Skip to main content
ARS Home » Plains Area » Fort Collins, Colorado » Center for Agricultural Resources Research » Soil Management and Sugarbeet Research » Research » Research Project #432311

Research Project: Management Practices for Long Term Productivity of Great Plains Agriculture

Location: Soil Management and Sugarbeet Research

2019 Annual Report

Objective 1: Develop and refine management practices for enhanced yields, nitrogen use efficiencies, carbon sequestration, soil biodiversity and function, and reduced greenhouse gas emissions from agricultural systems of the Great Plains. Sub-objective 1.1: Improve nutrient (especially nitrogen) management. Sub-objective 1.2: Reduce greenhouse gas emissions (CO2, N2O, CH4). Sub-objective 1.3: Characterize soil C and N stocks, fractions, isotopic signatures, and SOC chemistry with depth to develop BMPs that increase C-Seq. Sub-objective 1.4: Evaluate the effect of management practices on soil microbial structure and function. Sub-objective 1.5: Increase long-term productivity and economic returns. Objective 2: Improve procedures for national agricultural greenhouse gas inventories and indices to assess soil biology, soil health, and nutrient management. Sub-objective 2.1: Develop a new USDA ARS Nutrient Uptake and Outcome (NUOnet) database and improve nutrient indices and tools. Sub-objective 2.2: Improve procedures and tools for assessment of greenhouse gas emissions (CO2, N2O, CH4), NUE and C-Seq. Sub-objective 2.3: Develop a new national soil biology database. Sub-objective 2.4: Develop a new soil biology (soil health) index to quantify beneficial bacteria in soil. Objective 3: Assess the long-term consequences of management practices and cropping systems on nitrogen use efficiencies, greenhouse gas emissions, carbon sequestration, soil biodiversity and functions. Sub-objective 3.1: Implement a data management plan and procedures to facilitate data archiving and retrieval in the national databases developed in Objective 2 (NUOnet, GRACEnet, soil biology). Sub-objective 3.2: Improve long-term nutrient (especially nitrogen) management, while reducing the long-term emissions of greenhouse gases (CO2, N2O, CH4), increasing C-Seq, and enhancing soil health.

Often the management of agricultural lands has led to degradation of the soil resource, including the depletion of soil carbon and the loss of natural and synthetic nutrients. The lost carbon and nutrients negatively impact producer’s profit margins and have negative environmental impacts (lead to increased buildup of greenhouse gases (GHG) in the atmosphere and pollution of surface and ground water resources). Improved agricultural management can reverse this degradation, improve profit margins and minimize or even mitigate the negative environmental impacts. The overall goal of this project is to develop new and/or improved best management practices (BMPs), new and/or improved models, tools and databases, and sustainable production systems that can help us adapt to and/or mitigate climate change. We will use a combined approach that incorporates field applied studies to develop BMPs (Objective 1); develop and/or improve models, databases, and analytical tools (Objective 2); and conduct field analysis of long-term patterns and processes to assess if the performance of the BMPs is maintained, or improved, over time, and if the models and/or other tools can simulate measured values over decades (Objective 3). The scientific approach includes using different key performance variables of plant productivity such as crop yields; and soil health, nitrogen use efficiency, greenhouse gas emissions, soil carbon sequestration, and soil biological structure and function. A full economic analysis of each BMP will also be conducted. Additionally, basic mechanistic research to increase our knowledge of the basic science and processes of soil chemistry, soil physics, and soil biology, is also being conducted. The Soil Management and Sugar Beet Research Unit scientists have unique skills in each of these fields, and also bring outside collaborators together as part of a comprehensive and multi-faceted research program. As a result of this research, new and viable solutions are developed that address the complexities associated with soil and air management. Tools and information are provided to producers, land managers, and policy makers helping to ensure productive and healthy soils, climate change mitigation and adaptation, and improved air and water quality. Farm sustainability and profitability are improved while improving conservation and minimizing negative environmental impact.

