Articles | Volume 12, issue 1
https://doi.org/10.5194/soil-12-205-2026
© Author(s) 2026. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Special issue:
https://doi.org/10.5194/soil-12-205-2026
© Author(s) 2026. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Coupled C and N turnover in a dynamic pore scale model reveal the impact of exudate quality on microbial necromass formation
Maximilian Rötzer
CORRESPONDING AUTHOR
Modeling and Numerics, Department of Mathematics, University of Erlangen-Nürnberg, Erlangen, Germany
Mathematical Institute for Machine Learning and Data Science, Catholic University of Eichstätt-Ingolstadt, Ingolstadt, Germany
Henri Braunmiller
Root-Soil Interaction, School of Life Sciences, Technical University of Munich, Freising, Germany
Eva Lehndorff
Soil Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
Nadja Ray
Modeling and Numerics, Department of Mathematics, University of Erlangen-Nürnberg, Erlangen, Germany
Mathematical Institute for Machine Learning and Data Science, Catholic University of Eichstätt-Ingolstadt, Ingolstadt, Germany
Andrea Scheibe
Soil Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
Alexander Prechtel
Modeling and Numerics, Department of Mathematics, University of Erlangen-Nürnberg, Erlangen, Germany
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Andrea Scheibe, Carlos A. Sierra, and Marie Spohn
Biogeosciences, 20, 827–838, https://doi.org/10.5194/bg-20-827-2023, https://doi.org/10.5194/bg-20-827-2023, 2023
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We explored carbon cycling in soils in three climate zones in Chile down to a depth of 6 m, using carbon isotopes. Our results show that microbial activity several meters below the soil surface is mostly fueled by recently fixed carbon and that strong decomposition of soil organic matter only occurs in the upper decimeters of the soils. The study shows that different layers of the critical zone are tightly connected and that processes in the deep soil depend on recently fixed carbon.
Sascha Scherer, Benjamin Höpfer, Katleen Deckers, Elske Fischer, Markus Fuchs, Ellen Kandeler, Jutta Lechterbeck, Eva Lehndorff, Johanna Lomax, Sven Marhan, Elena Marinova, Julia Meister, Christian Poll, Humay Rahimova, Manfred Rösch, Kristen Wroth, Julia Zastrow, Thomas Knopf, Thomas Scholten, and Peter Kühn
SOIL, 7, 269–304, https://doi.org/10.5194/soil-7-269-2021, https://doi.org/10.5194/soil-7-269-2021, 2021
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This paper aims to reconstruct Middle Bronze Age (MBA) land use practices in the northwestern Alpine foreland (SW Germany, Hegau). We used a multi-proxy approach including biogeochemical proxies from colluvial deposits in the surroundings of a MBA settlement, on-site archaeobotanical and zooarchaeological data and off-site pollen data. From our data we infer land use practices such as plowing, cereal growth, forest farming and use of fire that marked the beginning of major colluvial deposition.
Cited articles
Baumert, V. L., Vasilyeva, N. A., Vladimirov, A. A., Meier, I. C., Kögel-Knabner, I., and Mueller, C. W.: Root exudates induce soil macroaggregation facilitated by fungi in subsoil, Frontiers in Environmental Science, 6, 1–17, https://doi.org/10.3389/fenvs.2018.00140, 2018. a
Baveye, P. C., Otten, W., Kravchenko, A., Balseiro-Romero, M., Beckers, É., Chalhoub, M., Darnault, C., Eickhorst, T., Garnier, P., Hapca, S., Kiranyaz, S., Monga, O., Mueller, C. W., Nunan, N., Pot, V., Schlüter, S., Schmidt, H., and Vogel, H.-J.: Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain, Frontiers in Microbiology, 9, 1–48, https://doi.org/10.3389/fmicb.2018.01929, 2018. a
