Articles | Volume 17, issue 7
https://doi.org/10.5194/gmd-17-2705-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-17-2705-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model description paper
| 
12 Apr 2024
Model description paper |
| 12 Apr 2024
| 12 Apr 2024
Optimal enzyme allocation leads to the constrained enzyme hypothesis: the Soil Enzyme Steady Allocation Model (SESAM; v3.1)
Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
Christian Reimers
Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
Bernhard Ahrens
Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
Marion Schrumpf
Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
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Biogeosciences, 21, 1827–1846, https://doi.org/10.5194/bg-21-1827-2024, https://doi.org/10.5194/bg-21-1827-2024, 2024
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We present a methodology to detect inconsistencies in perhaps the most important data source for measurements of ecosystem–atmosphere carbon, water, and energy fluxes. We expect that the derived consistency flags will be relevant for data users and will help in improving our understanding of and our ability to model ecosystem–climate interactions.
Christine Fischer-Bedtke, Johanna Clara Metzger, Gökben Demir, Thomas Wutzler, and Anke Hildebrandt
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Canopies change how rain reaches the soil: some spots receive more and others less water. It has long been debated whether this also leads to locally wetter and drier soil. We checked this using measurements of canopy drip and soil moisture. We found that the increase in soil water content after rain was aligned with canopy drip. Independently, the soil storage reaction was dampened in locations prone to drainage, like hig-macroporosity areas, suggesting that canopy drip enhances bypass flow.
Lin Yu, Silvia Caldararu, Bernhard Ahrens, Thomas Wutzler, Marion Schrumpf, Julian Helfenstein, Chiara Pistocchi, and Sönke Zaehle
Biogeosciences, 20, 57–73, https://doi.org/10.5194/bg-20-57-2023, https://doi.org/10.5194/bg-20-57-2023, 2023
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In this study, we addressed a key weakness in current ecosystem models regarding the phosphorus exchange in the soil and developed a new scheme to describe this process. We showed that the new scheme improved the model performance for plant productivity, soil organic carbon, and soil phosphorus content at five beech forest sites in Germany. We claim that this new model could be used as a better tool to study ecosystems under future climate change, particularly phosphorus-limited systems.
Sinikka Jasmin Paulus, Tarek Sebastian El-Madany, René Orth, Anke Hildebrandt, Thomas Wutzler, Arnaud Carrara, Gerardo Moreno, Oscar Perez-Priego, Olaf Kolle, Markus Reichstein, and Mirco Migliavacca
Hydrol. Earth Syst. Sci., 26, 6263–6287, https://doi.org/10.5194/hess-26-6263-2022, https://doi.org/10.5194/hess-26-6263-2022, 2022
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In this study, we analyze small inputs of water to ecosystems such as fog, dew, and adsorption of vapor. To measure them, we use a scaling system and later test our attribution of different water fluxes to weight changes. We found that they occur frequently during 1 year in a dry summer ecosystem. In each season, a different flux seems dominant, but they all mainly occur during the night. Therefore, they could be important for the biosphere because rain is unevenly distributed over the year.
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Geosci. Model Dev., 15, 8377–8393, https://doi.org/10.5194/gmd-15-8377-2022, https://doi.org/10.5194/gmd-15-8377-2022, 2022
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Soil microbes process soil organic matter and affect carbon storage and plant nutrition at the ecosystem scale. We hypothesized that decadal dynamics is constrained by the ratios of elements in litter inputs, microbes, and matter and that microbial community optimizes growth. This allowed the SESAM model to descibe decadal-term carbon sequestration in soils and other biogeochemical processes explicitly accounting for microbial processes but without its problematic fine-scale parameterization.
Zavud Baghirov, Markus Reichstein, Basil Kraft, Bernhard Ahrens, Marco Körner, and Martin Jung
EGUsphere, https://doi.org/10.5194/egusphere-2025-3123, https://doi.org/10.5194/egusphere-2025-3123, 2025
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We introduce a new global model that links how water and carbon move through land ecosystems. By combining process knowledge with artificial intelligence that learns from observations, we model daily changes in vegetation, water and carbon cycle processes. This model outperforms both purely data-driven and traditional process models, especially in dry and tropical regions. This advance could improve current understanding of water-carbon cycle relationships.
Marleen Pallandt, Marion Schrumpf, Holger Lange, Markus Reichstein, Lin Yu, and Bernhard Ahrens
Biogeosciences, 22, 1907–1928, https://doi.org/10.5194/bg-22-1907-2025, https://doi.org/10.5194/bg-22-1907-2025, 2025
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As soils warm due to climate change, soil organic carbon (SOC) decomposes faster due to increased microbial activity, given sufficient available moisture. We modelled the microbial decomposition of plant litter and residue at different depths and found that deep soil layers are more sensitive than topsoils. Warming causes SOC loss, but its extent depends on the litter type and its temperature sensitivity, which can either counteract or amplify losses. Droughts may also counteract warming-induced SOC losses.
Marijn Van de Broek, Gerard Govers, Marion Schrumpf, and Johan Six
Biogeosciences, 22, 1427–1446, https://doi.org/10.5194/bg-22-1427-2025, https://doi.org/10.5194/bg-22-1427-2025, 2025
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Soil organic carbon models are used to predict how soils affect the concentration of CO2 in the atmosphere. We show that equifinality – the phenomenon that different parameter values lead to correct overall model outputs, albeit with a different model behaviour – is an important source of model uncertainty. Our results imply that adding more complexity to soil organic carbon models is unlikely to lead to better predictions as long as more data to constrain model parameters are not available.
Guohua Liu, Mirco Migliavacca, Christian Reimers, Basil Kraft, Markus Reichstein, Andrew D. Richardson, Lisa Wingate, Nicolas Delpierre, Hui Yang, and Alexander J. Winkler
Geosci. Model Dev., 17, 6683–6701, https://doi.org/10.5194/gmd-17-6683-2024, https://doi.org/10.5194/gmd-17-6683-2024, 2024
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Our study employs long short-term memory (LSTM) networks to model canopy greenness and phenology, integrating meteorological memory effects. The LSTM model outperforms traditional methods, enhancing accuracy in predicting greenness dynamics and phenological transitions across plant functional types. