Microbiome of rhizosphere: from structure and functions

Abstract

Microbial composition and functions in the rhizosphere – an important microbial hotspot – are among the most fascinating yet elusive topics in microbial ecology. Based on the similarity of rhizosphere properties with respect to carbon availability and nutrient depletion, we hypothesized that (i) rhizobacterial populations are recruited from the bulk soil, but are preselected by excess released root carbon, so that bacterial diversity is lower in the rhizosphere and bacterial networks are less stable, (ii) the rhizosphere is home to more abundant copiotrophic bacteria than the bulk soil, and iii) the functional capacity involved in the carbon and nitrogen transformation would be greater in the rhizosphere.We used 557 pairs of published 16S rDNA amplicon sequences from the bulk soils and rhizosphere in natural and agricultural ecosystems (forests, grasslands, croplands) around the world to generalize bacterial characteristics with respect to community diversity, composition, and functions.The rhizosphere selects microorganisms from bulk soil to function as a seed bank, reducing microbial diversity. The rhizosphere is enriched in Bacteroidetes, Proteobacteria, and other copiotrophs. Highly modular but unstable bacterial networks in the rhizosphere (common for r-strategists) reflect the interactions and adaptations of microorganisms to dynamic conditions. Dormancy strategies in the rhizosphere are dominated by toxin–antitoxin systems, while sporulation is common in bulk soils. Functional predictions showed that genes involved in organic compound conversion, nitrogen fixation, and denitrification were strongly enriched in the rhizosphere (11–182%), while genes involved in nitrification were strongly depleted. Thus, rhizosphere is the most powerful factor shaping the composition, structure and functions of the soil microbiome and of biogenic element’s cycling.ReferenceLing N, Wang T, Kuzyakov Y 2022. Rhizosphere bacteriome structure and functions. Nature Communications 13, 836. https://doi.org/10.1038/s41467-022-28448-9