reaction)-based methods to analyze plant-associated bacterial communities. Development of novel primers will allow a less biased and more quantitative view of these global hotspots of microbial activity. Based on comparison of microbiome data for the different root-soil compartments and on knowledge of bacterial functions, a three-step enrichment model for shifts in community structure from bulk soil toward roots is presented. To unravel how plants shape their microbiome, a major research field is likely to be the coupling of reductionist and molecular ecological approaches, particularly for specific plant genotypes and mutants, to clarify causal relationships in complex root communities.
authors.affiliation: Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, D-28334 Bremen, Germany; email: breinhold@uni-bremen.de , wiebke.buenger@uni-bremen.de , claudia.burbano@uni-bremen.de , sabale@uni-bremen.de , thurek@uni-bremen.de.
authors.forename: Barbara
authors.initials: B
authors.lastname: Reinhold-Hurek
authors.forename: Wiebke
authors.initials: W
authors.lastname: Bünger
authors.forename: Claudia Sofía
authors.initials: CS
authors.lastname: Burbano
authors.forename: Mugdha
authors.initials: M
authors.lastname: Sabale
authors.forename: Thomas
authors.initials: T
authors.lastname: Hurek
mesh_terms: D018407:Bacterial Physiological Phenomena; D018517:Plant Roots / Q000382:microbiology*; D016133:Polymerase Chain Reaction; D058441:Rhizosphere; D012988:Soil Microbiology
keywords: culture-independent analysis; endophytes; endorhizosphere; metagenome; rhizoplane; rhizosphere soil