Skip to main content
ARS Home » Midwest Area » Ames, Iowa » National Laboratory for Agriculture and The Environment » Agroecosystems Management Research » Research » Research Project #432305

Research Project: Agroecosystem Benefits from the Development and Application of New Management Technologies in Agricultural Watersheds

Location: Agroecosystems Management Research

2019 Annual Report

1a. Objectives (from AD-416):
Objective 1: Design, place, and assess conservation practices for improved water quality and environmental benefits. Sub-objectives: 1.1: Develop and evaluate practices for reducing surface water contaminants in artificially drained landscapes; 1.2: Evaluate perennial systems to reduce runoff, sediment, and phosphorus (P) losses; and 1.3: Increase the efficacy of the Agricultural Conservation Planning Framework (ACPF) toolbox as an approach to conservation planning for improved water quality within Midwest watersheds. Objective 2: As part of the Long-Term Agroecosystem Research (LTAR) network, and in concert with similar long-term, land-based research infrastructure in the Upper Mississippi River Basin Region, use the Upper Mississippi River Basin Experimental Watersheds 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 region. 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 Greenhouse gas Reduction through Agricultural Carbon Enhancement network (GRACEnet) and/or Livestock GRACEnet projects. Objective 3: Quantify the effects of landscape attributes and management practices on the fate, transformation, and transport of antibiotics, antibiotic-resistant bacteria and other emerging contaminants in surface runoff, drainage water, and streams in agricultural watersheds.

1b. Approach (from AD-416):
This project will conduct research to investigate the effects of agricultural management practices at field and watershed scales, the dynamics of watershed hydrology, and fundamental processes relevant to contaminant behavior in watersheds. Under the first objective, field studies will evaluate practices that can reduce loss of nitrate-nitrogen from cropped fields. These practices include saturated buffers, bioreactors, fall planted cover crops, and protected surface inlets to subsurface drainage. Bioreactor denitrification capacities will be assessed with microbiological assessments, and modeling studies will be conducted to investigate management practices that may reduce N loss to subsurface drainage in the context of historical climate data. Research will be conducted to improve agricultural conservation planning across the Midwest. Conservation needs also exist in perennial agricultural systems and investigations into the water use, runoff, erosion, and P losses will be carried out. Under the second objective, field and watershed studies will be conducted as part of the Long-Term Agroecosystem Research (LTAR) network that will support research to sustain or enhance agricultural production and environmental quality in the Upper Mississippi River Basin region. The third objective will employ a mix of laboratory, field, and modeling studies to evaluate environmental transport of pathogens and veterinary pharmaceuticals under different landscape attributes and management practices. A breadth of watershed monitoring, controlled experiments in field and laboratory, and modeling techniques will be employed in the research. Publications, tools for conservation planning, and databases available to other scientists will be produced. Results are intended to enable agriculture to better manage water resources for multiple needs; particularly, in the Upper Mississippi River Basin.

3. Progress Report:
Objective 1.1. Three new saturated buffers were constructed across Iowa and instrumented to measure flow and determine nitrate concentrations in shallow groundwater. This brings the total saturated buffers being monitored to 11. All monitored sites indicate that saturated buffers remove from 40-90% of the nitrate that would normally flow into local streams. Three years of monitoring a woodchip bioreactor for nitrate removal have been completed. These results are being evaluated and the results will be published. Measurements of yield and water quality effects of fall-planted cover crops in a corn and soybean rotation continued. Cover crops removed more than 50% of the nitrate before it can move to surface waters. To evaluate organic crop management effect on N loss to subsurface drainage, daily weather records were organized and evaluated for 2010-2018 for input to the Root Zone Water Quality Model (RZWQM). As required for the evaluation of organic management practices, a new alfalfa model was developed for use with RZWQM and testing was conducted using field data from Colorado. As part of the effort to evaluate effect of winter rye cover crop in corn/soybean systems on N loss to drainage, we conducted an experiment with rye fertilized at several N rates and planted using several methods to determine N content and biomass of the rye. This information is essential to determine if fertilized and harvested rye could provide a revenue incentive for producers to plant winter rye cover crops while still reducing N loss to drainage as previous research suggests. Objective 1.2. Overhead pictures were taken from after harvest to early growing season to determine fraction ground cover in farmer's fields (seven-year rotation vs. corn or soybean). In addition to the ground cover measurements, rainfall simulation experiments were completed in the same fields in the fall of 2018. Manuscripts are in-press about leaf area index (growth of various plants over the season) and evapotranspiration (how much water the various plants and cropping systems use at different times of the year) in a comparison of organic and conventional crop systems. The developed techniques work well for assessing plant growth and water use for each plant type in a mix over the season (which varies with plant type). The longer-term rotations do indeed use more water in the spring and fall than conventional corn and soybean cropping systems. Measurements have continued on these fields. Leaf area index and evapotranspiration of crops, cover crops, and weeds have been analyzed in a new organic cover crop experiment. Objective 1.3. Significant progress was made extending the Agricultural Conservation Planning Framework (ACPF). ACPF databases are available online that now cover more than 11,000 small (Hydrologic Unit Code 12: 15,000-40,000 acre) watersheds. When watersheds in the Upper Illinois River basin in northwest Indiana are completed (currently underway), the ACPF HUC12 database will cover all the Upper Mississippi River basin to support regional scaling of Long Term Agroecosystem Research (LTAR). In the current year, all of Nebraska and most of eastern Missouri watersheds have been added to the database. The ACPF toolbox was also updated to version 3.0. The new ACPF toolbox and User Manual are available online. Improvements in version 3.0 include an option to incorporate wide rivers and waterbodies into the stream network, and a "riparian catchments tool" that discretizes a watershed to map land areas contributing runoff to every segment of riparian streambank. These additions substantially enhance the ACPF’s riparian analysis and outputs. A farm pond siting tool was also included in version 3. ACPF training videos were updated to incorporate these version changes and are also available online. New utilities were also included in ACPF version 3 that allow users to build input databases independently for any HUC12 watershed in the lower 48 states of the U.S. Access to the ACPF and training resources is provided through, a website that has been developed by the University of Wisconsin Division of Extension under a subordinate project with funding from Natural Resources Conservation Service (NRCS), received through an Interagency Agreement (IAA). The same funding has supported database development at Iowa State University and social science research to evaluate the utility of ACPF results for enhancing conservation planning and producer engagement outcomes. Research on results of ACPF watershed analysis was conducted. A virtual experiment was run to compare ACPF practice-siting results across 32 HUC12 watersheds representing dominant landform regions of Iowa. Two journal articles were submitted and are in review; these manuscripts characterize regional differences in conservation opportunities for upland and riparian landscapes of central and eastern Iowa and provide advice to ACPF users for selecting input parameters for several ACPF tools. We also continued to collaborate with ARS colleagues in Fort Collins, Colorado, by providing data from the South Fork Iowa River watershed for calibration and evaluation of the ARS Agricultural Ecosystem Services (AgES) watershed model and contributing to a submitted manuscript (in review). Objective 2.1. Hydrology, nitrate, and phosphate monitoring continued at the agricultural watersheds: Southfork of the Iowa River and Walnut Creek in Story County. Changes in Jasper County’s Walnut Creek’s nitrate-nitrogen concentrations were documented after 3,000 acres of tallgrass prairie reconstructions were initiated from 1993 through 2006 at the Neal Smith National Wildlife Refuge. The 20-year water quality record showed a consistent, slow decline in nitrate concentrations and loads. Data from the South Fork of the Iowa River were contributed to a multi-location LTAR effort to compare water balances in different agricultural systems and a manuscript is in preparation. Objective 2.2. The LTAR Common Experiment compares conventional and alternative managements with respect to nitrate and phosphorus losses in drainage water, yield, nutrient use efficiency, and greenhouse gas emissions. Two treatments, winter rye (Secale cereale) and Camelina sativa, were observed to reduce nitrate loss in drainage water. Camelina provided a yield of oil seed. Progress was made documenting the performance of these treatments. Objective 2.3. Watershed data were compiled and are stored in a database. Periodically these data are transferred to the Sustaining the Earth's Watersheds, Agricultural Research Data System (STEWARDS) database which provides public access to the Conservation Effects Assessment Project (CEAP) data. Additional agronomic and soil data at LTAR field sites (Brooks and Coles field) were organized and stored. Objective 3.1. Persistence of tetracycline and macrolide antibiotic-resistance genes were examined in the field with different manure application timings (early fall, late fall, and spring) providing an array of temperature conditions. Unexpectedly, few differences were observed in the persistence of antibiotic resistance genes except after spring application of manure resulted in increased persistence of one of the four genes. Analysis of antibiotics in the same research showed tetracyclines to be persistent. Sulfonamide antibiotics were occasionally detected and the macrolide antibiotic, tylosin, was only detected in manure and not in soil. Other related experiments documented the change in soil bacterial communities after application of swine manure. Unique DNA sequences (OTU) associated with 12 orders of bacteria were responsible for the majority of OTUs stimulated by manure application. Proteobacteria were most prevalent, followed by Bacteroidetes, Firmicutes, Actinobacteria, and Spirochaetes. While the majority of the 12 orders decreased after day 59, relative abundances of genes associated with Rhizobiales and Actinomycetales in soil increased. These shifts in community structure are being compared with the current analysis of dynamics of antibiotic resistance genes in the same experiment. Objective 3.2. At two different field sites rainfall simulations were performed to generate surface run-off. Progress was made with analysis of resistance genes and antibiotics in this surface runoff water.

