A robust initialization method for accurate soil organic carbon simulations

Abstract. Changes in soil organic carbon (SOC) stocks are a major
source of uncertainty for the evolution of atmospheric CO2
concentration during the 21st century. They are usually simulated by
models dividing SOC into conceptual pools with contrasted turnover times.
The lack of reliable methods to initialize these models, by correctly
distributing soil carbon amongst their kinetic pools, strongly limits the
accuracy of their simulations. Here, we demonstrate that PARTYSOC, a
machine-learning model based on Rock-Eval® thermal analysis,
optimally partitions the active- and stable-SOC pools of AMG, a simple and well-validated SOC dynamics model, accounting for effects of soil management
history. Furthermore, we found that initializing the SOC pool sizes of AMG
using machine learning strongly improves its accuracy when reproducing the
observed SOC dynamics in nine independent French long-term agricultural
experiments. Our results indicate that multi-compartmental models of SOC
dynamics combined with a robust initialization can simulate observed SOC
stock changes with excellent precision. We recommend exploring their
potential before a new generation of models of greater complexity becomes
operational. The approach proposed here can be easily implemented on soil
monitoring networks, paving the way towards precise predictions of SOC stock
changes over the next decades.

Topics

No keywords indexed for this article. Browse by subject →

References

89

[1]

Amelung, W., Bossio, D., de Vries, W., Kögel-Knabner, I., Lehmann, J., Amundson, R., Bol, R., Collins, C., Lal, R., Leifeld, J., Minasny, B., Pan, G., Paustian, K., Rumpel, C., Sanderman, J., van Groenigen, J. W., Mooney, S., van Wesemael, B., Wander, M., and Chabbi, A.: Towards a global-scale soil climate mitigation strategy, Nat. Commun., 11, 1–10, https://doi.org/10.1038/s41467-020-18887-7, 2020. 10.1038/s41467-020-18887-7

[2]

Andriulo, A. E., Mary, B., and Guerif, J.: Modelling soil carbon dynamics with various cropping sequences on the rolling pampas, Agronomie, 19, 365–377, 1999. 10.1051/agro:19990504

[3]

Aphalo, P. J.: Learn R as you learnt your mother tongue, Leanpub [code], available at: https://leanpub.com/learnr (last access: 19 January 2022), 2016.

[4]

Bailey, V. L., Bond-Lamberty, B., DeAngelis, K., Grandy, A. S., Hawkes, C. V., Heckman, K., Lajtha, K., Phillips, R. P., Sulman, B. N., Todd-Brown, K. E. O., and Wallenstein, M. D.: Soil carbon cycling proxies: Understanding their critical role in predicting climate change feedbacks, Glob. Chang. Biol., 24, 895–905, https://doi.org/10.1111/gcb.13926, 2018. 10.1111/gcb.13926

[5]

Baldock, J. A., Hawke, B., Sanderman, J., and Macdonald, L. M.: Predicting contents of carbon and its component fractions in Australian soils from diffuse reflectance mid-infrared spectra, Soil Res., 51, 577–595, https://doi.org/10.1071/SR13077, 2013. 10.1071/sr13077

[6]

Balesdent, J. and Arrouays, D.: Usage des terres et stockage de carbone dans les sols du territoire français. Une estimation des flux nets pour la période 1900–1999, Comptes rendus l'Académie d'Agriculture Fr., 85, 265–277, 1999.

[7]

Balesdent, J., Basile-Doelsch, I., Chadoeuf, J., Cornu, S., Derrien, D., Fekiacova, Z., and Hatté, C.: Atmosphere–soil carbon transfer as a function of soil depth, Nature, 559, 599–602, https://doi.org/10.1038/s41586-018-0328-3, 2018. 10.1038/s41586-018-0328-3

[8]

Barré, P., Montagnier, C., Chenu, C., Abbadie, L., and Velde, B.: Clay minerals as a soil potassium reservoir: Observation and quantification through X-ray diffraction, Plant Soil, 302, 213–220, https://doi.org/10.1007/s11104-007-9471-6, 2008. 10.1007/s11104-007-9471-6

[9]

Barré, P., Eglin, T., Christensen, B. T., Ciais, P., Houot, S., Kätterer, T., van Oort, F., Peylin, P., Poulton, P. R., Romanenkov, V., and Chenu, C.: Quantifying and isolating stable soil organic carbon using long-term bare fallow experiments, Biogeosciences, 7, 3839–3850, https://doi.org/10.5194/bg-7-3839-2010, 2010. 10.5194/bg-7-3839-2010

