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DOE OSTI2026

Data for Soil Oxygen Dynamics: A Key Mediator of Tile Drainage Impacts on Coupled Hydrological, Biogeochemical, and Crop Systems

Tile drainage removes excess water and is an essential, widely adopted management practice to enhance crop productivity in the US Midwest and throughout the world. Tile drainage has been shown to significantly change hydrological and biogeochemical cycles by lowering the water table and reducing the residence time of soil water, although examining the complex interactions and feedbacks in an integrated hydrology–biogeochemistry–crop system remains elusive. Oxygen dynamics are critical to unraveling these interactions and have been ignored or oversimplified in existing models. Understanding these impacts is essential, particularly so because tile drainage has been highlighted as an adaptation under projected wetter springs and drier summers in the changing climate in the US Midwest. We used the ecosys model that uniquely incorporates first-principle soil oxygen dynamics and crop oxygen uptake mechanisms to quantify the impacts of tile drainage on hydrological and biogeochemical cycles and crop growth in corn–soybean rotation fields. The model was validated with data from a multi-treatment, multi-year experiment in Washington, IA. The relative root mean square error (rRMSE) for the corn and soybean yield in validation is 5.66 % and 12.57 %, respectively. The Pearson coefficient (r) of the monthly tile flow during the growing season is 0.78. Plant oxygen stress turns out as an emergent property of the equilibrium between the soil oxygen supply and biological demand. The impact of tile drainage on the system is achieved through a series of coupled feedback mechanisms. The model results show that tile drainage reduces the soil water content and enhances soil oxygenation. It additionally increases the subsurface discharge and elevates inorganic nitrogen leaching, with seasonal variations influenced by climate and crop phenology. The improved aerobic condition alleviates crop oxygen stress during wet springs, thereby promoting crop root growth during the early growth stage. The development of greater root density, in turn, mitigates water stress during dry summers, leading to an overall increase in the crop yield by ∼6 %. These functions indicate the potential of tile drainage in bolstering crop resilience to climate change and the use of this modeling tool for large-scale assessments of tile drainage. The model reveals the underlying causal mechanisms that drive the agroecosystem response to drainage on the coupled hydrology, biogeochemistry, and crop system dynamics.

Modeling↗

DOE OSTI2026

Data for High Yield Production of 3-Hydroxypropionic Acid Using Issatchenkia orientalis

Biomanufacturing provides a more sustainable alternative to fossil-based chemical manufacturing. 3-Hydroxypropionic acid (3HP) is a top Department of Energy value-added chemical and precursor to bioplastics, yet cost-effective microbial production remains elusive. Here, we establish the acid-tolerant yeast Issatchenkia orientalis as a robust host for low-pH 3HP biosynthesis. Genome-scale modeling identifies the β-alanine pathway as optimal, offering the highest theoretical yield and lowest oxygen requirement. Thermodynamic analysis confirms its favorability under acidic conditions. Using sequence similarity network analysis, we discover highly active aspartate 1-decarboxylase (PAND), β-alanine-pyruvate aminotransferase (BAPAT), and 3HP dehydrogenase (YDFG), which significantly improve the pathway efficiency. Next, to further elevate the production, pathway optimization through multi-copy PAND integration, byproduct elimination (knockouts of pyruvate decarboxylase and glycerol-3-phosphate dehydrogenase), and reinforcement of aspartate flux by overexpression of pyruvate carboxylase and aspartate amino transferase improves the titer to 29 g/L in shake flasks. Fed-batch fermentation at pH 4 with low-cost corn steep liquor medium further increases the production to 92 g/L with 0.7 g/g yield and 0.55 g/L/h productivity. Techno-economic analysis indicates that such performance could potentially enable a financially viable process for sustainable acrylic acid production. This work establishes I. orientalis as a next-generation platform for cost-effective 3HP production and paves the way toward industrial commercialization.

