Nitrogen is one of the most powerful levers in modern agriculture. When supplies are inadequate, crops often produce less biomass, fewer seeds and smaller grains. Yet applying more nitrogen is not a simple solution. Crops commonly absorb only a fraction of the fertilizer supplied to fields; the remainder can leach into waterways, escape as nitrous oxide or undergo chemical transformations that contribute to air and climate pollution. Farmers therefore face a biological paradox: plants need enough nitrogen to build a productive canopy, but excessive applications are expensive and can damage ecosystems. Nitrogen-use efficiency, or NUE, describes how effectively a plant converts available nitrogen into harvestable yield. According to the review by Dmitry Veselov, Jiangzhe Zhao, Alla Korobova and colleagues, improving NUE will require understanding not just how nitrate enters roots, but how plants interpret its presence and coordinate their entire body in response.

The first step is nitrate perception. Plant roots use transporter proteins to acquire nitrate from soil, but some of these transporters also act as “transceptors”—molecules that combine transport activity with sensory functions. One of the best studied is NRT1.1, also known as CHL1 or NPF6.3 in Arabidopsis. Its activity changes with nitrate concentration, allowing roots to respond across a broad range of nutrient availability. At low nitrate levels, high-affinity NRT2 transporters help capture scarce ions; at higher concentrations, other transport systems become more important. NRT1.1 can also influence the distribution of auxin, another plant hormone, thereby altering the formation and elongation of lateral roots. This allows a plant to proliferate roots in nutrient-rich patches rather than spending the same amount of energy everywhere. Once nitrate is detected, calcium signals, protein phosphorylation and transcription factors such as NLP6 and NLP7 help activate a rapid nitrogen-response program.

Cytokinins add a second layer of control to this nutrient-sensing network. These hormones are produced in roots and shoots, and their concentration depends on a balance between biosynthesis, transport and breakdown. Nitrate availability can stimulate the expression of isopentenyl transferase, or IPT, enzymes involved in cytokinin production. In particular, nitrate-responsive changes in root IPT activity can increase the synthesis of cytokinin precursors, including forms that are converted into trans-zeatin, a biologically active cytokinin. Other enzymes, including cytokinin oxidases and dehydrogenases known as CKXs, remove or deactivate the hormones. The result is a dynamic system rather than a simple on–off switch: a change in nitrate supply can alter cytokinin production, chemical form and movement through the plant. Recent evidence highlighted in the review suggests that fluctuations in nitrate may even influence IPT3 through changes in chromatin and histone modification, allowing roots to adjust hormone production as nutrient conditions shift.

The direction of cytokinin movement is crucial. Root-derived cytokinins can travel upward through the xylem, carrying information about soil conditions to leaves and growing shoots. Transporters such as ABCG14 and related proteins help load and move cytokinin compounds over long distances, while purine permeases and other transport systems contribute to local distribution and hormone homeostasis. The shoot is not simply a passive recipient of this chemical message. It also sends information back to the roots through sugars, nitrogen-containing metabolites and mobile peptides. CEP peptides produced in roots under nitrogen limitation can be processed into signals that travel upward and stimulate shoot-to-root messages, including CEPD-like proteins that regulate nitrate uptake. Cytokinins therefore participate in a two-way conversation: roots report the availability of nitrate, while shoots communicate their demand for additional nitrogen. This feedback prevents the plant from absorbing nutrients indiscriminately when its leaves cannot use them efficiently.

The most visible consequence of this communication appears below ground, where nitrate and cytokinin signals help reshape root architecture. When nitrate is scarce, plants may favor deeper or more extensive roots capable of exploring a larger volume of soil. In a localized nitrate-rich patch, they can stimulate lateral root growth near the nutrient source. Cytokinins interact with auxin in this process, often exerting opposing effects on root and shoot development. High cytokinin activity in some root zones can limit primary root elongation, while reduced cytokinin levels may permit a larger root system. This explains why genetically or chemically reducing cytokinin degradation in roots can produce plants with enhanced root growth, improved mineral accumulation in shoots and greater drought tolerance. The effect is context-dependent, however. A root that grows farther is not automatically more efficient; constructing and maintaining extra tissue requires carbon. The plant must balance the energetic cost of exploration against the expected benefit of finding and absorbing more nitrate.

Above ground, cytokinins help determine whether newly acquired nitrogen becomes productive leaf area or is diverted elsewhere. Adequate cytokinin signaling promotes cell division, leaf expansion and chloroplast development, the process by which cells build the photosynthetic machinery that captures light. In rice, wheat and other cereals, higher cytokinin status has been associated with increased photosynthetic capacity under favorable nitrogen conditions. This connection is chemically logical: nitrogen is required to build chlorophyll and many photosynthetic proteins, including Rubisco, the enzyme that fixes carbon dioxide. Cytokinins can also influence stomatal behavior, chlorophyll maintenance and the expression of genes involved in carbon assimilation. By coordinating nitrogen uptake with photosynthetic activity, the plant can convert absorbed nitrate into sugars more efficiently. Those sugars, in turn, provide energy and carbon skeletons for nitrate assimilation, creating a feedback loop between carbon and nitrogen metabolism.

