Rhizosphere bacteriome structure and functions

Ning Ling,Tingting Wang,Yakov Kuzyakov

doi:10.1038/s41467-022-28448-9

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.

Highlights

Microbial composition and functions in the rhizosphere—an important microbial hotspot— are among the most fascinating yet elusive topics in microbial ecology
High-throughput sequencing of culture-independent marker genes, has greatly expanded the repertoire of microorganisms living in soils[14], and many studies have characterized root-associated microbial communities[9]
Bacterial alpha-diversity is depleted in the rhizosphere compared to the bulk soil in terms of observed species richness (−5.3%), Shannon’s diversity index (−0.9%), and Faith’s phylogenetic diversity (−3.7%) (Fig. 1)

Summary

Introduction

Microbial composition and functions in the rhizosphere—an important microbial hotspot— are among the most fascinating yet elusive topics in microbial ecology. All plants can exert general selective effects directed toward nutrient acquisition or pathogen suppression, regardless of their geographic origin or recent location These general patterns in the rhizosphere and bulk soils with respect to the taxonomic and functional profiles of bacterial communities remain largely unexplored. We analyzed and synthesized a very broad range of taxonomic and functional features of the bacteriome in the rhizosphere compared to bulk soil, and generalized these compositional changes to other factors such as plant species, geographic environment, and soil properties This provided general principles for the selection of microorganisms around living roots and laid the foundation for harnessing the power of the microbiome for sustainable terrestrial ecosystem functioning

Methods

Results

Conclusion