Research Project: Optimizing and Enhancing Sustainable and Profitable Dryland Wheat Production

Location: Columbia Plateau Conservation Research Center

2025 Annual Report

Objectives
Objective 1: Evaluate and seek to optimize climate-adaptive cropping system alternatives to the 2-year winter wheat-fallow system that reduce fallow periods in the dryland Pacific Northwest, increasing productivity, profitability, input-use efficiency, and sustainability. 1.A: Evaluate winter cover crops in low and intermediate precipitation regions. 1.B: Evaluate newly developed food-grade winter field peas as a rotational crop with nitrogen benefit. Objective 2: Increase resilience and profitability of the widely-used dryland wheat-fallow system by improving nutrient and weed management. 2.A: Develop liming practices to ameliorate the increasing soil acidity issues on wheat production systems in the low and intermediate regions of the PNW to increase productivity and yield. 2.B: Evaluate the effects of crop management on soil and grain nutrients. 2.C: Evaluate the impacts of integrated (chemical/mechanical) weed management and weed physiology on soil water dynamics in-field and under controlled settings. 2.D: Evaluate profitability of management strategies that ameliorate soil quality decline (e.g., soil pH) or reduce weed infestation. Objective 3: Develop tools to better assess agricultural soil microbiomes for enhancing nutrient cycling and optimizing desired biochemical degradative pathways in diverse agroecosystems. 3.A: Develop high-throughput standard protocols to assess soil biological function and diversity. 3.B: Assess the soil microbiome response to PFAS as an emerging concern in agriculture.

Approach
1.A: A dryland cover crop systems trial under low and intermediate rainfall will include fall-seeded cover crops of winter pea, winter canola, winter barley, and a mix of the three. Winter wheat-fallow will be the control. Analyses include grain yield and quality; cover crop and weed biomass, density and/or cover; soil fertility and soil biology; soil water dynamics; and economic assessments. 1.B: Studies will be established at two dryland sites under low and intermediate rainfall and an irrigated site. Treatments include food-grade green pea (MiCa), a food-grade yellow pea (Klondike), and a non-food-grade Austrian winter pea (Grainger), plus wheat and fallow. Analyses include plant phenology and growth; yield components; plant nitrogen and nitrogen fixation; soil fertility; soil moisture; and soil biology. Data will support development of the first mechanistic plant growth model for winter field peas (DSSAT CROPGRO; collaboration with University of Florida). 2.A: A lime micro-dosing method will be evaluated in dryland wheat cropping systems at sites with soil acidity constraints (pH <5.5) in the low and intermediate rainfall regions. Treatments will include a one-time application of lime using the traditional broadcast approach or micro-dosing with 10-50% lime recommendation. Analyses include soil chemistry (including exchangeable aluminum [Al3+], pH, and cation exchange capacity) and grain yield. 2.B: Archived soil samples from a long-term fertility trial at Pendleton, Oregon will be analyzed for secondary- and micro-nutrient contents and soil pH to identify historical trends in soil quality and crop yield. Separately, the effects of wheat genotype, production environment, and other variables on grain nutrient density will be assessed. 2.C: Weed management with chemical, mechanical or integrated (chemical/mechanical) practices will be assessed in dryland wheat-fallow under low and intermediate rainfall. Assessments include weed density, vegetation cover (UAV-based); grain yield; and soil water dynamics. Greenhouse and column assays will assess the potential belowground advantage of weeds on water extraction compared to wheat including permanent wilting point, rooting depth, and soil water extraction. 2.D: Standard enterprise budget analyses will be performed to determine cost-benefit relationships from lime micro-dosing and integrated weed management strategies. 3.A: A bench-scale assay for combined nutrient-cycling enzymes (carbon, nitrogen, sulfur, phosphate) will be modified for microplates with robotic-assisted liquid handling. Protocols and bioinformatic pipelines will be developed to assess archaeal and bacterial ammonia-oxidizing microbial communities based on DNA sequencing of the amoA gene (ammonia monooxygenase) using the Oxford Nanopore MinION platform. 3.B: Microbial communities from PFAS-contaminated and PFAS-naïve soils amended with PFAS will be assessed using molecular techniques to identify potential microbiota associated with PFAS degradation. PFAS compositional profiles and concentrations will be determined using liquid chromatography mass spectrometry.