The review also draws attention to cytokinin’s role in delaying leaf senescence, the orderly deterioration of leaves as plants age or face nutrient stress. During grain filling, cereal crops depend heavily on flag leaves to continue producing carbohydrates that are transported into developing seeds. Nitrogen availability and cytokinin signaling can help maintain these leaves for longer, preserving photosynthetic activity at a stage when grain weight is being determined. At the same time, cytokinin metabolism must be carefully controlled. Excessive or poorly timed signaling can disrupt the balance between vegetative growth and reproduction. Enzymes such as CKXs act as important regulators of this balance. Research in rice has shown that altering CKX activity can affect grain number, grain filling and the relationship between carbohydrate-producing leaves and developing grains. Some transport proteins may even carry both sugar and cytokinin, linking the movement of energy and growth signals directly within developing cereal grains.

Nitrogen and cytokinin signaling may also help crops cope with drought, salinity, heat and flooding—stresses that are becoming more consequential as climates change. Nitrate can influence stress-related gene expression, antioxidant defenses and the production of reactive oxygen species, molecules that serve as signals at controlled levels but can damage cells when they accumulate excessively. Cytokinins interact with abscisic acid, the hormone strongly associated with drought responses, as well as with ethylene and other signaling pathways. Under water deficit, changes in cytokinin production and transport can alter the balance between shoot growth and root investment, helping plants conserve resources while continuing to search for water. In some systems, stress-induced cytokinin synthesis has been linked to coordinated regulation of carbon and nitrogen assimilation. Nitrate nutrition has also been associated with improved tolerance to salinity and heat, although the benefits depend on dose, timing, species and environmental conditions. Too much nitrogen can intensify stress by stimulating growth that the plant cannot support with available water.

The authors emphasize that these findings do not justify simply adding hormones or more fertilizer to fields. Cytokinins are powerful regulators, and their effects vary with tissue, developmental stage, nitrate concentration and interactions with other hormones. Instead, the review points toward precision strategies that might match fertilizer placement and timing to the plant’s signaling capacity. Localized fertilizer application could encourage roots to forage in nutrient-rich zones without saturating the entire soil profile. Breeding or gene editing might target nitrate sensors, cytokinin transporters, IPT biosynthetic enzymes or CKX catabolic enzymes to create crops that maintain productivity with less nitrogen. Beneficial soil microbes that produce or modify cytokinins could provide another route, particularly under drought or nutrient stress, although field performance remains difficult to predict. The central message is that future high-efficiency crops may be designed not only to absorb more nitrate, but to make better decisions about when, where and why to use it. By treating nitrate as both food and information, agriculture could move closer to producing more grain with less fertilizer—and make the plant’s own communication network part of the solution.

Subject of Research: Interaction between nitrate signaling and cytokinin hormones in plant nitrogen-use efficiency, growth, stress resistance and crop productivity

Article Title: Interaction between nitrates and cytokinins in the regulation of nitrogen use efficiency, plant growth, abiotic stress resistance and productivity

Article References: Veselov, D., Zhao, J., Korobova, A. et al. “Interaction between nitrates and cytokinins in the regulation of nitrogen use efficiency, plant growth, abiotic stress resistance and productivity.” Plant and Soil (2026). Original research page

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09011-7

Keywords: nitrate uptake, nitrogen-use efficiency, cytokinin signaling, cytokinin transporters, root architecture, crop productivity, drought resistance, cereal grain filling

Duckweed, a tiny yet fast-growing aquatic plant, has been explored for its capacity to influence nitrogen dynamics in flooded rice fields. The study’s experimental framework incorporated state-of-the-art high-precision gas exchange measurement chambers, allowing for the rigorous quantification of five reactive nitrogen gases: nitrous acid (HONO), nitrogen oxides (NOx), ammonia (NH3), nitrous oxide (N2O), and related nitrogen compounds. The experimental design contrasted bare soil conditions, nitrogen-fertilized soil, and nitrogen-fertilized soil coupled with duckweed coverage, thus teasing apart the plant’s direct and indirect effects on nitrogen emissions.