Progress Report
This report is for a new project which began in February 2017. It continues the research from 3012-11000-011-00D. Objective 1. All milestones are fully met. Studies about management practices related to long-term productivity of Great Plains agriculture continue. Studies on increasing the sustainability of these systems to sequester soil carbon, reduce greenhouse gas emissions, increase nitrogen use efficiencies and economic returns, prevent soil/water degradation, enhance yields, and maintain soil biology continue to be conducted. Various management strategies related to 4R principles for nitrogen fertilizer (right time, source, type, rate) are being studied. The use of cover crops, crop residue management, and tillage practices that minimize soil disturbance is also being monitored. The use of alternative cropping systems as management practices (e.g., polycrops, sorghum sudangrass, and other rotations) is being assessed. These studies are providing information about how to improve long term management of cropping systems to be more sustainable with higher yields and higher nutrient use efficiencies. Research on the influence of a microbial inoculant in improving drought tolerance in winter wheat has been established at Colorado State University Agricultural Research, Development and Education Center (ARDEC). Study includes the use of various delivery systems for applying the microbial inoculant and its efficacy on multiple wheat varieties. Effects of management practices on soil microbial abundance and biodiversity are being monitored for irrigated corn (Colorado), wheat (Colorado, Oregon, and Idaho), and potato (Colorado). Preliminary greenhouse studies show the potential for biological soil amendments to increase drought resistance. A new method of inorganic carbon removal was implemented for quick analysis of stable isotopes, expanding the laboratory’s capacity to measure deep soil carbon in calcareous soils. Trace gas samples were collected from replicated field plots under different treatments to investigate the impacts of management practices including: fertilizer source (synthetic nitrogen, manure, enhanced efficiency fertilizer), fertilizer application rate (0 – 246 kg N/ha), residue management (50% removal, no removal), crop rotation (continuous corn, corn/barley rotation), and interactions with tillage intensity. Crop nitrogen uptake and use efficiencies were measured for all the long-term studies at ARDEC, and studies to assess long-term nitrogen budgets to determine long-term nitrogen use efficiencies and the potential to reduce losses of reactive nitrogen are progressing on schedule. Objective 2. All milestones are fully met. Carbon sequestration and greenhouse gas emissions: Data from the Greenhouse gas Reduction through Agricultural Carbon Enhancement network (GRACEnet) and Nutrient Uptake and Outcome network (NUOnet) have been incorporated into the Agricultural Collaborative Research Outcomes System (AgCROS), which also includes information from related ARS projects - Resilient Economic Agricultural Practices (REAP), Long Term Agroecosystem Research (LTAR), Agricultural Antibiotic Resistance (AgAR), and Food Data Central. The template has been modified to accommodate additional types of data from these projects, and visualization and other software improvements have been implemented. Publicly available data include crop yield, soil carbon, greenhouse gas (GHG) emission, land management, weather, and other information from 33 field sites across the U.S. with some studies beginning in the 1980s. In addition to observational data, the system now also generates maps of nitrous oxide (N2O) emissions based on the USDA GHG inventory for major crop types across the U.S. Long term harvested biomass, soil carbon stock, and nitrous oxide emissions data from studies in Colorado and other regions continue to be collected to improve and evaluate the DayCent model and perform meta analyses. Recent improvements in the DayCent model include more realistic representation of nitrogen retranslocation in plants as well as including a nitrogen storage pool that can be used to support new growth, implementing a submodule to simulate ammonia volatilization, and more mechanistic representation of enhanced efficiency fertilizers. The new model is currently being evaluated using crop yield, soil carbon, and N gas observations from research sites across the U.S. and around the world. Simulated soil N2O emissions are also being compared with observations derived from atmospheric inversions. The National Resources Inventory (NRI) is a statistically-based sample of all non-federal land in the U.S. and provides land cover and use information needed as model inputs for simulations conducted for the national GHG inventory. Newly available NRI data from 2013-2015 for over 350,000 points representing agricultural land and more detailed Conservation Effects Assessment Project (CEAP) data were compiled, entered into the model input file database, and quality controlled for accuracy. The database was then used to extend model input files to 2015 and simulations will be performed for next national GHG inventory published in 2020. The soil biology system (myPhyloDB) has been optimized to increase the speed for all data uploading and handling procedures. Several new univariate and multivariate analyses have also been added. 500 soil samples from the USDA Natural Resources Conservation Service Soil Health Assessment Initiative have been received and the first 300 samples have been analyzed for microbial community composition and beneficial gene abundance. These samples, in addition to nearly 1000 samples from ongoing research projects analyzed under this research project, are being used to develop indicator curves for selected beneficial genes (e.g., nitrogen fixation) and a general molecular assessment of soil health. A new prototype of the Data Entry Template (DET) for NUOnet was developed and used to collect and upload data from cooperators across 11 field sites in the U.S. The USDA-ARS NUOnet database was released in FY 2019. The new DET contains data on the impact of nutrient management, including how it affects yields and nutrient uptake, as well as data on how conservation practices affect off-site transport of nutrients via leaching, ammonia volatilization, surface runoff, and other loss pathways. The new NUOnet DET was developed as an AgCROS tool to help connect to other databases such as GRACEnet, REAP, Agricultural Antibiotic Resistance (AgAR), the Soil Health Assessment network (SHAnet), and the Long-Term Agroecosystem Research (LTAR) database. It will also interface with the USDA Food Data System (FooDS), which relates nutrient composition of food and biomarkers of human health. Objective 3. All milestones are fully met. Long-term studies were monitored at the Colorado State University Agricultural Research, Development and Education Center (ARDEC). Field sampling of nitrogen fertilization, no-tillage, and organic matter addition studies was completed for the 2018 field year, and laboratory analyses are in progress. Long-term data analysis is in progress and has resulted in one peer-reviewed publication on deep soil carbon under long-term no-tillage compared to strip tillage. Although strip-tillage improved yield by 13%, soil carbon was lost even with low-impact tillage. Laboratory analyses for field sampling of nitrogen fertilization, no-tillage, and organic matter addition studies are underway. Data analysis has resulted in on peer-reviewed publication on the impact of residue removal on soil microbial communities and soil carbon fractions. This publication was recently featured in the tri-society magazine CSA News in June. All of the long-term analysis of the nitrogen fertilizer plots using a nitrogen budget approach shows that nitrogen deposition is an important pathway for an irrigated no-till continuous corn rotation at this site in Northern Colorado. Additional long-term analyses of nitrogen budgets are being conducted for other crop rotations. Studies on the long-term effects on soil biological diversity and function, greenhouse gas emissions, carbon sequestration, nitrogen use efficiencies, and macro- and micro-nutrient dynamics are being conducted. Studies are aimed at continuing to assess the long-term effects of fertilizer, soil, and crop management to transfer best management practices that contribute to sustainability, higher resource use efficiencies, and increased economic returns. In cooperation with U.S. Agency for International Development (USAID), Virginia Tech, and Penn State, we are analyzing data from long-term studies conducted in the Andean region of Ecuador assessing the potential of conservation agriculture, using-no till, crop residue management and nitrogen fertilization, to increase sustainability and economic returns for farmers.

