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

Abstract

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.

Determining the footprint of breeding in the seed microbiome of a perennial cereal

“…Comparable to the current study, a previous investigation observed similar relative abundance patterns of nirK gene copy numbers in wheat seedlings [ 60 ]. In adult intermediate wheatgrass roots, however, they were almost 100-fold higher [ 15 ]. Though, the relative abundance of nirK and nifH gene copy numbers decreased over time in wheat and Brassica seedlings respectively, suggesting that the sampling timepoint may have a substantial influence on their occurrence [ 57 , 60 ].…”

“…Information on the positive ecosystem services of intermediate wheatgrass is increasingly available, however, knowledge of the microbiome of this crop is scarce. A limited number of studies addressed the microbiome of intermediate wheatgrass, targeting only below-ground compartments [ 14 , 15 ]. Perenniality and management influence the communities of soil nematodes, earthworms and bacteria associated with intermediate wheatgrass and the plants generally sustain more complex food webs compared to annual wheat [ 14 , 16 ].…”

“…Perenniality and management influence the communities of soil nematodes, earthworms and bacteria associated with intermediate wheatgrass and the plants generally sustain more complex food webs compared to annual wheat [ 14 , 16 ]. Furthermore, the deep roots of wheatgrass were shown to enrich potential plant-beneficial bacteria [ 15 ]. To date, no study has been published on endophytic microbial communities in intermediate wheatgrass.…”

The State of the Art in Root System Architecture Image Analysis Using Artificial Intelligence: A Review

“…Oft-cited methods of root harvesting are shovelomics [ 23 , 24 ], trenching (pioneered by [ 25 ]) [ 18 ], and coring [ 26 ]. These methods are labor-intensive and shovelomics, for example, requires destruction of the growth environment and removal of the sample plants by removing the root crown.…”