The results revealed a striking reduction in emissions of nitrogen oxides and nitrous acid when duckweed was present—a greater than 70 percent decrease in HONO and over 50 percent reduction in NOx compared to fertilized soil without duckweed. These gases are notorious contributors to atmospheric pollution and acid rain, and their suppression holds notable promise for air quality improvement. The mechanism underpinning this suppression was traced to duckweed’s modification of the soil microenvironment. By floating on the water surface, duckweed alters redox potential—shifting soil chemistry toward more oxidized conditions—and elevates pH levels. These changes foster a microbial community that favors pathways limiting reactive nitrogen oxide production, effectively transforming the biogeochemical cycling of nitrogen in the paddy ecosystem.

However, the study highlights a challenging trade-off. While the duckweed cover curtails nitrogen oxide emissions, it inadvertently stimulates a dramatic escalation of ammonia and nitrous oxide release. Ammonia emissions surged by a staggering 140-fold, and nitrous oxide emissions increased threefold compared to the fertilized control without duckweed. Nitrous oxide is a particularly potent greenhouse gas, with a global warming potential substantially exceeding that of carbon dioxide. The researchers attribute these elevated emissions to the decomposition of duckweed biomass, which introduces labile organic carbon and nitrogen into the soil. This influx fuels microbial processes such as nitrification and denitrification, intensifying the release of ammonia and N2O into the atmosphere.

Delving into the molecular realm, the researchers employed advanced metagenomic and transcriptomic tools to map shifts in the soil microbiome’s functional gene expression. Significant upregulation of genes associated with denitrification—as well as ammonia production—was documented in duckweed-treated soils. This genomic activation suggests that duckweed not only reshapes the chemical environment but actively remodels microbial metabolic pathways, steering nitrogen transformations toward enhanced gaseous loss. These findings underscore the intricate feedbacks between plant biomass input, soil chemistry, and microbial community dynamics underpinning nitrogen gas fluxes.

This complexity spotlights a critical implication: natural interventions that appear environmentally advantageous can incur unintended consequences if implemented in isolation. Duckweed, while reducing harmful nitrogen oxides, simultaneously amplifies emissions of other environmentally detrimental gases. Consequently, the study advocates a nuanced, integrated approach toward deploying duckweed in rice agriculture. Such strategies might involve periodic harvesting of duckweed biomass to prevent its decomposition on-site, thereby halting the chain reaction of increased ammonia and N2O emissions.

Additional soil amendments could further optimize outcomes. For instance, biochar incorporation might stabilize soil nitrogen and sequester carbon, while nitrification inhibitors can slow microbial conversion processes, collectively reducing gaseous nitrogen losses. These additive measures could leverage duckweed’s benefits while mitigating its drawbacks, positioning it as a component within a sophisticated toolkit for sustainable nitrogen management in rice paddies.

Co-author and senior researcher Dr. Zhimin Sha stresses that duckweed should not be seen as a silver bullet but rather as a promising piece in a complex puzzle. The research team calls for long-term, field-based studies to validate lab findings and quantify real-world impacts across diverse environmental conditions and rice cultivation systems. Such comprehensive monitoring is essential for developing adaptable, multifunctional approaches that reconcile agricultural productivity with environmental stewardship.

This study offers a paradigm shift in how biological interventions are evaluated in agroecosystems. It moves beyond simplistic assessments toward mechanistic insights into microbial ecology, biogeochemical feedbacks, and gas flux interactions. The researchers’ careful dissection of duckweed’s dual role serves as a cautionary tale against one-dimensional thinking and exemplifies the necessity of system-level perspectives in tackling global environmental challenges tied to food production.

In sum, the mechanistic evaluation of duckweed’s influence on nitrogen gas emissions represents a significant advance in understanding the subtleties of nitrogen cycling under flooded conditions. Its findings illuminate the promise and pitfalls of leveraging natural biological processes to curb harmful emissions from one of the planet’s most important crops. The enduring lesson is the power—and complexity—of tiny plants in shaping planetary-scale environmental outcomes, affirming the need for precision and integration in the design of sustainable agricultural practices.

Subject of Research: Not applicable

Article Title: Mechanistic evaluation of duckweed intervention on reactive nitrogen gas fluxes from paddy soils

News Publication Date: 28-Oct-2025

Web References: https://www.maxapress.com/nc

References: Lan Y, Xu S, Liu X, Li D, Chu Q, et al. 2025. Mechanistic evaluation of duckweed intervention on reactive nitrogen gas fluxes from paddy soils. Nitrogen Cycling 1: e008

Image Credits: Yiyu Lan, Shuhan Xu, Xiangyu Liu, Detian Li, Qingnan Chu, Dianming Wu, Yanwen Xu, Ping He, Chengrong Chen & Zhimin Sha

Keywords: Nitrogen, Nitrogen cycle, Sustainable agriculture

The challenge lies not only in the economic burden faced by farmers, as they wrestle with the escalating costs of imported nitrogen fertilizers, but also in the wider implications for water quality and climate change. When nitrogen escapes into groundwater, it leads to contamination, resulting in adverse effects such as harmful algae blooms that pose threats to aquatic ecosystems. Furthermore, the residual nitrogen in the soil undergoes microbial transformations into nitrous oxide, a potent greenhouse gas with a warming potential exponentially greater than that of carbon dioxide. Thus, the quest for enhanced nitrogen use efficiency represents a dual opportunity: to bolster agricultural productivity while supporting environmental sustainability.