4. Accomplishments
1. Field-edge nitrate removal. Saturated riparian buffers are a promising new practice for removing nitrate from farm field drainage; however, only limited data on the effectiveness of the practice is currently available. By monitoring six sites from two to nine years, ARS researchers in Ames, Iowa, in cooperation with researchers at Iowa State University have shown saturated riparian buffers can remove from 40% – 90% of nitrate leaving a farmer’s field before it enters a stream or river. In addition, these scientists have shown that nitrate removal is primarily from denitrification (conversion of nitrate to nitrogen gas) and that this conversion does not increase the generation of nitrous oxide – a powerful greenhouse gas. This research has led the USDA-Natural Resources Conservation Service (NRCS) to develop a new conservation practice standard (#604) and the installation of the practice across Midwest farms.

2. Two decades of water quality response to tallgrass prairie ecosystem restoration. It is important to understand environmental lag times that govern watershed responses to new agricultural conservation and ecosystem restoration practices. In south-central Iowa, ARS researchers from Ames, Iowa, in cooperation with Iowa’s State Geologist, measured changes in Walnut Creek’s nitrate-nitrogen concentrations after 3,000 acres of tallgrass prairie reconstructions were initiated from 1993 through 2006 at the Neal Smith National Wildlife Refuge. The 20-year water quality record showed a consistent, slow decline in nitrate concentrations and loads. Periods of flood and drought influenced the water quality record and limited the statistical approaches that could be used to analyze the data. Water quality improvement in agricultural watersheds depends on the extent of land use changes and on travel times of flow paths carrying pollutants to the stream. In the mostly naturally drained watershed, slow responses were caused by slow groundwater flow rates through the fine-grained sediments. This information extends the literature on environmental time lags in watersheds and is of interest to agricultural conservationists and others interested in documenting conservation effects in watersheds.

3. Assessing a precision conservation technology for planning and stakeholder engagement. The Agricultural Conservation Planning Framework (ACPF) provides an assessment of conservation practice placement options to help planners prioritize conservation investments and improve watershed water quality outcomes. Can conservation planners use these results to engage producers and better organize planning activities? Social scientists at Purdue University, with funding facilitated through the ARS in Ames, Iowa, examined this question using in-person interviews with conservation planners in six watersheds in Iowa and Minnesota. Results showed planners could use ACPF results with current planning approaches, and that ACPF results helped planners incorporate watershed perspectives and engage producers in planning. ACPF results were successfully applied using several "enabling" approaches that considered producer perspectives. While conservation planning is a localized process that must consider social dynamics, watershed planning technologies can be adapted in response to dynamics of landscapes and local communities. These results are of interest to USDA-Natural Resources Conservation Service (NRCS), state agencies, and non-governmental organizations who are seeking to improve water quality outcomes for agriculture.

