2013 Annual Report
1)methodology based on emission factors to estimate greenhouse gas (GHG) fluxes from agricultural systems for national inventories and reported to the United Nations Framework Convention on Climate Change (UNFCCC). Researchers from ARS in Fort Collins, CO and Colorado State University showed that the more sophicticated DayCent ecosystem model (IPCC Tier 3 methodology) can accurately predict N2O flux data for 13 field sites in the U.S. and Australia. In addition, the ability of the model to represent soil C stock changes was verified by comparing model outputs with observations from 47 field sites (mostly in North America). Consequently, use of the DayCent process based model to estimate GHG fluxes at the national scale reported by the US to the UNFCCC and published by EPA in 2013 (Inventory of U.S. Greenhouse Gas Emissions and Sinks: 1990–2011) have smaller uncertainty intervals than emissions reported by other nations using IPCC Tier 1 methodology. 4. DayCent simulations of biofuel systems validated. Biofuels have potential to reduce GHG emissions compared to fossil fuels but rigorous life cycle GHG accounting is required to quantify this reduction. ARS researchers at Fort Collins, CO, in collaboration with scientists from ARS-Pasture Systems and Watershed Management Research Unit in College Park, PA and with Colorado State University, compared biomass yields and N2O fluxes estimated by the DayCent ecosystem model with observations from biofuel studies in Pennsylvania. The model was shown to accurately represent yields and emissions for corn, soy, and alfalfa rotations, and continuous switchgrass and reed canary grass systems. DayCent has subsequently been applied to estimate soil GHG emissions for different biofuel systems in representative counties in the US. 5. Grazing intensity has little impact on soil carbon (SOC) and nitrogen (SON) stocks under bermudagrass. ARS researchers at Fort Collins, CO, in collaboration with scientists from the University of Florida evaluated rotational stocking (8-, 16-, and 24-cm postgraze stubble) and nitrogen (N) rates on a 14-yr-bermudagrass pasture near Gainesville, FL. Soil samples to 20-cm after 2 grazing years show intensity and N had no effect on SOC and SON. Lower intensity and N increased particulate organic C and <53-mm particle-size C and N. Stable C isotopes show C4-derived C was lost due to intensive grazing. Results demonstrate particulate organic C and <53 mm associated C were sensitive indicators of short-term impacts of pasture management strategies on SOC In sandy soils of subtropical regions. Diagnostic soil fractions are simple tools that can be used by researchers and farmers to evaluate short-term management impacts in soils. 6. Global climate change impacts soil organic C (SOC) and soil organic N (SON) in the US Great Plains. ARS researchers at Fort Collins, CO, evaluated gradient effects on soil C and N under native, conservation tillage and conventional tillage across the Great Plains. They found that soil C under all land-uses decreased. The potential effect of climate change, based on mean annual temperature (MAT) and the mean annual precipitation to potential evapotranspiration (MAP:PET) ratio in the U.S. Great Plains are that a 1 °C increase in MAT could result in loss of 486 Tg of SOC (1.78 Pg CO2eq) and release of 180 kg SON/ha from the top 10cm of soil over 30 yr. Increased warming and land conversion from CRP to cropping may significantly decrease SOC stock. Increased temperature could negatively impact soil fertility under agricultural management, but practices that minimize soil erosion and reduce evapotranspiration may offset C and N loss from increasing temperature. 7. Biochar (BC) amendment decreased N2O emissions up to 89% with increasing rate and sequestered recalcitrant C. Agriculture contributes substantially to greenhouse gas (GHG) emissions and soil organic carbon loss. ARS researchers at Fort Collins, CO, evaluated the ability of biochar additions to soils to decrease agricultural greenhouse gas emissions and sequester recalcitrant C in the laboratory. They found that increasing BC addition rates decreased N2O emissions exponentially and increased CO2 emissions linearly across all four soils. Expressed as CO2 equivalents, CO2 was the primary GHG emitted (97.5%), followed by N2O. All GHG emissions were small compared to the total soil carbon sequestered in the BC. Highly recalcitrant BC sequestered C and reduced GHG emissions. Biochar amendment to soil could be used to decrease N2O emissions and sequester soil C in a wide range of agricultural soils. These results provide data to modeling efforts of field application effects of biochar. 8. Biochar amendment to soils reduced N leaching. Nitrogen loss from agriculture contributes to downstream water pollution and greenhouse gas production. ARS researchers at Fort Collins, CO, evaluated the ability of biochar additions to soils to decrease agricultural N fertilizer leaching and N2O efflux in the laboratory. Biochar had no effect on NO3-, NH4+ or N2O for unfertilized soils and decreased extractable NO3- in N fertilized soils and had mixed effects on NH4+. Biochar amendment reduced N leaching and N2O emissions in neutral to acidic soils with high N content. This research confirms that biochar application is most effective in mitigating N loss through leaching and N2O in acidic, high C soils and could be used by producers to target N mitigation strategies. 9. Irrigated corn in the central Great Plains has a low ability to sequester soil organic carbon (SOC). Agricultural cultivation has significantly decreased SOC and irrigated cropping and N fertilization has been suggested as a means to increase SOC content by increasing crop productivity. Across 8 yr in a C sequestration study near Fort Collins, CO, ARS researchers evaluated continuous-irrigated corn grown under no-till (NT) and conventional till (CT) at three N-rates. Deep soil samples (120 cm) and stable-isotopic C techniques measured C4-C from corn and residual C3–C. Fertilizer N helped retain C4–C and slowed C3–C loss. NT maintained SOC better than CT. Despite greater crop productivity, irrigated corn has low potential to sequester SOC in the central Great Plains. Producers will use these results to more effectively manage irrigated corn production. 10. Rising temperature will limit soil organic carbon (SOC) in the US Great Plains. ARS researchers at Fort Collins, CO, evaluated temperature and moisture gradients effects on soil C and N under native, conservation tillage and conventional tillage across the Great Plains. They found that the relative stabilization of C in particulate organic matter (POM) and mineral-associated fractions (Cmin) in the near surface soil horizons is being assessed in relation to SOC stocks across 14 locations. Preliminary results suggest that soil C stocks and d13C in whole soil and in the POM and Cmin fractions are strongly driven by temperature gradients, with the greatest SOC in cool climates. Conservation practices that decrease SOC mineralization (no-tillage), minimize soil erosion and reduce evapotranspiration may offset C and N loss from increasing temperature. 11. Nitrogen source and rate affect furrow irrigated corn yields. Nitrogen rate studies were conducted by ARS scientists in Fort Collins, CO under furrow irrigated corn production to compare polymer-coated urea (PCU) and stabilized urea (SU) effects on corn yields, plant N uptake and N use efficiency (NUE) to conventional granular urea. PCU had a yield advantage (4 to 14%) over urea at N rates from 168 to 280 kg N/ha resulting in greater economic returns with PCU. The reduced fertilizer rates associated with PCU is also an effective means to reduce N2O emissions as compared to granular urea. Crop consultants and producers can use this information to utilize N more efficiently in irrigated corn production systems. 12. Plant tannins limit Phytophthora growth and sporulation. Phytophthora species are some of the most destructive and widespread pathogens, common to all crop and non-crop plant species. ARS scientists in Fort Collins, CO have identified a number of plant compounds that directly inhibit Phytophthora growth and sporulation contributing to disease resistance. In a recent paper, we have identified that plant tannins can disrupt the function of Phytophthora elicitin proteins, leading to reduced pathogen growth and sporulation. This is a novel mode of action for plant tannins providing a new line of evidence for their role as plant defense compounds. Therefore, plant tannins are a potential new tool to reduce Phytophthora diseases without the need for pesticide inputs. 13. Improving ethanolic fermentation for biofuels production. Acid hydrolysis is often the first step in the production of ethanolic biofuels. However, this step produces furfural, a toxic compound that can interfere with the fermentation of sugars to produce ethanol. ARS research in Fort Collins, CO shows that a pre-incubation treatment using bacteria can remove furfural and improve the subsequence fermentation.
