Lost and found: Rediscovering microbiome-associated phenotypes that reshape agricultural sustainability

Authors: FAVELA, ALONSO - University Of Arizona; KENT, ANGELA - University Of Illinois Urbana-Champaign; SIBLE, CONNOR - University Of Illinois Urbana-Champaign; Flint Garcia, Sherry; KLIMASMITH, ISAAC - University Of Illinois Urbana-Champaign; MUJJABI, CHRISTOPHER - University Of Illinois Urbana-Champaign; RAGLIN, SIERRA - University Of Illinois; BELOW, FRED - University Of Illinois Urbana-Champaign; BOHN, MARTIN - University Of Illinois Urbana-Champaign

Submitted to: Science Advances
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2025
Publication Date: 1/1/2026
Citation: Favela, A., Kent, A.D., Sible, C.N., Flint Garcia, S.A., Klimasmith, I.M., Mujjabi, C., Raglin, S.S., Below, F.E., Bohn, M.O. 2026. Lost and found: Rediscovering microbiome-associated phenotypes that reshape agricultural sustainability. Science Advances. 12(1). https://doi.org/10.1126/sciadv.aed3360.
DOI: https://doi.org/10.1126/sciadv.aed3360

Interpretive Summary: Nitrogen is one of the major inputs for corn production in modern agricultural systems. Nitrogen cycling in the soil is governed largely by microbial communities, where microbes alter nitrogen movement through the soil and nitrogen availability to growing plants. Plants can partially suppress some microbial activities (such as nitrification and denitrification) involved in nitrogen cycling, thereby reducing nitrogen losses before plants can use the nitrogen. These plant suppression mechanisms can improve soil nitrogen uptake by over 50%, resulting in higher yields under reduced nitrogen inputs. We previously found that corn’s wild ancestor, teosinte, was able to change soil microbial communities in favor of suppressing nitrification and denitrification. In this study, we tested whether teosinte-derived genes could alter nitrogen cycling and microbial communities in modern corn under field conditions. We determined that several chromosomal regions from teosinte allowed the plants to inhibit nitrification and denitrification. We determined that the teosinte genes produce chemicals related to sulfur metabolism, which can reprogram root chemistry and alter microbial communities. This work demonstrates the transformative effects on nitrogen cycling through shifts in corn root metabolites and microbial populations. Understanding the connections between plant genes and microbial activities is essential for breeders and geneticists to reintroduce genes from wild relatives into corn to improve nitrogen uptake by the corn crop. Ultimately, farmers will benefit from this research by reducing nitrogen fertilizer expenses in corn production.

Technical Abstract: Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification—key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and exudate metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. These findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture.