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Burford, J. R. and Bremner, J. M. 1975. Relationships between the denitrification capacities of soils and total, watersoluble and readily decomposable soil organic matter. Soil Biology & Biochemistry 7, 389-394.
Burford, J. R., and Stefanson, R. C. 1973. Measurements of gaseous losses of nitrogen from soils. Soil Biology & Biochemistry 5, 133-141.
Nitrogen Workshop 2012
Burger, M. and Jackson, L. E. 2004. Plant and microbial use and turnover: rapid conversion of nitrate to ammonium in soil with roots. Plant and Soil 266, 289-301.
Cavigelli, M. A. and Robertson, G. P. 2000. The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology 81, 1402-1414.
Chalk, P. M. and Smith, C. J. 1983. Chemodenitrification. In "Gaseous loss of nitrogen from plant soil systems" (J. R.
Freney and J. R. Simpson, eds.), pp. 65-89. Martinus Nijhoff and Dr W Junk, Dordrecht.
Cho, C. M., and Mills, J. G. 1979. Kinetic formulation of the denitrification process in soil. Canadian Journal of Soil Science 59, 249-257.
Clément, J.-C., Shrestha, J., Ehrenfeld, J. G., and Jaffé, P. R. 2005. Ammonium oxidation coupled to dissimilatory reduction of iron under anaerobic conditions in wetland soils. Soil Biology & Biochemistry 37, 2323-2328.
Dassonville, F. and Renault, P. 2002. Interactions between microbial processes and geochemical transformations under anaerobic conditions: a review. Agronomie 22, 51-68.
Davidson, E. A. and Seitzinger, S. 2006. The enigma of progress in dentrification research. Ecological Applications 16, 2057-2063.
Dendooven, L., and Anderson, J. M. 1994. Dynamics of reduction enzymes involved in the denitrification process in pasture soil. Soil Biology & Biochemistry 26, 1501-1506.
Dendooven, L., Splatt, P., Anderson, J. M. and Scholefield, D. 1994. Kinetics of the denitrification process in a soil under permanent pasture. Soil Biology & Biochemistry 26, 361-370.
Firestone, M. K. and Davidson, E. A. 1989. Microbiological basis of NO and N2O production and consumption in soil.
In "Exchange of trace gases between terrestrial ecosystems and the atmosphere" (M. O. Andreae and D. S. Schimel, eds.), pp. 7-21. John Wiley & Sons, New York.
Focht, D. D. 1974. The effect of temperature, pH, and aeration on the production of nitrous oxide and gaseous nitrogen
- a zero order kinetic model. Soil Science 118, 173-179.
Focht, D. D. and Verstraete, E. 1977. Biochemical ecology of nitrification and denitrification. In "Advances in Microbial Ecology" (M. Alexander, ed.), Vol. 1, pp. 135-214. Plenum Press, New York.
Galloway, J. N. and Cowling, E. B. 2002. Reactive nitrogen and the world: 200 years of change. Ambio 31, 64-71.
Greenwood, D. J. and Goodman, D. 1964. Oxygen diffusion and aerobic respiration in soil spheres. Journal of the Science of Food and Agriculture 15, 579-588.
Groffman, P. M. 1991. Ecology of nitrification and denitrification in soil evaluated at scales relevant to atmospheric chemistry. In "Microbial production and consumption of greenhouse gases: methane, nitrogen oxides and halomethanes" (J. E. Rogers and W. B. Whitman, eds.), pp. 201-217. American Society for Microbiology, Washington, D.C.
Groffman, P. M., Altabet, M. A., Böhlke, J. K., Butterbach-Bahl, K., David, M. B., Firestone, M. K., Giblin, A. E., Kana, T. M., Nielsen, L. P. and Voytek, M. A. 2006. Methods for measuring denitrification diverse approaches to a difficult problem. Ecological Applications 16, 2091-2122.
Groffman, P. M., Tiedje, J. M., Robertson, G. P. and Christensen, S. 1988. Denitrification at different temporal and geographical scales: proximal and distal controls. In "Advances in nitrogen cycling in agricultural ecosystems" (J. R.
Wilson, ed.), pp. 174-192. CAB International, Wallingford.
Hall, E. K., Maixner, F., Franklin, O., Daims, H., Richter, A. and Battin, T. 2011. Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches. Ecosystems 14, 261-273.
Jones, D. L., Shannon, D., Murphy, D. V. and Farrar, J. 2004. Role of dissolved organic nitrogen (DON) in soil N cycling in grassland soils. Soil Biology & Biochemistry 36, 749-756.
Knops, J. M. H., Bradley, K. L. and Wedin, D. A. 2002. Mechanisms of plant-species impacts on ecosystem nitrogen cycling. Ecology Letters 5, 454-466.
Knowles, R. 1982. Denitrification. Microbiological Reviews 46, 43-70.
Kohl, D. H., Vithayathil, F., Whitlow, P., Shearer, G. and Chien, S. H. 1976. Denitrificaiton kinetics in soil systems: the significance of good fits of data to mathematical forms. Soil Science Society of America Journal 40, 249-253.
Kool, D. M., Dolfing, J., Wrage, N. and van Groenigen, J. W. 2011. Nitrifier denitrification as a distinct and significant source of nitrous oxide from soil. Soil Biology & Biochemistry 43, 174-178.
Laudelout, H., Germain, L., Chabalier, P. F. and Chiang, C. N. 1977. Computer simulation of loss of fertilizer nitrogen through chemical decomposition of nitrite. Journal of Soil Science 28, 329-339.
Laughlin, R. J. and Stevens, R. J. 2002. Evidence for fungal dominance of denitrification and codenitrification in a grassland soil. Soil Science Society of America Journal 66, 1540-1548.
Li, C., Frolking, S. and Frolking, T. A. 1992. A model of nitrous oxide evolution from soil driven by rainfall events: 1.
model structure and sensitivity. Journal of Geophysical Research 97, 9759-9776.
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Liu, B., Mørkved, P. T., Frostegård, Å. and Bakken, L. R. 2010. Denitrification gene pools, transcriptionand kinetics of NO,N2O and N2 productionas affected bysoil pH. FEMS Microbiology Ecology 72, 407-417.
Manzoni, S., Jackson, R. B., Trofymow, J. A. and Porporato, A. 2008. The global stoichiometery of litter nitrogen mineralization. Science 321, 684-686.
McCarty, G. W. and Bremner, J. M. 1993. Factors affecting the availabiltiy of organic carbon for denitrification of nitrate in subsoils. Biology and Fertility of Soils 15, 132-136.
McElwain, D. L. S. 1978. A re-examination of oxygen diffusion in a spherical cells with Michaelis-Menten oxygen uptake kinetics. Journal of Theoretical Biology 71, 255-263.
McLaren, A. D. 1970. Temporal and vectorial reactions of nitrogen in soil: a review. Canadian Journal of Soil Science 50, 97-109.
Miller, M. N., Zebarth, B. J., Dandie, C. E., Burton, D. L., Goyer, C., and Trevors, J. T. 2009. Denitrifier community dynamics in soil aggregates under permanent grassland and arable cropping systems. Soil Science Society of America Journal 73, 1843-1851.
Molina, J. A. E., Clapp, C. E., Shaffer, M. J., Chichester, F. W. and Larson, W. E. 1983. NCSOIL, A model of nitrogen and carbon transformations in soil: sescription, calibration, and behavior. Soil Science Society of America Journal 47, 85-91.
Morley, N. and Baggs, E. M. 2010. Carbon and oxygen controls on N2O and N2 production during nitrate reduction.
Soil Biology & Biochemistry 42, 1864-1871.
Morozkina, E. V. and Kurakov, A. V. 2007. Dissimilatory nitrate reduction in fungi under conditions of hypoxia and anoxia: a review. Applied Biochemistry and Microbiology 43, 544-549.
Myrold, D. D., and Tiedje, J. M. 1985a. Diffusional constraints on denitrification in soil. Soil Science Society of America Journal 49, 651-657.
Myrold, D. D., and Tiedje, J. M. 1985b. Establishment of denitrification capacity in soil: effects of carbon, nitrate and moisture. Soil Biology & Biochemistry 17, 819-822.
Nõmmik, H. 1956. Investigations on denitrification in soil. Acta Agriculturæ Scandinavica 6, 195-228.
Nunan, N., Wu, K., Young, I. M., Crawford, J. W. and Ritz, K. 2002. In situ spatial patterns of soil bacterial poplulataions, mapped at multiple scales, in an arable land. Microbial Ecology 44, 296-305.
Osler, G. H. R. and Sommerkorn, M. 2007. Toward a complete soil C and N cycle: incorporating the soil fauna.
Ecology 88, 1611-1621.
Parkin, T. B. 1987. Soil microsite as a source of denitrification variabilitiy. Soil Science Society of America Journal 51, 1194-1199.
Parton, W., Silver, W. L., Burke, I. C., Grassens, L., Harmon, M. E., Currie, W. S., King, J. Y., Adair, E. C., Brandt, L.
A., Hart, S. C., and Fasth, B. 2007. Global-scale similarities in nitrogen release patterns during long-term decomposition. Science 315, 361-364.
Parton, W. J., Schimel, D. S., Cole, C. V. and Ojima, D. S. 1987. Analysis of factors controlling soil organic matter levels in great plains grasslands. Soil Science Society of America Journal 51, 1173-1179.
Payne, W. J. 1973. Reduction of nitrogenous oxides by microorganisms. Bacteriological Reviews 37, 409-452.
Philippot, L. 2005. Tracking nitrate reducers and denitrifiers in the environment. Biochemical Society Transactions 33, 200-204.
Philippot, L., Andert, J., Jones, C. M., Bru, D. and Hallin, S. 2011. Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil. Global Change Biology 17, 1497-1504.
Philippot, L., Čuhel, J., Saby, P. A., Chèneby, D., Chroňáková, A., Bru, D., Arrouays, D., Martin-Laurent, F. and Šimek, M. 2009. Mapping field-scale spatial patterns of size and activity of the denitrifier community. Environmental Microbiology 11, 1518-1526.