Bioproducts↗

DOE OSTI2026

Data for Clumping Index Estimation With 30°-tilted Cameras in Row Crops: Evaluation of Methods and Segment Size Effects

The clumping index (CI) quantifies the spatial distribution of foliage elements and is essential for accurately estimating the plant area index (PAI), canopy radiative transfer, and photosynthesis. Traditionally, the finite-length averaging method (LX), the gap size distribution method (CC), and a combined approach of CC and LX (CLX) have been applied to instruments like TRAC and digital hemispherical photography to estimate CI. However, a comprehensive evaluation of these methods in row crops remains limited, especially regarding the influence of segment size on CI. Meanwhile, digital cameras offer a cost-effective and user-friendly solution for canopy measurements in row crops, yet their application in this context remains underexplored. In this study, we employed a new approach using a 30°-tilted digital camera to estimate CI in corn and soybean fields, applying the LX, CC, and CLX methods. We systematically assessed the performance of these three methods by combining field measurements in real-world fields with simulations using the LESS 3D radiative transfer model. Our results showed that CLX applied to the whole image and 45° segment offered accurate estimation of CI (bias within ±0.1, RMSE < 0.2) and PAI (bias within ±0.4, RMSE < 1) in real-world fields and LESS simulations. The accuracy of the LX method was highly sensitive to segment size, with the best performance observed at the 15° segment (PAI bias within ±0.4). In contrast, the CC method remained stable across different segment sizes, and its performance was generally comparable to that of LX, except at the 15° segment. Across view zenith angles, CI derived from CC generally showed a continuous increase, while those from LX and CLX followed a rising trend at small zenith angles but began to decline at 68°, likely due to an increasing proportion of no-gap segments. Seasonally, LX tended to show decreasing CI during early growth stages but increased as the canopy matured, whereas CC and CLX showed gradually increasing CI before plateauing at peak PAI. The 30°-tilted camera effectively captured CI variations across different angles and growth stages, making it a practical and robust instrument for row crop canopy structure analysis. Applying these CI methods to digital cameras offers a low-cost and accessible CI estimation alternative, improving canopy structure monitoring accuracy in row crops.

Modeling↗

DOE OSTI2019

Computational modeling of continuum scale constitutive equations to improve biomass feedstock material handling and conveying systems

Existing design practices for common feedstock handling equipment such as hoppers and screw feeders have not been successful in many situations. The lack of an appropriate toolset to characterize and model biomass flow behavior is deemed the root cause of plugging, stalls, and flow-related issues in biomass handling systems design and operations. New standardized characterization protocols in conjunction with appropriate constitutive models will lead to successful biomass handling system design and operations. This study investigates constitutive models for bulk solid flow based on the first principles to overcome issues in biomass handling. The focus is on two major issues in biomass handling, i.e., initiating and sustaining of flow in the hopper that is widely used in biomass conveying operation. Accordingly, this article focuses on analytical models of biomass hopper flow. Mohr-Coulomb, Drucker-Prager, and modified Cam-clay models are investigated as constitutive bulk solid flow models. Parameters of those models are determined using a set of triaxial tests. Triaxial tests are conducted using the cubical triaxial tester (CTT) in the Food and Biomaterials Lab of the Pennsylvania State University. Milled 1mm corn stover and 2mm wood chip biomass materials having different flow characteristics are examined, and their respective flow behavior out of a hopper are simulated using the Finite Element method implementing identified constitutive models and determined fundamental mechanical properties. It is found that, with the same hopper geometry, ground corn stover 1mm tends to exhibit funnel flow whereas ground Douglas fir 2 mm tends to exhibit mass flow. These simulation results are validated with hopper flow experiments. This study demonstrates how biomass flow problems can be predicted and mitigated by numerically modeled fundamental constitutive equations.

