How roots, climate, and edaphic controllers shape the rhizosphere microbiome of a wild annual grass

Background/Question/Methods

The interface between roots and soil, known as the rhizosphere, is a dynamic habitat in the soil ecosystem. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the diversity of plant-microbial interactions that occur in soil. The goal of this study was to determine how the selective influence of a root compares to other factors that shape the soil microbial community, such as soil characteristics and the regional climate. We identified the bacteria present in the soil immediately adjacent to the roots of Avena sp.(wild oat) in three California grasslands using Illumina 16S sequencing. Each site contained a natural mixed plant community where the soils had not been tilled for at least the previous 10 years (in most cases >50 years). Each site was characterized for a suite of edaphic characteristics (e.g., pH, soil texture, cation exchange capacity (CEC), salinity, total carbon and nitrogen, phosphorus, and iron), climatic characteristics (e.g., soil moisture, 8-month soil temperature range), and biological characteristics (e.g. plant biomass, above ground primary productivity, and total microbial biomass).

Results/Conclusions

The rhizosphere soils were more similar to each other than to the background soils from which each was derived, despite the fact that the three grasslands studied were separated by hundreds of kilometers. The rhizosphere communities were more influenced by factors related to regional climatic conditions than the background soil (soil moisture, soil temperature), while the background soil communities were more influenced by soil characteristics (pH, CEC, exchangeable cations, clay content). Avena selected for a root-specific microbiome that was strongly phylogenetically clustered, which was primarily composed of families within the alpha-Proteobacteria, the Bacteroidetes, a single family within the Actinobacteria, as well as other less abundant phyla (Verrucomicrobia, Armatimonadetes (formerly OP10)). Even with a robust sequencing depth of approximately 70,000 sequences per sample, 17% of the taxa detected consistently in the rhizosphere soils were not detected in any of the background soils. This indicates that the root selects for populations of bacteria that can be rare in background soil. These results support the hypothesis that roots are agents of natural selection, which episodically enrich less abundant or rare populations in the soil microbial community.