Skip to main content
ARS Home » Midwest Area » Columbia, Missouri » Cropping Systems and Water Quality Research » Research » Research Project #432224

Research Project: Long-term Management of Water Resources in the Central Mississippi River Basin

Location: Cropping Systems and Water Quality Research

2022 Annual Report

Objective 1: Determine linkages between stream water quality and field characteristics through field and watershed scale studies. 1a: Improve the Phosphorus (P) Index on claypan soils. 1b: Determine nutrient fluxes from surface drained land in the lower Mississippi River basin. 1c: Assess stream water quality within the northern Missouri/southern Iowa Region (NMSIR). Objective 2: Assess the effectiveness of conservation practices to mitigate the impacts of agriculture on water quality in the Central Mississippi River Basin. 2a: Assess the effect of grasses and vegetative buffers on the fate of organic contaminants. 2b: Determine effectiveness of buffer strips, crop rotations and cover crops. Objective 3: As part of the LTAR network, and in concert with similar long-term, land-based research infrastructure in the Central Mississippi River Region, use the Goodwater Creek Experimental Watershed LTAR site to improve the observational capabilities and data accessibility of the LTAR network and support research to sustain or enhance agricultural production and environmental quality in agroecosystems characteristic of the Central Mississippi River basin. Research and data collection are planned and implemented based on the LTAR site application and in accordance with the responsibilities outlined in the LTAR Shared Research Strategy, a living document that serves as a roadmap for LTAR implementation. Participation in the LTAR network includes research and data management in support of the ARS GRACEnet and/or Livestock GRACEnet projects. 3a: Establish an observatory for weather and discharge monitoring representative of the CMRB. 3b: Establish and conduct an experiment comparing the performance of two farming systems: one business as usual (BAU) that reflects the dominant agricultural practices in the CMRB and one aspirational (ASP) that is hypothesized to result in less adverse environmental impacts and improved economic output. 3c: Investigate greenhouse gas (GHG) as a function of crops and top soil depth. 3d: Assess denitrification in claypan soils. 3e: Assess climate change impacts in CMRB.

Increased sustainability of agriculture in the Mississippi River Basin will be studied at field, farm, and watershed scales. This research will focus in understanding how alternative farming systems can become more resilient and sustainable through increased food production, less environmental impacts on water and air resources, and climate regulation. The overall goal of this project is to improve understanding of, and help manage water resources for sustainable agricultural production in the Central Mississippi River Basin (CMRB). Emphasis is given to long-term study, i.e., 50 year window. Thus, we will design and implement a monitoring infrastructure for this research. The project will focus on edge of field studies that link water quantity and quality to field characteristics, soil, crop and agronomic management practices, and conservation practices (e.g., buffer strips); on watershed studies that link inherent vulnerability caused by soils and topography to stream water quality; on regional studies that broaden the scope of our plot, field, and watershed research. The observatory of the Long-Term Agroecosystems Research (LTAR) infrastructure will provide long-term data of weather and stream flow in our research watershed to reveal possible manifestations of climate change, as well as interpret experimental observations and drive simulation models. The Common Experiment, within the LTAR project, will compare production, surface runoff quantity and quality, soil health, and biological indicators between “Business-As-Usual” (BAU) and Aspirational (ASP) systems and inform environmental (e.g., crop residue reducing soil erosion potential) and economic (e.g., crop yield and quality) aspects of relative sustainability of the two systems. Long-term assessment of water, carbon, and nutrient budgets will show how the respective components are affected by climate change and management. Measurement of instantaneous energy, water, and carbon fluxes will provide needed data for full interpretation of the differences observed between these management systems. Short term plot studies are included to investigate processes, including soil emissions of greenhouse gases and denitrification, where interaction between management (e.g., tillage, crop type, fertilizer) and soil landscape properties (e.g., landscape position, soil horizonation) may be a significant factor. These plot studies will provide guidance to design and implement the long-term nfrastructure.

