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Searching for the missing nitrogen: biogenic nitrogen gases in groundwater and streams

  • R. J. FOX (a1), T. R. FISHER (a1), A. B. GUSTAFSON (a1), T. E. JORDAN (a2), T. M. KANA (a1) and M. W. LANG (a3)...


Biogenic nitrogen (N2) and nitrous oxide (N2O) accumulations were measured in groundwater, streams and the vadose zone of small agricultural watersheds in the Mid-Atlantic USA. In general, N2 and N2O in excess of atmospheric equilibrium were found in groundwater virtually everywhere that was sampled. Excess N2 in groundwater ranged from undetectable to 616 μmol N2-N/l, the latter representing c. 50% of background N2. The N2O-N concentrations varied from undetectable to 75 μm, and usually greatly exceeded values at atmospheric equilibrium (25–30 nM); however, N2O was generally 1–10% of excess N2. Intermediate levels of deficit and excess N2 in flowing streams (−65 to +250 μmol N2-N/L) resulting from both abiotic and biotic processes were also measured. In vadose zone gases, multiple N2/Ar gas profiles were measured which exhibited seasonal variations with below atmospheric values when the soil was warming in spring/summer and above atmospheric values when groundwater was cooling in fall/winter. Both abiotic and biotic processes contributed to the excess N2 and N2O that was observed. The current data indicate that large concentrations of excess N gases can accumulate within soil, groundwater, and streams of agriculturally dominated watersheds. When excess N gases are exchanged with the atmosphere, the net fluxes to the atmosphere may represent an important loss term for watershed N budgets.


