Abstract
Soil contains the largest terrestrial pool of organic matter, and the cycling of organic carbon in soils plays a crucial role in controlling atmospheric carbon dioxide (CO2) and global climate change. Although considerable progress has been made in previous modeling studies on the fate of soil organic matter (SOM), only a few models used a process-based approach for investigating these strongly coupled and complex soil systems, which involve SOM oxidation, transient water flow, and mass transport processes in aqueous and gaseous phases. Typically, physically based models for water flow, as well as solute and gas transport, are not coupled with state-of-the-art SOM degradation models. Reactive transport models (RTMs) provide a flexible framework for implementing different SOM degradation concepts and integrating biogeochemical processes with water flow and mass transport. Given the complex nature of carbon cycling in soils coupled with flow and mass transport, code intercomparison using well-defined benchmarks is in many cases the only practical method of model verification. The benchmark presented in this manuscript focuses on SOM oxidation under variably saturated flow conditions. The benchmark consists of three problems characterized by increasing complexity. The problems were solved using two different reactive transport codes, namely HP1 and MIN3P-THCm. The first supporting problem introduces a batch-type simulation to assess kinetic networks of SOM degradation. In the second supporting problem, transient water flow, solute transport, gas generation, and diffusive gas transport are considered. The principal problem combines the kinetic networks of SOM degradation with reactive transport under variably saturated flow conditions, including CO2 transport from soils to the atmosphere. Simulation results for the benchmark problems demonstrate an overall excellent agreement between the two codes, building confidence in the ability of RTMs to simulate complex C-cycling in dynamic environments.
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References
Paul, E. A.: Soil Microbiology, Ecology and Biochemistry, 3rd Ed. Academic Press, M.A. (2007).
Jenkinson, D.S., Adams, D.E., Wild, A.: Model estimates of CO2 emissions from soil in response to global warming. Nature. 351, 304–306 (1991)
Dungait, J.A.J., Hopkins, D.W., Gregory, A.S., Whitmore, A.P.: Soil organic matter turnover is governed by accessibility not recalcitrance. Glob Chang Biol. 18, 1781–1796 (2012)
Campbell, E.E. and Paustian, K.: Current developments in soil organic matter modeling and the expansion of model applications: a review. Environ Res Lett 10. (2015).
Vereecken, H., et al.: Modeling soil processes: review, key challenges, and new perspectives. Vadose Zone J 15(5), (2016).
Adair, E., Parton, W., Del Grosso, S., Silver, W., Harmon, M., Hall, S., Burke, I., Hart, S.: Simple three-pool model accurately describes patterns of long-term litter degradation in diverse climates. Glob Change Biol. 14, 2636–2660 (2008)
Manzoni, S., Porporato, A.: Soil carbon and nitrogen mineralization: theory and models across scales. Soil Biol Biochem. 41, 1355–1379 (2009)
Jenkinson, D.: The turnover of organic carbon and nitrogen in soil. Philos Trans R Soc Lond B. 329, 361–368 (1990)
Porporato, A., D’Odorico, P., Laio, F., Rodriguez-Iturbe, I.: Hydrologic controls on soil carbon and nitrogen cycles. I. Modeling scheme. Adv Water Resour. 26, 45–58 (2003)
Bosatta, E., Ågren, G.I.: Theoretical-analysis of degradation of heterogeneous substrates. Soil Biol Biochem. 17, 601–610 (1985)
Sierra, C.A., Müller, M., Trumbore, S.E.: Models of soil organic matter degradation: the SoilR package, version 1.0. Geosci Model Dev. 5, 1045–1060 (2012)
Wutzler, T., Reichstein, M.: Colimitation of decomposition by substrate and decomposers—a comparison of model formulations. Biogeosciences. 5, 749–759 (2008)
Grant, R.F., Juma, N.G., McGill, W.B.: Simulation of carbon and nitrogen transformations in soil: microbial biomass and metabolic products. Soil Biol Biochem. 25, 1331–1338 (1993)
Herbst, M., Hellebrand, H.J., Bauer, J., Huisman, J.A., Simunek, J., Weihermuller, L., Graf, A., Vanderborght, J., Vereecken, H.: Multiyear heterotrophic soil respiration: evaluation of a coupled CO2 transport and carbon turnover model. Ecol Model. 214, 271–283 (2008)
Del Grosso, S.J., Parton, W.J., Mosier, A.R., Ojima, D.S., Kulmala, A.E., Phongpan, S.: General model for N2O and N2 gas emissions from soils due to denitrification. Glob Biogeochem Cycles. 14, 1045–1060 (2000)
Parton, W.J., Holland, E.A., Del Grosso, S.J., Hartman, M.D., Martin, R.E., Mosier, A.R., Ojima, D.S., Schimel, D.S.: Generalized model for NOx and N2O emissions from soils. J Geophys Res. 106, 17403–17417 (2001)
Braakhekke, M.C., Beer, C., Hoosbeek, M.R., Reichstein, M., Kruijt, B., Schrumpf, M., Kabat, P.: SOMPROF: A vertically explicit soil organic matter model. Ecol Model. 222(10), 1712–1730 (2011)
Fang, C., Moncrieff, J.B.: A model for soil CO2 production and transport 1: model development. Agr Forest Meteorol 95, 225–236 (1999)
Jassal, R.S., Black, T.A., Drewitt, G.B., Novak, M.D., Gaumont-Guay, D., Nesic, Z.: A model of the production and transport of CO2 in soil: predicting soil CO2 concentrations and CO2 efflux from a forest floor. Agric For Meteorol. 124, 219–236 (2004)
Šimůnek, J., Suarez, D.L.: Modeling of carbon dioxide transport and production in soil, 1, Model development. Water Resour Res. 29(2), 487–497 (1993)
Pansu, M., Sarmiento, L., Rujano, M.A., Ablan, M., Acevedo, D., Bottner, P.: Modeling organic transformations by microorganisms of soils in six contrasting ecosystems: validation of the MOMOS model. Glob Biogeochem Cycles 24 (2010).