1. The USDA Agricultural Collaborative Research Outcomes System (AgCROS) network meets a long-standing need for availability of agricultural data. There was a longstanding need in the U.S. for a “network of networks” to support long-term availability of agricultural data to facilitate data discovery. To address this need, ARS scientists in Fort Collins, Colorado, led the development of the Agricultural Collaborative Research Outcomes System (AgCROS) portal and continue to lead ARS and non-ARS collaborator efforts across the U.S. in populating the system using standardized data reporting templates. As a result, numerous ARS databases including the Greenhouse gas Reduction through Agricultural Carbon Enhancement network (GRACEnet), Resilient Economic Agricultural Practices (REAP), NUOnet (Nutrient Uptake and Outcome network), LTAR (Long Term Agricultural Research), SHAnet (Soil Health Assessment network), DAPP (Dairy Agriculture for People and the Planet), and AgAR (Agricultural Antibiotic Resistance) are now publicly available in AgCROS. The databases (networks) in AgCROS contain more than 522,000 records, and there have been 359 downloads from 156 registered users. Additionally, the AgCROS webpages have been viewed more than 13,600 times. AgCROS established the needed “net-work of networks” to enhance the scale and impact of agricultural research, enabling researchers to develop solutions to challenges that cannot be sufficiently addressed with finer-scale studies while also providing a large volume of open-access datasets to researchers, students, consultants, and the general public to enhance the discovery of information.

