Modeling soil moisture and oxygen effects on soil biogeochemical cycles including dissimilatory nitrate reduction to ammonium (DNRA)

Hillel, 1998

Schlesinger, 1997

Moyano, 2012, The moisture response of soil heterotrophic respiration: interaction with soil properties, Biogeosciences, 9, 1173, 10.5194/bg-9-1173-2012

Or, 2007, Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review, Adv Water Resour, 30, 1505, 10.1016/j.advwatres.2006.05.025

Schimel, 2007, Microbial stress-response physiology and its implications for ecosystem function, Ecology, 88, 1386, 10.1890/06-0219

Manzoni, 2012, Responses of soil microbial communities to water-stress: results from a meta-analysis, Ecology, 93, 930, 10.1890/11-0026.1

Skopp, 1990, Steady-state aerobic microbial activity as a function of soil water content, Soil Sci Soc Am J, 54, 1619, 10.2136/sssaj1990.03615995005400060018x

Ilstedt, 2000, Optimum soil water for soil respiration before and after amendment with glucose in humid tropical acrisols and a boreal mor layer, Soil Biol Biochem, 32, 1591, 10.1016/S0038-0717(00)00073-0

Linn, 1984, Effect of water-filled pore space on carbon dioxide and nitrous oxide production in tilled and nontilled soils, Soil Sci Soc Am J, 48, 1267, 10.2136/sssaj1984.03615995004800060013x

Liptzin, 2010, Temporal dynamics in soil oxygen and greenhouse gases in two humid tropical forests, Ecosystems, 14, 171, 10.1007/s10021-010-9402-x

Rubol, 2012, Hydrologic control on redox and nitrogen dynamics in a peatland soil, Sci Total Environ, 432, 37, 10.1016/j.scitotenv.2012.05.073

Butterbach-Bahl, 2013, Nitrous oxide emissions from soils: how well do we understand the processes and their controls?, Philos Trans R Soc London Ser B Biol Sci, 368, 20130122, 10.1098/rstb.2013.0122

Conrad, 1996, Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO), Microbiol Mol Biol Rev, 60, 609

Khdyer, 1983, Nitrification and denitrification of nitrogen fertilizers in a soil column, Soil Sci Soc Am J, 47, 1134, 10.2136/sssaj1983.03615995004700060015x

Silver, 2001, Dissimilatory nitrate reduction to ammonium in upland tropical forest soils, Ecology, 82, 2410, 10.1890/0012-9658(2001)082[2410:DNRTAI]2.0.CO;2

Rütting, 2011, Assessment of the importance of dissimilatory nitrate reduction to ammonium for the terrestrial nitrogen cycle, Biogeosci Discuss, 8, 1169, 10.5194/bgd-8-1169-2011

Silver, 2005, Nitrogen cycling in tropical plantation forests: potential controls on nitrogen retention, Ecol Appl, 15, 1604, 10.1890/04-1322

Manzoni, 2009, Soil carbon and nitrogen mineralization: Theory and models across scales, Soil Biol Biochem, 41, 1355, 10.1016/j.soilbio.2009.02.031

Wang, 2012, A review on parameterization and uncertainty in modeling greenhouse gas emissions from soil, Geoderma, 170, 206, 10.1016/j.geoderma.2011.11.009

Sanchez-Vila, 2013, An analytical solution to study substrate-microbial dynamics in soils, Adv Water Resour, 54, 181, 10.1016/j.advwatres.2013.02.004

Li, 1992, A model of nitrous oxide evolution from soil driven by rainfall events: 2 model applications, J Geophys Res, 97, 9777, 10.1029/92JD00510

Venterea, 2000, Nitric and nitrous oxide emissions following fertilizer application to agricultural soil: biotic and abiotic mechanisms and kinetics, J Geophys Res Atmos, 105, 15117, 10.1029/2000JD900025

Kaharabata, 2003, Comparing measured and expert-N predicted N2O emissions from conventional till and no till corn treatments, Nutr Cycling Agroecosyst, 66, 107, 10.1023/A:1023978830307

Wang, 2013, Evaluation of a soil greenhouse gas emission model based on Bayesian inference and MCMC: model uncertainty, Ecol Modell, 3, 97, 10.1016/j.ecolmodel.2012.09.010

Maggi, 2008, A mechanistic treatment of the dominant soil nitrogen cycling processes: model development, testing, and application, J Geophys Res Biogeosci, 113, G2, 10.1029/2007JG000578

Groffman, 2006, Methods for measuring denitrification: diverse approaches to a difficult problem, Ecol Appl, 16, 2091, 10.1890/1051-0761(2006)016[2091:MFMDDA]2.0.CO;2