Batlle-Aguilar, J., Brovelli, A., Porporato, A., Barry, D.A.: Modelling soil carbon and nitrogen cycles during land use change. A review. Agron Sustain Dev. 31(2), 251–274 (2011)
Fontaine, S., Barot, S.: Size and functional diversity of microbe populations control plant persistence and long-term soil carbon accumulation. Ecol Lett. 8, 1075–1087 (2005)
Thaysen, E.M., Jacques, D., Jessen, S., Andersen, C.E., Laloy, E., Ambus, P., Postma, D., Jakobsen, I.: Inorganic carbon fluxes across the vadose zone of planted and unplanted soil mesocosms. Biogeosciences. 11, 7179–7192 (2014)
Jacques, D., Šimůnek, J., Mallants, D., van Genuchten, M.T.: Modeling coupled hydrologic and chemical processes: long-term uranium transport following phosphorus fertilization. Vadose Zone J. 7, 698–711 (2008)
Jacques, D., Šimůnek, J., Mallants, D., van Genuchten, M.T.: The HPx software for multicomponent reactive transport during variably-saturated flow: recent developments and applications. J Hydrol Hydromech 66, 211–226 (2018)
Steefel, C.I., Yabusaki, S.B., Mayer, K.U.: Reactive transport benchmarks for subsurface environmental simulation. Comput Geosci. 19, 439–443 (2015)
Carrayrou, J., Hoffmann, J., Knabner, P., Krautle, S., de Dieuleveult, C., Erhel, J., van der Lee, J., Lagneau, V., Mayer, K.U., Macquarrie, K.T.B.: Comparison of numerical methods for simulating strongly nonlinear and heterogeneous reactive transport problems-the MoMaS benchmark case. Comput Geosci. 14(3), 483–502 (2010)
Mayer, K.U., Frind, E.O., Blowes, D.W.: Multicomponent reactive transport modelling in variably saturated porous media using a generalized formulation for kinetically controlled reactions. Water Resour Res. 37, 1174 (2002)
Bea, S.A., Wilson, S.A., Mayer, K.U., Dipple, G.M., Power, I.M., Gamazo, P.: reactive transport modeling of natural carbon sequestration in ultramafic mine tailings. Vadose Zone J. 11, 1–17 (2012)
Steefel, C.I., Appelo, C.A.J., Arora, B., Jacques, D., Kalbacher, T., Kolditz, O., Lagneau, V., Lichtner, P.C., Mayer, K.U., Meeussen, J.C.L., Molins, S., Moulton, D., Shao, H., Simunek, J., Spycher, N., Yabusaki, S.B., Yeh, G.T.: Reactive transport codes for subsurface environmental simulation. Comput Geosci. 19, 445–478 (2015)
Manzoni, S., Porporato, A.: Theoretical analysis of nonlinearities and feedbacks in soil carbon and nitrogen cycles. Soil Biol Biochem. 39, 1542–1556 (2007)
Moore, W. J.: Physical Chemistry, 4th Ed. Prentice-Hall, N. J (1972).
Millington, R.J.: Gas diffusion in porous media. Science. 130, 100–102 (1959)
van Genuchten, M.T.: Closed-form equation for predicting the hydraulic conductivity of unsaturated soils. Soil Sci Soc Am J. 44, 892–898 (1980)
Mayer, K.U., Alt-Ep**, P., Jacques, D., Arora, B., Steefel, C.I.: Benchmark problems for reactive transport modeling of the generation and attenuation of acid rock drainage. Comput Geosci. 19, 599–611 (2015)
Gérard, F., Blitz-Frayret, C., Hinsinger, P., Pagès, L.: Modelling the interactions between root system architecture, root functions and reactive transport processes in soil. Plant Soil. 413, 161–180 (2017)
Nowack, B., Mayer, K.U., Oswald, S.E., van Beinum, W., Appelo, C.A.J., Jacques, D., Seuntjens, P., Gérard, F., Jaillard, B., Schnepf, A., Roose, T.: Verification and intercomparison of reactive transport codes to describe root-uptake. Plant Soil. 14, 305–321 (2006)
Leterme, B., Blanc, P., Jacques, D.: A reactive transport model for mercury fate in soil—application to different anthropogenic pollution sources. Environ Sci Pollut Res. 21(21), 12279–12293 (2014)
Kuka, K., Franko, U., Ruhlmann, J.: Modelling the impact of pore space distribution on carbon turnover. Ecol Model. 208, 295–306 (2007)
Keiluweit, M., Nico, P.S., Kleber, M., Fendorf, S.: Are oxygen limitations under recognized regulators of organic carbon turnover in upland soils? Biogeoch. 127, 157–171 (2016)
Funding
Funding for this research was provided by Agriculture and Agri-Food Canada through the project Valuing diversity in agro-ecosystems: The interplay of natural habitat, integrated BMPs, and field crop** systems on GHG emissions and carbon stocks, supporting M. Jia with a Research Assistantship and through an NSERC (Natural Sciences and Engineering Research Council of Canada) discovery grant held by K. Ulrich Mayer.
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Jia, M., Jacques, D., Gérard, F. et al. A benchmark for soil organic matter degradation under variably saturated flow conditions. Comput Geosci 25, 1359–1377 (2021). https://doi.org/10.1007/s10596-019-09862-3
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DOI: https://doi.org/10.1007/s10596-019-09862-3