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DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗
DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗
DOE OSTI2025

Unveiling the drivers contributing to global wheat yield shocks through quantile regression

Sudden reductions in crop yield (i.e., yield shocks) severely disrupt the food supply, intensify food insecurity, depress farmers' welfare, and worsen a country's economic conditions. Here, we study the spatiotemporal patterns of wheat yield shocks, quantified by the lower quantiles of yield fluctuations, in 86 countries over 30 years. Furthermore, we assess the relationships between shocks and their key ecological and socioeconomic drivers using quantile regression based on statistical (linear quantile mixed model) and machine learning (quantile random forest) models. Using a panel dataset that captures spatiotemporal patterns of yield shocks and possible drivers in 86 countries, we find that the severity of yield shocks has been increasing globally since 1997. Moreover, our cross-validation exercise shows that quantile random forest outperforms the linear quantile regression model. Despite this performance difference, both models consistently reveal that the severity of shocks is associated with higher weather stress, nitrogen fertilizer application rate, and gross domestic product (GDP) per capita (a typical indicator for economic and technological advancement in a country). While the unexpected negative association between more severe wheat yield shocks and higher fertilizer application rate and GDP per capita does not imply a direct causal effect, they indicate that the advancement in wheat production has been primarily on achieving higher yields and less on lowering the possibility and magnitude of sharp yield reductions. Hence, in the context of growing extreme weather stress, there is a critical need to enhance the technology and management practices that mitigate yield shocks to improve the resilience of the world food systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Historical and Future Global Irrigation Energy Consumption by Fuel and Region

Irrigation energy use is a significant component of agricultural production costs, contributing directly to the energy and emissions intensity of crop production and ultimately to food prices. Understanding the existing structure of irrigation energy consumption help achieve food-energy-water security and environmental goals. We present a comprehensive global data set detailing country-level irrigation energy consumption, emphasizing the comparative use of electric, diesel, and emerging solar pumps. To our knowledge, no such data set exists. We draw from a literature review to develop a logistic transformed regression model to estimate the shares of fuel sources for irrigation across countries over historical years to construct a global data set of country-level irrigation energy consumption by multiple fuel sources. Additionally, we compare our estimates of irrigation energy use with agricultural energy use as reported by the International Energy Agency and other external sources. We then use this data to project future irrigation energy use with the Global Change Analysis Model, which is a multisector dynamics model, to showcase the usage of this data set. Projections under the reference scenario show a global shift in fuel types for irrigation pumping, while patterns vary across regions, with India and Pakistan leading in solar-powered irrigation growth and countries like the USA and China continuing to rely primarily on grid electricity. This data set provides a resource to understand the role of irrigation fuel choices within the broader energy sector, as well as the connected agricultural, land use, and water sectors under alternative future scenarios, enabling informed decision making toward efficient agricultural practices.

Global Change Analysis Model (GCAM)↗
DOE OSTI2021

Decreased land use intensity improves surface soil quality on marginal lands

The Conservation Reserve Program (CRP) has been a major factor in land transitions out of intensive row-crop management on marginally productive lands in the central United States. While CRP can protect these more environmentally sensitive lands against erosion and potential nutrient loss, information on how CRP affects soil quality over time is limited. Using a chronosequence with 0–40 yr of CRP conversion history, we evaluated soil quality under different land use intensities (CRP, pasture, row crop) using the Soil Management Assessment Framework (SMAF). Effects of slope classes (higher [14–25%] and lower [2–14%]) and soil depth (0–120 cm) were also evaluated. Our results show that the soils were functioning at 84 and 78% of their theoretical capacity under CRP and row crop, respectively. Conversion to CRP enhanced overall soil quality by increasing soil biological, physical, and chemical attributes, but soil nutrient availability decreased due to the absence of fertilizer application. Increasing soil organic C (SOC) enhanced overall soil quality because of its impact on soil biological, physical, chemical, and nutrient conditions. Conversion to CRP will likely have greater benefits for more environmentally sensitive soils (i.e., higher slope) as demonstrated by structural equation modeling. Land use effects were also depth dependent, with more prominent effects within the 0-to-5-cm than the 5-to-15-cm depth increment. Overall, our methods focused on key soil quality indicators, confirmed ecological benefits of CRP conversion, and provided guidance for improved and simplified land management recommendations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Nitrogen-Fixing Gamma Proteobacteria Azotobacter vinelandii—A Blueprint for Nitrogen-Fixing Plants?

The availability of fixed nitrogen limits overall agricultural crop production worldwide. The so-called modern “green revolution” catalyzed by the widespread application of nitrogenous fertilizer has propelled global population growth. It has led to imbalances in global biogeochemical nitrogen cycling, resulting in a “nitrogen problem” that is growing at a similar trajectory to the “carbon problem”. As a result of the increasing imbalances in nitrogen cycling and additional environmental problems such as soil acidification, there is renewed and increasing interest in increasing the contributions of biological nitrogen fixation to reduce the inputs of nitrogenous fertilizers in agriculture. Interestingly, biological nitrogen fixation, or life’s ability to convert atmospheric dinitrogen to ammonia, is restricted to microbial life and not associated with any known eukaryotes. It is not clear why plants never evolved the ability to fix nitrogen and rather form associations with nitrogen-fixing microorganisms. Perhaps it is because of the large energy demand of the process, the oxygen sensitivity of the enzymatic apparatus, or simply failure to encounter the appropriate selective pressure. Whatever the reason, it is clear that this ability of crop plants, especially cereals, would transform modern agriculture once again. Successfully engineering plants will require creating an oxygen-free niche that can supply ample energy in a tightly regulated manner to minimize energy waste and ensure the ammonia produced is assimilated. Nitrogen-fixing aerobic bacteria can perhaps provide a blueprint for engineering nitrogen-fixing plants. This short review discusses the key features of robust nitrogen fixation in the model nitrogen-fixing aerobe, gamma proteobacteria Azotobacter vinelandii, in the context of the basic requirements for engineering nitrogen-fixing plants.

Microbiology↗
DOE OSTI2023

Local adaptation of switchgrass drives trait relations to yield and differential responses to climate and soil environments

Abstract Switchgrass, a potential biofuel crop, is a genetically diverse species with phenotypic plasticity enabling it to grow in a range of environments. Two primary divergent ecotypes, uplands and lowlands, exhibit trait combinations representative of acquisitive and conservative growth allocation strategies, respectively. Whether these ecotypes respond differently to various types of environmental drivers remains unclear but is crucial to understanding how switchgrass varieties will respond to climate change. We grew two upland, two lowland, and two intermediate/hybrid cultivars of switchgrass at three sites along a latitudinal gradient in the central United States. Over a 4‐year period, we measured plant functional traits and biomass yields and evaluated genotype‐by‐environment (G × E) interaction effects by analyzing switchgrass responses to soil and climate variables. We found substantial evidence of G × E interactions on biomass yield, primarily due to deviations in the response of the southern lowland cultivar Alamo, which produced more biomass in hotter and drier environments relative to other cultivars. While lowland cultivars had the highest potential for yield, their yields were more variable year‐to‐year compared to other cultivars, suggesting greater sensitivity to environmental perturbations. Models comparing soil and climate principal components as explanatory variables revealed soil properties, especially nutrients, to be most effective at predicting switchgrass biomass yield. Also, positive correlations between biomass yield and conservative plant traits, such as high stem mass and tiller height, became stronger at lower latitudes where the climate is hotter and drier, regardless of ecotype. Lowland cultivars, however, showed a greater predisposition to exhibit these conservative traits. These results suggest switchgrass trait allocation trade‐offs that prioritize aboveground biomass production are more tightly associated in hot, dry environments and that lowland cultivars may exhibit a more specialized strategy relative to other cultivars. Altogether, this research provides essential knowledge for improving the viability of switchgrass as a biofuel crop.

09 BIOMASS FUELS↗
DOE OSTI2026

Integrating Carbon Capture, Utilization, & Sequestration into Chemical Pulp Mills

The U.S. pulp and paper industry presents a unique and largely untapped opportunity for large- scale carbon dioxide removal (CDR). Unlike most industrial sectors, pulp mills rely heavily on biomass, meaning that much of their carbon emissions originate from atmospheric CO₂ that was recently captured by plants. If this biogenic CO₂ can be captured and permanently stored, pulp mills can be transformed from carbon emitters into net carbon removal facilities. This project was motivated by that opportunity and aimed to develop and evaluate integrated, low-cost strategies for capturing, utilizing, and sequestering CO₂ within existing chemical pulping operations. The scope of this work focused on four complementary innovations designed to integrate seamlessly into kraft pulp mill infrastructure: (1) in situ CO₂ capture within the recovery cycle, (2) oxy-fuel retrofitting of the rotary lime kiln to produce a high-purity CO₂ stream, (3) ex situ CO₂ capture and mineralization using pulp mill residues (dregs, grits, and lime mud), and (4) beneficial reuse of these residues as mineral carbonate fertilizers. The project combined process modeling, laboratory experimentation, life cycle assessment (LCA), and field trials to evaluate the technical feasibility, economic viability, and environmental impact of these approaches. The results demonstrate that pulp mills can serve as effective platforms for carbon removal when equipped with integrated carbon capture systems. Process modeling showed that combining sodium spiking with oxy-fuel calcination significantly enhances CO₂ capture efficiency while reducing costs by up to 31% compared to conventional configurations. Experimental work further revealed that calcination behavior in high-CO₂ environments differs substantially from traditional systems, leading to the development of a new kinetic model that predicts reaction rates under these conditions. This model provides essential design guidance for next-generation decarbonized lime kilns. In parallel, the project demonstrated that alkaline mineral residues generated during pulping operations can be repurposed as a sustainable alternative to agricultural lime. Across a wide range of soils in the southeastern United States, these materials performed equivalently to commercial lime in adjusting soil pH while offering lower greenhouse gas emissions and reduced cost. Field and greenhouse studies confirmed that crop and tree growth responses were comparable, supporting their viability as a drop-in replacement. This co-product pathway provides a practical utilization strategy that offsets costs and improves overall system economics. A major contribution of this project is the first comprehensive life cycle assessment of carbon removal in pulp and paper systems across multiple system boundaries. Results show that retrofitted mills can achieve carbon removal efficiencies ranging from 12% to 92%, depending on how the system is defined. This finding highlights a critical issue in carbon accounting: reported performance is highly sensitive to methodological choices. By explicitly quantifying these differences, this work provides valuable guidance for policymakers, carbon registries, and project developers working to standardize carbon removal metrics. From a commercialization perspective, the technologies investigated in this project are well- aligned with existing industrial infrastructure, minimizing the need for entirely new facilities. 3 DE-EE0009413 Industry engagement throughout the project—including collaboration with pulp and paper companies, equipment manufacturers, and carbon removal developers—has accelerated the transition from research to deployment. Notably, a commercial developer is actively pursuing carbon capture projects at pulp mills in the southeastern United States and has cited this research as a contributing foundation. The emergence of voluntary carbon markets and long-term offtake agreements further strengthens the business case for implementation. The broader public benefits of this work are significant. By enabling large-scale carbon removal using existing industrial systems, this approach offers a near-term pathway to reduce atmospheric CO₂ concentrations while supporting domestic manufacturing and rural economies. The reuse of industrial residues as fertilizers reduces reliance on mined materials, lowers costs for farmers, and decreases environmental impacts associated with conventional lime production. In addition, the project has supported workforce development by training graduate students and researchers in carbon capture technologies, helping to build capacity in a critical area of national interest. In conclusion, this project demonstrates that integrated carbon capture, utilization, and sequestration in pulp mills is both technically feasible and economically promising. By combining process innovation, experimental validation, and systems-level analysis, the work advances the understanding of how biomass-based industries can contribute to climate mitigation. The findings provide a strong foundation for commercial deployment and offer a scalable solution for transforming a major U.S. industry into a source of durable carbon removal.

09 BIOMASS FUELS↗
DOE OSTI2021

Remote Sensing-Based Estimation of Advanced Perennial Grass Biomass Yields for Bioenergy

A sustainable bioeconomy would require growing high-yielding bioenergy crops on marginal agricultural areas with minimal inputs. To determine the cost competitiveness and environmental sustainability of such production systems, reliably estimating biomass yield is critical. However, because marginal areas are often small and spread across the landscape, yield estimation using traditional approaches is costly and time-consuming. This paper demonstrates the (1) initial investigation of optical remote sensing for predicting perennial bioenergy grass yields at harvest using a linear regression model with the green normalized difference vegetation index (GNDVI) derived from Sentinel-2 imagery and (2) evaluation of the model’s performance using data from five U.S. Midwest field sites. The linear regression model using midsummer GNDVI predicted yields at harvest with R2 as high as 0.879 and a mean absolute error and root mean squared error as low as 0.539 Mg/ha and 0.616 Mg/ha, respectively, except for the establishment year. Perennial bioenergy grass yields may be predicted 152 days before the harvest date on average, except for the establishment year. The green spectral band showed a greater contribution for predicting yields than the red band, which is indicative of increased chlorophyll content during the early growing season. Although additional testing is warranted, this study showed a great promise for a remote sensing approach for forecasting perennial bioenergy grass yields to support critical economic and logistical decisions of bioeconomy stakeholders.

09 BIOMASS FUELS↗
DOE OSTI2022

Frontiers and opportunities in bioenergy crop microbiome research networks

Researchers from across the four U.S. Department of Energy Bioenergy Research Centers engaged in a microbiome workshop that focused on identifying challenges and collaboration opportunities to better understand bioenergy-relevant plant–microbe interactions. The virtual workshop included hands-on educational sessions and a keynote address on current best practices in microbiome science and community microbiome standards, as well as breakout sessions aimed at identifying microbiome-related data and measurements that should be prioritized, opportunities for and barriers to integrating plant metabolites to microbiome research, and strategies for more effectively integrating microbiome data and processes into existing models. Based on participant discussion, key findings of the workshop were the need to prioritize scaling data sharing across BRCs and the broader research community and securing collaborative infrastructure in the areas of microbiome-ecosystem modeling and molecular plant-microbe interactions. This workshop review highlights additional main findings from this event, to encourage cross-site and more holistic meta-analyses while promoting wide scientific community engagement across plant microbiome sciences.

09 BIOMASS FUELS↗
DOE OSTI2025

Stepping into the Midwest Bioeconomy: Stakeholder Engagement and Geospatial Tools to Assist in Perennial Bioenergy Crop Decision Making and Entrepreneurship

This project, “Ecosystem Services and Farm Entrepreneurship Technical Assistance,” was a three-year project originally planned for FY22–FY24. Due to a late start and a few extensions, it is being completed in early FY25. This project explored opportunities to support the deployment of a bioeconomy with a circular, more sustainable supply chain. Using a tool developed by Argonne to identify agricultural areas suitable for use in the bioeconomy, we sought to create opportunities in the bioeconomy as biomass producers, bioenergy users, and environmental entrepreneurs. We proposed to focus at the beginning on enhancing the tool’s capabilities, while engaging with key stakeholders to improve and expand the tool’s functionality for all potential stakeholders in the bioeconomy. We believe that expanding our tools and technologies, coupled with conversations in agricultural spaces, will be needed as we continue to explore how best to offer farmers whole-of supply-chain opportunities to participate in the bioeconomy. Through this project we have continued to gain a better understanding of the ways in which farmers, landowners, bioenergy users, and environmental entrepreneurs may approach the bioeconomy. In addition, as we improve our analytic toolkit, we can continue to refine our communication and the ways in which we can valuate the bioeconomy. Refining these tools allows us to dive deeper into conversations around plausible policies and drivers for future bioeconomy investment and engagement by stakeholders. By working with farmers and agricultural landowners to enable a sustainable bioeconomy business model, enhance their energy options, and recover resources from their waste streams, this project directly responds to the Bioenergy Technology Office’s (BETO) priorities of building a resilient energy economy. It addresses BETO’s focus on fostering the development and adoption of energy technologies that enable the conversion of waste to energy, efficient land use, and robust job creation. By establishing a technical assistance program that develops capabilities and practices in agricultural areas to implement a bioeconomy future, this program will develop an important linkage between technology being developed at U.S. Department of Energy national laboratories and the agricultural communities of the Midwest. This project focuses on farmers with lower productivity farmland. Because less productive lands create a more difficult revenue stream for conventional crops, these farmers may therefore be more open to alternative agricultural land management regimes. Consequently, the technical assistance program and the methodologies for targeting perennial bioenergy crop application on marginal land provide a distinct opportunity to engage with and invest in the bioeconomy in these economically stressed areas. Stakeholders in this project include farmers and landowners, local conservation organizations (NRCS, SWCS, etc.), universities, non-profit environmental and agricultural entities, farm consultants, environmental regulators, and industry, including the industries working on conversion technologies, anaerobic digestion, pyrolysis, and biochar generation, and the companies interested in trading or purchasing/supporting the valuation of ecosystem services (ES).

09 BIOMASS FUELS↗
DOE OSTI2024

Cortical cell size regulates root metabolic cost

SUMMARY It has been hypothesized that vacuolar occupancy in mature root cortical parenchyma cells regulates root metabolic cost and thereby plant fitness under conditions of drought, suboptimal nutrient availability, and increased soil mechanical impedance. However, the mechanistic role of vacuoles in reducing root metabolic cost was unproven. Here we provide evidence to support this hypothesis. We first show that root cortical cell size is determined by both cortical cell diameter and cell length. Significant genotypic variation for both cortical cell diameter (~1.1‐ to 1.5‐fold) and cortical cell length (~ 1.3‐ to 7‐fold) was observed in maize and wheat. GWAS and QTL analyses indicate cortical cell diameter and length are heritable and under independent genetic control. We identify candidate genes for both phenes. Empirical results from isophenic lines contrasting for cortical cell diameter and length show that increased cell size, due to either diameter or length, is associated with reduced root respiration, nitrogen content, and phosphorus content.RootSlice, a functional‐structural model of root anatomy, predicts that an increased vacuolar: cytoplasmic ratio per unit cortical volume causes reduced root respiration and nutrient content. Ultrastructural imaging of cortical parenchyma cells with varying cortical diameter and cortical cell length confirms thein silicopredictions and shows that an increase in cell size is correlated with increased vacuolar volume and reduced cytoplasmic volume. Vacuolar occupancy and its relationship with cell size merits further investigation as a phene for improving crop adaptation to edaphic stress.

Plant Sciences↗
DOE OSTI2021

New Orthophoto Generation Strategies from UAV and Ground Remote Sensing Platforms for High-Throughput Phenotyping

Remote sensing platforms have become an effective data acquisition tool for digital agriculture. Imaging sensors onboard unmanned aerial vehicles (UAVs) and tractors are providing unprecedented high-geometric-resolution data for several crop phenotyping activities (e.g., canopy cover estimation, plant localization, and flowering date identification). Among potential products, orthophotos play an important role in agricultural management. Traditional orthophoto generation strategies suffer from several artifacts (e.g., double mapping, excessive pixilation, and seamline distortions). The above problems are more pronounced when dealing with mid- to late-season imagery, which is often used for establishing flowering date (e.g., tassel and panicle detection for maize and sorghum crops, respectively). In response to these challenges, this paper introduces new strategies for generating orthophotos that are conducive to the straightforward detection of tassels and panicles. The orthophoto generation strategies are valid for both frame and push-broom imaging systems. The target function of these strategies is striking a balance between the improved visual appearance of tassels/panicles and their geolocation accuracy. The new strategies are based on generating a smooth digital surface model (DSM) that maintains the geolocation quality along the plant rows while reducing double mapping and pixilation artifacts. Moreover, seamline control strategies are applied to avoid having seamline distortions at locations where the tassels and panicles are expected. The quality of generated orthophotos is evaluated through visual inspection as well as quantitative assessment of the degree of similarity between the generated orthophotos and original images. Several experimental results from both UAV and ground platforms show that the proposed strategies do improve the visual quality of derived orthophotos while maintaining the geolocation accuracy at tassel/panicle locations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

How High to Fly? Mapping Evapotranspiration from Remotely Piloted Aircrafts at Different Elevations

Recent advancements in remotely piloted aircrafts (RPAs) have made frequent, low-flying imagery collection more economical and feasible than ever before. The goal of this work was to create, compare, and quantify uncertainty associated with evapotranspiration (ET) maps generated from different conditions and image capture elevations. We collected optical and thermal data from a commercially irrigated potato (Solanum tuberosum) field in the Wisconsin Central Sands using a quadcopter RPA system and combined multispectral/thermal camera. We conducted eight mission sets (24 total missions) during the 2019 growing season. Each mission set included flights at 90, 60, and 30 m above ground level. Ground reference measurements of surface temperature and soil moisture were collected throughout the domain within 15 min of each RPA mission set. Evapotranspiration values were modeled from the flight data using the High-Resolution Mapping of Evapotranspiration (HRMET) model. We compared HRMET-derived ET estimates to an Eddy Covariance system within the flight domain. Additionally, we assessed uncertainty for each flight using a Monte Carlo approach. Results indicate that the primary source of uncertainty in ET estimates was the optical and thermal data. Despite some additional detectable features at low elevation, we conclude that the tradeoff in resources and computation does not currently justify low elevation flights for annual vegetable crop management in the Midwest USA.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Self-Supervised Anomaly Detection via Neural Autoregressive Flows with Active Learning

Many self-supervised methods have been proposed with the target of image anomaly detection. These methods often rely on the paradigm of data augmentation with predefined transformations such as flipping, cropping, and rotations. However, it is not straightforward to apply these techniques for non-image data, such as time series or tabular data, while the performance of the existing deep approaches has been under our expectation on tasks beyond images. In this work, we propose a novel active learning (AL) scheme that relied on neural autoregressive flows (NAF) for self-supervised anomaly detection, specifically on small-scale data. Unlike other generative models such as GANs or VAEs, flow-based models allow to explicitly learn the probability density and thus can assign accurate likelihoods to normal data which makes it usable to detect anomalies. The proposed NAF-AL method is achieved by efficiently generating random samples from latent space and transforming them into feature space along with likelihoods via invertible mapping. The samples with lower likelihoods are selected and further checked by outlier detection using Mahalanobis distance. The augmented samples incorporating with normal samples are used for training a better detector so as to approach decision boundaries. Compared with random transformations, NAF-AL can be interpreted as a likelihood-oriented data augmentation that is more efficient and robust. Extensive experiments show that our approach outperforms existing baselines on multiple time series and tabular datasets, and a real-world application in advanced manufacturing, with significant improvement on anomaly detection accuracy and robustness over the state-of-the-art.

Zhang, Jiaxin↗
DOE OSTI2024

Quantifying leaf symptoms of sorghum charcoal rot in images of field‐grown plants using deep neural networks

Abstract Charcoal rot of sorghum (CRS) is a significant disease affecting sorghum crops, with limited genetic resistance available. The causative agent, Macrophomina phaseolina (Tassi) Goid, is a highly destructive fungal pathogen that targets over 500 plant species globally, including essential staple crops. Utilizing field image data for precise detection and quantification of CRS could greatly assist in the prompt identification and management of affected fields and thereby reduce yield losses. The objective of this work was to implement various machine learning algorithms to evaluate their ability to accurately detect and quantify CRS in red‐green‐blue images of sorghum plants exhibiting symptoms of infection. EfficientNet‐B3 and a fully convolutional network emerged as the top‐performing models for image classification and segmentation tasks, respectively. Among the classification models evaluated, EfficientNet‐B3 demonstrated superior performance, achieving an accuracy of 86.97%, a recall rate of 0.71, and an F1 score of 0.73. Of the segmentation models tested, FCN proved to be the most effective, exhibiting a validation accuracy of 97.76%, a recall rate of 0.68, and an F1 score of 0.66. As the size of the image patches increased, both models’ validation scores increased linearly, and their inference time decreased exponentially. This trend could be attributed to larger patches containing more information, improving model performance, and fewer patches reducing the computational load, thus decreasing inference time. The models, in addition to being immediately useful for breeders and growers of sorghum, advance the domain of automated plant phenotyping and may serve as a foundation for drone‐based or other automated field phenotyping efforts. Additionally, the models presented herein can be accessed through a web‐based application where users can easily analyze their own images.

Gonzalez, Emmanuel M.↗
DOE OSTI2023

Response patterns of simulated corn yield and soil nitrous oxide emission to precipitation change

Abstract Background Precipitation plays an important role in crop production and soil greenhouse gas emissions. However, how crop yield and soil nitrous oxide (N 2 O) emission respond to precipitation change, particularly with different background precipitations (dry, normal, and wet years), has not been well investigated. In this study, we examined the impacts of precipitation changes on corn yield and soil N 2 O emission using a long-term (1981–2020, 40 years) climate dataset as well as seven manipulated precipitation treatments with different background precipitations using the DeNitrification-DeComposition (DNDC) model. Results Results showed large variations of corn yield and precipitation but small variation of soil N 2 O emission among 40 years. Both corn yield and soil N 2 O emission showed near linear relationships with precipitation based on the long-term precipitation data, but with different response patters of corn yield and soil N 2 O emission to precipitation manipulations. Corn yield showed a positive linear response to precipitation manipulations in the dry year, but no response to increases in precipitation in the normal year, and a trend of decrease in the wet year. The extreme drought treatments reduced corn yield sharply in both normal and wet years. In contrast, soil N 2 O emission mostly responded linearly to precipitation manipulations. Decreases in precipitation in the dry year reduced more soil N 2 O emission than those in the normal and wet years, while increases in precipitation increased more soil N 2 O emission in the normal and wet years than in the dry year. Conclusions This study revealed different response patterns of corn yield and soil N 2 O emission to precipitation and highlights that mitigation strategy for soil N 2 O emission reduction should consider different background climate conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Growing grasses in unprofitable areas of US Midwest croplands could increase species richness

The US has large potential to grow perennial energy crops, but because these crops are rarely grown in current agricultural landscapes, it is unclear how biodiversity may be affected. Over time, as agriculture has increased, many grassland species have declined. In addition, not all agricultural land is profitable for growing annual crops. Unprofitable areas were responsible for a loss of approximately $110 million USD per year from 2013 to 2016. Based on this, we want to know how converting less-profitable portions of agricultural fields to switchgrass, a native prairie grass, would influence species occurrence. To address this question, we developed an alternative landscape in which clustered corn/soy acres with a low return on investment (ROI) were replaced with grassland. We also developed and validated species distribution models to predict changes in species occurrence for 28 avian species in Iowa in response to landscape management. Furthermore, we compared results for three different models: Random forest (RF), Stochastic gradient boosting (GBM), and Neural network (Nnet) and found that all models performed well and predicted similar species distribution. Predicted species richness increased by 3.66% (RF), 2.79% (GBM), and 7.51% (Nnet) when we simulated a change in management for ~3% of Iowa's low ROI corn/soybean areas to grassland. If harvested, these areas could generate approximately 7.6 million dry tons/year of switchgrass for bioenergy, thereby increasing farmers earnings. Unprofitable areas tended to occur along streams, which suggest that incorporating partially harvested riparian buffers can benefit avian biodiversity, while improving water quality and reducing unnecessary costs for farmers.

59 BASIC BIOLOGICAL SCIENCES↗