09 BIOMASS FUELS↗

DOE OSTI2018

Water impacts of U.S. biofuels: Insights from an assessment combining economic and biophysical models

Biofuels policies induce land use changes (LUC), including cropland expansion and crop switching, and this in turn alters water and soil management practices. Policies differ in the extent and type of land use changes they induce and therefore in their impact on water resources. We quantify and compare the spatially varying water impacts of biofuel crops stemming from LUC induced by two different biofuels policies by coupling a biophysical model with an economic model to simulate the economically viable mix of crops, land uses, and crop management choices under alternative policy scenarios. We assess the outputs of an economic model with a high-resolution crop-water model for major agricultural crops and potential cellulosic feedstocks in the US to analyze the impacts of three alternative policy scenarios on water balances: a counterfactual ‘no-biofuels policy’ (BAU) scenario, a volumetric mandate (Mandate) scenario, and a clean fuel-intensity standard (CFS) scenario incentivizing fuels based on their carbon intensities. While both biofuel policies incentivize more biofuels than in the counterfactual, they differ in the mix of corn ethanol and advanced biofuels from miscanthus and switchgrass (more corn ethanol in Mandate and more cellulosic biofuels in CFS). The two policies differ in their impact on irrigated acreage, irrigation demand, groundwater use and runoff. Net irrigation requirements increase 0.7% in Mandate and decrease 3.8% in CFS, but in both scenarios increases are concentrated in regions of Kansas and Nebraska that rely upon the Ogallala aquifer for irrigation water. Our study illustrates the importance of accounting for the overall LUC and shifts in agricultural production and management practices in response to policies when assessing the water impacts of biofuels.

09 BIOMASS FUELS↗

DOE OSTI2019

PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production

Lignocellulosic biomass offers a sustainable source for biofuel production that does not compete with food-based cropping systems. Importantly, two critical bottlenecks prevent economic adoption: many industrially relevant microorganisms cannot ferment pentose sugars prevalent in lignocellulosic medium, leaving a significant amount of carbon unutilized. Furthermore, chemical biomass pretreatment required to release fermentable sugars generates a variety of toxins, which inhibit microbial growth and metabolism, specifically limiting pentose utilization in engineered strains. Here we dissected genetic determinants of anaerobic xylose fermentation and stress tolerance in chemically pretreated corn stover biomass, called hydrolysate. We previously revealed that loss-of-function mutations in the stress-responsive MAP kinase HOG1 and negative regulator of the RAS/Protein Kinase A (PKA) pathway, IRA2, enhances anaerobic xylose fermentation. However, these mutations likely reduce cells’ ability to tolerate the toxins present in lignocellulosic hydrolysate, making the strain especially vulnerable to it. We tested the contributions of Hog1 and PKA signaling via IRA2 or PKA negative regulatory subunit BCY1 to metabolism, growth, and stress tolerance in corn stover hydrolysate and laboratory medium with mixed sugars. We found mutations causing upregulated PKA activity increase growth rate and glucose consumption in various media but do not have a specific impact on xylose fermentation. In contrast, mutation of HOG1 specifically increased xylose usage. We hypothesized improving stress tolerance would enhance the rate of xylose consumption in hydrolysate. Surprisingly, increasing stress tolerance did not augment xylose fermentation in lignocellulosic medium in this strain background, suggesting other mechanisms besides cellular stress limit this strain’s ability for anaerobic xylose fermentation in hydrolysate.

09 BIOMASS FUELS↗

DOE OSTI2016

AmeriFlux US-Bo1 Bondville

This is the AmeriFlux version of the carbon flux data for the site US-Bo1 Bondville. Site Description - Agriculture, continuous no-till since 1986, Annual rotation between corn (C4) and soybeans (C3). The field was planted with corn during 2005 and 2007, with soybeans during 2006 and 2008.

Meyers, Tilden↗

DOE OSTI2025

AmeriFlux US-IAC Iowa State University SE tower

This is the AmeriFlux version of the carbon flux data for the site US-IAC Iowa State University SE tower. Site Description - This is a 4 ha (200 m x 200 m) sorghum-corn-soybean rotation established at the Sustainable Advanced Bioeconomy Research (SABR) farm at Iowa State University. The site has a long history of conventional row-cropping, predominantly corn-soy rotations. In the immediately preceding growing season, soybeans were grown at the SABR farm.

(Rojda), Guler Aslan Sungur↗

DOE OSTI2026

AmeriFlux US-CLN Coles Farm North

This is the AmeriFlux version of the carbon flux data for the site US-CLN Coles Farm North. Site Description - The land was given to Iowa State University in 1974, and was a corn-soybean rotation with conventional tillage operation until 2015. In 2016, the management was moved to strip tillage corn-soybean rotation with cover crops. The field is located east of Williams, IA.