Progress Report
This is the final report for this project which terminated in January 2022. See the report for the replacement project, 5070-12000-001-000D, “Linkages Between Crop Production Management and Sustainability in the Central Mississippi River Basin” for additional information. Objective 1. Over five years, this objective resulted in a published dataset, along with a data paper, which includes runoff, sediment and phosphorus loss from agricultural fields, and management and soil characteristics associated with these losses. This dataset, available at:, is useful to evaluate phosphorus loss models and indices. In collaboration with the University of Missouri, successive projects have evaluated the Natural Resources Conservation Service (NRCS) Soil Vulnerability Index (SVI), which classifies inherent soil vulnerability of cropland (field characteristics) to loss of sediment and nutrients by runoff and leaching). Several papers were published, including one recently submitted. Research has produced recommendations regarding the SVI use and improvement, and it is continuing to include climatic characteristics. Lack of support personnel prevented work toward determining nutrient fluxes in the lower Mississippi River basin for much of the project cycle. Once the position was filled, inspection of the sites showed equipment loss caused by weather and changes in the site characteristics that would cause incompatibility of new data with previously collected data. With only one year remaining in the project, restarting monitoring was deemed not worthwhile. Objective 2. All data have been collected and water samples analyzed in the study of vegetative buffers. The results on estrogen and veterinary antibiotics were not as expected and not sufficiently meaningful to describe in a publication. Three manuscripts were developed on the topic of phytochemical and microbial contributions to atrazine degradation, two of which are published method papers and one is a research paper submitted this spring. Five years of discharge and water quality samples were collected in the plot study of buffers, rotations, and cover crops. Laboratory analysis of the water samples is complete for all dissolved constituents. A backlog for total nutrient analyses is being resolved. Certification is 60% completed and continuing. Modeling of the buffers and cover crops is progressing but hindered by the change to and the calibration of a new version of the Agricultural Policy/Environmental eXtender (APEX) model. This objective will continue under Objective 1 of the replacement project 5070-12000-001-000D entitled “Linkages Between Crop Production Management and Sustainability in the Central Mississippi River Basin”. Objective 3. Monitoring and upkeep of the Long-Term Agroecosystems Research (LTAR) observatory and of the cropping systems needed for the Common Experiment are continuing, including all field operations for the cropping systems and plant, soil, water, and air sampling at three scales: small plots, large plots, and fields. Data from the weather station at the Central Mississippi River Basin (CMRB) LTAR site are going to the Agricultural Collaborative Research Outcomes System (AgCROS) Server; data are flagged for inconsistencies with the experimental range of values obtained at these sites. Further quality control processes, which involve visual inspection, comparison with nearby data, possible replacement, and approval are ongoing. Collection, certification and uploading of flow and water quality monitoring are on-going at plot, field, and watershed scale. Water quality analyses of water samples are completed for dissolved constituents and the backlog of total nutrient analyses is being addressed. Collection and certification of eddy flux measurements are ongoing at three locations, two of which have been approved for inclusion in the Ameriflux network, the Department of Energy supported network of sites measuring ecosystem carbon, water, and energy fluxes in North, Central and South America. Data from these two stations are available on-line. We are addressing the quality assurance and quality control of eddy flux data at the third site, which is part of Objective 3 of the replacement project 5070-12000-001-000D. During the life of the project, we have defined and implemented the two contrasting (i.e., aspirational (ASP) and one business-as-usual (BAU)) management scenarios for the LTAR Common Experiment. These were initiated in 2015 and 2016 with implementation of these management systems in fields, replicated large plots, and small research plots. The basic ASP rotation started as a no-till corn-soybean-wheat rotation with cover crops and a precision agriculture nutrient and pesticide management system. Adaptive adjustments to this system include a longer rotation and perennialization (that is, a hay crop that remains more than one year). The BAU scenario started in 2016 in a producer operated field. Replication of these two management systems occurs on the large and small plots. Crop yields from 2016 to 2021 are complete and certified. Crop phenology images are transmitted automatically to the PhenoCam Network, a network of sites equipped with cameras that provide automated sensing of phenology (nature’s calendar, as described by plant emergence or plant maturity for example). Analysis of the Common Experiment data will continue under Objectives 1 and 4 of the replacement project 5070-12000-001-000D. Aboveground net primary productivity and plant tissue chemistry samples and soil samples from 2016 to 2020 have been collected according to protocol and processing is ongoing for assessment of biomass production, microbial abundance, diversity, and function. Further collection and analysis of the data will continue under Objective 3 of the replacement project 5070-12000-001-000D in collaboration with a Michigan State University faculty member (formerly at the University of Missouri) and the LTAR Archbold Biological Station-University of Florida (ABS-UF) site. Greenhouse gas measurements, along with soil moisture, oxygen, and temperature data were implemented for 19 small plots at the University of Missouri South Farm. It took several years to get the field equipment and gas chromatograph operational and a complete and valid weekly greenhouse gas (GHG) data set was obtained for the BAU and ASP plots during the 2019 growing season. Following the scientist retirement in 2020, this objective was redefined by a recently hired scientist with university collaborators and will continue under Objective 3 of the replacement project 5070-12000-001-000D. Data collection for assessing denitrification in claypan soils is completed. Two manuscripts have been submitted: 1) spatial distribution and landscape dependence of potential and actual denitrification from BAU and ASP fields; 2) assessment of RNA-based methods for quantifying denitrification. The field-scale estimates of denitrification for BAU and ASP fields are completed but are not publishable without comparison to an existing denitrification model. A multi-site denitrification paper with results from LTAR sites in Pennsylvania, Georgia, and Missouri has been published. The assessment of water availability and productivity in the Goodwater Creek Experimental and Mark Twain Lake watersheds under varying climate includes one cross-location report and three papers that assess changes in water balance, as well as future flood and drought risks in these watersheds and the effects of possible management options. A fourth manuscript was accepted for publication in early fall. A book chapter on the modeling approach to address soil water management under climate change was accepted for publication in December 2022.