4. Corn stover harvest and N loss to drainage. Harvesting corn stover for bioenergy feedstock is projected to increase over the next few decades. Because of projections of increasing fertilizer nitrogen (N) use and the associated environmental problems, the U.S. National Academy of Engineering has listed "Manage the Nitrogen Cycle" as one of 14 grand challenges for the 21st century. While it is known that corn stover harvest removes nutrients such as N from fields, the effects on subsurface drainage and other N losses are uncertain. To maintain acceptable corn production, most published modeling studies have assumed supplemental N fertilizer is required to replace the N removed. ARS researchers in Ames, Iowa, and Fort Collins, Colorado, along with University collaborators from Penn State and Iowa State used the Root Zone Water Quality Model (RZWQM) to examine N losses with and without corn stover removal in a corn and soybean rotation. Surprisingly, the simulated annual corn yields and N loss to drainage were nearly the same with or without stover harvest, despite more N removed from the stover harvest treatments and the same N fertilizer applied to both treatments. These results are important to optimizing the energy and nitrogen budgets associated with corn stover harvest. This research will help model developers, model users, agricultural scientists, and the bioenergy industry more clearly understand N losses and energy budgets under subsurface drained conditions and corn stover harvest, which will help in development of a sustainable bioenergy industry.

Review Publications
Gellis, A.C., Fuller, C.C., Van Metre, P.C., Filstrup, C.T., Tomer, M.D., Cole, K.J., Sabitov, T. 2018. Combining sediment fingerprinting with age-dating sediment using fallout radionuclides for an agricultural stream, Walnut Creek, Iowa, USA. Journal of Soils and Sediments. p. 1-23.
Beck, W.J., Moore, P.L., Schilling, K.E., Wolter, C.F., Isenhart, T.M., Cole, K.J., Tomer, M.D. 2019. Changes in lateral floodplain connectivity accompanying stream channel evolution: Implications for sediment and nutrient budgets. Science of the Total Environment. 660:1015-1028.
Malone, R.W., Herbstritt, S., Ma, L., Richard, T., Cibin, R., Gassman, P., Zhang, H., Karlen, D.L., Hatfield, J.L., Obrycki, J., Helmers, M., Jaynes, D.B., Kaspar, T.C., Parkin, T.B. 2019. Corn stover harvest and N losses in central Iowa. Science of the Total Environment. 663:776-792.
Zhao, L., Li, L., Cai, H., Fan, J., Chau, H.W., Malone, R.W., Zhang, C. 2019. Organic amendments improve wheat root growth and yield through regulating soil properties. Agronomy Journal. 111(2):482-495.
Zhang, H., Malone, R.W., Ma, L., Ahuja, L.R., Anapalli, S.S., Marek, G.W., Gowda, P.H., Evett, S.R., Howell, T.A. 2018. Modeling evapotranspiration and crop growth of irrigated and non-irrigated corn in the Texas high plains using RZWQM. Transactions of the ASABE. 61(5):1653-1666.
Tomer, M.D., Shilling, K.E., Cole, K.J. 2019. Nitrate on a slow decline: Watershed water quality response during two decades of tallgrass prairie ecosystem reconstruction in Iowa. Journal of Environmental Quality. 48:579-585.
Ranjan, P., Singh, A.S., Tomer, M.D., Lewandowski, A.M., Prokopy, L.S. 2019. Lessons learned from using a decision-support tool for precision placement of conservation practices in six agricultural watersheds in the US midwest. Journal of Environmental Management. 239:57-65.
Rieke, E.L., Soupir, M.L., Moorman, T.B., Yang, F., Howe, A. 2018. Temporal dynamics of bacterial communities in soil and leachate water after swine manure application. Frontiers in Microbiology. 9(3197).
Martin, E.A., Davis, M.P., Moorman, T.B., Isenhart, T.M., Soupir, M.L. 2019. Impact of hydraulic residence time on nitrate removal in pilot-scale woodchip bioreactors. Journal of Environmental Management. 237:424-432.
Davis, M.P., Groh, T.A., Jaynes, D.B., Parkin, T.B., Isenhart, T.M. 2018. Nitrous oxide emissions from saturated riparian buffers: Are we trading a water quality problem for an air quality problem? Journal of Environmental Quality. 48(2):261-269.
Groh, T.A., Davis, M.P., Isenhart, T.M., Jaynes, D.B., Parkin, T.B. 2018. In situ denitrification in saturated riparian buffers. Journal of Environmental Quality. 48(2):376-384.
Young, E.O., Ross, D.S., Jaynes, D.B. 2019. Riparian buffer nutrient dynamics and water quality. Frontiers in Environmental Science. 7:76.
Jaynes, D.B., Isenhart, T.M. 2018. Performance of saturated riparian buffers in Iowa, USA. Journal of Environmental Quality. 48(2):289-296.