Neale, Christopher [Daugherty Water for Food Insti↗

DOE OSTI2026

AmeriFlux US-CLS Coles Farm South

This is the AmeriFlux version of the carbon flux data for the site US-CLS Coles Farm South. Site Description - The land was given to Iowa State University in 1974, and was a corn-soybean rotation with conventional tillage operation until 2015. In 2016, the management was moved to strip tillage corn-soybean rotation with cover crops. The field is located east of Williams, IA.

Prueger, John H. [National Laboratory for Agricult↗

DOE OSTI2026

AmeriFlux FLUXNET-1F US-IAC Iowa State University SE tower

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-IAC Iowa State University SE tower. This is the FLUXNET version of the carbon flux data for the site US-IAC Iowa State University SE tower produced by applying the standard ONEFlux (1F) software. Site Description - This is a 4 ha (200 m x 200 m) sorghum-corn-soybean rotation established at the Sustainable Advanced Bioeconomy Research (SABR) farm at Iowa State University. The site has a long history of conventional row-cropping, predominantly corn-soy rotations. In the immediately preceding growing season, soybeans were grown at the SABR farm.

(Rojda), Guler Aslan Sungur↗

DOE OSTI2015

Refinery Upgrading of Hydropyrolysis Oil From Biomass

Cellulosic and woody biomass can be converted to bio-oils containing less than 10% oxygen by a hydropyrolysis process. Hydropyrolysis is the first step in Gas Technology Institute’s (GTI) integrated Hydropyrolysis and Hydroconversion IH2®. These intermediate bio-oils can then be converted to drop-in hydrocarbon fuels using existing refinery hydrotreating equipment to make hydrocarbon blending components, which are fully compatible with existing fuels. Alternatively, cellulosic or woody biomass can directly be converted into drop-in hydrocarbon fuels containing less than 0.4% oxygen using the IH2 process located adjacent to a refinery or ethanol production facility. Many US oil refineries are actually located near biomass resources and are a logical location for a biomass to transportation fuel conversion process. The goal of this project was to work directly with an oil refinery partner, to determine the most attractive route and location for conversion of biorenewables to drop in fuels in their refinery and ethanol production network. Valero Energy Company, through its subsidiaries, has 12 US oil refineries and 11 ethanol production facilities, making them an ideal partner for this analysis. Valero is also part of a 50- 50 joint venture with Darling Ingredients called Diamond Green Diesel. Diamond Green Diesel’s production capacity is approximately 11,000 barrels per day of renewable diesel. The plant is located adjacent to Valero’s St Charles, Louisiana Refinery and converts recycled animal fats, used cooking oil, and waste corn oil into renewable diesel. This is the largest renewable diesel plant in the U.S. and has successfully operated for over 2 years For this project, 25 liters of hydropyrolysis oil from wood and 25 liters of hydropyrolysis oils from corn stover were produced. The hydropyrolysis oil produced had 4-10% oxygen. Metallurgical testing of hydropyrolysis liquids was completed by Oak Ridge National Laboratories (Oak Ridge) and showed the hydropyrolysis oils had low acidity and caused almost no corrosion in comparison to pyrolysis oils, which had high acidity and caused significant levels of corrosion.