Brax, M., Buchmann, C., Kenngott, K., Schaumann, G. E., and Diehl, D.: Influence of the physico-chemical properties of root mucilage and model substances on the microstructural stability of sand, Biogeochemistry, 147, 35–52, https://doi.org/10.1007/s10533-019-00626-w, 2020. a, b
Bucka, F. B., Kölbl, A., Uteau, D., Peth, S., and Kögel-Knabner, I.: Organic matter input determines structure development and aggregate formation in artificial soils, Geoderma, 354, 113881, https://doi.org/10.1016/j.geoderma.2019.113881, 2019. a, b
Buckeridge, K. M., Creamer, C., and Whitaker, J.: Deconstructing the microbial necromass continuum to inform soil carbon sequestration, Functional Ecology, 36, 1396–1410, 2022. a
Chandel, A. K., Jiang, L., and Luo, Y.: Microbial models for simulating soil carbon dynamics: A review, Journal of Geophysical Research: Biogeosciences, 128, e2023JG007436, https://doi.org/10.1029/2023JG007436, 2023. a, b
Cochran, V., Horton, K., and Cole, C.: An estimation of microbial death rate and limitations of N or C during wheat straw decomposition, Soil Biology and Biochemistry, 20, 293–298, 1988. a
Cookson, W., Osman, M., Marschner, P., Abaye, D., Clark, I., Murphy, D., Stockdale, E., and Watson, C.: Controls on soil nitrogen cycling and microbial community composition across land use and incubation temperature, Soil Biology and Biochemistry, 39, 744–756, 2007. a
Crawford, J. W., Verrall, S., and Young, I. M.: The origin and loss of fractal scaling in simulated soil aggregates, European Journal of Soil Science, 48, 643–650, https://doi.org/10.1111/j.1365-2389.1997.tb00564.x, 1997. a
Crawford, J. W., Deacon, L., Grinev, D., Harris, J. A., Ritz, K., Singh, B. K., and Young, I.: Microbial diversity affects self-organization of the soil – Microbe system with consequences for function, Journal of the Royal Society Interface, 9, 1302–1310, https://doi.org/10.1098/rsif.2011.0679, 2012. a
Dungait, J. A., Hopkins, D. W., Gregory, A. S., and Whitmore, A. P.: Soil organic matter turnover is governed by accessibility not recalcitrance, Global Change Biology, 18, 1781–1796, https://doi.org/10.1111/j.1365-2486.2012.02665.x, 2012. a
Endress, M.-G., Dehghani, F., Blagodatsky, S., Reitz, T., Schlüter, S., and Blagodatskaya, E.: Spatial substrate heterogeneity limits microbial growth as revealed by the joint experimental quantification and modeling of carbon and heat fluxes, Soil Biology and Biochemistry, 197, 109509, https://doi.org/10.1016/j.soilbio.2024.109509, 2024. a
Gregory, P. J., George, T. S., and Paterson, E.: New methods for new questions about rhizosphere/plant root interactions, Plant and Soil, 476, 699–712, https://doi.org/10.1007/s11104-022-05437-x, 2022. a
He, X., Abs, E., Allison, S. D., Tao, F., Huang, Y., Manzoni, S., Abramoff, R., Bruni, E., Bowring, S. P. K., Chakrawal, A., Ciais, P., Elsgaard, L., Friedlingstein, P., Georgiou, K., Hugelius, G., Holm, L. B., Li, W., Luo, Y., Marmasse, G., Nunan, N., Qiu, C., Sitch, S., Wang, Y.-P., and Goll, D. S.: Emerging multiscale insights on microbial carbon use efficiency in the land carbon cycle, Nature Communications, 15, 8010, https://doi.org/10.1038/s41467-024-52160-5, 2024. a, b
Kleber, M., Sollins, P., and Sutton, R.: A conceptual model of organo-mineral interactions in soils: self-assembly of organic molecular fragments into zonal structures on mineral surfaces, Biogeochemistry, 85, 9–24, https://doi.org/10.1007/s10533-007-9103-5, 2007. a
Kwabiah, A. B., Palm, C. A., Stoskopf, N. C., and Voroney, R. P.: Response of soil microbial biomass dynamics to quality of plant materials with emphasis on P availability, Soil Biology and Biochemistry, 35, 207–216, https://doi.org/10.1016/S0038-0717(02)00253-5, 2003. a