2. Critical enhancements to USDA GRACEnet facilitate improved assessment of agricultural management. While Greenhouse gas Reduction through Agricultural Carbon Enhancement network (GRACEnet) is an important tool that can be used to calibrate, improve, and develop predictive and process models and decision support tools used for national greenhouse gas inventories in the U.S., improvement of discovery of data available in GRACEnet was needed. ARS researchers in Fort Collins, Colorado, led the development of critical enhancements to GRACEnet such as the establishment of field/laboratory measurement protocols, a standardized data entry template, software to perform quality control of data entry, and a user-friendly web access. The GRACEnet data have been incorporated into the Agricultural Collaborative Research Outcomes System (AgCROS), which includes information from many related ARS projects. Publicly available data include crop yield, soil carbon, greenhouse gas (GHG) emission, land management, weather, and other information from 20 field sites across the U.S., with some studies beginning in the 1980s. In addition to observational data, the system now generates maps of N2O emissions based on the USDA GHG inventory for major crop types across the U.S. Additional data visualization capabilities include automatically generated figures to compare soil emissions and other variables across field sites. GRACEnet contains more than 475,000 total records including 120,000 soil GHG emission and 83,000 soil measurements. GRACEnet datasets have been downloaded more than 350 times, and the GRACEnet webpage has been viewed more than 7,800 times to date this year. These critical greenhouse gas datasets are contributing to improvement of models that are addressing wide-scale agricultural management impacts on soil carbon and GHG emissions at local, regional, and national levels.

3. The USDA Nutrient Uptake and Outcome network (NUOnet) provides important data on nutrient management impacts. There is a need for a new regional and national database on best practices for nitrogen management, including cover crops, crop rotations, and manure and other byproduct inputs. Additionally, multidisciplinary results are needed to connect nutrient management and human and animal nutrition related to crop nutritional composition. To address these needs, ARS scientists in Fort Collins, Colorado, developed the open-access USDA Nutrient Uptake and Outcome network (NUOnet). The NUOnet webpages have been viewed more than 3,300 times. NUOnet contains data from 11 ARS sites across the U.S. including data on yield impact, nutrient uptake, and conservation practices’ effectiveness in reducing off-site transport via leaching, ammonia volatilization, surface runoff, and other pathways. Additionally, a Data Entry Template was developed to facilitate the upload of data and to help connect NUOnet and the Gas Reduction through Agricultural Carbon Enhancement network (GRACEnet) databases, which enhanced GRACEnet utility in calibrating and validating tools for assessing nitrogen emissions. NUOnet also contains datasets on other nutrients such as phosphorus and macro- and micro-nutrients, and it is part of the Dairy Agriculture for People and the Planet (DAPP) Grand Challenge, providing an integral link to connect data from the field to the table that will benefit farmers, ranchers, scientists, extension personnel, conservationists, consumers, and the general public.

4. The myPhyloDB database is a cutting-edge tool that aids in the standardization, normalization, and technology transfer of metagenomics data. The advent of next-generation sequencing has led to a dramatic increase in analysis of genetic material for microbial populations from a variety of sources (e.g., soil, human, animal). However, current analysis platforms do not allow for convenient storage or the standardization necessary for efficient technology transfer and cross-study analyses. ARS scientists in Fort Collins, Colorado, developed myPhyloDB to fill the need for a database that includes soil biology and soil biology responses to management. This new web-based tool is a significant advancement that provides an easy-to-use graphical interface and adds new functionality to the DNA sequence processing capabilities of Mothur – the most widely cited bioinformatics program (4000+ citations). myPhyloDB has been adopted as the designated platform for the ARS Soil Biology Group and is being integrated into the USDA Agricultural Collaborative Research Outcomes System (AgCROS) network. myPhyloDB has been downloaded or distributed via CD-ROM to more than 200 different international research groups in fields ranging from soil microbial ecology to human health and nutrition.

