Research Project: Enhancing Photosynthesis for Agricultural Resiliency and Sustainability

Location: Global Change and Photosynthesis Research

2024 Annual Report

Objectives
Objective 1: Develop, test, and quantify the benefits of specific strategies for agricultural greenhouse gas mitigation, including enhanced rock weathering, overwintering corn and soybean, expanded use of cover crops, and genetic manipulations to increase photosynthetic efficiency. Sub-objective 1.A: Apply micrometeorological techniques to quantify ecosystem-scale fluxes of greenhouse gases, energy, and water in response to environmental variability, land-use change, and variable management practices. Sub-objective 1.B: Test the effect of basalt application on maize and soybean leaf and seed nutrient content. Objective 2: Adapt crops to future atmospheric conditions through identifying key genes and loci associated with CO2 response, N use efficiency, crop quality and ozone tolerance. Sub-Objective 2.A: Identify the genetic factors that coordinate photosynthesis with N availability and characterize how manipulation of these factors impacts plant traits. Sub-objective 2.B: Test whether the ability to obtain biologically fixed N provides an advantage to how plants acclimate to elevated CO2 and characterize the factors that signal C/N status between source and sink tissues. Sub-objective 2.C: Test soybean response to elevated ozone and drought stress. Sub-objective 2.D: Design an experiment to disentangle the relative contributions of high temperature and increased vapor pressure deficit on the physiology, growth, and yields of soybean. Objective 3: Develop and apply tools using a field-based high-throughput phenotyping platform to quantify growth, physiology, yield quantity, yield quality, and scalability of crop adaptations to current and future environmental conditions. Sub-objective 3.A: Develop multi- and hyper- spectral techniques for high-throughput phenotyping of leaf, plant, and canopy growth, physiological, and nutritional properties to associate genotype to phenotype and to quantify physiological responses to genetic manipulations to increased photosynthetic efficiency. Sub-objective 3.B: Develop and test hyperspectral methods to measure soil characteristics, including water content, and iron and zinc concentrations. Objective 4: Develop, train, and validate computer models of crop nutrient uptake and growth in order to identify traits and genes that will improve crop quality and yield. Sub-objective 4.A: Develop models of yield for key crops that include effects of CO2 concentration, temperature, soil characteristics and vapor pressure. Sub-objective 4.B: Develop soil and root nutrient uptake and distribution models.

Approach
Research aims to understand and reduce the negative impacts of agriculture by quantifying greenhouse gas fluxes using Eddy covariance techniques, investigating the effectiveness of soil amendments to store carbon, and developing state-of-the-art high-throughput techniques for fast and accurate measurements of crop traits. Experiments will test how elevated carbon dioxide impacts enhanced rock weathering in corn and soybean ecosystems and will monitor carbon dioxide, water and ozone fluxes in long-term experimental facilities. Research will test how interrelated metabolic and stress response pathways are coordinated at the genetic scale, generate crop models that identify trait and gene targets for crop improvement, and develop novel high throughput phenotyping techniques to measure plant and canopy traits and efficiently process immense data streams from sensors. Experimental approaches scale from the molecular to the ecosystem level, combining biophysics, physiology, molecular biology, genetics, and genomics. Research will take advantage of unique field and greenhouse experimental and monitoring facilities, along with integrated collaborations with other ARS and university researchers and commercial farmers.

