Research Project: Agricultural Management for Long-Term Sustainability and Soil Health

Location: Soil Management and Sugarbeet Research

2023 Annual Report

Objectives
1. Evaluate the influence of conservation practices (e.g., tillage, cover crops, and soil amendments) on C and nutrient cycling through the soil profile to inform management and cropping system practices regarding optimization of C and nutrient cycling for increased productivity, sustainability, and ecosystem services. o Sub-Objectives 1.A-1.D can be found in uploaded post plan in Related Docs. 2. Investigate the effects of integrating multiple conservation practices (e.g., tillage, cover crops) on crop productivity and soil health to provide information and support development of tools to producers and managers in response to conservation practice adoption. o Sub-Objectives 2.A and 2.B can be found in uploaded post plan in Related Docs. 3. Evaluate the long-term ecosystem benefits of conservation practices resilient to climatic variation to provide data and tools to producers and farm managers for assessing best conservation practices. o Sub-Objectives 3.A-3.C can be found in uploaded post plan in Related Docs. 4. Develop management practices incorporating the latest technology developments for a field-size aspirational four-year dryland crop rotation system with precision nutrient, agrichemical, and weed control and crop population management. 212 C4 PS4A,4B. 5. Evaluate potential alternative crops and management practices for introduction into the aspirational wheat-based dryland rotation system. 212 C4 PS4A, 4B.

Approach
Soil function is an interplay of physical, chemical, and biological processes, and soil microbes play a direct role in driving soil chemical and physical processes important for overall ecosystem function. There remains, however, substantial uncertainty regarding how critical factors such as the soil’s microbiome, variabilities in nutrient cycling, management strategies, and variabilities in environment and/or climate change all interact to determine agricultural productivity and environmental outcomes. This project utilizes a holistic systems approach to develop new Best Management Practices and understanding of the interactive nature and interdependence of the Genetics x Environment x Management (GxExM) factors that result in highly productive and resilient agricultural systems. The objectives of this research are designed to integrate the scientists’ expertise related to soil function, crop productivity, and ecosystem services; each scientist is an expert in his/her field and responsible for the measurement of performance variables including, but not limited to, nutrient cycling, GHG monitoring and modeling, soil C sequestration and cycling, and soil biology structure and function. The knowledge and outcomes of this work will contribute to increased yield and profit sustainability for farmers; protection of ecosystems; increased nutrient use efficiency (NUE) and reduced losses of N from of N input application; and improved understanding of N cycling in cropping systems. Additionally, this research will increase C sequestration (C-Seq), reduce greenhouse gas (GHG) emissions, enhance soil quality/soil health, and increase resilience to climate change. These studies will contribute to improved agricultural production supported by a deeper understanding of soil biological processes; they will also contribute to improved soil biological properties and functions and to the development of sustainable agricultural systems in the Great Plains.