Kästner, M., Miltner, A., Thiele-Bruhn, S., and Liang, C.: Microbial Necromass in Soils – Linking Microbes to Soil Processes and Carbon Turnover, Frontiers in Environmental Science, https://doi.org/10.3389/fenvs.2021.756378, 2021. a
Langeveld, J., Bouwman, A. F., van Hoek, W. J., Vilmin, L., Beusen, A. H., Mogollón, J. M., and Middelburg, J. J.: Estimating dissolved carbon concentrations in global soils: a global database and model, SN Applied Sciences, 2, 1626, https://doi.org/10.1007/s42452-020-03290-0, 2020. a
Lavallee, J. M., Soong, J. L., and Cotrufo, M. F.: Conceptualizing soil organic matter into particulate and mineral-associated forms to address global change in the 21st century, Global Change Biology, 26, 261–273, 2020. a
Lehmann, J. and Kleber, M.: The contentious nature of soil organic matter, Nature, 528, 60–68, https://doi.org/10.1038/nature16069, 2015. a, b
Liang, C., Amelung, W., Lehmann, J., and Kästner, M.: Quantitative assessment of microbial necromass contribution to soil organic matter, Global Change Biology, 25, 3578–3590, https://doi.org/10.1111/gcb.14781, 2019. a, b, c, d
Lucas, M., Vetterlein, D., Vogel, H. J., and Schlüter, S.: Revealing pore connectivity across scales and resolutions with X-ray CT, European Journal of Soil Science, 72, 546–560, https://doi.org/10.1111/ejss.12961, 2021. a
Manzoni, S.: Flexible Carbon-Use Efficiency across Litter Types and during Decomposition Partly Compensates Nutrient Imbalances – Results from Analytical Stoichiometric Models, Frontiers in Microbiology, 8, 661, https://doi.org/10.3389/fmicb.2017.00661, 2017. a
Manzoni, S., Taylor, P., Richter, A., Porporato, A., and Ågren, G. I.: Environmental and stoichiometric controls on microbial carbon-use efficiency in soils, New Phytologist, 196, 79–91, 2012. a
Manzoni, S., Čapek, P., Porada, P., Thurner, M., Winterdahl, M., Beer, C., Brüchert, V., Frouz, J., Herrmann, A. M., Lindahl, B. D., Lyon, S. W., Šantrůčková, H., Vico, G., and Way, D.: Reviews and syntheses: Carbon use efficiency from organisms to ecosystems – definitions, theories, and empirical evidence, Biogeosciences, 15, 5929–5949, https://doi.org/10.5194/bg-15-5929-2018, 2018. a
Miao, Y., Lv, J., Huang, H., Cao, D., and Zhang, S.: Molecular characterization of root exudates using Fourier transform ion cyclotron resonance mass spectrometry, Journal of Environmental Sciences, 98, 22–30, https://doi.org/10.1016/j.jes.2020.05.011, 2020. a
Nazari, M., Bickel, S., Benard, P., Mason-Jones, K., Carminati, A., and Dippold, M. A.: Biogels in soils: plant mucilage as a biofilm matrix that shapes the rhizosphere microbial habitat, Frontiers in Plant Science, 12, 798992, https://doi.org/10.3389/fpls.2021.798992, 2022. a
Niedeggen, D., Rüger, L., Oburger, E., Santangeli, M., Ahmed, M., Vetterlein, D., Blagodatsky, S., and Bonkowski, M.: Microbial utilisation of maize rhizodeposits applied to agricultural soil at a range of concentrations, European Journal of Soil Science, 75, 1–14, https://doi.org/10.1111/ejss.13530, 2024. a, b, c, d, e, f, g, h, i, j, k, l
Poeplau, C., Begill, N., Liang, Z., and Schiedung, M.: Root litter quality drives the dynamic of native mineral-associated organic carbon in a temperate agricultural soil, Plant and Soil, 491, 439–456, https://doi.org/10.1007/s11104-023-06127-y, 2023. a, b
Portell, X., Pot, V., Garnier, P., Otten, W., and Baveye, P. C.: Microscale Heterogeneity of the Spatial Distribution of Organic Matter Can Promote Bacterial Biodiversity in Soils: Insights From Computer Simulations, Frontiers in Microbiology, 9, 1–16, https://doi.org/10.3389/fmicb.2018.01583, 2018. a, b
Pot, V., Portell, X., Otten, W., Garnier, P., Monga, O., and Baveye, P. C.: Accounting for soil architecture and microbial dynamics in microscale models: Current practices in soil science and the path ahead, European Journal of Soil Science, 73, e13142, https://doi.org/10.1111/ejss.13142, 2021. a, b