Progress Report
This project began in June 2023 and aims to understand and reduce the negative impacts of agriculture by quantifying greenhouse gas fluxes, investigating the effectiveness of soil amendments to remove carbon dioxide (CO2) from the atmosphere, and developing high-throughput techniques for fast and accurate measurements of crop traits. In support of Objective 1, researchers in Urbana, Illinois measured ecosystem water, carbon and energy fluxes in maize/soybean, C4 bioenergy crop and pasture ecosystems using eddy covariance techniques. These fluxes provide critical ground-truth measurements for assessing the carbon budgets of agroecosystems. Ten site years of data were added to the Ameriflux network in 2023/2024 and have been downloaded by the community over 1000 times. In support of Sub-objective 1B, ARS researchers in Urbana, Illinois, grew soybean with and without crushed basalt rock at ambient and elevated CO2 concentration at the Free Air Concentration Enrichment (FACE) facility. The multi-year experiment tests the potential for elevated CO2 to interact with enhanced rock weathering (ERW) to improve CO2 sequestration in agricultural ecosystems. ERW is the biogeochemical improvement of cropland soils with crushed basalt, an abundant natural silicate rock, for carbon sequestration. ERW involves the acceleration of silicate mineral dissolution that occurs when rock grains react with rainfall and CO2 in soil to sequester CO2. Measurements of crop development, photosynthesis, stomatal conductance, soil respiration, soil nitrous oxide emissions, soil moisture, water chemistry, soil pH and cation exchange capacity and rates of in situ rock weathering were made throughout the season. Samples for leaf and grain quality and nutritional status are being analyzed currently. In support of Sub-objectives 2A and 2B, ARS researchers in Urbana, Illinois, grew alfalfa lines with and without nitrogen fixation capabilities in different nitrogen and CO2 concentrations. Specifically, these experiments test the hypothesis that legumes will have an advantage at elevated CO2 as they can exchange excess carbon from greater photosynthesis with nitrogen-fixing bacteria. The nitrogen-fixing bacteria could provide a greater sink for carbohydrate and in return exchange nitrogen to the plant at elevated CO2. The experiments showed that symbiosis with nitrogen fixing bacteria provided a significant advantage to the plant, especially at elevated CO2. Gene regulatory networks identified important genetic regulators that integrated nitrogen and carbon signaling including two classes of transcription factors. In support of Sub-objective 2C, soybean was grown with combined ozone and drought stress to test if the timing of stressors impacted the physiological response. A preliminary experiment was performed to optimize the timing of treatments and to identify a drought stress treatment that elicited a moderate response without killing the plants. Reducing soil moisture by 30% provided a moderate drought treatment where we could then investigate interactions with elevated ozone stress. In support of Sub-objective 2D, ARS researchers in Urbana, Illinois, grew soybeans under rising temperature with and without additional humidity using in-field infrared heaters and misting systems to test how physiology, growth, and yield responded to rising temperature and vapor pressure deficit. Preliminary results discovered that much of soybean physiological responses to rising temperature were driving by lower vapor pressure deficit. This is a significant result that emphasizes the importance of considering vapor pressure deficit in ecosystem models of crop responses to climate change. Objective 3 aims to develop and apply high-throughput phenotyping platforms to quantify growth, physiology, yield quantity, yield quality, and scalability of crop adaptations to current and future environmental conditions. In support of this objective, ARS researchers in Urbana, Illinois, assessed soybean seed quality with near infrared reflectance and statistical models to estimate seed protein and oil content. It was discovered that in a soybean genotype that showed a significant yield increase in elevated CO2, soybean oil content significantly decreased at elevated CO2. Additionally, genetic variability in photosynthetic capacity in a recombinant inbred population of soybean was assessed by leaf hyperspectral reflectance and current research is identifying genetic markers associated with changes in photosynthetic capacity at elevated CO2. Also in support of Objective 3, ARS scientists in Urbana, Illinois, tested the performance of two estimation techniques, namely voxelization and a convex hull algorithm, for estimating biomass from lidar scans. Research focused on three crops: corn (Zea mays), broom corn (Sorghum bicolor variety Tx430), and energy sorghum (Sorghum bicolor) and the digital biomass estimations were tested against conventional destructive biomass harvest data. The results showed that both estimation techniques could be accurately used, and in fact, the digital biomass estimation techniques were more accurate than conventional biomass harvests. This research, published in Remote Sensing, advances non-destructive biomass measurement capabilities and offers insights into the strengths and weaknesses of existing technical and statistical methodologies. In support of the CERCA project, ARS scientists in Urbana, Illinois explored potential genetic variation in maize cold tolerance and specific genes that may confer cold tolerance. Sixty-three maize landraces adapted to altitudes above 2500m were planted in a fall field trial along with 250 doubled haploid lines from a stiff stalk multi-parent advanced generation inter-cross (MAGIC) population and monitored for health following freezing events. The fall planting experiment complemented work in New York, Wisconsin, and Texas and aimed to identify lines with tolerance to freezing temperatures. ARS scientists also grew five maize hybrids in five replicated plots to investigate the nitrogen budget in the different lines. ARS scientists purchased four nitrous oxide trace gas analyzers and distributed those to collaborators in New York, North Carolina, and Florida where replicated trials are also being done. ARS scientists established a uniform protocol for measuring nitrous oxide emissions from the plots grown in different states and are identifying if there is variation in nitrous oxide emissions associated with maize hybrids. This work is foundational to building accurate computational models of nitrogen budgets in maize agriculture.