Progress Report
This report documents progress for project 2074-21600-001-000D, titled, “Optimizing and Enhancing Sustainable and Profitable Dryland Wheat Production ", which started September 2023. Significant progress was made on Objective 1 in optimizing alternatives to the traditional two-year winter wheat-fallow dryland cropping system under low to moderate annual precipitation including both cover cropping (Sub-objective 1.A) and crop diversification with food-grade winter peas as a rotational crop (Sub-objective 1.B). In support of Sub-objective 1.A, sample collection and analysis of soil, water, and plant samples continued for the second year of the trial that is managed through a Congressionally mandated agreement with Oregon State University. Similar to last year, winter barley, winter pea, and the mixed cover crop had strong establishment in the field, but winter canola treatments were unsuccessful. All plots at both sites encountered inadvertent but significant herbicide spray damage in the spring. The herbicide damage negatively impacted both soil water and soil microbiological assessments, but plant biomass sampling was carried out with care taken to avoid damaged plot areas. The cover crops were sampled in mid-May to determine biomass productivity and the level of weed infestation in each cropping system. Biomass samples are being prepared for total nitrogen (N) and N15 analyses which will be used to assess system N balances and biological N fixation of legume cover crops. Crop and weed cover assessments from unpiloted aerial systems (UAS)-based imagery were completed by collaborators at Oregon State University. At physiological maturity, plots in the wheat cash crop phase were sampled to assess grain yield, yield component parameters, and residue production. The plots were also harvested by a small-plot combine to determine yield at greater scale. Soil cores for gravimetric water and chemistry were collected to a 3-ft depth prior to fall planting and after cover crop termination in areas with limited herbicide damage. Infiltration measurements were taken during the first year of the study, but in the second year the plots were instrumented with water potential sensors and soil moisture sensors as a proxy for water infiltration due to high labor and equipment costs. Significant herbicide damage occurred in areas of sensor placement; therefore, assessment of daily soil water use was infeasible. Although the fall preplant soils were analyzed for soil enzyme activity and archived for soil community analyses, the spring soil collection for microbiology was not conducted since the patchy distribution of plants would confound inferences on cover crop effects in the following wheat phase. Significant progress was made on Sub-objective 1.B. Field trials with three winter pea varieties (two novel food-grade winter peas and Austrian winter peas) and wheat were successfully established at three sites for the second year. The trials are providing foundational scientific information on crop growth, yield, and other traits of the newly developed food-grade dry peas and supporting the development of a CROPGRO module for field peas in the DSSAT crop growth simulation model. Data on various response variables were collected from time-series measurements to capture changes in growth and biomass partitioning over the entire crop life cycle in different environments. The data from the first and second year of the project was analyzed for its agronomic, agroecological, and physiological value and provided to collaborators at the University of Florida for parameterization of the CROPGRO-PEA module. Significant progress was made in identifying the belowground benefits of field peas compared to wheat with completion of soil nitrogen cycling enzyme activity and near-completion of soil chemistry and DNA sequencing for pre-plant (bulk) soils and in-crop (root-impacted) soils. The project was expanded to evaluate winter peas in a rotational cropping system by assessing their impact on the following wheat crop. The soil microbiome and nodule analyses are performed in collaboration with ARS in Pullman, Washington. For Objective 2, significant progress was made on Sub-objectives 2.B2 and 2.C, but Sub-objectives 2.A, 2.B1, and 2.D were delayed due to critical vacancies in agronomy and agricultural economics. The wheat mineral density study of Sub-objective 2.B (Hypothesis 2.B2) was successfully completed and published