Microbial feedbacks to climate: How climate and edaphic controllers shape the rhizosphere microbiome of a wild annual grass
The millimeters of soil that directly surround a root, known as the rhizosphere, plays a crucial role in all vegetated ecosystems, yet we know little about how a changing climate will alter this microhabitat. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the response of microbial communities to climate. The goal of this study was to determine the factors that shape rhizosphere microbial community assembly, such as climatic soil variables (temperature and moisture), abiotic soil characteristics, and dispersal limitation. We collected rhizosphere soil and the surrounding background soil from in-situ wild communities of Avena sp.(wild oat) using a nested-sampling design in three California grasslands, where the sampling sites spanned from 10 cm to 1 km (52 samples per site). Microbial communities were analyzed by 16S Illumina sequencing. Each site was characterized for a suite of edaphic characteristics (e.g., pH, soil texture, cation exchange capacity (CEC), total carbon and nitrogen), climatic characteristics (e.g., soil moisture, 8-month soil temperature range), and biological characteristics (e.g. above ground primary productivity, and total microbial biomass).
Rhizosphere soils were more similar to each other than to the background soils from which each was derived, and were more influenced by factors related to climate (soil moisture, temperature) than the background soil. Our results suggest that rhizosphere communities may be shaped by the host plants’ response to climate. Background soil community composition, on the other hand, was most strongly influenced by soil characteristics (pH, CEC, exchangeable cations, clay content). Using multiple regression, we have tested how soil moisture and temperature predicts rhizosphere community assembly (deterministic processes), as opposed to dispersal limitation (neutral processes). Our results suggest Avena selects for a root-specific microbiome that is strongly phylogenetically clustered, and even with a robust sequencing depth of approximately 70,000 sequences per sample, 17% of the taxa detected consistently in the rhizosphere were not detected in the background soil. This suggests that roots enrich less abundant or possibly rare populations in soil. We hypothesize that that some of these bacterial lineages have made a physiological trade-off for rhizosphere competence at the expense of competitiveness in soil outside the rhizosphere.