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At least 145 records · Page 8

Fully‐Printed Ion Sensor Arrays for Measuring Agricultural Nitrogen and Potassium Concentrations Using Nernstian and AI Models

Abstract The chemical composition of growing media is a key factor for plant growth, impacting agricultural yield and sustainability. However, there is a lack of affordable chemical sensors for ubiquitous nutrient ion monitoring in agricultural applications. This work investigates using fully printed ion‐sensor arrays to measure the concentrations of nitrate, ammonium, and potassium in mixed‐electrolyte media. Ion sensor arrays composed of nitrate, ammonium, and potassium ion‐selective electrodes and a printed silver‐silver chloride (Ag/AgCl) reference electrode are fabricated and characterized in aqueous solutions in a range of concentrations that encompass what is typical for agricultural growing media (0.01 m m –1 m ). The sensors are also tested in mixed‐electrolyte solutions of NaNO 3 , NH 4 Cl, and KCl of varying concentrations, and the recorded potentials are input into Nernstian and artificial neural network models to compare the prediction accuracy of the models against ground truth. The artificial neural network models demonstrated higher accuracy over the Nernstian model, and the model using only ion‐sensor inputs is 7.5% more accurate than the Nernstian model under the same conditions. By enabling more precise and efficient fertilizer application, these sensor arrays coupled to computational models can help increase crop yields, optimize resource use, and reduce environmental impact.

Goodrich, Payton [University of California Berkele↗

Halophytes and heavy metals: A multi‐omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima

Abstract Premise The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we usedCakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole‐genome triplication with closely related salt‐sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy. Methods Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response inC. maritimaand identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium. Results Cakile maritimais tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool inC. maritimaand likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved inC. maritimaabiotic stress tolerance. Conclusions These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.

Plant Sciences↗

Planting miscanthus instead of row crops may increase the productivity and economic performance of farmed potholes

Abstract Climate change projections indicate that precipitation events in the central United States are expected to become more intense, more frequent in the spring, and less frequent in the summer. Such a precipitation shift could adversely impact crop yields, especially in subfield areas known as farmed potholes, which are highly susceptible to flooding and ponding, and crop death is more likely to occur, particularly early in the growing season. This suggests that planting alternative crops, such as more flood tolerant perennials, in these areas may be a more profitable option. Using observations of crop growth and yield along with ponding depth of a specific field and farmed pothole in the central United States, we developed a spatially explicit version of the agroecosystem model Agro‐IBIS to estimate water depth and crop yield. After evaluating the model, we conducted a case study for a specific farmed pothole with a range of future precipitation scenarios with Agro‐IBIS to simulate the effects of contemporary (2002–2016) and future precipitation on a conventional corn/soybean ( Zea mays L. and Glycine max Merr.) rotation and an alternative perennial miscanthus ( Miscanthus × giganteus Greef et Deu.) cropping system. The depth and frequency of ponding increased under most future precipitation scenarios. The corn/soybean rotation had greater total loss (i.e., no yield) on average (>30%) for all scenarios in comparison to miscanthus (<10%). Under one future precipitation scenario with increased spring precipitation, both the corn/soybean rotation and miscanthus simulations showed an increase in yield. A simple budget analysis indicated that it is more profitable to plant miscanthus instead of corn or soybeans where yields in farmed potholes are consistently poor. Our findings show that potholes can be individually modeled, and their influence on yield can be quantified for use in future management decisions dictated by change in climate.

54 ENVIRONMENTAL SCIENCES↗

Impact of vertical and seasonal variation in leaf traits on simulating soybean canopy photosynthesis via 1D and 3D modeling

Accurate modeling of photosynthesis is crucial for predicting crop productivity and quantifying the carbon cycle in agroecosystems. Leaf traits are essential inputs for modeling canopy photosynthesis. Yet, many existing models still use fixed plant functional type (PTF)-based values to parameterize leaf traits under a big-leaf or two-big-leaf assumption, neglecting their vertical profiles and seasonal changes. This simplification may introduce significant uncertainties in estimating gross primary productivity (GPP). In this study, we simulated soybean GPP and tested the effects of vertical and seasonal variation in three key leaf photosynthetic traits: the maximum carboxylation rate at 25 °C (Vcmax 25 ), leaf chlorophyll content (LCC), and leaf mass per area (LMA) in the 1D-SCOPE and 3D-Helios models. Weekly field measurements were conducted during the growing season of 2024 to support the simulation. We designed ten leaf trait parameterization schemes by incorporating different combinations of vertical profiles and seasonal changes, while assuming homogeneous canopy architecture in both models. Our results revealed that Vcmax 25 vertical and seasonal variation had the strongest influence on simulated GPP in both 1D and 3D models, while LCC and LMA effects were minimal. Particularly, the scheme with an empirically parameterized Vcmax 25 profile achieved comparable performance to the scheme with the measured Vcmax 25 profile. Both 1D-SCOPE and 3D-Helios accurately modeled GPP (SCOPE: R 2 = 0.87, Bias = 0.55 µmol m⁻² s⁻¹; Helios: R 2 = 0.9, Bias = 0.22 µmol m⁻² s⁻¹) under the most complex scheme, and their responses to vertical and seasonal variation in leaf traits were consistent, demonstrating the robustness of our findings. Based on our findings, we propose a scalable framework for parameterizing leaf traits to improve GPP simulations. This study contributes to improving the representation of leaf trait dynamics in canopy-level photosynthesis models, potentially enhancing our ability to predict crop productivity and understand agroecosystem carbon dynamics.

54 ENVIRONMENTAL SCIENCES↗

Cycles-L: A Coupled, 3-D, Land Surface, Hydrologic, and Agroecosystem Landscape Model

Managing landscapes to increase agricultural productivity and environmental stewardship can be informed by spatially-distributed models that operate at spatial and temporal scales that are intervention-relevant. This paper presents Cycles-L, a landscape-scale agroecosystem and hydrologic modeling system, using as a test case a watershed in Pennsylvania. Cycles-L emerges from melding the landscape and hydrology structure of Flux-PIHM, a 3-D land surface hydrologic model, with the agroecosystem processes in the Cycles model. Consequently, Cycles-L can simulate processes affected by topography, soil heterogeneity, and management practices, owing to its physically-based hydrology that can simulate horizontal and vertical transport of solutes with water. The model was tested at a 730-ha experimental watershed within the Mahantango Creek watershed. Cycles-L simulated well stream water and mineral nitrogen discharge (Nash-Sutcliffe coefficient 0.55 and 0.60, respectively) and grain yield (root mean square error 1.2 Mg ha -1 ). Cycles-L outputs are as good or better than those obtained with the uncoupled Flux-PIHM (water discharge) and Cycles (grain yield) models. Modeled spatial patterns of nitrogen fluxes like denitrification illustrate the combined control of crop management and topography. For example, denitrification is almost twice as high when simulated with Cycles-L than when simulated with Cycles 1-D. Due to its spatial and temporal resolution, Cycles-L fills a gap in the availability of models that operate at a scale relevant to evaluate interventions in the landscape. Cycles-L can become a central component in tools for climate change scenario analysis, precision agriculture, precision conservation, and artificial intelligence-based decision support systems.

54 ENVIRONMENTAL SCIENCES↗

Elucidation of Triacylglycerol Overproduction in the C4 Bioenergy Crop Sorghum bicolor by Constraint-Based Analysis

Upregulation of triacylglycerols (TAGs) in vegetative plant tissues such as leaves has the potential to drastically increase the energy density and biomass yield of bioenergy crops. In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. Here we present a core metabolism model for the C 4 biomass crop Sorghum bicolor ( iTJC1414 ) along with a minimal model for photosynthetic CO 2 assimilation, sucrose and TAG biosynthesis in C 3 plants. Extending iTJC1414 to a four-cell diel model we simulate C 4 photosynthesis in mature leaves with the principal photo-assimilatory product being replaced by TAG produced at different levels. Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. For plant generic pathways, ATP- and NADPH-demands per CO 2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the photosynthetic supply in ATP and NADPH in iTJC1414 is adjusted to be balanced for sucrose as the sole photo-assimilatory product, overproduction of TAG is predicted to cause a substantial surplus in photosynthetic ATP. This means that if TAG synthesis was the sole photo-assimilatory process, there could be an energy imbalance that might impede the process. Adjusting iTJC1414 to a photo-assimilatory rate that approximates field conditions, we predict possible daily rates of TAG accumulation, dependent on varying ratios of carbon partitioning between exported assimilates and accumulated oil droplets (TAG, oleosin) and in dependence of activation of futile cycles of TAG synthesis and degradation. We find that, based on the capacity of leaves for photosynthetic synthesis of exported assimilates, mature leaves should be able to reach a 20% level of TAG per dry weight within one month if only 5% of the photosynthetic net assimilation can be allocated into oil droplets. From this we conclude that high TAG levels should be achievable if TAG synthesis is induced only during a final phase of the plant life cycle.

59 BASIC BIOLOGICAL SCIENCES↗

Considering uncertainties expands the lower tail of maize yield projections

Crop yields are sensitive to extreme weather events. Improving the understanding of the mechanisms and the drivers of the projection uncertainties can help to improve decisions. Previous studies have provided important insights, but often sample only a small subset of potentially important uncertainties. Here we expand on a previous statistical modeling approach by refining the analyses of two uncertainty sources. Specifically, we assess the effects of uncertainties surrounding crop-yield model parameters and climate forcings on projected crop yield. We focus on maize yield projections in the eastern U.S.in this century. We quantify how considering more uncertainties expands the lower tail of yield projections. We characterized the relative importance of each uncertainty source and show that the uncertainty surrounding yield model parameters is the main driver of yield projection uncertainty.

59 BASIC BIOLOGICAL SCIENCES↗

CORN (Crop Optimization Realized through Neuralnets)

Traditional models of predicting plant traits are limited because they often rely on linear assumptions that do not fully capture the complexity of biological interactions and DNA-based markers which are static across environments. This project generated a set of RNA-based data from large multi-environment field trials and combined it with advanced machine learning techniques to account for these complex interactions and improve the accuracy of predictions.

59 BASIC BIOLOGICAL SCIENCES↗

Community Input on the Need, Scope, and Development Roadmap of a Proposed National Virtual Biosecurity for Bioenergy Crops Center (NVBBCC)

Brookhaven National Laboratory (BNL) was awarded a pilot project in FY22 under the U.S. Department of Energy (DOE) Office of Science Biopreparedness Research Virtual Environment (BRaVE) initiative, to define research priorities, needs, and requirements for a national virtual center devoted to the biosecurity of bioenergy crops. The mission of the proposed center, referred to as the National Virtual Biosecurity for Bioenergy Crop Center (NVBBCC), would be to provide the scientific basis and tools to detect, characterize, model, and mitigate biothreats to bioenergy crops. This function will be essential to ensure the projected increased US reliance over the next few decades on key plant-based energy products, such as biojet fuel. The NVBBCC is envisioned as a distributed, virtual center with multiple national laboratories at its core to maximize the use of existing unique facilities and expertise across the DOE complex. A major goal of the pilot project was to develop a roadmap for establishing NVBBCC through a series of meetings to gather community input. A total of about 150 individuals, drawn from DOE laboratories, the USDA, academia, NIH, DHS and the private sector participated in six planning meetings held in FY23. Four of the meetings were focused on specific research topics (disease detection, dispersion and disease propagation, biomolecular characterization of plant-pathogen interaction, and mitigation strategies). These four meetings were followed by a meeting that focused on computational needs to support collaborative, data-intensive research within a distributed center as well as workforce development. A final meeting focused on establishing and maintaining preparedness within NVBBCC to respond to an emerging disease within bioenergy crops and how it would collaborate and coordinate with USDA and DHS.

09 BIOMASS FUELS↗

Quantifying carbon budget, crop yields and their responses to environmental variability using the ecosys model for U.S. Midwestern agroecosystems

As one of the major agricultural production areas in the world, the United States (U.S.) Midwest plays a vital role in the global food supply and agricultural ecosystem services. Although significant efforts have been made in modeling the carbon cycle dynamics over this area, large uncertainty still exists in the previous simulations in terms of reproducing individual components of the carbon cycle and their responses to environmental variability. Here we evaluated the performance of an advanced agroecosystem model, ecosys, in simulating carbon budgets over the U.S. Midwest, considering both the magnitude of carbon flux/yield and its response to environmental (climate and soil) variability. We conducted model simulations and evaluations at 7 cropland eddy-covariance sites as well as over 293 counties of Illinois, Indiana, and Iowa in the U.S. Midwest. The site-level simulations showed that ecosys captured both the magnitude and seasonal patterns of carbon fluxes (i.e., net ecosystem carbon exchange (NEE), ecosystem gross primary production (GPP), and ecosystem respiration (Reco)), leaf area index (LAI), and dynamic plant carbon allocation processes, with R2 equal to 0.92, 0.87, 0.87, and 0.78 for GPP, NEE, Reco, and LAI, respectively across all the sites compared with the observations. For regional scale simulations, ecosys reproduced the spatial distribution and interannual variability of corn and soybean yields with the constraints of observed yields and a new remotely sensed GPP product, with R2 of multi-year averaged simulated and observed yield equal 0.83 and 0.80 for corn and soybean, respectively. The simulated responses of carbon cycle dynamics to environmental variability were consistent with that from the empirical observations at both site and regional scales. Furthermore, our results demonstrated the applicability of ecosys in simulating the carbon cycle and soil carbon dynamics of the U.S. Midwestern agroecosystems under different climate and soil conditions.

54 ENVIRONMENTAL SCIENCES↗

Evaluating SWAT + model uncertainties for human and natural outcomes: Application in a Great Lakes agricultural watershed

Nutrient exports from agricultural lands in the Great Lakes Region pose significant threats to water quality and ecological health through eutrophication, hypoxia, and harmful algal blooms. Climate change and agricultural adaptation practices complicate future nutrient loading due to intensified hydrologic cycles and land use decisions. Our research focuses on evaluating the Soil and Water Assessment Tool (SWAT) plus model parametric uncertainties for human and natural outcomes across different scales. These factors are integral to ensuring a balance between productive agricultural practices and maintaining the health of watershed hydrology. However, uncertainties in modeling such complex interactions pose significant challenges, limiting our ability to precisely determine critical factors that influence crop yield and soil moisture. Our analysis employs Sobol global sensitivity analysis to evaluate first-order, second order, and total-order indices for SWAT crop growth parameter, ensuring comprehensive assessment of individual and interactive effects on model outputs. The objective is to identify the parameters that significantly affect model outputs for crop yield and soil moisture and improve our understanding of their interactions at the basin and hydrological response unit (HRU) scale. Our case study, the Portage River Watershed, which drains into Lake Erie, is chosen to better capture finer scale interactions crucial for predicting nutrient loading under future climate scenarios. This foundational work is aimed at setting the stage for the future development of an agent-based model (ABM). The ABM model would incorporate SWAT outputs to dynamically simulate decision-making processes.

Bunyon, Enock↗

Evaluation of Global Fire Simulations in CMIP6 Earth System Models

Fire is the primary form of terrestrial ecosystem disturbance on a global scale and an important Earth system process. Most Earth system models (ESMs) have incorporated fire modeling, with 19 of them submitting model outputs of fire-related variables to the Coupled Model Intercomparison Project Phase 6 (CMIP6). This study provides the first comprehensive evaluation of CMIP6 historical fire simulations by comparing them with multiple satellite-based products and charcoal-based historical reconstructions. Our results show that most CMIP6 models simulate the present-day global burned area and fire carbon emissions within the range of satellite-based products. They also capture the major features of observed spatial patterns and seasonal cycles, the relationship of fires with precipitation and population density, and the influence of the El Niño–Southern Oscillation (ENSO) on the interannual variability of tropical fires. Regional fire carbon emissions simulated by the CMIP6 models from 1850 to 2010 generally align with the charcoal-based reconstructions, although there are regional mismatches, such as in southern South America and eastern temperate North America prior to the 1910s and in temperate North America, eastern boreal North America, Europe, and boreal Asia since the 1980s. The CMIP6 simulations have addressed three critical issues identified in CMIP5: (1) the simulated global burned area being less than half of that of the observations, (2) the failure to reproduce the high burned area fraction observed in Africa, and (3) the weak fire seasonal variability. Furthermore, the CMIP6 models exhibit improved accuracy in capturing the observed relationship between fires and both climatic and socioeconomic drivers and better align with the historical long-term trends indicated by charcoal-based reconstructions in most regions worldwide. However, the CMIP6 models still fail to reproduce the decline in global burned area and fire carbon emissions observed over the past 2 decades, mainly attributed to an underestimation of anthropogenic fire suppression, and the spring peak in fires in the Northern Hemisphere midlatitudes, mainly due to an underestimation of crop fires. In addition, the model underestimates the fire sensitivity to wet–dry conditions, indicating the need to improve fuel wet-ness estimation. Based on these findings, we present specific guidance for fire scheme development and suggest a postprocessing methodology for using CMIP6 multi-model outputs to generate reliable fire projection products.

Wildfire, Earth system models↗

The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum

Abstract Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.

59 BASIC BIOLOGICAL SCIENCES↗

The effect of increasing temperature on crop photosynthesis: from enzymes to ecosystems

Abstract As global land surface temperature continues to rise and heatwave events increase in frequency, duration, and/or intensity, our key food and fuel cropping systems will likely face increased heat-related stress. A large volume of literature exists on exploring measured and modelled impacts of rising temperature on crop photosynthesis, from enzymatic responses within the leaf up to larger ecosystem-scale responses that reflect seasonal and interannual crop responses to heat. This review discusses (i) how crop photosynthesis changes with temperature at the enzymatic scale within the leaf; (ii) how stomata and plant transport systems are affected by temperature; (iii) what features make a plant susceptible or tolerant to elevated temperature and heat stress; and (iv) how these temperature and heat effects compound at the ecosystem scale to affect crop yields. Throughout the review, we identify current advancements and future research trajectories that are needed to make our cropping systems more resilient to rising temperature and heat stress, which are both projected to occur due to current global fossil fuel emissions.