09 BIOMASS FUELS↗

DOE OSTI2015

Life-cycle Analysis of Bioproducts and Their Conventional Counterparts in GREET

To further expand upon the literature in this field and to develop a platform for bioproduct LCA, we developed LCA results for ten bioproducts produced either from algal glycerol or from corn stover-derived sugars. We used Argonne National Laboratory’s Greenhouse gases, Regulated Emissions, and Energy use in Transportation (GREETTM) model as the platform for this study. The data and calculations reported herein are available to GREET users in a bioproducts module included in the fall 2015 GREET release. This report documents our approach to this analysis and the results. In Chapter 2, we review the process we underwent to select the bioproducts for analysis based on market and technology readiness criteria. In Chapter 3, we review key parameters for production of the two feedstocks we considered: corn stover and algae. Given the lack of publicly available information about the production of bioproducts, which is caused in large part by the emerging nature of the industry, we developed Aspen Plus® simulations of the processes that could be used to produce each bioproduct. From these simulations, we extracted the energy and material flows of these processes, which were important inputs to the GREET bioproducts module. Chapter 4 provides the details of these Aspen Plus simulations. It is important to compare the LCA results for bioproducts to those for their petroleum counterparts. We therefore also developed material and energy flow data for conventional products based mostly on the literature. These data are described in Chapter 5 and are also included in the GREET bioproducts module. In Chapter 6, we present results from this analysis and examine areas for refinement and future research.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Renewable Enhanced Feedstocks for Advanced Biofuels and Bioproducts (REFABB)

The basic concept of the REFABB project was that by genetically engineering the biomass crop switchgrass to produce a natural polymer PHB, which is readily broken down by heating (thermolysis) into the chemical building block crotonic acid, sufficient additional economic value would be added for the grower and processor to make it an attractive business at small scale. Processes for using thermolysis to upgrade biomass to densified pellets (char) or bio-oil are well known and require low capital investment similar to a corn ethanol facility. Several smaller thermolysis plants would then supply the densified biomass, which is easier to handle and transport to a centralized biorefinery where it would be used as the feedstock. Crotonic acid is not by itself a large volume commodity chemical, however, the project demonstrated that it can be used as a feedstock to produce a number of large volume chemicals including butanol which itself is a biofuel target. In effect the project would try to address three key technology barriers, feedstock logistics, feedstock supply and cost effective biomass conversion. This project adds to our understanding of the potential for future biomass biorefineries in two main areas. The first addressed in Task A was the importance and potential of developing an advanced value added biomass feedstock crop. In this Task several novel genetic engineering technologies were demonstrated for the first time. One important outcome was the identification of three novel genes which when re-introduced into the switchgrass plants had a remarkable impact on increasing the biomass yield based on dramatically increasing photosynthesis. These genes also turned out to be critical to increasing the levels of PHB in switchgrass by enabling the plants to fix carbon fast enough to support both plant growth and higher levels of the polymer. Challenges in the critical objective of Task B, demonstrating conversion of the PHB in biomass to crotonic acid at over 90% yield, demonstrated the need to consider up-front the limitations of trying to adopt existing equipment to a task for which subsequent basic research studies indicated it was not suitable. New information was developed in the most complex of the chemical conversions studied, advanced catalysis to make acrylic acid, a chemical used widely to make paints, and this was published in a scientific journal. In regard to the technical effectiveness, the crop science aspects were for the most part remarkably effective in addressing the underlying objectives indicating the soundness of the technical approach. With time, it should be possible to fully develop the advanced biomass biorefinery feedstock. Challenges within the thermolysis step to recover crotonic acid meant that by the end of the project we were not able to demonstrate an economic case based on data from scaled up equipment. Solving this will take further research and development work. As a general statement, the broadest public good is in demonstrating the value of funding a very unique approach to the complex problem of enabling large-scale biomass biorefineries which resulted in significant progress towards the ultimate goal and a clearer understanding of the technical hurdles remaining. Perhaps not surprisingly, some of the broader benefits to the public come from the use of the REFABB project innovations in areas unrelated to the initial objective. It is worth highlighting the breakthrough developments in identifying three single global regulator genes which can be engineered into plants to dramatically increase photosynthesis and carbon capturing ability. These genes have tremendous potential for use in major food crops, in particular corn to enhance grain yield and based on recent findings, increase the root density, a critical key to increasing carbon sequestration in agriculture and improving the sustainability of global food and biofuel production.