in the journal Crop Science and the research was also highlighted by invitation of the editorial board in CSA News (the trade magazine for the Crops, Soils, and Agronomy societies of America, CSSA/SSSA/ASA). Significant progress was made on Sub-objective 2.C in evaluating weed management strategies and weed physiology on soil water dynamics. Sub-objective 2.C is managed in part by a Congressionally mandated Non-Assistance Cooperative Agreement with Oregon State University under the Pacific Northwest Herbicide Resistance Initiative. The second-year field study evaluating integrated weed management strategies was successfully implemented and data collection was continued. Soil moisture was assessed at all three sites (two in the intermediate and one in the low annual precipitation region) in spring and fall with soil infiltration analyzed for wheat-phase plots in the spring. The spatial distribution of weed cover in the fallow plots at the intermediate precipitation site was assessed using UAS-based imagery. At the low precipitation site, UAS-imagery was not feasible due to constraints in operation timing, labor, and weather; therefore, weed cover was assessed by ground surveys as stated in the research plan contingency. Assessments of grain yield and ground-based surveys of weed cover were performed by Oregon State University. Significant progress was also made on Sub-objective 2.C with the early completion of the growth chamber experiment (2.C2). The full dataset has been collected, summarized, and analyzed, and a manuscript is currently in preparation. In addition, significant progress was made on the Congressionally funded research of the PNW Herbicide Resistance Initiative to develop web-based tools that facilitate herbicide-resistant weed management including a regional interactive herbicide resistance map that provides real-time data on the prevalence and spread of resistant weed populations. Progress was made on all aspects of Objective 3 with modification from the research plan. For the development of robot-assisted protocols in Sub-objective 3.A, optimizations were completed that improved the accuracy of the liquid volume transfer and reduced the number of pipet tips that were used for the liquid transfers. Critical vacancies delayed completion of the robot-assisted, color-based soil enzyme activity assay; however, significant progress was made on the completion of a robot-assisted mineralization assay. The mineralization assay was prioritized based on research need and urgency to complete ongoing research. The protocol couples the measurement of ammonia for the 7-day anaerobic mineralization method with the analysis of nitrate thereby streamlining the two analyses (i.e., mineralization and soil inorganic nitrogen). The mineralization assay has been shared with ARS collaborators for validation of the method. Significant progress was made on Sub-objective 3.A2 in developing molecular and DNA sequence analysis (e.g., bioinformatic) tools to assess ammonia oxidizing microbial communities. A quantitative polymerase chain reaction (qPCR) assay (e.g., a method that measures the number of specific genes in a DNA sample) was developed for comammox bacteria, a group that performs complete nitrification compared to the more commonly assessed group of bacteria and archaea that carry out only the step of ammonia oxidation. Bioinformatic protocols were developed to analyze community diversity and composition of bacterial ammonia oxidizers from DNA sequence data collected on the Oxford Nanopore MinION next generation DNA sequencing platform. Progress on Sub-objective 3.B, to characterize the response of the microbiome to per- and polyfluoroalkyl substances (PFAS) was made through collaboration with an ARS scientist at University Park, Pennsylvania in which ongoing projects can be leveraged to identify potential sites based on background PFAS levels. The PFAS work has been expanded to include a retroactive study on the potential for and legacy of PFAS contamination of soil from biosolid amendments at ARS in Adams, Oregon. Archived soils from a study that commenced in 2007 are being analyzed for PFAS through a collaboration with Penn State (University Park, Pennsylvania). This work has the potential to identify how PFAS persists in the soil under moderate rainfall and dryland wheat-fallow cropping with the added benefit to reassess the study site over 20-years following the final biosolid amendments.

