At the heart of this groundbreaking research lies the intricate interplay between corn genetics and soil microbiology. Corn fields traditionally suffer from substantial nitrogen loss, which not only diminishes soil fertility but also contributes to environmental pollution and climate change. Nitrogen fertilizers are a cornerstone of modern agriculture, yet a significant portion of applied nitrogen escapes into air and water systems through microbial processes known as nitrification and denitrification. The microbes responsible transform beneficial ammonium nitrogen into nitrate and nitrogen gases, some of which are potent greenhouse gases like nitrous oxide.

Angela Kent, lead researcher and professor at the Department of Natural Resources and Environmental Sciences at the University of Illinois, elaborates on these microbial dynamics. “Nitrifying bacteria convert ammonium into nitrate, which easily leaches into waterways causing eutrophication. Meanwhile, denitrifying bacteria convert nitrate into gaseous forms. Under certain conditions common in conventional farming—like oxygen-rich soil or carbon-poor environments—these bacteria produce nitrous oxide, a greenhouse gas far more potent than carbon dioxide.”

The researchers dug deeper into the genetic origins of these traits by revisiting corn’s ancestral lines. During the Green Revolution, breeding focused primarily on aboveground traits such as yield and pest resistance, inadvertently neglecting root traits and the rhizosphere—the microbe-rich zone surrounding the roots. This oversight allowed nitrifying and denitrifying bacteria to flourish, exacerbating nitrogen loss issues. The team posited that genes lost during modern breeding might be present in teosinte, the wild and weedy ancestor of modern maize.

Previous findings from 2021 revealed that teosinte roots secrete chemicals capable of suppressing the activity of nitrifying and denitrifying microbes. This fascinating microbial inhibition maintains soil nitrogen in the more stable ammonium form, reducing losses and enhancing nitrogen use efficiency. The new study expanded on this insight by examining near-isogenic lines (NILs), which are modern corn lines containing small gene segments from teosinte. By growing 42 NILs alongside pure B73 (a well-characterized modern inbred corn line) and teosinte itself in field trials, they monitored changes in rhizosphere microbial populations and nitrification potential.

The results were remarkable. Two NILs exhibited a striking 50% decrease in nitrification activity compared to B73, while two others showed similarly robust suppression of denitrification. Many additional lines reduced denitrification to varying extents. These introgressed teosinte genes selectively modulated root chemistry in a way that negatively impacted nitrifier and denitrifier activity without compromising the plant’s ability to absorb nitrogen. Moreover, these microbiome-mediated traits are robust; they behave dominantly, persisting even when introgressed into hybrid corn backgrounds, and crucially, they do so without any yield penalty.

Alonso Favela, assistant professor at the University of Arizona and first author of the study, highlights the significance of these findings. “The nitrification inhibition trait appears to be dominant, and when bred into hybrid corn backgrounds, it preserves yield. This means we can engineer high-performing crops that are simultaneously sustainable, conserving nitrogen and mitigating greenhouse gas emissions.”

Corn is grown on over 97 million acres in the United States alone. If the nitrification inhibition trait were scaled to this level, it could revolutionize nitrogen management across the country’s vast corn belt. The potential environmental benefits are vast, including reductions in water pollution, lower nitrous oxide emissions, and decreased reliance on synthetic nitrogen fertilizers — the manufacture of which consumes tremendous fossil fuel resources.

From a technical standpoint, the research underscores a new paradigm in plant breeding, extending selection to include effects on the rhizosphere microbiome. This “extended phenotype” approach centers on the plant’s influence over the soil microbial community, a dynamic and critical interface in nutrient cycling and plant health. By harnessing genetic loci from wild relatives, breeders can reintroduce beneficial microbial interactions lost during decades of focusing on aboveground traits.

This innovation also raises intriguing prospects for integrating other beneficial microbial functions into crops. Kent envisions combining microbiome traits that conserve nitrogen with those that enable symbiotic nitrogen fixation, a process currently absent in cereal crops like maize. Such synergies could lead to breakthrough reductions in the need for synthetic fertilizers, pushing agriculture towards true sustainability.

Further research funded by major agencies including the National Institute of Food and Agriculture, National Science Foundation, and the Department of Energy’s Center for Advanced Bioenergy and Bioproducts Innovation aims to decipher the precise genes and molecular pathways responsible for these interactions. The maize genetic resources housed at the Maize Genetics Cooperation Stock Center provide an invaluable repository for identifying candidate genes controlling rhizosphere chemistry.

Looking ahead, translating these findings from experimental lines into commercially viable varieties will hinge not only on breeding but also on regulatory approvals and farmer adoption. However, the absence of yield penalties paired with significant environmental benefits strengthens the case for adoption in modern agriculture. As nitrogen pollution remains a global challenge, innovations like this could play a critical role in balancing food security with ecosystem health.

In summary, rediscovering the genomic legacy of corn’s wild ancestor offers a promising avenue to mitigate the environmental footprint of one of the world’s most important crops. By embracing the microbial ecology beneath our feet, scientists are pioneering novel strategies to conserve resources, reduce pollution, and build a resilient agricultural future. This study exemplifies the power of combining cutting-edge genetics with ecological insights to address some of the most pressing challenges facing global food production and environmental stewardship.

