Gene-by-environment interaction significantly drives bacterial endophyte communities in maize stalks

Authors: LI, HANXIA - University Of Georgia; GRIFFIS, HOLLY - University Of Georgia; Edwards, Jode; Flint Garcia, Sherry; HIRSCH, CANDICE - University Of Minnesota; Holland, James; Knoll, Joseph; LIMA, DAYANE - University Of Wisconsin; DE LEON, NATALIA - University Of Wisconsin; MURRAY, SETH - Texas A&M University; SINGH, MANINDERPAL - Michigan State University; SCHNABLE, JAMES - University Of Nebraska; SEKHON, RAJANDEEP - Clemson University; THOMISON, PETER - The Ohio State University; THOMPSON, ADDIE - Michigan State University; WALLACE, JASON - University Of Georgia

Submitted to: bioRxiv
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/24/2025
Publication Date: 12/24/2025
Citation: Li, H., Griffis, H.K., Edwards, J.W., Flint-Garcia, S.A., Hirsch, C., Holland, J.B., Knoll, J.E., Lima, D., de Leon, N., Murray, S.C., Singh, M., Schnable, J.C., Sekhon, R.S., Thomison, P., Thompson, A.M., Wallace, J. 2025. Gene-by-environment interaction significantly drives bacterial endophyte communities in maize stalks. bioRxiv. https://doi.org/10.64898/2025.12.23.696053.
DOI: https://doi.org/10.64898/2025.12.23.696053

Interpretive Summary: Microbes associated with plants supply vital nutrients to the plant, manipulate growth, and provide other essential benefits to the plant. However, harnessing and manipulating microbes to benefit agriculture has been very elusive. Researchers at the University of Georgia in collaboration with multiple USDA ARS research labs and universities have quantified the roles of field locations (environment), maize hybrids (genetics), and soil factors in determining what microbes associate with corn plants. Researchers found that the field location where hybrids were grown was a much stronger determinant of microbe communities in corn plants than the genetics of the corn plant. It was also found that the microbe communities were influenced by soil pH and soil potassium level. The results of this study will help researchers better understand the factors that influence microbial communities and inform further research on how to manipulate these communities to benefit maize production.

Technical Abstract: Plant-associated microbes can benefit their host by supplying nutrients, manipulating hormone levels, and producing secondary metabolites. There has been great interest in harnessing beneficial plant-microbe interactions to improve agriculture; however, most microbes that show early promise fail to translate to field settings. Although there are likely several reasons for this, one key aspect is that the interactions between plants and microbes can vary across different host genetics and different environments. However, quantitative data for these differences is still scarce. To understand the environmental context of plant-microbe interactions, we sampled maize stalks from 20 specific hybrid varieties across 15 locations. We quantified the bacterial endophyte community in each sample by 16s amplicon sequencing and determined core microbiomes across environments and genotypes. We find that the stalk microbiome is highly variable, especially at finer taxonomic levels (genus, species), and that very few clades are prevalent enough to count as "core." We then determined the relative contribution of host genotype, environment, and genotype-by-environment (GxE) interactions in determining the makeup of these communities. We found large effects of the environment and GxE on individual microbes, the overall community composition, and predicted metabolic profiles. Host genotype by itself, however, had little to no consistent effects across environments. Although these communities were living in maize stalks, we identified soil factors (pH and potassium) as the most significant environmental drivers of the community. Our results indicate that while host genetics significantly affects the stalk microbial community, its effects are almost entirely predicated on interactions with the environment. These results imply harnessing crop microbiomes for agriculture will require significant investment in multilocation trials to accurately estimate GxE effects on microbial products.