Ray, N., Rupp, A., and Prechtel, A.: Discrete-continuum multiscale model for transport, biomass development and solid restructuring in porous media, Advances in Water Resources, 107, 393–404, https://doi.org/10.1016/j.advwatres.2017.04.001, 2017. a, b
Rupp, A., Knabner, P., and Dawson, C.: A local discontinuous Galerkin scheme for Darcy flow with internal jumps, Computational Geosciences, 22, 1149–1159, 2018a. a
Rupp, A., Totsche, K. U., Prechtel, A., and Ray, N.: Discrete-Continuum Multiphase Model for Structure Formation in Soils Including Electrostatic Effects, Frontiers in Environmental Science, 6, 1–13, https://doi.org/10.3389/fenvs.2018.00096, 2018b. a, b, c
Schimel, J. P. and Weintraub, M. N.: The implications of exoenzyme activity on microbial carbon and nitrogen limitation in soil: a theoretical model, Soil Biology and Biochemistry, 35, 549–563, 2003. a
Schweizer, S. A., Bucka, F. B., Graf-Rosenfellner, M., and Kögel-Knabner, I.: Soil microaggregate size composition and organic matter distribution as affected by clay content, Geoderma, 355, 113901, https://doi.org/10.1016/j.geoderma.2019.113901, 2019. a
Simon, E., Guseva, K., Darcy, S., Alteio, L., Pjevac, P., Schmidt, H., Jenab, K., Ranits, C., and Kaiser, C.: Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates, The ISME Journal, 18, https://doi.org/10.1093/ismejo/wrae156, 2024. a
Sokol, N. W., Whalen, E. D., Jilling, A., Kallenbach, C., Pett-Ridge, J., and Georgiou, K.: Global distribution, formation and fate of mineral-associated soil organic matter under a changing climate: A trait-based perspective, Functional Ecology, 36, 1411–1429, https://doi.org/10.1111/1365-2435.14040, 2022. a, b
The MathWorks Inc.: MATLAB version: R2024a, https://www.mathworks.com (last access: 19 February 2026), 2024. a
Totsche, K. U., Amelung, W., Gerzabek, M. H., Guggenberger, G., Klumpp, E., Knief, C., Lehndorff, E., Mikutta, R., Peth, S., Prechtel, A., Ray, N., and Kögel-Knabner, I.: Microaggregates in soils, Journal of Plant Nutrition and Soil Science, 181, 104–136, https://doi.org/10.1002/jpln.201600451, 2018. a
Varney, R. M., Chadburn, S. E., Burke, E. J., and Cox, P. M.: Evaluation of soil carbon simulation in CMIP6 Earth system models, Biogeosciences, 19, 4671–4704, https://doi.org/10.5194/bg-19-4671-2022, 2022. a
Vetterlein, D., Carminati, A., Kögel-Knabner, I., Bienert, G. P., Smalla, K., Oburger, E., Schnepf, A., Banitz, T., Tarkka, M. T., and Schlüter, S.: Rhizosphere Spatiotemporal Organization – A Key to Rhizosphere Functions, Frontiers in Agronomy, https://doi.org/10.3389/fagro.2020.00008, 2020. a
Vetterlein, D., Lippold, E., Schreiter, S., Phalempin, M., Fahrenkampf, T., Hochholdinger, F., Marcon, C., Tarkka, M., Oburger, E., Ahmed, M., Javaux, M., and Schlüter, S.: Experimental platforms for the investigation of spatiotemporal patterns in the rhizosphere – Laboratory and field scale, Journal of Plant Nutrition and Soil Science, 184, 35–50, https://doi.org/10.1002/jpln.202000079, 2021. a, b, c, d, e, f
Vogel, H. J., Balseiro-Romero, M., Kravchenko, A., Otten, W., Pot, V., Schlüter, S., Weller, U., and Baveye, P. C.: A holistic perspective on soil architecture is needed as a key to soil functions, European Journal of Soil Science, 73, 1–14, https://doi.org/10.1111/ejss.13152, 2022. a
Vogel, H.-J., Amelung, W., Baum, C., Bonkowski, M., Blagodatsky, S., Grosch, R., Herbst, M., Kiese, R., Koch, S., Kuhwald, M., König, S., Leinweber, P., Lennartz, B., Müller, C. W., Pagel, H., Rillig, M. C., Rüschhoff, J., Russell, D., Schnepf, A., Schulz, S., Siebers, N., Vetterlein, D., Wachendorf, C., Weller, U., and Wollschläger, U.: How to adequately represent biological processes in modeling multifunctionality of arable soils, Biology and Fertility of Soils, 60, 263–306, https://doi.org/10.1007/s00374-024-01802-3, 2024. a
Wang, B., Brewer, P. E., Shugart, H. H., Lerdau, M. T., and Allison, S. D.: Soil aggregates as biogeochemical reactors and implications for soil–atmosphere exchange of greenhouse gases – A concept, Global Change Biology, 25, 373–385, https://doi.org/10.1111/gcb.14515, 2019. a
Wei, L., Ge, T., Zhu, Z., Ye, R., Peñuelas, J., Li, Y., Lynn, T. M., Jones, D. L., Wu, J., and Kuzyakov, Y.: Paddy soils have a much higher microbial biomass content than upland soils: A review of the origin, mechanisms, and drivers, Agriculture, Ecosystems & Environment, 326, 107798, https://doi.org/10.1016/j.agee.2021.107798, 2022. a
Wiesenbauer, J., König, A., Gorka, S., Marchand, L., Nunan, N., Kitzler, B., Inselsbacher, E., and Kaiser, C.: A pulse of simulated root exudation alters the composition and temporal dynamics of microbial metabolites in its immediate vicinity, Soil Biology and Biochemistry, 189, 109259, https://doi.org/10.1016/j.soilbio.2023.109259, 2023. a
Witzgall, K., Vidal, A., Schubert, D. I., Höschen, C., Schweizer, S. A., Buegger, F., Pouteau, V., Chenu, C., and Mueller, C. W.: Particulate organic matter as a functional soil component for persistent soil organic carbon, Nature Communications, 12, 4115, https://doi.org/10.1038/s41467-021-24192-8, 2021. a
Zech, S., Dultz, S., Guggenberger, G., Prechtel, A., and Ray, N.: Microaggregation of goethite and illite evaluated by mechanistic modeling, Applied Clay Science, 198, 105845, https://doi.org/10.1016/j.clay.2020.105845, 2020. a
Zech, S., Ritschel, T., Ray, N., Totsche, K. U., and Prechtel, A.: How water connectivity and substrate supply shape the turnover of organic matter – Insights from simulations at the scale of microaggregates, Geoderma, 405, 115394, https://doi.org/10.1016/j.geoderma.2021.115394, 2022a. a, b, c, d
Zech, S., Schweizer, S. A., Bucka, F. B., Ray, N., Kögel-Knabner, I., and Prechtel, A.: Explicit spatial modeling at the pore scale unravels the interplay of soil organic carbon storage and structure dynamics, Global Change Biology, 28, 4589–4604, 2022b. a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q
Zech, S., Prechtel, A., and Ray, N.: Coupling scales in process‐based soil organic carbon modeling including dynamic aggregation, Journal of Plant Nutrition and Soil Science, 187, 130–142, https://doi.org/10.1002/jpln.202300080, 2024. a
Zechmeister-Boltenstern, S., Keiblinger, K. M., Mooshammer, M., Peñuelas, J., Richter, A., Sardans, J., and Wanek, W.: The application of ecological stoichiometry to plant–microbial–soil organic matter transformations, Ecological Monographs, 85, 133–155, https://doi.org/10.1890/14-0777.1, 2015. a, b
Zhang, Y., Gao, Y., Zhang, Y., Huang, D., Li, X., Gregorich, E., McLaughlin, N., Zhang, X., Chen, X., Zhang, S., Liang, A., and Xiang, Y.: Effect of long-term tillage and cropping system on portion of fungal and bacterial necromass carbon in soil organic carbon, Soil and Tillage Research, 218, 105307, https://doi.org/10.1016/j.still.2021.105307, 2022. a
Short summary
In soil, many factors influence how much carbon is stored: the structure of soil particles, microbial activity, and the balance of carbon and nitrogen. Using small-scale simulations, we can quantify and study their interplay. Nitrogen availability limits the microbial efficiency, and dead microbes contribute to long-term carbon storage by becoming occluded in aggregated soil particles. Our study offers new insights into how soils hold carbon, which is crucial for understanding climate change.
In soil, many factors influence how much carbon is stored: the structure of soil particles,...
Special issue