Leading this charge is Gloria Coruzzi, the Carroll & Milton Petrie Professor in the Department of Biology at NYU. Coruzzi articulates the transformative potential of their research, emphasizing that through pinpointing critical genes responsible for nitrogen utilization, scientists can either select for favorable traits in breeding or even modify the genes themselves. Such advancements could lead to the development of crop varieties that utilize nitrogen more effectively, promising a vast reduction in fertilizer applications and a corresponding decrease in environmental degradation.

The approach taken by Coruzzi’s research team integrates machine learning with insights from plant genetics, a revolutionary perspective that leverages vast datasets to uncover patterns linking genes with traits of interest. Central to their study is the comparative analysis between corn, a staple crop for the U.S. economy, and Arabidopsis, a model organism in plant biology studies. This cross-species examination provides a unique vantage point from which to explore genetic similarities and functional relationships that govern NUE.

Previous research laid the groundwork by identifying conserved nitrogen-responsive genes between corn and Arabidopsis, validating their contributions to nitrogen use. Building on this foundation, the current study dives deeper into the genome, revealing that traits such as nitrogen use efficiency are regulated by groups of genes, known as “regulons.” These regulons are collectively controlled by transcription factors—a class of proteins that regulate gene expression and orchestrate the plant’s response to nitrogen treatment.

The researchers utilized RNA sequencing to analyze how corn and Arabidopsis genes respond when exposed to nitrogen. By harnessing machine learning algorithms, they created models capable of predicting nitrogen use efficiency based on both genotypic and phenotypic data. The evolutionarily conserved genes identified in this study were grouped into NUE regulons and their collective machine learning scores were calculated and ranked. The rigorous methodology employed by the researchers highlights the beauty of machine learning: it reveals complex relationships between multiple genes, rather than attributing physiological traits to singular genetic influencers.

Among the significant findings, two transcription factors were highlighted—ZmMYB34/R3 in corn and AtDIV1 in Arabidopsis. The former regulates 24 nitrogen-related genes in corn, while the latter governs 23 target genes sharing a genetic lineage with corn. This cross-species verification not only strengthens the model but also provides empirical evidence supporting the predicted roles of the identified genes in nitrogen utilization. Furthermore, feeding these validated NUE regulons back into the AI models significantly bolstered predictions for nitrogen use efficiency across various corn varieties grown in field conditions.

The implications of identifying these NUE regulons are profound. By screening corn hybrids at the seedling stage for the expression of identified genes tied to nitrogen use efficiency, farmers can make informed decisions about the varieties they cultivate. Implementing molecular markers at an early growth stage allows for the selection of hybrids most adept at efficiently utilizing nitrogen prior to field planting, ultimately presenting a proactive solution for modern agricultural challenges.

Coruzzi’s vision extends beyond immediate agricultural benefits. The potential to significantly mitigate nitrogen pollution and its cascading environmental effects underlines the importance of this research in the context of global sustainability efforts. Through this innovative intersection of plant genetics and artificial intelligence, the research represents a critical evolution in accurately predicting and managing nitrogen use in crops, echoing the call for environmentally responsible agricultural practices that harmonize productivity with ecological preservation.

The research, listed in a special focus issue of The Plant Cell, emphasizes translational research from model organisms to crop plants, celebrating milestones in plant genomics. New York University has filed a patent covering this pioneering work, suggesting that the implications of these findings could soon shift from academic theory to practical applications in agricultural practice, showcasing the ever-increasing significance of interdisciplinary collaboration in addressing real-world problems.

As this research unfolds, it captures the imagination not only of scientists but of farmers and consumers alike, pointing to tangible pathways toward a more sustainable future in food production. The integration of machine learning within plant genetics promises a new era of precision agriculture, wherein the focus shifts to optimizing resources and achieving ecological balance while continuing to meet the nutritional demands of a growing global population.

Subject of Research: Nitrogen Use Efficiency in Crops
Article Title: NUE regulons conserved model-to-crop enhance machine learning predictions of nitrogen use efficiency
News Publication Date: 14-May-2025
Web References: https://www.nyu.edu/about/news-publications/news/2021/september/machine-learning-uncovers-genes-of-importance.html
References: Coruzzi, G., et al. (2025). NUE regulons conserved model-to-crop enhance machine learning predictions of nitrogen use efficiency. The Plant Cell. DOI: 10.1093/plcell/koaf093.
Image Credits: Tracey Friedman/NYU

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