Progress Report
Objective 1. All field sampling has been conducted to evaluate the fine-scale seasonal dynamics in soil parameters in conventional and no-tillage continuous corn. Two-years of samples were collected up to twice per week during the growing season and twice per month during the off-season for a total of 66 sample dates. All laboratory analyses of living microbial biomass, total and dissolved soil Carbon (C) and Nitrogen (N) contents and soil greenhouse gas (GHG) emissions have been analyzed and a preliminary model predicting microbial biomass has been developed. A variety of field, greenhouse, and modeling studies have been conducted to evaluate soil amendments, bio-stimulants, and enhanced efficiency fertilizers to reduce direct and indirect N loses to the environment promoting nitrogen-use-efficiency (NUE), crop productivity, and yield. Two greenhouse studies examining the impact of environmentally-safe nitrogen (ESN) on plant biomass and soil microbial community structure and function have been completed. Field plots have been installed at Colorado State University's Agricultural Research, Development and Education Center (ARDEC), and sampling protocols and measurements are currently being developed. DayCent model simulations have recently been conducted to estimate the GHG mitigation that could be achieved by applying enhanced efficiency fertilizers to cropped soils across the United States. Studies to evaluate cover crops to promote soil health, stress tolerance, and crop productivity are currently being conducted. Field sampling and analyses have been conducted from two cover crop trials in collaboration with Natural Resource Conservation Service (NRCS) Plant Material Center locations in Oregon and Kansas. In addition, collaborative efforts with Pendleton, Oregon to evaluate cover crops in dryland wheat are ongoing. Soil samples from the first year of this experiment have been collected and are currently being analyzed for soil health and microbial community structure and function. Research also continues on the impact of residue placement on soil organic carbon stabilization and loss using d13C to quantify carbon dioxide (CO2) efflux, incorporation into microbial biomass, and soil C fractions. Samples have been collected and laboratory analyses are in progress. Objective 2. A field study at ARDEC is currently in its second year to evaluate the effect of conservation practice stacking on ecosystem benefits (e.g., N losses, C/N storage and cycling, GHG reduction potentials), soil health (e.g., microbial biomass, beneficial bacteria), and crop yield. Annual sampling and all appropriate laboratory analyses are up to date. Several efforts dedicated to the continued refinement and development of models, indices, and decision support tools that evaluate the effect of conservation practices on ecosystem benefits, soil health, and crop productivity are currently underway. For example, on-going studies at ARDEC, and world-wide, continue to be used in the development and expansion of nitrogen tools such as a new Nitrogen Index for assessment of the effects of N management on the risk of N losses and potential impacts to soil health. An improved version of DayCent continues to be developed that includes an improved model of microbial biomass; testing and model validation with new datasets; and efforts to reduce model input burdens. Particular emphasis is being placed on using the projects under Objective 1 to improve modelled estimates of microbial biomass and including nitrification inhibitors into DayCent. Objective 3. Long-term studies continue at ARDEC evaluating N fertilization rates under tillage management, residue removal, and organic vs inorganic N sources. A study at ARDEC is currently in its third year to explore the impact of conservation practice stacking (i.e., tillage and cover crops) on resilience and/or resistance of yield, productivity, and ecosystem benefits to climate variability. ARS researchers in Fort Collins, Colorado, continue to have a strong focus on enhancing data stewardship and tech-transfer through improved databases, such as Agricultural Collaborative Research Outcomes (AgCROS). New data coordination, meta-data and data-sharing platforms and file formats are being developed for handling in-house and collaborative long-term research studies. We also continue to develop, test, and refine standardized procedures for all phases of soil biological analyses, such as sample, collection and handling, analytical techniques, and data storage and analyses. A standardized protocol cross-laboratory comparison of molecular analysis for soil microbial community composition has been conducted to explore sources of variation and the repeatability of molecular microbial analyses conducted in different laboratories. New experiments to explore metagenomic approaches to evaluate microbial communities and their contribution to soil C sequestration are being developed and plan with 11 different ARS laboratories.

Accomplishments
1. Plant traits influence carbon sequestration success. Accounting for the form and longevity of plant roots to soils is critical in developing carbon (C) markets and accurate mitigation assessments. Plant traits determine the longevity of soil C and the benefits of deep-rooted perennial grasses (switchgrass and big bluestem) for bioenergy. ARS scientists in Fort Collins, Colorado, and cooperators at Boise State University and Argonne National Laboratory assessed root traits, chemistry, and soil C accumulation in a long-term bioenergy study. They found that the larger root system of big bluestem had greater C accumulation despite greater recalcitrant root chemistry of the switchgrass. Cultivar selection and continued focus in plant breeding programs on traits that influence the longevity of soil C will be critical for farmers and producers to improve bioenergy and soil C sequestration.

2. Snowmelt/soil thaw pulses of soil nitrous oxide (N2O). ARS researchers in Fort Collins, Colorado, and university partners showed that atmospheric trace gas inversions and newly implemented bottom-up modeling approaches exhibit large nitrous oxide pulses in the northcentral region of the United States during early spring. Accounting for these snowmelt/soil thaw induced pulses increases annual N2O emissions from croplands and grasslands by 6 to 16%. These improved estimates are now being incorporated into the Environmental Protection Agency's annual Inventory of U.S. Greenhouse Gas Emissions and Sinks. This report is made available to the public and is developed in collaboration with Unit scientists and their public and private collaborators.

3. Improved carbon modeling and greenhouse gas inventories added to the Greenhouse Gas Reduction through Agricultural Carbon Enhancement Network (GRACEnet) project. There is a need to improve the functionality of GRACEnet by addressing widescale agricultural management impacts on soil carbon and greenhouse gas (GHG) emissions. ARS researchers in Fort Collins, Colorado, in cooperation with numerous ARS locations led GRACEnet updates such that the portal now contains data from 17 ARS locations with more than 450,000 total records including 116,000 soil GHG emission measurements and 83,000 soil measurements. GRACEnet data increased the accuracy of GHG emission estimates reported in the U.S. national GHG inventories, including the latest Environmental Protection Agency inventory published during FY 2017. Additionally, project data have been used to develop scaling factors to quantify the GHG reductions for improved management practices imbedded in decision support tools. GRACEnet data are now being used to validate the USDA Natural Resources Conservation Service Carbon Management Evaluation Tool [COMET]-Farm and COMET Planner tools. COMET-Farm is used by Boulder County, Colorado to estimate entity level management impacts on GHG fluxes for the Restore Colorado project, while COMET-Planner is used to estimate the outcomes of practices (e.g., cover crops, no-till, reduced till, mulching, compost application) for the California Healthy Soils Program.