Accomplishments
1. Fact check: new diagnostics and reference soils to validate soil microbial DNA sequencing results. Soil biology is an important factor driving the productivity and sustainability of soils. To understand the diversity and function of soil microbes, DNA sequencing methods are now commonly employed, but reproducibility and the potential to introduce error throughout the workflow steps are ongoing challenges. In response, twelve ARS researchers in Adams, Oregon; Beltsville, Maryland; Brookings, South Dakota; Columbia, Missouri; Fayetteville, Arkansas; Fayetteville, New York; Florence, South Carolina; Fort Collins, Colorado; Lincoln, Nebraska; Morris, Minnesota; Riverside, California; and Stoneville, Mississippi, conducted a cross-laboratory study to evaluate sources of variability in soil community sequencing experiments and develop diagnostics to detect errors. One of the seven sequencing runs in the experiment produced results that were clearly incorrect based on comparison to the other runs, yet the internal control (microbial mock community) and standard diagnostics did not suggest errors. This study provides new, simple bioinformatic diagnostics to identify erroneous sequence results and recommends reference soils rather than simple “mock” communities to validate sequence results. Researchers and commercial facilities following these guidelines can have greater confidence in the accuracy and reproducibility of soil community sequence results.

2. Shining light on grain mineral nutrition of wheat. The United States is the fourth largest exporter of wheat worldwide, with the Pacific Northwest region being renowned for its production of high-quality soft white winter wheat sold primarily to Asian markets. Many populations in developing Asian countries rely on U.S. wheat exports as a primary source of mineral nutrients, but concern exists that certain breeding selection traits of soft white wheat have led to a decline in grain mineral concentrations, perhaps even greater than the well-established mineral decline observed in hard red wheat over the past 60 years. To address this concern, ARS researchers in Adams, Oregon, collaborated with scientists at Washington State University, University of Idaho, and Oregon State University to develop global benchmark grain mineral concentrations for modern wheat as a comparative tool for assessment of soft white and hard red wheat both in the Pacific Northwest and wheat worldwide, and to assess the effects of grain milling and processing on the mineral density of flour. Overall, it was found that grain mineral concentrations of soft white wheat have declined over time, but do not differ from hard red wheat or wheat grown globally. There is wide variation in grain mineral density between different wheat varieties and, more so, from wheat produced in different agronomic environments. Additionally, the flour refining process consistently and severely reduced mineral nutritional quality. This research highlights opportunities to enhance grain mineral density through the genetic variation and underlines the central roles that production site and whole, unrefined grains can play in providing essential nutrients in malnourished populations.

3. New data and tools to enable holistic nutrient management of small grains at farm and regional scales. Wheat and barley rely on essential mineral nutrients supplied by the soil or by fertilizer to support growth. Research on nutrient management in small grains has focused on nitrogen, leaving a void of information on the amounts of secondary macronutrients and micronutrients taken up by small grain crops across broad spatial scales. To better develop effective, holistic management and modeling of mineral nutrients in small grain cropping systems, ARS researchers in Adams, Oregon, and Kimberly, Idaho, collaborated with University of Idaho scientists to characterize wheat and barley uptake of eight essential nutrients at farm- and regional-scales. Easy-to-use tools designed for producers were developed to estimate nutrients contained in grain and residue as a function of grain yield. The results highlighted the largely unrecognized and untenably high long-term economic costs associated with soil nutrient consumption from residue removal (baling), which is a common practice in the Pacific Northwest and other areas. The knowledge and tools provided through this research improves the economic and environmental sustainability of small grain nutrient management regionally and worldwide.

4. National survey of soil health response to crop management across the United States. Microbes are a crucial component of soil health and drive productivity and sustainability of agricultural systems. Regional factors and management practices impact microbial communities and affect functions essential to crop productivity such as nutrient cycling, soil organic matter, aggregation, water availability, and disease. To understand the microbial response within a national context, 22 ARS scientists from 15 ARS locations across the U.S. collaborated to elucidate the effects of environment, soil properties, and conservation practices on the structure (diversity and composition) and function (i.e., nutrient cycling capacity) of the soil microbial communities important to soil health. Overall, soil organic carbon and conservation practices were strong drivers of the soil microbial communities in which reduced tillage, cover cropping and manure had larger effects on microbial groups than increased crop diversity. Researchers in Pendleton, Oregon, provided crucial insights for dryland agricultural systems with direct impacts to producers seeking to improve fallow periods by either cover cropping or reducing tillage intensity. This work is important in developing healthy soils and sustaining crop productivity both regionally and nationally.