[10]

Barré, P., Plante, A. F., Cécillon, L., Lutfalla, S., Baudin, F., Bernard, S., Christensen, B. T., Eglin, T., Fernandez, J. M., Houot, S., Kätterer, T., Le Guillou, C., Macdonald, A., van Oort, F., and Chenu, C.: The energetic and chemical signatures of persistent soil organic matter, Biogeochemistry, 130, 1–12, https://doi.org/10.1007/s10533-016-0246-0, 2016. 10.1007/s10533-016-0246-0

[11]

Barthès, B. G., Brunet, D., Hien, E., Enjalric, F., Conche, S., Freschet, G. T., d'Annunzio, R., and Toucet-Louri, J.: Determining the distributions of soil carbon and nitrogen in particle size fractions using near-infrared reflectance spectrum of bulk soil samples, Soil Biol. Biochem., 40, 1533–1537, https://doi.org/10.1016/j.soilbio.2007.12.023, 2008. 10.1016/j.soilbio.2007.12.023

[12]

Baudin, F., Disnar, J. R., Aboussou, A., and Savignac, F.: Guidelines for Rock-Eval analysis of recent marine sediments, Org. Geochem., 86, 71–80, https://doi.org/10.1016/j.orggeochem.2015.06.009, 2015. 10.1016/j.orggeochem.2015.06.009

[13]

Behar, F., Beaumont, V., and De B. Penteado, H. L.: Rock-Eval 6 Technology: Performances and Developments, Oil Gas Sci. Technol., 56, 111–134, https://doi.org/10.2516/ogst:2001013, 2001. 10.2516/ogst:2001013

[14]

An approach for estimating net primary productivity and annual carbon inputs to soil for common agricultural crops in Canada

M.A. Bolinder, H.H. Janzen, E.G. Gregorich et al.

Agriculture, Ecosystems & Environment 10.1016/j.agee.2006.05.013

[15]

Bruun, S. and Jensen, L. S.: Initialisation of the soil organic matter pools of the Daisy model, Ecol. Modell., 153, 291–295, 2002. 10.1016/s0304-3800(02)00017-0

[16]

Cagnarini, C., Renella, G., Mayer, J., Hirte, J., Schulin, R., Costerousse, B., Della Marta, A., Orlandini, S., and Menichetti, L.: Multi-objective calibration of RothC using measured carbon stocks and auxiliary data of a long-term experiment in Switzerland, Eur. J. Soil Sci., 70, 819–832, https://doi.org/10.1111/ejss.12802, 2019. 10.1111/ejss.12802

[17]

Cécillon, L.: A dual response, Nat. Geosci., 14, 262–263, https://doi.org/10.1038/s41561-021-00749-6, 2021a. 10.1038/s41561-021-00749-6

[18]

Cécillon, L.: lauric-cecillon/PARTYsoc: Second version of the PARTYSOC statistical model, Zenodo [code], https://doi.org/10.5281/zenodo.4446138, 2021b.

[19]

Cécillon, L., Baudin, F., Chenu, C., Houot, S., Jolivet, R., Kätterer, T., Lutfalla, S., Macdonald, A., van Oort, F., Plante, A. F., Savignac, F., Soucémarianadin, L. N., and Barré, P.: A model based on Rock-Eval thermal analysis to quantify the size of the centennially persistent organic carbon pool in temperate soils, Biogeosciences, 15, 2835–2849, https://doi.org/10.5194/bg-15-2835-2018, 2018. 10.5194/bg-15-2835-2018

[20]

Cécillon, L., Baudin, F., Chenu, C., Christensen, B. T., Franko, U., Houot, S., Kanari, E., Kätterer, T., Merbach, I., van Oort, F., Poeplau, C., Quezada, J. C., Savignac, F., Soucémarianadin, L. N., and Barré, P.: Partitioning soil organic carbon into its centennially stable and active fractions with machine-learning models based on Rock-Eval® thermal analysis (PARTYSOCv2.0 and PARTYSOCv2.0EU), Geosci. Model Dev., 14, 3879–3898, https://doi.org/10.5194/gmd-14-3879-2021, 2021. 10.5194/gmd-14-3879-2021

[21]

Chassé, M., Luftalla, S., Cécillon, L., Baudin, F., Abiven, S., Chenu, C., and Barré, P.: Long-term bare fallow soil fractions reveal thermo-chemical properties controlling soil organic carbon dynamics, Biogeosciences, 18, 1703–1718, https://doi.org/10.5194/bg-18-1703-2021, 2021. 10.5194/bg-18-1703-2021

[22]

Modeling soil organic carbon evolution in long-term arable experiments with AMG model

Hugues Clivot, Jean-Christophe Mouny, Annie Duparque et al.

