Rhizosphere bacteriome structure and functions

TLDR

The rhizosphere is a dynamic microbial hotspot that selects for copiotrophic taxa such as Bacteroidetes and Proteobacteria, reduces overall diversity, and supports highly modular yet unstable bacterial networks driven by toxin–antitoxin dormancy strategies. We analyzed 557 pairs of published 16S rDNA amplicon sequences from bulk soils and rhizospheres across diverse ecosystems to generalize bacterial community diversity, composition, and functional traits. Functional predictions revealed that rhizosphere communities are enriched for genes involved in organic compound conversion, nitrogen fixation, and denitrification (by 11–182%) while genes for nitrification are depleted.

Abstract

Abstract Microbial composition and functions in the rhizosphere—an important microbial hotspot—are among the most fascinating yet elusive topics in microbial ecology. We used 557 pairs of published 16S rDNA amplicon sequences from the bulk soils and rhizosphere in different ecosystems 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.