09 BIOMASS FUELS↗

DOE OSTI2015

Investigation of Coal-biomass Catalytic Gasification using Experiments, Reaction Kinetics and Computational Fluid Dynamics

A collaborative effort involving experiments, kinetic modeling, and computational fluid dynamics (CFD) was used to understand co-gasification of coal-biomass mixtures. The overall goal of the work was to determine the key reactive properties for coal-biomass mixed fuels. Sub-bituminous coal was mixed with biomass feedstocks to determine the fluidization and gasification characteristics of hybrid poplar wood, switchgrass and corn stover. It was found that corn stover and poplar wood were the best feedstocks to use with coal. The novel approach of this project was the use of a red mud catalyst to improve gasification and lower gasification temperatures. An important results was the reduction of agglomeration of the biomass using the catalyst. An outcome of this work was the characterization of the chemical kinetics and reaction mechanisms of the co-gasification fuels, and the development of a set of models that can be integrated into other modeling environments. The multiphase flow code, MFIX, was used to simulate and predict the hydrodynamics and co-gasification, and results were validated with the experiments. The reaction kinetics modeling was used to develop a smaller set of reactions for tractable CFD calculations that represented the experiments. Finally, an efficient tool was developed, MCHARS, and coupled with MFIX to efficiently simulate the complex reaction kinetics.

09 BIOMASS FUELS↗

DOE OSTI2016

ESTIMATING WATER FOOTPRINT AND MANAGING BIOREFINERY WASTEWATER IN THE PRODUCTION OF BIO-BASED RENEWABLE DIESEL BLENDSTOCK

This analysis covers the entire biorefinery operation. The study focuses on net water consumed for the production of a unit of biofuel: blue, green, and grey water footprint. Blue water is defined as the water consumed in the biorefinery that is withdrawn from surface and ground water. Blue water footprint includes enzyme cultivation, pretreatment, hydrolysis, bioreactor, cooling system, boiler, fuel upgrading, combustor track, and on-site WWT. Grey water is defined as wastewater generated from the biorefinery and was evaluated based on the wastewater treatment plant design. Green water, defined as rainwater consumed for the production, is not required in the RDB process. Approximately 7–15 gal of water are required to produce a gallon of RDB when corn stover or non-irrigated perennial grasses, switchgrass and Miscanthus x giganteus (Miscanthus), serve as the feedstock in the contiguous United States. Bioelectricity generation from the biorefinery resulted in a net water credit, which reduced the water footprint. The life cycle grey water footprint for nitrogen is primarily from nitrogen in the feedstock production stage because no wastewater is discharged into the environment in the RDB process. Perennial grasses-based RDB production shows a promising grey water footprint, while corn stover-based RDB production has a relatively low green water footprint. Results from the study can help improve our understanding of the water sustainability of advanced biofuel technology under development. Make-up water for cooling and boiling remains a major demand in the biorefinery. The work revealed a key issue or trade-off between achieving zero liquid discharge to maximize water resource use and potentially increasing cost of fuel production. Solid waste disposal was identified as a management issue, and its inverse relationship with wastewater management could affect economic sustainability.

09 BIOMASS FUELS↗

DOE OSTI2017

Organic acid production from food wastes using Gluconobacter oxydans: A possible source of cheaper lixiviants for leaching REE from end-of-life products

Gluconobacter oxydans is an acidophilic bacterium that is used in industry for producing organic acids, such as gluconic acid, from sugars such as glucose. Recently it has been discovered that the organic acids produced by G. oxydans has potential to be used in the recovery of rare earth elements (REE), especially gluconic acid. Producing gluconic acid from pure glucose has been deemed costly and so research has been conducted to find more economically friendly feedstock. In this work corn stover, potato peel waste, market rejected fruits, and apple processing and holding pond waters were investigated for their ability to provide G. oxydans sufficient sugar to grow and produce organic acid for bioleaching. Substrates such as the corn stover and fruits provided more than 20 g/L of glucose, and the bacterium grew well on all but the apple processing and holding pond water.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Carbon Calculator for Land Use Change from Biofuels Production (CCLUB) Users’ Manual and Technical Documentation

The Carbon Calculator for Land Use Change from Biofuels Production (CCLUB) calculates carbon emissions from land use change (LUC) for four different ethanol production pathways including corn grain ethanol and cellulosic ethanol from corn stover, Miscanthus, and switchgrass, and a soy biodiesel pathway. This document discusses the version of CCLUB released September 30, 2017 which includes five ethanol LUC scenarios and four soy biodiesel LUC scenarios.

09 BIOMASS FUELS↗