14. Bioremediation of selenite contaminated soil and water. Selenite, a toxic metalloid, is a common irrigation and ground water contaminant; consumption of food or water contaminated with high levels of selenite is a health risk to farm animals and humans. Fort Collins, CO ARS research demonstrated a method for identifying specific proteins that interact with selenite and biochemical pathways whose functions are impeded by selenite. This information can help determine health issues associated with selenite poisoning, the intracellular target of toxic selenite, and aid in removing selenite from contaminated water. 15. Impact of soil microbiomes on the leaf metabolome and herbivore feeding behavior. It is known that environmental factors can affect the biosynthesis of leaf metabolites. ARS researchers in Fort Collins, CO in cooperation with CSU, analyzed experimentally how diverse soil microbiomes applied to the roots of Arabidopsis thaliana were able to modulate plant growth and the leaf metabolome, as assessed by GC-MS analyses. Further, we determined the effects of soil microbiome-driven changes in leaf metabolomics on the feeding behavior of Trichopulsia ni larvae. This study is of one the first of its kind to show that soil microbes can influence leaf chemistry and insect feeding behavior. 16. Soil microbiomes vary in their ability to confer drought tolerance. Drought is a major constraint on agricultural production. Crop genetic improvement for drought tolerance has received much attention and there is ample information about the ability of specific soil microbes to influence drought tolerance in plants. However, there is a need to understand the cumulative effect of these multiple interactions on a plant’s ability to overcome abiotic stresses such as drought. ARS researchers in Fort Collins, CO in cooperation with CSU, have identified a set of soil microbes that when present in the soil can modify the plant’s ability to sense drought stress and increase its biomass production. Targeted testing with the individual microbes identified in this study will be continued. 17. Isolation and characterization of lignin-degrading bacteria. The deconstruction of lignin to enhance the release of fermentable sugars from plant cell walls presents a challenge for biofuels production from lignocellulosic plant biomass. The discovery of novel lignin-degrading enzymes from bacteria provide advantages over fungal enzymes in terms of their production and relative ease of protein engineering. Two Bacillus strains were identified by ARS researchers in Ft. Collins, CO that degraded lignin and its most abundant building block, guaiacylglycerol-b-guaiacyl ether. These findings provide important evidence that bacterial enzymes can degrade and/or modify lignin and contribute to the release of fermentable sugars from lignocellulose. 18. Removal of nitrate in groundwater beneath cattle-pens. Nitrate is often a major agricultural groundwater contaminant in areas where cattle are raised. A Fort Collins, CO ARS field study found that biobarriers placed in shallow vadose zone soils beneath the cattle pens can intercept and remove nitrate from percolating soil water protecting the underlying aquifer from contamination. 19. Bioproduction of value added products. Fort Collins, CO ARS research shows that a novel bacterial isolate obtained from a tropical rainforest soil can convert ferulic acid, an inexpensive chemical common in crop residues, to 4-Vinylguaiacol, a much more valuable chemical used as a flavoring. The conversion was rapid and highly efficient. 20. Root exudation and the associated microbiome follow specific patterns that are developmentally programmed. Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. In a study by ARS researchers in Ft. Collins, CO, it was found that that the composition of root exudates varied with plant developmental stage, such that the levels of sugars and sugar alcohols were highest in young plants and the levels of amino acids and phenolics increased over time. A strong correlation between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development was observed. This work is among the first studies to show a functional link between root exudation and the root-associated microbial community throughout plant development. 21. Harnessing the rhizosphere microbiome through plant breeding and agricultural management. The need to enhance the sustainability of intensive agricultural systems is widely recognized. One promising approach is to encourage beneficial services provided by soil microorganisms to decrease the inputs of fertilizers and pesticides. However, limited success of this approach in field applications raises questions as to how this might be best accomplished. ARS researchers in Ft. Collins, CO highlight connections between root exudates and the rhizosphere microbiome, and discuss the possibility of using plant exudation characteristics to selectively enhance beneficial microbial activities and microbiome characteristics. The article outlines strategies for more effectively exploiting beneficial microbial services on agricultural systems, and calls attention to topics that require additional research. 22. Nitrogen fertilizer source influences soil nitrous oxide emissions from no-till corn. Nitrous oxide (N2O) is a potent greenhouse gas emitted when inorganic N fertilizers are applied to agricultural crops. ARS Scientists in Fort Collins, CO compared N2O emissions from enhanced-efficiency N fertilizer (EENF) sources to commonly used granular urea and liquid urea-ammonium nitrate (UAN) fertilizers in an irrigated, no-till corn system. Some EENF sources reduced growing season N2O emissions up to 62% compared to urea and 37% compared to UAN. Cropping system managers and policy makers need to consider selection of N fertilizer source as a mitigation practice for reducing N2O emissions and global warming potential in the semi-arid western U.S.
23. Nitrogen source effects on ammonia volatilization. Ammonia (NH3) volatilization is one of the main pathways of nitrogen (N) loss from agricultural cropping systems. The NH3-N loss from four urea based N sources [urea, urea-ammonium nitrate (UAN), SuperU, and a polymer-coated urea, ESN] surface band applied at a rate of 200 kg N ha-1 to irrigated, strip-till corn production systems was evaluated for 2 yr using semi-static chambers by ARS scientists at Fort Collins, CO. Irrigation with 16-19 mm of water one day after N fertilization limited NH3-N volatilization from surface applied N fertilizers to a range of 0.1-4.0% of total N applied. SuperU, which contains a urease inhibitor, had the lowest level of NH3-N loss when compared to other N sources. Estimated NH3-N losses for the N sources were in the order: ESN=UAN>urea>SuperU. The open-chamber method was a viable, low cost method for estimating NH3–N loss from small field plots. 24. Kentucky nitrogen and phosphorous index. The new Kentucky Nitrogen (N) and Phosphorous (P) Index tool was transferred to the state of Kentucky by ARS researchers in Ft. Collins, CO. There is the need to increase nitrogen use efficiencies to reduce losses of reactive nitrogen to the environment and to reduce the off-site transport of phosphorous, which can contribute to negative impacts such as hypoxia problems that lower water quality of surface waters. The Kentucky Natural Resources Conservation Service released its new Nutrient Management Conservation Practice Standard 590 in March of 2013, and this new N and P risk assessment tool is referenced in the standard as an official risk assessment tool for Kentucky. The tool was CCE certified by NRCS and this application is a power 25. An improved Mexico Nitrogen Index tool with N2O Index capabilities. An ARS scientist in Fort Collins improved the Mexico Nitrogen Index tool and added a new capability to assess N2O emissions, to the tool. This new bilingual tool (available in the English and Spanish languages) was transferred to Enhancing Capacity for Low Emission Development Strategies (EC-LEDS), a U.S. Government program cooperating with Mexico. There is a bilateral cooperation between the U.S. and Mexico in a new, joint program to expand the implementation of conservation agriculture (CA) for climate change adaptation across Mexico. This new Mexico Nitrogen Index tool, developed by an ARS scientist in Fort Collins, is being used to assess the risk of nitrogen losses to the environment, to increase nitrogen use efficiency, and to reduce emissions of N2O. This new bilingual tool can help users implement conservation practices for mitigation of and adaptation to climate change, and can help enhance communication between technical personnel and farmers across Mexico about how to implement best management practices that reduce N2O emissions.
Stewart, C.E., Zheng, J., Botte, J., Cotrufo, M. 2013. Co-generated fast pyrolysis biochar mitigates green-house gas emissions and increases carbon sequestration in temperate soils. Global Change Biology Bioenergy. 5:153-164.
Silveira, M., Liu, K., Sollenberger, L., Follett, R.F., Vendramini, J. 2012. Short-term effects of grazing intensity and nitrogen fertilization on soil organic carbon pools under perennial grass pastures in the Southeastern USA . Journal of Soil Biology and Biochemistry. 58:(2013)42-49.
Chaparro, J.M., Badri, D.V., Bakker, M.G., Sugiyama, A., Manter, D.K., Vivanco, J.M. 2013. Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS One. 8:e55731.