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Aeschbach-Hertig, W., Peeters, F., Beyerle, U. & Kipfer, R. (1999). Interpretation of dissolved atmospheric noble gases in natural water. Water Resources Research 35, 27792792.
Aeschbach-Hertig, W., El-Gamal, H., Wieser, M., & Palcsu, L. (2008). Modeling excess air and degassing in groundwater by equilibrium partitioning with a gas phase. Water Resources Research 44, W08449, DOI:10.1029/2007WR006454.
Beaulieu, J. J., Tank, J. L., Hamilton, S. K., Wollheim, W. M., Hall, R. O. Jr, Mulholland, P. J., Peterson, B. J., Ashkenas, L. R., Cooper, L. W., Dahm, C. N., Dodds, W. K., Grimm, N. B., Johnson, S. L., McDowell, M. W., Poole, G. C., Valett, H. M., Arango, C. P., Bernot, M. J., Burgin, A. J., Crenshaw, C. L., Helton, A. M., Johnson, L. T., O'Brien, J. M., Potter, J. D., Sheibley, R. W., Sobota, D. J. & Thomas, S. M. (2011). Nitrous oxide emission from denitrification in stream and river networks. Proceedings of the National Academy of Sciences USA 108, 214219.
Benitez, J. A. & Fisher, T. R. (2004). Historical land cover conversion (1665–1850) in the Choptank watershed, Eastern USA. Ecosystems 7, 219232.
Bohlke, J.-K. & Denver, J. M. (1995). Combined use of groundwater dating, chemical, and isotopic analyses to resolve the history and fate of nitrate contamination in two agricultural watersheds, Atlantic coastal plain, Maryland. Water Resources Research 31, 23192339.
Boyer, E. W., Goodale, C. L., Jaworski, N. A. & Howarth, R. W. (2002). Anthropogenic nitrogen sources and relationships to riverine nitrogen export in the northeastern USA. Biogeochemistry 57/58, 137169.
Burgin, A. J. & Hamilton, S. K. (2007). Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways. Frontiers in Ecology & the Environment 5, 8996.
Colt, J. (1984). Computation of Dissolved Gas Concentrations in Water as Functions of Temperature, Salinity, and Pressure. Special Publication no. 14. Bethesda, MD, USA: American Fisheries Society.
David, M. B. & Gentry, L. E. (2000). Anthropogenic inputs of nitrogen and phosphorus and riverine export for Illinois, USA. Journal of Environmental Quality 29, 494508.
Denver, J. M., Ator, S. W., Lang, M. W., Fisher, T. R., Gustafson, A. B., Fox, R., Clune, J. W. & McCarty, G. W. (2014). Nitrate fate and transport through current and former depressional wetlands in an agricultural landscape, Choptank Watershed, Maryland, USA. Journal of Soil and Water Conservation 69, 527542.
Falkengren-Grerup, U. (1995). Interspecies differences in the preference of ammonium and nitrate in vascular plants. Oecologia 102, 305311.
Fisher, T. R., Hagy, J. D. III, Boynton, W. R. & Williams, M. R. (2006). Cultural eutrophication in the Choptank and Patuxent estuaries of Chesapeake Bay. Limnology and Oceanography 51, 435447.
Fisher, T. R., Jordan, T. E., Staver, K. W., Gustafson, A. B., Koskelo, A. I., Fox, R. J., Sutton, A. J., Kana, T., Beckert, K. A., Stone, J. P., McCarty, G. & Lang, M. (2010). The Choptank Basin in transition: intensifying agriculture, slow urbanization, and estuarine eutrophication. In Coastal Lagoons: Systems of Natural and Anthropogenic Change (Eds Kennish, M. J. & Paerl, H. W.), pp. 135166. New York: CRC Press.
Fox, R. J. (2011). Dynamics of metabolic gases in groundwater and the vadose zone of soils on Delmarva. PhD Thesis, University of Maryland, College Park, MD, USA.
Glass, A. D. M., Britto, D. T., Kaiser, B. N., Kinghorn, J. R., Kronzucker, H. J., Kumar, A., Okamoto, M., Rawat, S., Siddiqi, M. Y., Unkles, S. E. & Vidmar, J. J. (2002). The regulation of nitrate and ammonium transport systems in plants. Journal of Experimental Botany 53, 855864.
Green, C. T., Fisher, L. H. & Bekins, B. A. (2008). Nitrogen fluxes through unsaturated zones in five agricultural settings across the United States. Journal of Environmental Quality 37, 10731085.
Groffman, P. M., Gold, A. J. & Addy, K. (2000). Nitrous oxide production in riparian zones and its importance to national emission inventories. Chemosphere – Global Change Science 2, 291299.
Howarth, R. W., Billen, G., Swaney, D., Townsend, A., Jaworski, N., Lajtha, K., Downing, J. A., Elmgren, R., Caraco, N., Jordan, T., Berendse, F., Freney, J., Kudeyarov, V., Murdoch, P. & Zhao-Liang, Z. (1996). Regional nitrogen budgets and riverine N & P fluxes for the drainages to the North Atlantic Ocean: natural and human influences. Biogeochemistry 35, 75139.
Ingram, R. G. S., Hiscock, K. M. & Dennis, P. F. (2007). Noble gas excess air applied to distinguish groundwater recharge conditions. Environmental Science and Technology 41, 19491955.
Jordan, T. E. & Weller, D. W. (1996). Human contributions to terrestrial nitrogen flux. BioScience 46, 655664.
Jordan, T. E., Correll, D. L. & Weller, D. E. (1997). Effects of agriculture on discharges of nutrients from coastal plain watersheds of Chesapeake Bay. Journal of Environmental Quality 26, 836848.
Kana, T. M., Darkangelo, C., Hunt, M. D., Oldham, J. B., Bennett, G. E. & Cornwell, J. C. (1994). A membrane inlet mass spectrometer for rapid high precision determination of N2, O2, and Ar in environmental water samples. Analytical Chemistry 66, 41664170.
Langford, A. O., Fehsenfeld, F. C., Zachariassen, J. & Schimel, D. S. (1992). Gaseous ammonia fluxes and background concentrations in terrestrial ecosystems of the United States. Global Biogeochemical Cycles 6, 459483.
Laursen, A. E. & Seitzinger, S. P. (2004). Diurnal patterns of denitrification, oxygen consumption, and nitrous oxide production in rivers measured at the whole-reach scale. Freshwater Biology 49, 14481458.
Lee, K.-Y., Fisher, T. R. & Rochelle-Newall, E. (2001). Modeling the hydrochemistry of the Choptank River basin using GWLF and Arc/Info: 2. Model Application. Biogeochemistry 56, 311348.
McCutchan, J. H. Jr, Saunders, J. F. III, Pribyl, A. L. & Lewis, W. M. Jr. (2003). Open-channel estimation of denitrification. Limnology and Oceanography: Methods 1, 7481.
Mehnert, E., Hwang, H.-H., Johnson, T. M., Sanford, R. A., Beaumont, W. C. & Holm, T. R. (2007). Denitrification in the shallow ground water of a tile-drained, agricultural watershed. Journal of Environmental Quality 36, 8090.
Norton, M. M. & Fisher, T. R. (2000). The effects of forest on stream water quality in two coastal plain watersheds of the Chesapeake Bay. Ecological Engineering 14, 337362.
Pessarakli, M. (1999). Handbook of Plant and Crop Stress, 2nd edn. New York: Marcel Dekker Inc.
Schaefer, S. C. & Alber, M. (2007). Temperature controls a latitudinal gradient in the proportion of watershed nitrogen exported to coastal ecosystems. Biogeochemistry 85, 333346.
Schaefer, S. C., Hollibaugh, J. T. & Alber, M. (2009). Watershed nitrogen input and riverine export on the west coast of the US. Biogeochemistry 93, 219233.
Seitzinger, S., Harrison, J. A., Bohlke, J.-K., Bouwman, A. F., Lowrance, R., Peterson, B., Tobias, C. & Van Drecht, G. (2006). Denitrification across landscapes and waterscapes: a synthesis. Ecological Applications 16, 20642090.
Silver, W. L., Lugo, A. E. & Keller, M. (1999). Soil oxygen availability and biogeochemistry along rainfall and topographic gradients in upland wet tropical forest soils. Biogeochemistry 44, 301328.
Sutton, A. J., Fisher, T. R. & Gustafson, A. B. (2010). Effects of restored stream buffers on water quality in non-tidal streams in the Choptank River basin. Water, Air and Soil Pollution 208, 101118.
van Breemen, N., Boyer, E. W., Goodale, C. L., Jaworski, N. A., Paustian, K., Seitzinger, S. P., Lajtha, K., Mayer, B., Van Dam, D., Howarth, R. W., Nadelhoffer, K. J., Eve, M. & Billen, G. (2002). Where did all the nitrogen go? Fate of nitrogen inputs to large watershed in the northeastern U.S.A. Biogeochemistry 57/58, 267293.
Vilain, G., Garnier, J., Tallec, G. & Tournebize, J. (2012). Indirect N2O emissions from shallow groundwater in an agricultural catchment (Seine Basin, France). Biogeochemistry 111, 253271.
Vogel, J. C., Talma, A. S. & Heaton, T. H. E. (1981). Gaseous nitrogen as evidence of denitrification in groundwater. Journal of Hydrology 50, 191200.
Wilson, G. B. & McNeill, G. W. (1997). Noble gas recharge temperatures and the excess air component. Applied Geochemistry 12, 747762.
Yang, W. H. & Silver, W. H. (2012). Application of the N2/Ar technique to measuring soil-atmosphere N2 fluxes. Rapid Communications in Mass Spectrometry 26, 449459.
Zumft, W. G. (1997). Cell biology and molecular basis of denitrification. Microbiology and Molecular Biology Reviews 61, 533616.
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