Rastetter, E. B., Ågren, G. I. and Shaver, G. R. 1997. Responses of N-limited ecosystems to increased CO2:a balancednutrition, coupled-element-cycles model. Ecological Applications 7, 444-460.
Robertson, L. A. and Kuenen, J. G. 1984. Aerobic denitrification - old wine in new bottles? Antonie van Leeuwenhoek 50, 525-544.
Robertson, L. A. and Kuenen, J. G. 1990. Physiological and ecological aspects of aerobic denitrification. In "Denitrification in soil and sediment" (N. P. Revsbech and J. Sørensen, eds.), pp. 91-104. Plenum Press, New York.
Rütting, T., Boeckx, P., Müller, C. and Klemedtsson, L. 2011. Assessment of the importance of dissimilatory nitrate reduction to ammonium for the terrestrial nitrogen cycle. Biogeosciences 8, 1779-1791.
Sanderman, J. and Amundson, R. 2003. Biogeochemistry of decomposition and detrital processing. In "Biogeochemistry" (W. H. Schlesinger, ed.), Vol. 8, pp. 350-419. Elsevier, Amsterdam.
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Sexstone, A. J., Revsbech, N. P., Parkin, T. B. and Tiedje, J. M. 1985. Direct Measurement of Oxygen Profiles and Denitrification Rates in Soil Aggregates. Soil Science Society of America Journal 49, 645-651.
Šimek, M. and Cooper, J. E. 2002. The influence of soil pH on denitrification: progress towards the understanding of this interaction over the last 50 years. European Journal of Soil Science 53, 345-354.
Spott, O., Russow, R. and Stange, C. F. 2011. Formation of hybrid N2O and hybrid N2 due to codenitrification: First review of a barely considered process of microbially mediated N-nitrosation. Soil Biology & Biochemistry 43, 1995Stevens, R. J., Laughlin, R. J., and Malone, J. P. 1998. Soil pH affects the processes reducing nitrate to nitrous oxide and di-nitrogen. Soil Biology & Biochemistry 30, 1119-1126.
Thomsen, J. K., Geest, T., and Cox, R. P. 1994. Mass spectrometer studies of the effect of pH on the accumulatin of intermediates in denitrification by Paracoccus denitrificans. Applied and Environmental Microbiology 60, 536-541.
Tiedje, J. M. 1988. Ecology of denitrification and dissimilatory nitrate reduction to ammonium. In "Biology of anaerobic microorganisms" (A. J. B. Zehnder, ed.), pp. 179-244. John Wiley & Sons, New York.
Tiedje, J. M., Sexstone, A. J., Myrold, D. D. and Robinson, J. A. 1982. Denitrification: ecological niches, competition and survival. Antonie van Leeuwenhoek 48, 569-583.
Uchida, Y., Clough, T. J., Kelliher, F. M., Hunt, J. E. and Sherlock, R. R. 2011. Effects of bovine urine, plants and temperature on N2O and CO2 emissions from a sub-tropical soil. Plant and Soil 345, 171-186.
van der Ploeg, R. R., Böhm, W. and Kirkham, M. B. 1999. On the origin of the theory of mineral nutrition of plants and the law of the minimum. Soil Science Society of America Journal 63, 1055-1062.
Van Kessel, C., Clough, T. J. and Van Groenigen, J. W. 2009. Dissolved organic nitrogen: an overlooked pathway of nitrogen loss from agricultural systems? Journal of Environmental Quality 38, 393-401.
Wrage, N., Velthof, G. L., van Beusichem, M. L. and Oenema, O. 2001. Role of nitrifier denitrification in the production of nitrous oxide. Soil Biology & Biochemistry 33, 1723-1732.
Zak, D. R., Holmes, W. E., White, D. C., Peacock, A. D. and Tilman, D. 2003. Plant diversity, soil microbial communities, and ecosystem function: are there any links? Ecology 84, 2042-2050.
Zumft, W. G. 1997. Cell biology and molecular basis of denitrification. Microbiology and Molecular Biology Reviews 61, 533-616.
Can molecular microbial ecology provide new understanding of soil nitrogen dynamics?
Firestone, M., Blazewicz, S. bPetersen, D.G., and 3Placella, S.
a University of California, Berkeley CA USA b Aarhus University.
c Michigan State University
1. Introduction The past several decades has seen rapid and profound advances in methodology capable of identifying and characterizing at a molecular level the complex communities that mediate nitrogen transformations in soil as well as their genetic capacities to carry out N processes.
Molecular approaches to identifying and quantifying the genes that code for enzymes mediating the N cycle have given us a capacity to assess the relationships among genes, environmental controllers, and rates of processes (e.g. Petersen et al., 2012)
Figure 1. Nitrogen cycle diagram including gene notations for some relevant N transformations It seems that every two to three years there is renewed promise that “soon” there will be a revolution in our understanding of the microbial bases of nitrogen cycling that will transform the substantial knowledge that has accrued over the past century.