Accomplishments
1. Determined drought and heat stress do not affect the sensitivity of soybean to ozone pollution. Increasing drought, higher temperatures and increased levels of ozone, a damaging air pollutant, are co-occurring stresses associated with climate change. The effects of ozone on soybean may vary with environmental factors including drought and high temperature. ARS scientists in Urbana, Illinois, examined 15 growing seasons of data from an in- field open-air ozone experiment and found that elevated ozone reduced soybean seed yield from as little as 5.3% in 2005 to 35.2% in 2010. Soybean lines showed greater seed yield losses to elevated ozone when grown at drier or hotter conditions compared to wetter or cooler years, because the hotter and drier conditions were associated with greater ozone dose. However, the sensitivity of soybean to the same increase in ozone concentration was not affected by growing season water availability or temperature. These results enable more accurate modeling of the effects of rising ozone pollution on crops and suggest that proposed management practices to mitigate ozone stress including irrigation may not be effective in reducing crop sensitivity to ozone.

2. Identified two classes of transcription factors that integrate nitrogen and light signals to coordinate photosynthesis and optimize yield. The coordination of nitrogen nutrient uptake from the soil and photosynthetic carbon assimilation is important for achieving optimal biomass/yield. Through integration of transcriptomic and physiological trait datasets, ARS researchers in Urbana, Illinois, identified important transcription factors that coordinate nitrogen and light signals. Transcription factors were enriched among the bZIP and MYB families. Photosynthetic genes were among the most enriched targets of these transcription factors. These results provide candidate targets for crop manipulation and breeding efforts for breeders and plant biotechnologists.

3. Developed soybean nitrogen uptake model to identify strategies for improving seed protein content. Soybean seed protein concentration is a critical trait contributing to soybean meal price. Although soybean yield has increased over the past several decades, seed protein concentration has declined, resulting in lower prices. Nitrogen is a primary constituent of protein, and a mathematical model describing nitrogen uptake and distribution could be used to identify biochemical steps that limit seed protein concentration. ARS researchers in Urbana, Illinois, developed a basic nitrogen uptake model which indicates that translocation of nitrogen from shoots to seeds is a key limiting step, implicating processes such as protein degradation during senescence and vascular amino acid transport as steps that limit seed protein concentration. This model has been coupled to the soybean growth model for further analysis. This information provides key strategies for increasing protein content in soybean which is important for the food and feed processing industries.