Review Publications
Delgado, J.A., Vandenberg, B.C., Kaplan, N.E., Neer, D.L., Wilson, G.J., D Adamo, R.E., Carter, J.D., Ogan, L., Grow, N.O., Marquez, R.D., Arthur, D.K., Eve, M.D., Del Grosso, S.J., Johnson, J.M., Karlen, D.L., Durso, L.M., Finley, J.W., Acosta Martinez, V., Harmel, R.D., Derner, J.D. 2018. Agricultural Collaborative Research Outcomes System: AgCROS - An emerging network of networks for national food and environmental security and human health. Journal of Soil and Water Conservation. 73(6):158A-164A.
Nummer, S.A., Qian, S.S., Harmel, R.D. 2018. Assessing the effects of conservation practices and fertilizer application methods on nitrogen and phosphorus losses from farm fields – a meta analysis. Journal of Environmental Quality. 47(5):1172-1178.
Hertzberger, A., Pittelkow, C., Harmel, R.D., Christianson, L.E. 2019. The MANAGE Drain Concentration database: A new tool compiling North American drainage nutrient concentrations. Agricultural Water Management. 216:113-117.
Allan-Perkins, E., Manter, D.K., Jung, G. 2019. Soil microbial communities on roughs, fairways, and putting greens of cool-season golf courses. Crop Science. 59(4):1753-1767.
Delgado, J.A., Barrera Mosquera, V.H., Escudero López, L.O., Cartagena Ayala, Y.E., Alwang, J.R., Stehouwer, R.C., Arévalo Tenelema, J.C., D Adamo, R.E., Domínguez Andrade, J.M., Valverde, F., Alvarado Ochoa, S.P. 2019. Conservation agriculture increases profits in an Andean region of South America. Agrosystems, Geosciences & Environment. 2(1):1-8.
Dilegge, M.J., Manter, D.K., Vivanco, J.M. 2019. A novel approach to determine generalist nematophagous microbes reveals Mortierella globalpina as a new biocontrol agent against Meloidogyne spp. nematodes. Scientific Reports. 9(7521):1-9.
Perveen, N., Barot, S., Maire, V., Cotrufo, F., Shahzad, T., Blagodatskaya, E., Stewart, C.E., Ding, W., Siddiq, M., Dimassi, B., Mary, B., Fontaine, S. 2019. Universality of priming effect: an analysis using thirty five soils with contrasted properties sampled from five continents. Soil biology and biochemistry. 134:162-171.
Salem, G., Weir, T., Byrne, P., Stromberger, M., Manter, D.K., El-Feki, W. 2018. Water stress tolerance of winter wheat (Triticum aestivum L.) genotypes is improved by ACC deaminase bacteria. Functional Plant Biology. 8:1-7.
Sherrod, L.A., Vigil, M.F., Stewart, C.E. 2019. Do fulvic, humic and humin c fractions represent meaningful biological, physical and chemical carbon pools? Journal of Environmental Quality.
Stewart, C.E., Roosendaal, D.L., Sindelar, A.J., Jin, V.L., Schmer, M.R. 2019. Does no-tillage mitigate stover removal in irrigated continuous corn? A multi-location assessment. Soil Science Society of America Journal. 83(3):733-742.
Stull, V., Finer, E., Bermans, R.S., Febvre, H., Longhurst, C., Manter, D.K., Patz, J., Weir, T.L. 2018. Impact of edible cricket consumption on gut microbiota in healthy adults, a double-blind, randomized crossover trail. Scientific Reports. 8(10762):1-13.
Xu, H., Sieverding, H., Kwon, H., Clay, D., Stewart, C.E., Johnson, J.M., Qin, Z., Karlen, D.L., Wang, M. 2019. A global meta-analysis of soil organic carbon response to corn stover removal. Global Change Biology Bioenergy. 00:1-19.
Del Grosso, S.J., Parton, W.J. 2019. History of ecosystem model development at Colorado State University and current efforts to address contemporary ecological issues. American Society of Agronomy. 8:53-70.
Manter, D.K., Delgado, J.A., Moore-Kucera, J. 2018. Integrated soil health management: A framework for soil health, conservation and regeneration. In: Reicosky, D. Managing Soil Health for Sustainable Agriculture, Volume 2. Sawston, Cambridge: Burleigh Dodds Science Publishing Limited. p.69-87.
Ramlow, M., Foster, E., Del Grosso, S.J., Cotrufo, M. 2017. The limited benefits of biochar in limited irrigation maize. Agriculture, Ecosystems and Environment. 269:71-81.
Miner, G.L., Delgado, J.A., Ippolito, J.A., Barbarick, K.A., Stewart, C.E., Manter, D.K., Del Grosso, S.J., Halvorson, A.D., Floyd, B.A., D Adamo, R.E. 2018. Long-term nitrogen fertilization rates affect crop micronutrient concentrations but not soil micronutrient availability. Field Crops Research. 228:170-182.
Febvre, H., Rao, S., Gindin, M., Goodwin, N., Finer, E., Vivanco, J., Lu, S., Manter, D.K., Wallace, T., Weir, T. 2019. Phage study: effects of supplemental bacteriophage intake on inflammation and gut microbiota in healthy adults. Nutrients. 11(3):666.
Sassenrath, G.F., Delgado, J.A. 2018. Precision conservation and precision regulation. In: Delgado, J.A., Sasenrath, G.F., Mueller, T., editors. Precision Conservation: Geospatial Techniques for Agricultural and Natural Resources Conservation. Madison, WI: American Society of Agronomy and Crop Science Society of America, Inc. p. 361-384.