Bailey, R.T., Gates, T.K., Halvorson, A.D. 2013. Simulating variably-saturated reactive transport of selenium and nitrogen in agricultural groundwater systems. Journal of Contaminant Hydrology. http://dx.doi.org/10.1016/j.jconhyd.2013.03.001.
Badri, D.V., De-La-Pena, C., Vivanco, J.M., Lei, Z., Manter, D.K., Guimaraes, R., Summer, L.W. 2012. Defense-and stress-related proteins are involved in early events related to plant-plant recognition prior to competition. PLoS Biology. 7:e46640.
Bakker, M., Manter, D.K., Sheflin, A., Weir, T., Vivanco, J. 2012. Marshner Review: Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant and Soil. DOI: 10.1007/s1104-012-1361-x.
Cavigelli, M.A., Del Grosso, S.J., Liebig, M.A., Snyder, C.S., Fixen, P.E., Venterea, R.T., Leytem, A.B., McLain, J.E., Watts, D.B. 2013. US agricultural nitrous oxide emissions: context, status, and trends. Frontiers in Ecology and the Environment. 10:537-546.
Delgado, J.A., Nearing, M.A., Rice, C. 2013. Conservation practices for climate change. Advances in Agronomy. 121:47-115.
Follett, R.F., Jantalia, C.P., Halvorson, A.D. 2013. Soil Carbon Dynamics for Irrigated Corn under Two Tillage Systems. Soil Science Society of America Journal. 77:951-963.
Halvorson, A.D., Snyder, C.S., Blaylock, A.D., Del Grosso, S.J. 2013. Enhanced-efficiency nitrogen fertilizers: potential role in nitrous oxide emission mitigation. Agronomy Journal. Vol. 106:715:722..
Halvorson, A.D., Bartolo, M. 2014. Nitrogen source and rate effects on furrow irrigated corn yields and NUE. Agronomy Journal. Vol. 106:681-693..
Hansen, L., Delgado, J.A., Ribaudo, M., Crumpton, W. 2012. Cost effectiveness of on- and off-field conservation practices designed to reduce nitrogen in downstream water. Journal of Environmental Economics and Management. 67:162A-166A.
Huang, X., Santhanam, N., Badri, D., Hunter, W.J., Manter, D.K., Decker, S., Vivanco, J., Reardon, K. 2013. Isolation and characterization of lignin-degrading bacteria from rainforest soils. Biotechnology and Bioengineering. 110:1616-1626.
Stong, R.A., Kolodny, E., Kelsey, R., González-Hernández, M.P., Manter, D.K. 2013. Effect of plant sterols and tannins on Phytophthora ramorum growth and sporulation. Journal of Chemical Ecology. 39:733-743.
Jantalia, C.P., Halvorson, A.D., Follett, R.F., Alves, B.R., Polidoro, J.C., Urquiaga, S. 2012. Nitrogen source effects on ammonia volatilization as measured with semi-static chamber. Agronomy Journal. Vol. 104:1595-1603. Kelsey, R.G., Beh, M., Shaw, D., Manter, D.K. 2013. Ethanol attracts scolytid beetles to Phytophthora ramorum cankers on coast live oak. Journal of Chemical Ecology. 39:494-506.
Monar, C., Saavedra, A., Escudero, L., Delgado, J.A., Alwang, J., Barrera, V., Botello, R. 2013. Positive impacts in soil and water conservation in an Andean region of South America: Case scenarios from a USAID multidisciplinary cooperative project. Journal of Soil and Water Conservation. 68:25A-30A.
Sugiyama, A., Bakker, M., Badri, D., Manter, D.K., Vivanco, J. 2012. Relationships between Arabidopsis thaliana and soil bacterial communities. Botany. 91:123-126.
Venterea, R.T., Halvorson, A.D., Kitchen, N.R., Liebig, M.A., Cavigelli, M.A., Del Grosso, S.J., Motavalli, P.P., Nelson, K.A., Spokas, K.A., Singh, B.P., Stewart, C.E., Ranaivoson, A., Strock, J., Collins, H.P. 2012. Challenges and opportunities for mitigating nitrous oxide emissions from fertilized cropping systems. Frontiers in Ecology and the Environment. 10(10)562-570.
