The rhizosphere revisited: root microbiomics

Abstract

The rhizosphere was defined over 100 years ago as the zone around the root where microorganisms and processes important for plant growth and health are located. Recent studies show that the diversity of microorganisms associated with the root system is enormous. This rhizosphere microbiome extends the functional repertoire of the plant beyond imagination. The rhizosphere microbiome of Arabidopsis thaliana is currently being studied for the obvious reason that it allows the use of the extensive toolbox that comes with this model plant. Deciphering plant traits that drive selection and activities of the microbiome is now a major challenge in which Arabidopsis will undoubtedly be a major research object. Here we review recent microbiome studies and discuss future research directions and applicability of the generated knowledge.

Keywords: Arabidopsis thaliana; Pseudomonas spp; extended phenotype; microbial communities; plant roots.

FIGURE 1

(A) Numbers (log cfu g^-1) of culturable aerobic bacteria and Pseudomonas spp. in bulk (black bars) and rhizosphere soil of Arabidopsis (gray bars) and Tobacco (white bars). Plants were grown for 7 weeks on a potting soil–sand mixture or a clay soil, which were either untreated or autoclaved twice heat treatment (HT) before planting. Different letters indicate significant differences within each soil type. (B) Denaturing gradient gel electrophoresis (DGGE) profile showing the Pseudomonas spp. community structure from bulk soils (top gel: potting soil; bottom gel: clay soil), and the rhizospheres of Arabidopsis and tobacco grown on these soils. M, reference marker; lanes 1 and 10, Arabidopsis rhizosphere grown on non-autoclaved soil; lanes 2 and 6, autoclaved bulk soil; lanes 3 and 9, tobacco rhizosphere grown on autoclaved soil; lanes 4 and 12, non-autoclaved bulk soil; lanes 5 and 7, tobacco rhizosphere grown on non-autoclaved soil; lanes 8 and 11, Arabidopsis rhizosphere grown on non-autoclaved soil. (C) Ordination biplot generated by redundancy analysis (RDA) of Pseudomonas-specific DGGE fingerprints of bulk soil and the rhizospheres of Arabidopsis and tobacco grown on (a) potting soil–sand mixture; (b) autoclaved potting soil–sand mixture; (c) clay soil; (d) autoclaved clay soil. Open triangles, bulk; open circles, Arabidopsis rhizosphere; open squares, tobacco rhizosphere; gray triangles, centroid position of variables.