Environmental Modelling & Software 10.1016/j.envsoft.2019.04.004

[23]

Coleman, K., Jenkinson, D. S., Crocker, G. J., Grace, P. R., Klír, J., Körschens, M., Poulton, P. R., and Richter, D. D.: Simulating trends in soil organic carbon in long-term experiments using RothC-26.3, Geoderma, 81, 29–44, https://doi.org/10.1016/S0016-7061(97)00079-7, 1997. 10.1016/s0016-7061(97)00079-7

[24]

Colomb, B., Debaeke, P., Jouany, C., and Nolot, J. M.: Phosphorus management in low input stockless cropping systems: Crop and soil responses to contrasting P regimes in a 36-year experiment in southern France, Eur. J. Agron., 26, 154–165, https://doi.org/10.1016/j.eja.2006.09.004, 2007. 10.1016/j.eja.2006.09.004

[25]

Cotrufo, M. F., Ranalli, M. G., Haddix, M. L., Six, J., and Lugato, E.: Soil carbon storage informed by particulate and mineral-associated organic matter, Nat. Geosci., 12, 989–994, https://doi.org/10.1038/s41561-019-0484-6, 2019. 10.1038/s41561-019-0484-6

[26]

The global soil community and its influence on biogeochemistry

Thomas W. Crowther, Johan van den Hoogen, J. Wan et al.

Science 10.1126/science.aav0550

[27]

Dangal, S. R. S., Schwalm, C., Cavigelli, M. A., Gollany, H. T., Jin, V. L., and Sanderman, J.: Improving soil carbon estimates by linking conceptual pools against measurable carbon fractions in the DAYCENT Model Version 4.5, ESSOAR, https://doi.org/10.1002/essoar.10507190.1, 2021. 10.1002/essoar.10507190.1

[28]

Dignac, M.-F., Derrien, D., Barré, P., Barot, S., Cécillon, L., Chenu, C., Chevallier, T., Freschet, G. T., Garnier, P., Guenet, B., Hedde, M., Klumpp, K., Lashermes, G., Maron, P.-A., Nunan, N., Roumet, C., and Basile-Doelsch, I.: Increasing soil carbon storage: mechanisms, effects of agricultural practices and proxies. A review, Agron. Sustain. Dev., 37, 14, https://doi.org/10.1007/s13593-017-0421-2, 2017. 10.1007/s13593-017-0421-2

[29]

Dimassi, B., Mary, B., Wylleman, R., Labreuche, J. Ô., Couture, D., Piraux, F., and Cohan, J. P.: Long-term effect of contrasted tillage and crop management on soil carbon dynamics during 41 years, Agr. Ecosyst. Environ., 188, 134–146, https://doi.org/10.1016/j.agee.2014.02.014, 2014. 10.1016/j.agee.2014.02.014

[30]

Disnar, J. R., Guillet, B., Keravis, D., Di-Giovanni, C., and Sebag, D.: Soil organic matter (SOM) characterization by Rock-Eval pyrolysis: Scope and limitations, Org. Geochem., 34, 327–343, https://doi.org/10.1016/S0146-6380(02)00239-5, 2003. 10.1016/s0146-6380(02)00239-5

[31]

Erb, K. H., Luyssaert, S., Meyfroidt, P., Pongratz, J., Don, A., Kloster, S., Kuemmerle, T., Fetzel, T., Fuchs, R., Herold, M., Haberl, H., Jones, C. D., Marín-Spiotta, E., McCallum, I., Robertson, E., Seufert, V., Fritz, S., Valade, A., Wiltshire, A., and Dolman, A. J.: Land management: data availability and process understanding for global change studies, Glob. Chang. Biol., 23, 512–533, https://doi.org/10.1111/gcb.13443, 2017. 10.1111/gcb.13443

[32]

FAO: Recarbonization of global soils: a dynamic response to offset global emissions, FAO, Rome, Italy, 8 pp., available at: https://www.fao.org/documents/card/en/c/e4839d17-c6aa-44ca-85cc-b4a6de25c143/ (last access: 19 January 2022), 2019.

[33]

FAO: Technical specifications and country guidelines for Global Soil Organic Carbon Sequestration Potential Map (GSOCseq), FAO, Rome, Italy, 48 pp., available at: https://www.fao.org/3/cb0353en/CB0353EN.pdf (last access: 19 January 2022), 2020.

[34]

Farina, R., Sándor, R., Abdalla, M., Álvaro-Fuentes, J., Bechini, L., Bolinder, M. A., Brilli, L., Chenu, C., Clivot, H., De Antoni Migliorati, M., Di Bene, C., Dorich, C. D., Ehrhardt, F., Ferchaud, F., Fitton, N., Francaviglia, R., Franko, U., Giltrap, D. L., Grant, B. B., Guenet, B., Harrison, M. T., Kirschbaum, M. U. F., Kuka, K., Kulmala, L., Liski, J., McGrath, M. J., Meier, E., Menichetti, L., Moyano, F., Nendel, C., Recous, S., Reibold, N., Shepherd, A., Smith, W. N., Smith, P., Soussana, J. F., Stella, T., Taghizadeh-Toosi, A., Tsutskikh, E., and Bellocchi, G.: Ensemble modelling, uncertainty and robust predictions of organic carbon in long-term bare-fallow soils, Glob. Chang. Biol., 27, 904–928, https://doi.org/10.1111/gcb.15441, 2021. 10.1111/gcb.15441

[35]

Fuchs, R., Herold, M., Verburg, P. H., Clevers, J. G. P. W., and Eberle, J.: Gross changes in reconstructions of historic land cover/use for Europe between 1900 and 2010, Glob. Chang. Biol., 21, 299–313, https://doi.org/10.1111/gcb.12714, 2015. 10.1111/gcb.12714

[36]

Gregorich, E. G., Gillespie, A. W., Beare, M. H., Curtin, D., Sanei, H., and Yanni, S. F.: Evaluating biodegradability of soil organic matter by its thermal stability and chemical composition, Soil Biol. Biochem., 91, 182–191, https://doi.org/10.1016/j.soilbio.2015.08.032, 2015. 10.1016/j.soilbio.2015.08.032

[37]

He, Y., Trumbore, S. E., Torn, M. S., Harden, J. W., Vaugh, L. J. S., Allison, S. D., and Randerson, J. T.: Radiocarbon constraints imply reduced carbon uptake by soils during the 21st century, Science, 353, 1419–1424, https://doi.org/10.1126/science.aad4273, 2016. 10.1126/science.aad4273

[38]

Hemingway, J. D., Rothman, D. H., Grant, K. E., Rosengard, S. Z., Eglinton, T. I., Derry, L. A., and Galy, V. V.: Mineral protection regulates long-term global preservation of natural organic carbon, Nature, 570, 228–231, https://doi.org/10.1038/s41586-019-1280-6, 2019. 10.1038/s41586-019-1280-6

[39]

Hénin, S. and Dupuis, M.: Essai de bilan de la matière organique du sol, in: Ann. Agron. 11, Dunod (impr. de Chaix), Paris, 17–29, 1945.

[40]

Herbst, M., Welp, G., Macdonald, A., Jate, M., Hädicke, A., Scherer, H., Gaiser, T., Herrmann, F., Amelung, W., and Vanderborght, J.: Correspondence of measured soil carbon fractions and RothC pools for equilibrium and non-equilibrium states, Geoderma, 314, 37–46, https://doi.org/10.1016/j.geoderma.2017.10.047, 2018. 10.1016/j.geoderma.2017.10.047

[41]

IPCC: Climate Change and Land: an IPCC special report on climate change, desertification, land degradation, sustainable land management, food security, and greenhouse gas fluxes in terrestrial ecosystems, edited by: Shukla, P. R., Skea, J., Calvo Buendia, E., Masson-Delmotte, V., Pörtner, H.-O., Roberts, D. C., Zhai, P., Slade, R., Connors, S., van Diemen, R., Ferrat, M., Haughey, E., Luz, S., Neogi, S., Pathak, M., Petzold, J., Portugal Pereira, J., Vyas, P., Huntley, E., Kissick, K., Belkacemi, M., and Malley, J., The Intergovernmental Panel on Climate Change, available at: https://www.ipcc.ch/srccl/ (last access: 19 January 2022), 2019.