Review Publications
Sapkota, B.R., Adams, C.B., Su, Q., Ale, S. 2024. Remote detection of water stress in cotton using a center pivot irrigation system-mounted sensor package. Scientific Reports. 14. Article 23436. https://doi.org/10.1038/s41598-024-74092-2.
Raman, R., Neely, H., Rajan, N., Bhandari, M., Siegfried, J., Ibrahim, A., Adams, C.B., Hardin, R. 2025. UAS-derived vegetation indices detect wheat leaf rust infection and its influence on grain yield and canopy temperature. Crop Science. 65(3). Article e70062. https://doi.org/10.1002/csc2.70062.
Adams, C.B., Kongraksawech, T., Ross, A., Long, D.S., Neely, C., Marshall, J., Graebner, R.C., Reardon, C.L., Liang, X. 2024. As grain mineral densities have declined over time, have densities converged across wheat classes?—Insights from the US Pacific Northwest and worldwide benchmarks. Crop Science. 65(1). Article e21409. https://doi.org/10.1002/csc2.21409.
Barroso, J., Reardon, C.L., Singh, S., Machado, S., Gourlie, J., Namdar, G., Oreja, F., Pritchett, L., Kriete, L., Calderon, F., Berry, P., McGee, R.J., Durfee, N.M., Adams, C.B., Hagerty, C.H. 2025. Biomass production, weed suppression, and soil water use of cover crops in dryland wheat production systems. Agronomy Journal. 117(2). Article e70053. https://doi.org/10.1002/agj2.70053.
Adams, C.B., Neely, C., Graebner, R.C. 2025. Yield variation, plasticity, adaptation, and performance ranking of winter wheat varieties across the environmental gradient of the US Pacific Northwest. Crop Science. 65(1). Article e70018. https://doi.org/10.1002/csc2.70018.
Adams, C.B., Rogers, C.W., Marshall, J., Walsh, O., Thurgood, G., Dari, B., Loomis, G. 2025. Wheat mineral nutrient uptake, harvest indices, and grain density from a regional perspective. Agronomy Journal. 117(3). Article e070066. https://doi.org/10.1002/agj2.70066.
Adams, C.B., Rogers, C.W., Marshall, J., Hatzenbuehler, P., Walsh, O., Thurgood, G., Dari, B., Loomis, G., Tarkalson, D.D. 2024. Uptake and economic value of macro- and micronutrient minerals in wheat residue. Agronomy. 14(8). Article 1795. https://doi.org/10.3390/agronomy14081795.
Manley, A., Ravelombola, W., Adams, C.B., Shrestha, R., Hinson, P.O., Trostle, C. 2025. 13C isotope discrimination variation in guar [Cyamopsis tetragronoloba (L.) Taub.] under water-deficit conditions. International Journal of Plant Biology. 16(1). Article 31. https://doi.org/10.3390/ijpb16010031.
Boote, K., Hoogenboom, G., Ale, S., Adams, C.B., Shrestha, R., Mvuyekure, R.F., Himanshu, S., Grover, K., Angadi, S. 2023. Adapting the CROPGRO model to simulate growth and yield of guar, Cyamopsis tetragonoloba L, an industrial legume crop. Industrial Crops and Products. 197. Article 116596. https://doi.org/10.1016/j.indcrop.2023.116596.
Manter, D.K., Reardon, C.L., Ashworth, A.J., Ibekwe, A.M., Lehman, R.M., Maul, J.E., Miller, D.N., Creed, T.B., Ewing, P.M., Park, S., Ducey, T.F., Tyler, H.L., Veum, K.S., Weyers, S.L., Knaebel, D.B. 2024. Unveiling errors in soil microbial community sequencing: A case for reference soils and improved diagnostics for nanopore sequencing. Communications Biology. 7. Article e913. https://doi.org/10.1038/s42003-024-06594-8.
Hogaboam, O., Manning, V., Reardon, C.L., Trippe, K.M. 2025. Hot or not: Quantifying isothiocyanates in plants, soil, and other media. Biosensors and Bioelectronics. 24. Article 100599. https://doi.org/10.1016/j.biosx.2025.100599.
Dungan, R.S., Acosta Martinez, V., Lehman, R.M., Manter, D.K., Mikha, M.M., Reardon, C.L., Tarkalson, D.D., Veum, K.S., Weyers, S.L., White, Jr., P.M. 2024. Short-term effects of a heavy dairy manure application on soil chemical and biological indicators in an irrigated semiarid cropping system. Agronomy Journal. 117(1). Article e21737. https://doi.org/10.1002/agj2.21737.
Roper III, W.R., Acosta Martinez, V., Veum, K.S., Burgess, C.J., Moore, J.M., Manter, D.K., Stewart, C.E., Emmett, B.D., Liebig, M.A., Fischel, M.H., Lehman, R.M., Franco Jr, J.G., Johnson, J.M., Weyers, S.L., Mikha, M.M., Trippe, K.M., Maul, J.E., Dungan, R.S., Gollany, H.T., Ducey, T.F., Hale, L.E., Jin, V.L., Cavadini, J., Reardon, C.L. 2025. Unraveling edaphic, environmental, and management drivers of soil microbial communities via ester-linked fatty acid methyl esters using a multilocation agroecosystem study. Geoderma. 453. Article 117158. https://doi.org/10.1016/j.geoderma.2024.117158.
Adams, C.B., Cosner, J.M. 2025. Field pea cardinal temperatures, growth and vigor traits of winter- and spring-adapted germplasm at germination and seedling stages. Scientific Reports. 15. Article 21759. https://doi.org/10.1038/s41598-025-06342-w.