The shared rhizosphere bacteriome of multiple plant species reveals species-specific and neighbor-specific recruitment

Authors: NEWBERGER, DEREK - Colorado State University; Deel, Heather; Manter, Daniel; VIVANCO, JORGE - Colorado State University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/14/2025
Publication Date: 1/27/2025
Citation: Newberger, D.R., Deel, H.L., Manter, D.K., Vivanco, J.M. 2025. The shared rhizosphere bacteriome of multiple plant species reveals species-specific and neighbor-specific recruitment. PLOS ONE. 20(1). Article e0316676. https://doi.org/10.1371/journal.pone.0316676.
DOI: https://doi.org/10.1371/journal.pone.0316676

Interpretive Summary: Root and rhizosphere studies often focus on analyzing single-plant microbiomes; however, the rhizosphere of crop plants are subject to both intraspecific (i.e., monoculture) and interspecific (i.e., polyculture) interactions. These influence of these two different types of plant-plant interactions on the plant's microbiome were analyzed in a microcosm study containing different combinations and densities of common cover crops, such as alfalfa, mustards, and fescues. Rhizobacterial beta diversity was promoted by increasing plant diversity; however, this effect can be reduced if planting densities are too high. This work shows the potential trade-offs between plant diversity and density on the resulting diversity of microbes in the soil.

Technical Abstract: Root and rhizosphere studies often focus on analyzing single-plant microbiomes, with the literature containing minimum empirical information about the shared rhizosphere microbiome of multiple plants. Here, the rhizosphere of individual plants was analyzed in a microcosm study containing different combinations and densities of cover crops: Medicago sativa, Brassica sp., and Fescue sp. Rhizobacterial beta diversity was promoted by increasing plant diversity around the target plant species. In contrast, rhizobacterial beta diversity was reduced by increasing plant density around the target plant species. Regardless of plant neighbor identity or density, a low number of rhizobacteria were strongly associated with each target species. Nonetheless, a few bacterial taxa were shown to have conditional associations such as being enriched within only high plant densities, which may alleviate plant competition between these species. Also, we found evidence of bacterial sharing of nitrogen fixers from alfalfa to fescue. Although rhizosphere bacterial networks had overlapping bacterial modules, the modules showing the largest percentage of the network changed depending on plant neighbor. In summary, this supports that intraspecific competition helps establish a plant’s microbiome. Additionally, interspecific competition brought on by polyculture and intercropping is not detrimental to a plant’s bacterial recruitment which indicates the possibility of co-existence between plant species.