Zheng, J., Stewart, C.E., Cotrufo, M. 2012. Biochar and N fertilizer alters soil N dynamics and greenhouse gas fluxes from two temperate soils. Journal of Environmental Quality. 41:1361-1370.
Zolla, G., Badri, D., Manter, D.K., Vivanco, J. 2013. Soil microbiomass vary in their ability to confer drought tolerance to Arabidopsis. Applied Soil Ecology. 68:1-9.
Delgado, J.A. 2012. Nitrogen Leaching Index. In: Sven Erik Jorgensen, Editor. Encyclopedia of Environmental Management. New York, NY: CRC Press Taylor & Francis Group. P. 1761-1767.
Delgado, J.A. 2012. Nitrogen trading tool. In: Sven Erik Jorgensen Editor.Encyclopedia of Environmental Management. New York, NY: CRC Press Taylor & Francis Group. P. 1772-1784.
Halvorson, A.D., Richardson, J. 2012. Management of dryland saline seeps. In: Wallender, W.W. and Tanjni, K.K. editors. Agricultural Salinity Assessment and Management. ASCE Manuals and Reports on Engineering Practice No. 71, 2nd edition. Reston, VA:American Society of Civil Engineers. p. 561-589.
Zolla, G., Bakker, M., Chaparro, J., Sheflin, A., Badri, D., Manter, D.K., Vivanco, J.M. 2013. Understanding root-microbiome interactions. In: Frans J. de Bruijn, editor. Molecular Microbial Ecology of the Rhrizosphere. New York, NY: Wiley & Sons, p. 743-754.
Badri, D., Zolla, G., Baker, M., Manter, D.K., Vivanco, J. 2013. Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior. New Phytologist. 198:264-273.
Del Grosso, S.J., White, J.W., Wilson, G., Vandenberg, B.C., Karlen, D.L., Follett, R.F., Johnson, J.M., Franzluebbers, A.J., Archer, D.W., Gollany, H.T., Liebig, M.A., Ascough II, J.C., Reyes-Fox, M.A., Starr, J.L., Barbour, N.W., Polumsky, R.W., Gutwein, M., James, D.E., Pellack, L.S. 2013. Introducing the GRACEnet/REAP data contribution, discovery and retrieval system. Journal of Environmental Quality. 42:1274-1280. DOI:10.2134/jeq2013.03.0097.
Delgado, J.A., Kowalski, K.D., Tebbe, C.R. 2013. The first nitrogen index app for mobile devices: using portable technology for smart agricultural management. Computers and Electronics in Agriculture. 91:121-123.
Dijkstra, F., Morgan, J.A., Follett, R.F., Lecain, D.R. 2013. Climate change reduces the net sink of CH4 and N2O in a semiarid grassland. Global Change Biology. 19:1816-1826.
Halvorson, A.D., Del Grosso, S.J. 2012. Nitrogen source and placement effects on soil nitrous oxide emissions from no-till corn. Journal of Environmental Quality. 41: 1349-1360.
Mikha, M.M., Benjamin, J.G., Halvorson, A.D., Nielsen, D.C. 2013. Soil carbon changes influenced by soil management and calculation method. Open Journal of Soil Science. 3:123-131.
Halvorson, A.D., Del Grosso, S.J. 2013. Nitrogen placement effects on soil nitrous oxide emissions from irrigated corn. Journal of Environmental Quality. 42:312-322.
Hunter, W.J. 2013. Pilot-scale vadose zone microbial biobarriers removed nitrate leaching from a cattle corral. Current Microbiology. 68:52-59.
Del Grosso, S.J., Cavigelli, M.A. 2012. Climate stabilization wedges revisited: can agricultural production and greenhouse gas reduction goals be accomplished? Frontiers in Ecology and the Environment. 10:571-578.
Lal, R., Delgado, J.A., Nielsen, D.C., Rice, C., Van Pelt, R.S. 2012. Adapting agriculture to drought and extreme events. Journal of Soil and Water Conservation. 67:162A-166A.