59 BASIC BIOLOGICAL SCIENCES↗

Land-use and atmospheric shifts jointly amplify U.S. drought-driven crop losses

Agricultural drought (AD) poses a major threat to food security, yet its future risk remains uncertain under co-evolving atmospheric conditions and land-use trajectories. Using an integrated, multi-sector modeling framework, we project AD risks for major crops across the contiguous United States (CONUS) through 2055 under a range of plausible futures that capture thermodynamic changes and land-use and land-cover change (LULCC) trajectories. Model projections reveal that drought-driven crop production losses increase sharply by nearly 60% for corn, 250% for wheat, and 135% for soybean relative to historical levels. The primary drivers of these increases, which include atmospheric shifts and LULCC, vary by region and crop type. LULCC acting as an important risk amplifier in regions experiencing cropland expansion into drought-prone regions, such as the Great Plains and northwestern U.S. Wheat exhibits the largest projected loss increases, a result that remains robust across scenarios. These findings highlight that interactions between atmospheric conditions and land-use trajectories shape future agricultural drought risk and should be jointly considered to support effective adaptation and food-system planning.

Yao, Lili↗

Contrasting Carbon–Water–Energy Dynamics in Perennial and Annual Bioenergy Agroecosystems Using Eddy Covariance and Interpretable Machine Learning

Understanding how agroecosystems respond to environmental variability is fundamental to predicting productivity and sustainability under a changing climate. We analyzed 55 site-years of high-frequency eddy covariance observations from five agroecosystems—two perennial grasses (miscanthus and switchgrass), two annual rotation systems (maize–soybean and sorghum–soybean), and a restored native prairie—to examine ecosystem-scale carbon, water, and energy fluxes. Using an interpretable machine-learning framework with regression tree ensembles, Shapley Additive Explanations, and Accumulated Local Effects, we quantified how environmental and temporal factors regulate gross primary productivity (GPP), evapotranspiration (ET), water-use efficiency, and the Bowen ratio. Perennials exhibited stronger physiological buffering and maintained fluxes across a broader range of temperature and moisture conditions, reflecting deeper rooting and persistent canopy cover. Annuals, in contrast, showed greater short-term variability and stronger coupling to atmospheric demand, with GPP and ET declining rapidly under low humidity or soil moisture. Differences in temperature sensitivity of Bowen ratio further revealed that perennials sustained proportionally greater sensible heat flux under cool conditions, whereas annuals exhibited constrained energy exchange when evaporative demand was low. Together, these results demonstrate that crop life cycle and canopy structure are fundamental determinants of ecosystem-scale carbon–water–energy coupling. By integrating long-term flux observations with interpretable machine learning, this study identifies the environmental drivers that shape agroecosystem function and highlights how conversion from annual to perennial feedstocks can enhance climatic resilience and alter land–atmosphere energy feedbacks. These findings provide a data-driven basis for improving crop and Earth-system models and for guiding bioenergy landscape design under future climate scenarios.

Accumulated Local Effects↗

An adaptive adversarial domain adaptation approach for corn yield prediction

Recently, statistical machine learning and deep learning methods have been widely explored for corn yield prediction. Though successful, machine learning models generated within a specific spatial domain often lose their validity when directly applied to new regions. To address this issue, we designed an unsupervised adaptive domain adversarial neural network (ADANN). Specifically, through domain adversarial training, the ADANN model reduced the impact of domain shift by projecting data from different domains into the same subspace. Also, the ADANN model was designed to be trained in an adaptive way, which guaranteed the model can learn the domain-invariant features and perform accurate yield prediction simultaneously. Informative variables including time-series vegetation indices and sequential weather observations were first collected from multiple data sources and aggregated to the county level. Then, we trained the ADANN model with the extracted features and corresponding reported county-level corn yield from the U.S. Department of Agriculture (USDA). Finally, the trained model was evaluated in four testing years 2016–2019. The U.S. corn belt was used as the study area and counties under study were grouped into two diverse ecological regions. Overall, the experimental results showed that the developed ADANN model had better performance than three other state-of-the-art machine learning models in both local experiments (train and test in the same region) and transfer experiments (train and test in different regions). As the first study using adversarial learning for crop yield prediction, this research demonstrates a novel solution for improving model transferability on crop yield prediction.

59 BASIC BIOLOGICAL SCIENCES↗