No abstract

Deep-rooted plants can obtain water and nutrients from the subsurface, making them more resilient to climatic changes such as drought. In addition, the deeper root network also allow the plants to recruit bacteria from a larger reservoir in the soil. These bacteria might contribute to nutrient acquisition and provide other plant beneficial traits to the plant. However, the deep rhizosphere communities' compositions and their assembly dynamics are unknown. Here, we show, using three perennial crops, Kernza, lucerne and rosinweed, grown in 4 m RootTowers, that deep rhizosphere bacterial communities are plant specific, but clearly distinct from the shallow communities. We found that the diversity decreased with depth in the rhizosphere, whereas abundance of 16S rRNA gene copies did not change with depth in lucerne and rosinweed. Furthermore, we identified a subgroup (4-8%) of ASVs in the rhizosphere communities that could not be retrieved in the corresponding bulk soil communities. The abundances of genes determined by qPCR involved in N-cycling: amoA, nifH, nirK, nirS and nosZ differed significantly between plant species, suggesting differences in N content in the root exudates of the plant species. Our results suggest that colonization of the rhizosphere by bulk soil bacteria is not limited by carbon supply, but rather by dispersal. Furthermore, the abundance of N cycling genes indicate that deep rhizosphere bacteria have the potential to provide N through nitrogen fixation.

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 are 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 RootTowers, under semi-natural conditions. Across the plant species, higher bacterial abundance and lower diversity were found in the root-associated communities compared to 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 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.