1. Identified factors influencing denitrification in claypan soils. Greenhouse gas production in the agricultural landscape has important implications for climate change. Claypan soils, which are prone to saturation of the topsoil layer, are particularly vulnerable to denitrification when fertilized for grain crop production. ARS scientists in Columbia, Missouri, and collaborators at the University of Missouri evaluated how management of cropping systems interacted with landscape characteristics to impact denitrification and production of nitrous oxide, a potent greenhouse gas. On these degraded claypan soils, emissions were dominated by nitrogen gas (> 85%) rather than nitrous oxide. Investigators also found that long-term erosion patterns across the landscape and the associated differences in soil properties exerted more control over denitrification than current management practices in these cropping systems. However, fertilizer management practices affected denitrification enzyme activity and actual denitrification, with more frequent and lower nitrogen application rates resulting in overall lower fluxes relative to a single annual application as is usually the case. This study benefits scientists and producers by highlighting the importance of landscape level and management factors that may influence greenhouse gas production from agricultural systems.

2. Discovered that climate trends in Northeast Missouri may cause conflicts among water users. Claypan soils, which are common in Northeast Missouri, have limited water storage capacity and high runoff potential, and are sensitive to overly wet and dry conditions. Most agricultural production on claypan soils is rain-fed and vulnerable to temperature increase and precipitation shortage during the growing season. ARS scientists in Columbia, Missouri, and collaborators at the University of Missouri and Pennsylvania State University developed a method to evaluate future water allocation in the Salt River Basin in Northeast Missouri given projections of future climate and changing land management practices. The watershed contains a major reservoir, Mark Twain Lake, which is the regional source of drinking water, and allows for hydroelectric production. Under current land use and management, the average annual difference between water demand and supply was projected to double from three to six million cubic meters because of climate change. A dramatic increase of irrigated cropland in the watershed resulted in a projected water shortage of up to 38.5 million cubic meters. Water withdrawals from Mark Twain Lake for agriculture purposes may help alleviate the projected shortages; however, on-farm pond storage would likely be more practical and cost-effective. This study informs decision makers on the effects of long-term climatic trends on water allocation, particularly for watersheds with significant agricultural activity.

Review Publications
Bean, G.M., Ransom, C.J., Kitchen, N.R., Scharf, P.C., Veum, K.S., Camberato, J.J., Ferguson, R.B., Fernandez, F.G., Franzen, D.W., Laboski, C.A., Nafziger, E.D., Sawyer, J.E., Nielsen, R.L. 2021. Soil hydrologic grouping guide which soil and weather properties best estimate corn nitrogen need. Agronomy Journal. 113(6):5541-5555.
Helmers, M.J., Abendroth, L.J., Reinhart, B.D., Chighladze, G., Pease, L., Bowling, L., Youssef, M., Ghane, E., Ahiablame, L., Brown, L., Fausey, N., Frankenberger, J., Jaynes, D., King, K.W., Kladivko, E., Nelson, K., Strock, J. 2021. Impact of controlled drainage on subsurface drain flow and nitrate load: A synthesis of studies across the U.S. Midwest and Southeast. Agricultural Water Management. 259. Article 107265.
Mire, M., Kim, C., Baffaut, C., Liu, F., Wuliji, T., Zheng, G. 2022. Escherichia cryptic clade II through clade VIII: Rapid detection and prevalence in feces and surface water. Science of the Total Environment. 848. Article 157741.
Nunes, M.R., Veum, K.S., Parker, P.A., Holan, S.H., Karlen, D.L., Amsili, J.P., Van Es, H.M., Wills, S.A., Seybold, C.A., Moorman, T.B. 2021. The soil health assessment protocol and evaluation applied to soil organic carbon. Soil Science Society of America Journal. 85(4):1196-1213.
Veum, K.S., Acosta Martinez, V., Lehman, R.M., Li, C., Cano, A., Nunes, M.R. 2021. PLFA and EL-FAME indicators of microbial community composition. In: Karlen, D.L., Stott, D.E., Mikha, M.M., editors. Laboratory Methods for Soil Health Analysis, Volume 2. John Wiley and Sons, Inc. p. 251-288.
Williams, M.R., Welikhe, P., Bos, J.H., King, K.W., Akland, M., Augustine, D.J., Baffaut, C., Beck, G., Bierer, A.M., Bosch, D.D., Boughton, E., Brandani, C., Brooks, E., Buda, A.R., Cavigelli, M.A., Faulkner, J., Feyereisen, G.W., Fortuna, A., Gamble, J.D., Hanrahan, B.R., Hussain, M., Kohmann, M., Kovar, J.L., Lee, B., Leytem, A.B., Liebig, M.A., Line, D., Macrae, M., Moorman, T.B., Moriasi, D.N., Nelson, N., Ortega-Pieck, A., Osmond, D., Pisani, O., Ragosta, J., Reba, M.L., Saha, A., Sanchez, J., Silveira, M., Smith, D.R., Spiegal, S.A., Swain, H., Unrine, J., Webb, P., White, K.E., Wilson, H., Witthaus, L.M. 2022. P-FLUX: A phosphorus budget dataset spanning diverse agricultural production systems in the United States and Canada. Journal of Environmental Quality. 51:451–461.
Zhou, P., Sudduth, K.A., Veum, K.S., Li, M. 2022. Extraction of reflectance spectra features for estimation of surface, subsurface, and profile soil properties. Computers and Electronics in Agriculture. 196. Article 106845.