[42]

Jobbagy, E. G. and Jackson, R. B.: The vertical distribution of Soil Organic Carbon and its relation to climate and vegetation, Ecol. Appl., 10, 423–436, 2000. 10.1890/1051-0761(2000)010[0423:tvdoso]2.0.co;2

[43]

Khedim, N., Cécillon, L., Poulenard, J., Barré, P., Baudin, F., Marta, S., Rabatel, A., Dentant, C., Cauvy-Fraunié, S., Anthelme, F., Gielly, L., Ambrosini, R., Franzetti, A., Azzoni, R. S., Caccianiga, M. S., Compostella, C., Clague, J., Tielidze, L., Messager, E., Choler, P., and Ficetola, G. F.: Topsoil organic matter build-up in glacier forelands around the world, Glob. Change Biol., 27, 1662–1677, https://doi.org/10.1111/gcb.15496, 2021. 10.1111/gcb.15496

[44]

Lee, J., Viscarra Rossel, R. A., Zhang, M., Luo, Z., and Wang, Y.-P.: Assessing the response of soil carbon in Australia to changing inputs and climate using a consistent modelling framework, Biogeosciences, 18, 5185–5202, https://doi.org/10.5194/bg-18-5185-2021, 2021. 10.5194/bg-18-5185-2021

[45]

Lehmann, J., Hansel, C. M., Kaiser, C., Kleber, M., Maher, K., Manzoni, S., Nunan, N., Reichstein, M., Schimel, J. P., Torn, M. S., Wieder, W. R., and Kögel-Knabner, I.: Persistence of soil organic carbon caused by functional complexity, Nat. Geosci., 13, 529–534, https://doi.org/10.1038/s41561-020-0612-3, 2020. 10.1038/s41561-020-0612-3

[46]

Leifeld, J., Reiser, R., and Oberholzer, H. R.: Consequences of conventional versus organic farming on soil carbon: Results from a 27-year field experiment, Agron. J., 101, 1204–1218, https://doi.org/10.2134/agronj2009.0002, 2009a. 10.2134/agronj2009.0002

[47]

Leifeld, J., Zimmermann, M., Fuhrer, J., and Conen, F.: Storage and turnover of carbon in grassland soils along an elevation gradient in the Swiss Alps, Glob. Change Biol., 15, 668–679, https://doi.org/10.1111/j.1365-2486.2008.01782.x, 2009b. 10.1111/j.1365-2486.2008.01782.x

[48]

Levavasseur, F., Mary, B., Christensen, B. T., Duparque, A., Ferchaud, F., Kätterer, T., Lagrange, H., Montenach, D., Resseguier, C., and Houot, S.: The simple AMG model accurately simulates organic carbon storage in soils after repeated application of exogenous organic matter, Nutr. Cycl. Agroecosyst., 117, 215–229, https://doi.org/10.1007/s10705-020-10065-x, 2020. 10.1007/s10705-020-10065-x

[49]

Lubet, E., Plénet, D., and Juste, C.: Effet à long terme de la monoculture sur le rendement en grain du maïs (Zea mays L) en conditions non irriguées, Agronomie, 13, 673–683, https://doi.org/10.1051/agro:19930801, 1993. 10.1051/agro:19930801

[50]

Lugato, E., Lavallee, J. M., Haddix, M. L., Panagos, P., and Cotrufo, M. F.: Different climate sensitivity of particulate and mineral-associated soil organic matter, Nat. Geosci., 14, 295–300, https://doi.org/10.1038/s41561-021-00744-x, 2021. 10.1038/s41561-021-00744-x

Showing 50 of 89 references

Metrics

27

Citations

89

References

Details

Published: Jan 24, 2022
Vol/Issue: 19(2)
Pages: 375-387
License: View

Authors

Université Paris‐Saclay INRAE AgroParisTech UMR Ecosys Thiverval‐Grignon France

BioEcoAgro Joint Research Unit INRAE Université de Liège Université de Lille Université de Picardie Jules Verne Barenton‐Bugny France

L

Laure Soucémarianadin

C

Claire Chenu

10Ecosys, INRAE–AgroParisTech, Thiverval-Grignon, France

P

Pierre Barré

Funding

Agence Nationale de la Recherche Award: Store Soil C

Agence de la transition écologique Award: PhD grant for E.K.

Cite This Article

Eva Kanari, Lauric Cécillon, François Baudin, et al. (2022). A robust initialization method for accurate soil organic carbon simulations. Biogeosciences, 19(2), 375-387. https://doi.org/10.5194/bg-19-375-2022

A robust initialization method for accurate soil organic carbon simulations

You May Also Like