Review Publications
Digrado, A., Montes, C.M., Baxter, I., Ainsworth, E.A. 2024. Seed quality under elevated CO2 differs in soybean cultivars with contrasting yield responses. Global Change Biology. 30(2). Article e17170. https://doi.org/10.1111/gcb.17170.
Brooks, M.D., Szeto, R.C. 2024. Biological nitrogen fixation maintains carbon/nitrogen balance and photosynthesis at elevated CO2. Plant Cell and Environment. 47(6):2178-2191. https://doi.org/10.1111/pce.14873.
Wu, G., Guan, K., Ainsworth, E.A., Martin, D.G., Kimm, H., Yang, X. 2023. Solar-induced chlorophyll fluorescence captures the effects of elevated ozone on canopy structure and acceleration of senescence in soybean. Journal of Experimental Botany. 75(1):350-363. https://doi.org/10.1093/jxb/erad356.
Li, S., Leakey, A.D.B., Moller, C., Montes, C.M., Sacks, E., Lee, D.K., Ainsworth, E.A. 2023. Similar photosynthetic but different yield responses of C3 and C4 crops to elevated O3. Proceedings of the National Academy of Sciences (PNAS). 120(46). Article e2313591120. https://doi.org/10.1073/pnas.2313591120.
Miner, G.L., Stewart, C.E., Delgado, J.A., Ippolito, J.A., Mason, R.E., Haley, S.D., Guttieri, M.J., Ainsworth, E.A., McGrath, J.M., Beebout, S.E. 2024. Global change impacts on mineral nutritional quality of cereal grains: Coordinated datasets and analyses to advance a systems-based understanding. Field Crops Research. 310. Article e109338. https://doi.org/10.1016/j.fcr.2024.109338.
Bernacchi, C.J., Ruiz-Vera, U.M., Siebers, M.H., DeLucia, N.J., Ort, D.R. 2023. Short- and long-term warming events on photosynthetic physiology, growth, and yields of field grown crops. Biochemical Journal. 480(13):999-1014. https://doi.org/10.1042/BCJ20220433.
Kantola, I., Blanc-Betes, E., Masters, M., Chang, E., Marklein, A., Moore, C., von Haden, A., Bernacchi, C.J., Wolf, A., Epihov, D., Beerling, D.J., DeLucia, E. 2023. Improved net carbon budgets in the US Midwest through direct measured impacts of enhanced weathering. Global Change Biology. 29(24):6829-7192. https://doi.org/10.1111/gcb.16903.
Siebers, M.H., Fu, P., Blakely, B.J., Long, S.P., Bernacchi, C.J., McGrath, J.M. 2024. Fast, nondestructive and precise biomass measurements are possible using lidar-based convex hull and voxelization algorithms. Remote Sensing. 16(12). Article 2191. https://doi.org/10.3390/rs16122191.
Huang, J., Katari, M.S., Juang, C., Coruzzi, G.M., Brooks, M.D. 2023. Building high-confidence gene regulatory networks by integrating validated TF-target gene interactions using ConnecTF. In: Kaufman, K., Vandepoele, K., editors. Plant Gene Regulatory Networks. 2nd edition. New York, NY: Humana. p. 195-220. https://doi.org/10.1007/978-1-0716-3354-0.
Alvarez, J.M., Hinckley, W., Leonelli, L., Brooks, M.D., Coruzzi, G.M. 2023. DamID-seq: A genome-wide DNA methylation method that captures both transient and stable TF-DNA interactions in plant cells. Book Chapter. p. 87-107. https://doi.org/10.1007/978-1-0716-3354-0.
Williams II, M.M., Hausman, N.E., Saballos, A., Landau, C.A., Brooks, M.D., Flannery, P., Tracy, W., Thompson, C. 2024. First report of severe tolpyralate sensitivity in corn (Zea mays) discovers a novel genetic factor conferring crop response to a herbicide. Pest Management Science. 80(3):1645-1653. https://doi.org/10.1002/ps.7896.
Cho, Y.B., Boyd, R.A., Ren, Y., Lee, M., Jones, S.I., Ruiz-Vera, U.M., McGrath, J.M., Master, M.D., Ort, D.R. 2023. Reducing chlorophyll levels in seed-filling stages results in higher seed nitrogen without impacting canopy carbon assimilation. Plant Cell and Environment. 47(1):278-293. https://doi.org/10.1111/pce.14737.
Guo, Y., Boughton, E., Bohlman, S., Bernacchi, C.J., Bohlen, P., Boughton, R., DeLucia, E., Fauth, J., Gomzez-Casanovas, N., Jenkins, D. et al. 2023. Grassland intensification effects cascade to alter multifunctionality of wetlands within metaecosystems. Nature Communications. 14. Article 8267. https://doi.org/10.1038/s41467-023-44104-2.
Yang, Y., Peng, B., Guan, K., Pan, M., Franz, T., Cosh, M.H., Bernacchi, C.J. 2024. Within-field soil moisture variability and time-invariant spatial structures of agricultural fields in the US Midwest. Vadose Zone Journal. Article e20337. https://doi.org/10.1002/vzj2.20337.
Berardi, D.M., Hartman, M.D., Brzostek, E.R., Bernacchi, C.J., DeLucia, E., von Haden, A.C., Kantola, I., Moore, C.E., Yang, W.H., Hudiburg, T.W., Parton, W.J. 2024. Microbial-explicit processes and refined perennial plant traits improve modeled ecosystem carbon dynamics. Geoderma. 443. Article 116851. https://doi.org/10.1016/j.geoderma.2024.116851.
Boughton, R.K., Smith, B.W., Boughton, E.H., Gomez-Casanovas, N., Bernacchi, C.J., DeLucia, E., Sparks, J., Swain, H.M. 2024. Patch-burn management changes grazing behavior of cattle in humid subtropical grasslands. Agriculture Ecosystems and the Environment. 368. Article 109012. https://doi.org/10.1016/j.agee.2024.109012.
Gomez-Casanovas, N., Mwebaze, P., Khanna, M., Branham, B., Time, A., DeLucia, E.H., Bernacchi, C.J., Knapp, A., Hoque, M.J., Du, X., et al. 2023. Knowns, uncertainties, and challenges in agrivoltaics to sustainably intensify energy and food production. Cell Reports Physical Science. 4(8). Article 101518. https://doi.org/10.1016/j.xcrp.2023.101518.