Groffman, 2009, Challenges to incorporating spatially and temporally explicit phenomena (hotspots and hot moments) in denitrification models, Biogeochemistry, 93, 49, 10.1007/s10533-008-9277-5

Porporato, 2003, Hydrologic controls on soil carbon and nitrogen cycles: I modeling scheme, Adv Water Resour, 26, 45, 10.1016/S0309-1708(02)00094-5

El Hassan, 1985, Kinetics of denitrifying growth by fast-growing cowpea rhizobia, Appl Environ Microbiol, 49, 517, 10.1128/AEM.49.3.517-521.1985

Reddy, 1975, Effect of alternate aerobic and anaerobic conditions on redox potential, organic matter decomposition and nitrogen loss in a flooded soil, Soil Biol Biochem, 7, 87, 10.1016/0038-0717(75)90004-8

Sylvia, 1999

Kapralek, 1982, Two sites of oxygen control in induced synthesis of respiratory nitrate reductase in Escherichia coli, J Bacteriol, 149, 1142, 10.1128/JB.149.3.1142-1145.1982

Giles, 2012, Soil nitrate reducing processes – drivers, mechanisms for spatial variation, and significance for nitrous oxide production, Front Microbiol, 3, 407, 10.3389/fmicb.2012.00407

Rodríguez-Iturbe, 2004

Wrage N, Kool DM, Oenema O, Van Groenigen JW. Nitrifier denitrification: what we know, don’t know and thought we knew 2007. In: ASA–CSSA–SSSA international annual meetings, a Century of Integrated Crops, Soils & Environment, New Orleans, Louisiana

Venterea, 2007, Nitrite-driven nitrous oxide production under aerobic soil conditions: kinetics and biochemical control, Global Change Biol, 13, 1798, 10.1111/j.1365-2486.2007.01389.x

Kadlec, 2009

Baggs, 2011, Soil microbial sources of nitrous oxide: recent advances in knowledge, emerging challenges and future direction, Curr Opin Environ Sustainability, 3, 321, 10.1016/j.cosust.2011.08.011

Schmidt, 2011, Constraining the conditions conducive to dissimilatory nitrate reduction to ammonium in temperate arable soils, Soil Biol Biochem, 43, 1607, 10.1016/j.soilbio.2011.02.015

Simunek, 1993, Modeling of carbon dioxide transport and production in soil 1. Model development, Water Resour Res, 29, 487, 10.1029/92WR02225

Stumm, 1970

Hamamoto, 2010, Excluded-volume expansion of Archie’s law for gas and solute diffusivities and electrical and thermal conductivities in variably saturated porous media, Water Resour Res, 46, W06514, 10.1029/2009WR008424

Olesen, 2001, Tortuosity, diffusivity, and permeability in the soil liquid and gaseous phases, Soil Sci Soc Am J, 65, 613, 10.2136/sssaj2001.1585

Vereecken, 2010, Using pedotransfer functions to estimate the van Genuchten–Mualem soil hydraulic properties: a review, Vadose Zone J, 9, 795, 10.2136/vzj2010.0045

Luckner, 1989, A consistent set of parametric models for the two-phase flow of immiscible fluids in the subsurface, Water Resour Res, 25, 2187, 10.1029/WR025i010p02187

Brovelli, 2012, Analysis of carbon and nitrogen dynamics in riparian soils: model development, Sci Total Environ, 429, 231, 10.1016/j.scitotenv.2012.04.027

Laio, 2001, Plants in water-controlled ecosystems: active role in hydrologic processes and response to water stress: II. Probabilistic soil moisture dynamics, Adv Water Resour, 24, 707, 10.1016/S0309-1708(01)00005-7

Papendick, 1966, Transient-state oxygen diffusion in soil: II. A case when rate of oxygen consumption varies with time, Soil Sci, 102, 10.1097/00010694-196610000-00002

Maggi, 2008, A mechanistic treatment of the dominant soil nitrogen cycling processes: model development, testing, and application, J Geophys Res Biogeosci, 113, G02016, 10.1029/2007JG000578

Šimůnek, 1993, Modeling of carbon dioxide transport and production in soil: 1. Model development, Water Resour Res, 10.1029/92WR02225

Saltelli, 2008

Rubin, 2003

Ye, 2008, On model selection criteria in multimodel analysis, Water Resour Res, 44, 10.1029/2008WR006803

Porporato, 2004, Soil water balance and ecosystem response to climate change, Am Nat, 164, 625, 10.1086/424970

Moyano, 2013, Responses of soil heterotrophic respiration to moisture availability: an exploration of processes and models, Soil Biol Biochem, 59, 72, 10.1016/j.soilbio.2013.01.002

Maag, 1996, Nitrous oxide emission by nitrification and denitrification in different soil types and at different soil moisture contents and temperatures, Appl Soil Ecol, 4, 5, 10.1016/0929-1393(96)00106-0

Burgin, 2012, Soil O2 controls denitrification rates and N2O yield in a riparian wetland, J Geophys Res, 117, G01010, 10.1029/2011JG001799

Khalil, 2004, Nitrous oxide production by nitrification and denitrification in soil aggregates as affected by O2 concentration, Soil Biol Biochem, 36, 687, 10.1016/j.soilbio.2004.01.004

Steinweg, 2012, Modeling the effects of temperature and moisture on soil enzyme activity: linking laboratory assays to continuous field data, Soil Biol Biochem, 55, 85, 10.1016/j.soilbio.2012.06.015

Groffman, 1991, Replationships between denitrification, CO2 production and air-filled porosity in soils of different texture and drainage, Soil Biol Biochem, 23, 299, 10.1016/0038-0717(91)90067-T

Thomas, 1994, Effects of oxygen, pH and nitrate concentration on denitrification by Pseudomonas species, FEMS Microbiol Lett, 118, 181, 10.1111/j.1574-6968.1994.tb06823.x

Burgin, 2007, Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways, Front Ecol Environ, 5, 89, 10.1890/1540-9295(2007)5[89:HWOTRO]2.0.CO;2

Kirschbaum, 1995, The temperature dependence of soil organic matter decomposition, and the effect of global warming on soil organic C storage, Soil Biol Biochem, 27, 753, 10.1016/0038-0717(94)00242-S

Schindlbacher, 2004, Effects of soil moisture and temperature on NO, NO2, and N2O emissions from European forest soils, J Geophys Res, 109, 10.1029/2004JD004590

Rodriguez-Iturbe, 1999, Probabilistic modelling of water balance at a point: the role of climate, soil and vegetation, Proc R Soc London Ser A Math Phys Eng Sci, 455, 3789, 10.1098/rspa.1999.0477

Clapp, 1978, Empirical equations for some soil hydraulic properties, Water Resour Res, 14, 601, 10.1029/WR014i004p00601

Henze, 2000

Bonin, 1989, Effects of oxygen on each step of denitrification on Pseudomonas nautica, Can J Microbiol, 35, 1061, 10.1139/m89-177

Ratkowsky, 1982, Relationship between temperature and growth rate of bacterial cultures, J Bacteriol, 149, 1, 10.1128/JB.149.1.1-5.1982

Daly, 2009, The effects of elevated atmospheric CO2 and nitrogen amendments on subsurface CO2 production and concentration dynamics in a maturing pine forest, Biogeochemistry, 94, 271, 10.1007/s10533-009-9327-7

Sander R. Compilation of Henry’s law constants for inorganic and organic species of potential importance in environmental chemistry. Max-Planck Institute of Chemistry, Air Chemistry Department; 1999.

Fagerbakke, 1996, Aquat Microb Ecol, 10, 15, 10.3354/ame010015

Stumm, 1996

Pritchard, 1982, Diffusion of coefficients of carbon dioxide, nitrous oxide, ethylene and ethane in air and their measurement, J Soil Sci, 33, 175, 10.1111/j.1365-2389.1982.tb01757.x

Kindred, 1989, Contaminant transport and biodegradation: 2. Conceptual model and test simulations, Water Resour Res, 25, 1149, 10.1029/WR025i006p01149

Šimůnek J, Sejna M, Van Genuchten MT. The HYDRUS-1D software package for simulating the one-dimensional movement of water, heat, and multiple solutes in variably-saturated media. University of California, Riverside, Research Reports, 2005. p. 240.

Davis, 2008, Denitrification and nitrate consumption in an herbaceous riparian area and perennial ryegrass seed cropping system, Soil Sci Soc Am J, 72, 1299, 10.2136/sssaj2007.0279

Lawrence, 2009, Does adding microbial mechanisms of decomposition improve soil organic matter models? A comparison of four models using data from a pulsed rewetting experiment, Soil Biol Biochem, 41, 1923, 10.1016/j.soilbio.2009.06.016

Evans, 2011, Nitrogen mineralization in riparian soils along a river continuum within a multi-land-use basin, Soil Sci Soc Am J, 75, 719, 10.2136/sssaj2010.0162

Groffman, 2000, Nitrous oxide production in riparian zones and its importance to national emission inventories, Chemosphere Global Change Sci, 2, 291, 10.1016/S1465-9972(00)00018-0