Subject of Research: Agricultural sustainability, soil microbiome modulation, nitrogen cycling in corn
Article Title: Lost and found: Rediscovering microbiome-associated phenotypes that reshape agricultural sustainability
Web References: DOI: 10.1126/sciadv.aed3360
Image Credits: Lauren Quinn, University of Illinois
Keywords: corn genetics, teosinte, nitrification inhibition, denitrification suppression, soil microbiome, nitrogen loss, greenhouse gas emissions, sustainable agriculture, rhizosphere, nitrogen cycling

In an innovative departure from traditional breeding methods focused solely on plant genetics, researchers led by Wolfram Weckwerth at the University of Vienna are pioneering a new approach rooted in the holobiont concept. This paradigm recognizes the intimate, co-evolutionary relationships between plants and their associated microbiomes—the communities of microbes inhabiting the root and leaf environments. By targeting this intricate plant-microbe symbiosis, breeders can harness natural biological mechanisms to reduce dependence on synthetic nitrogen fertilizers and enhance crop resilience against climate pressures.

Central to this approach is the exploitation of biological nitrification inhibitors (BNIs), naturally occurring compounds exuded by certain plant roots that suppress the microbial processes converting soil ammonium to nitrate. Since nitrate tends to be more mobile and prone to leaching, BNIs effectively slow nitrogen loss and improve nitrogen use efficiency. Although BNIs have been identified in a few species, understanding their variation within major crops like wheat has remained elusive due to the complexity of microbial interactions and biochemical pathways.

To address this, the research team conducted a detailed examination of root exudates from a diverse set of elite wheat cultivars, discovering significant variation in BNI activity across genotypes. This natural variability represents a powerful genetic resource. By profiling these root secretions using advanced metabolomic techniques and integrating microbiome sequencing data, scientists can now identify high-BNI lines capable of fostering beneficial soil microbiomes that promote nitrogen retention and soil health.

Arindam Ghatak, the first author of the study, emphasizes the sophistication required in characterizing root exudates, which encompass a complex mixture of metabolites that modulate microbial community structures in the rhizosphere. Such chemical dialogues select for microbial strains adept at inhibiting nitrification, thereby stabilizing nitrogen in forms more accessible to plants. Cultivating wheat varieties expressing robust BNI activity thus emerges as a promising strategy to reduce fertilizer inputs without sacrificing yield.

To scale this concept beyond the laboratory, the team developed a novel data-driven breeding framework that integrates plant genomics, soil microbiome profiling, and PANOMICS datasets—including transcriptomics, metabolomics, and proteomics. This systems biology approach, deployed through machine learning algorithms, can unravel multifaceted interactions within the plant holobiont and predict plant genotypes with optimal microbiome assembly and nitrogen use traits. The international collaboration spanned continents—from Europe to Asia and the Americas—reflecting the global imperative of sustainable agriculture.

Wolfram Weckwerth underscores that this holobiont-based breeding platform represents a paradigm shift in crop improvement. By bridging ecology, molecular biology, and breeding technology, it transcends conventional genotype-to-phenotype models and embraces agriculture as a complex ecosystem process. Enhancing natural nitrogen management via plant-microbe partnerships holds promise not only for climate change mitigation but also for restoring soil fertility and biodiversity in agroecosystems.

Moreover, crops developed under this framework are expected to exhibit greater resilience to abiotic stresses such as drought and extreme temperatures, conditions increasingly exacerbated by climate change. Improving root exudate profiles to shape beneficial microbiomes could also reduce the need for chemical pesticides by promoting pathogen-suppressive soil communities. This integrative strategy paves the way toward truly sustainable farming systems that harmonize productivity with ecological stewardship.

While the promise is substantial, challenges remain in translating these findings into field-scale practices. The complexity and context-dependence of soil microbiomes necessitate extensive validation across diverse environments to ensure stable BNI expression and beneficial microbiome assembly. Additionally, breeding for microbiome traits requires new phenotyping methods and robust computational tools to manage vast datasets. Nonetheless, the early successes demonstrated by Weckwerth’s team provide a beacon for the future of agro-biotechnology.

In parallel with experimental breeding, advances in synthetic biology and microbiome engineering offer complementary routes to harness plant holobionts. The integration of bioinformatics, remote sensing, and precision agriculture technologies will further enable targeted management of plant-microbe interactions in situ. Together, these innovations are set to revolutionize how agriculture addresses its environmental footprint, feeding a burgeoning population while safeguarding planetary health.

This research ultimately aligns with the goals of the United Nations Sustainable Development Goals, particularly those related to zero hunger, climate action, and life on land. By fostering crops that optimize natural nitrogen cycling, reduce greenhouse gas emissions, and enhance soil ecosystem services, the holobiont breeding concept stands at the forefront of sustainable agroecosystem design. Continued interdisciplinary efforts will be crucial to realize this vision on a global scale.

As nitrogen management increasingly emerges as a linchpin of agricultural sustainability, integrating biological insights into crop improvement heralds a new era. The convergence of molecular systems biology, ecology, and breeding illustrated by the work of Weckwerth and colleagues inspires transformative pathways to balance human food security with environmental resilience. This holistic perspective may well define the next generation of climate-smart agriculture.

Subject of Research: Nitrogen use efficiency in wheat through plant-microbiome interactions and biological nitrification inhibitors

Article Title: Natural variation of the holobiont for sustainable agroecosystems.

News Publication Date: 27-Jun-2025

Web References: http://dx.doi.org/10.1016/j.tplants.2025.05.006

Image Credits: Weckwerth

Keywords: nitrogen fertilizers, biological nitrification inhibitors, holobiont concept, wheat breeding, soil microbiome, climate change resilience, sustainable agriculture, PANOMICS, machine learning, plant-microbe interactions, nitrogen loss mitigation, agroecosystems