4. Development and standardization of new technology for soil microbial quantification. Illumina MiSeq is the current standard for characterizing microbial communities in soil. The Oxford Nanopore Technologies MinION sequencer is quickly gaining popularity because of the low initial cost and longer sequence reads. ARS scientists in Fort Collins, Colorado, compared the output of short MiSeq to short and full-length MinION 16S ribosomal RNA amplicons using similar bioinformatic methods with a mock community and agricultural soil samples. While significant platform biases exist, both platforms are suitable for identifying alpha- and beta-diversity differences between agricultural sites. The low cost and accuracy of the MinION sequencer is currently being leveraged in ARS laboratories nationally to develop standardized, low-cost, high-throughput protocols and diagnostics for robust and consistent metrics aimed at quantifying soil microbial community structure and function. These developments provide guidelines and methods applicable to public and private laboratories for conducting consistent and robust soil microbial community analyses.

5. Evaluating GHG reduction potentials associated with conservation practice adoption on U.S. croplands. Conservation agricultural practices have the potential to reduce greenhouse gas (GHG) emissions. To provide land managers, producers, and researchers estimates of greenhouse gas reduction potential from the implementation of climate-smart practices, ARS researchers in Corvallis, Oregon and Fort Collins, Colorado developed the Carbon Reduction Potential Evaluation (CaRPE) Tool (https://carppe.shinyapps.io/CarpeTool/). CaRPE is a web-based interactive tool to visualize and estimate the climate benefits of implementing conservation practices on croplands and grazing lands. A framework for applying CaRPE-based estimates to croplands under six cropland management practices and the Conservation Reserve Program (CRP) was applied to existing (2017) and projected conservation practice adoption on croplands. Current estimates suggest that 134.2 M tonnes of carbon dioxide equivalents (CO2e) per year have been or continue to be reduced by these conservation management practices on a cumulative total of 133.5 Mha of cropland. Projected estimates, assuming a business-as-usual scenario, predict an additional reduction potential of 48.7 M tonnes CO2e year-1 over the next 10 years for these same practices. The CaRPE tool and assessment framework provide land managers and conservation planners with a suite of tools for optimizing and selecting conservation practices for maximum GHG reduction potentials.

