Deep-Rooted Plant Species Recruit Distinct Bacterial Communities in the Subsoil

Deep-rooted plants can obtain water and nutrients from the subsoil, making them resilient to climatic changes. Plant growth and health may depend on interactions with root-associated bacteria but the composition and assembly dynamics of deep-root-associated bacterial communities are unknown, as is their ability to supply plants with nitrogen (N). Here, we investigated the root-associated communities of the three deep-rooted perennial crops-lucerne (Medicago sativa), intermediate wheatgrass (Thinopyrum intermedium), and rosinweed (Silphium integrifolium)-grown in 4-m-tall Root Towers under seminatural conditions. Across the plant species, higher bacterial abundance and lower diversity were found in the root-associated communities compared with the bulk soil communities. The deep-root-associated communities were enriched in the genera Pseudarthrobacter, Pseudomonas, Rhizobium, and Streptomyces, genera found to harbor a wide variety of bacterial species expressing plant beneficial traits. The composition of the deep-root-associated bacterial communities were plant species specific, and clearly distinct from the shallow communities. Additionally, the deep-root-associated communities comprised primarily amplicon sequence variants (ASVs) that were omnipresent in the bulk soil and, to a limited extent, ASVs that could have been transported from the topsoil or potentially from the seed. Abundances of genes involved in N-cycling (amoA, nifH, nirK, nirS, and nosZ) showed plant-species-specific patterns, and indicated that intermediate wheatgrass and lucerne recruit N-fixing bacteria even at 3 m of depth for N supply. This work provides the first steps toward understanding plant-microbe interactions of deep-rooted crops, which are important for evaluating these crops for use in future sustainable cropping systems.