Microbiome of the Rhizosphere: from Structure to Functions

Abstract

Microbial composition and functioning in the rhizosphere are among the most fascinating but hidden topics in microbial ecology. We generalized bacterial traits regarding community diversity, composition and functions using published 16s rDNA amplicon sequences of 584 pairs of bulk soils vs rhizosphere of crops. The lower bacterial diversity in the rhizosphere (-7% richness) compared to root-free soil reflects the excess of available organic substances near the root. The rhizosphere is enriched by Bacteroidetes, Proteobacteria and Cyanobacteria as well as other copiotrophic bacteria (r strategists). Complex but unstable bacterial networks in rhizosphere reflect tight microbial interactions and adaptations to fluctuating conditions common for r strategists. The dominant dormancy strategy in the rhizosphere is the toxin-antitoxin system, while sporulation is common in bulk soil. Function prediction analysis showed that the rhizosphere is strongly enriched (50–115%) in methanol oxidation, ureolysis, cellulolysis, chitinolysis and nitrogen fixation, but strongly depleted in functions related to N-cycling.

Visualization and quantification of carbon “rusty sink” by rice root iron plaque: Mechanisms, functions, and global implications

“…Many factors control plaque formation by Fe 3+ precipitation, including ROL by roots, root density and biomass, Fe 2+ concentration in soil solution and plant water uptake, alternative electron acceptors, and the corresponding redox reactions (Weiss et al, 2003). The Fe plaque shapes FeOB and FeRB communities in paddy soils (Ling et al, 2022; Liu, Qin, et al, 2019; Weiss et al, 2003). The higher relative abundance of fast‐growing microorganisms, such as Proteobacteria and Firmicutes, in the control and after Fe addition in the rhizosphere increase the calorespirometric ratio (corresponding to the decrease of substrate use efficiency) compared with that under P addition (Figures 3D and 4A).…”