Review Publications
Kim, J., Ale, S., Kreuter, U., Teague, R., Del Grosso, S.J., Dowhower, S.L. 2022. Evaluating the impacts of alternative grazing management practices on soil carbon sequestration and soil health indicators. Agriculture, Ecosystems and Environment. 342. Article e108234. https://doi.org/10.1016/j.agee.2022.108234.
Harmel, R.D., Kleinman, P.J., Hopkins, A., Millhouser, P., Ippolito, J.A., Sahoo, D. 2022. Updates to the MANAGE database to facilitate regional analyses of nutrient runoff. Agricultural and Environmental Letters. 7(2). Article e20095. https://doi.org/10.1002/ael2.20095.
Kelly-Slatten, M., Stewart, C.E., Tfaily, M., Jastrow, J., Sasso, A., de Graaf, M. 2023. Root traits of perennial C4 grasses contribute to cultivar variations in soil chemistry and species patterns in particulate and mineral-associated carbon pool formation. Global Change Biology Bioenergy. 15(4):613-628. https://doi.org/10.1111/gcbb.13041.
Newberger, D.R., Minas, I.S., Manter, D.K., Vivanco, J.M. 2023. A microbiological approach to alleviate soil replant syndrome in peaches. Microorganisms. 11(6). Article e1448. https://doi.org/10.3390/microorganisms11061448.
Miner, G.S., Stewart, C.E., Vigil, M.F., Poss, D.J., Haley, S.D., Jones-Diamond, S.M., Mason, E.R. 2022. Does agroecosystem management mitigate historic climate impacts on dryland winter wheat yields? Agronomy Journal. 114(6):3515-3530. https://doi.org/10.1002/agj2.21198.
Delgado, J.A., Halvorson, A.D., D'Adamo, R.E., Stewart, C.E., Floyd, B.A., Del Grosso, S.J. 2023. Long-term nitrogen balance of an irrigated no-till soil-corn system. Nutrient Cycling in Agroecosystems. 126:229-243. https://doi.org/10.1007/s10705-023-10287-9.
Delgado, J.A., Barrera, V.H., Alwang, J.R., Cartagena, Y.E., Escudero, L.O., Neer, D.L., D'Adamo, R.E., Zapata, A.C. 2023. Nitrogen management can increase potato yields and food security for climate change adaptation in the Andean region. American Journal of Potato Research. https://doi.org/10.1007/s12230-023-09912-8.
Manter, D.K., Hamm, A.K., Deel, H.L. 2023. Community structure and abundance of ACC deaminase containing bacteria in soils with 16S-PICRUSt2 inference or direct acdS gene sequencing. Journal of Microbiological Methods. 211. Article e106740. https://doi.org/10.1016/j.mimet.2023.106740.
Manter, D.K., Moore, J.M. 2022. CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands. Database: The Journal of Biological Databases and Curation. 2022. Article baac105. https://doi.org/10.1093/database/baac105.
Stevens, B.M., Creed, T.B., Reardon, C.L., Manter, D.K. 2023. Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil. Scientific Reports. 13. Article e9323. https://doi.org/10.1038/s41598-023-36101-8.
Meinen, R.J., Beegle, D.B., Vishwanath, S., Kleinman, P.J., Saporito, L.S., Spargo, J., Karsten, H., Dillon, J. 2023. Monolith soil core sampling to develop nitrate testing protocol for manure injection. Soil Science Society of America Journal. 87(2):378-389. https://doi.org/10.1002/saj2.20509.
Buda, A.R., Reed, S.M., Folmar, G.J., Kennedy, C.D., Millar, D.J., Kleinman, P.J., Miller, D.A., Drohan, P.J. 2022. Applying the NWS’s distributed hydrologic model to short-range forecasting of quickflow in the Mahantango Creek watershed. Journal of Hydrometeorology. https://doi.org/10.1175/JHM-D-21-0189.1.
Kleinman, P.J., Osmond, D.L., Christianson, L.E., Flaten, D.N., Ippolito, J.A., Jarvie, H.P., Kaye, J.P., King, K.W., Leytem, A.B., McGrath, J.M., Nelson, N.O., Shober, A.L., Smith, D.R., Staver, K.W., Sharpley, A.N. 2022. Addressing conservation practice limitations and trade-offs for reducing phosphorus loss from agricultural fields. Agricultural and Environmental Letters. 7(2). Article e20084. https://doi.org/10.1002/ael2.20084.
Bittman, S., Worth, D., Hunt, D.E., Spiegal, S.A., Kleinman, P.J., Vendramini, J., Silveira, M., Flynn, K.C., Reid, K., Martin, T., Vanderzaag, A., Javorek, S., Nanayakkara, S. 2023. Distribution of livestock sectors in Canada: Implications for manureshed management. Journal of Environmental Quality. 52(3):596-609. https://doi.org/10.1002/jeq2.20457.
Acharya, P., Ghimire, R., Paye, W., Ganguli, A., Del Grosso, S.J. 2022. Net greenhouse gas balance with cover crops in semi-arid irrigated cropping systems. Scientific Reports. 12. Article e12386. https://doi.org/10.1038/s41598-022-16719-w.
Hamm, A.K., Manter, D.K. 2022. Assessing the effects of no-till cultivation practices on soil health. In: Horwath, W., editor. Improving Soil Health. London: Burleigh Dodds Science Publishing. p. 123-146.
Moore, J.M., Manter, D.K., Bowman, M., Hunter, M., Bruner, E., McClelland, S. 2023. A framework to estimate climate mitigation potential for US cropland using publicly available data. Journal of Soil and Water Conservation. 78(2):193-206. https://doi.org/10.2489/jswc.2023.00132.
Pantigoso, H.A., He, Y., Manter, D.K., Fonte, S.J., Vivanco, J.M. 2022. Phosphorus solubilizing bacteria isolated from the rhizosphere of wild potato Solanum bulbocastanum enhance growth of modern potato varieties. Genetics, Genomics and Breeding of Potatoes. 46. Article e224. https://doi.org/10.1186/s42269-022-00913-x.
DiLegge, M.J., Manter, D.K., Vivanco, J.M. 2022. Soil microbiome disruption reveals specific and general plant-bacterial relationships in three agroecosystem soils. PLOS ONE. 17(11). Article e0277529. https://doi.org/10.1371/journal.pone.0277529.
Saha, A., Saha, G., Cibin, R., Spiegal, S.A., Kleinman, P.J., Veith, T.L., White, C., Drohan, P., Tsegaye, T.D. 2023. Evaluating water quality benefits of manureshed management in the Susquehanna River Basin. Journal of Environmental Quality. 52(2):328-340. https://doi.org/10.1002/jeq2.20429.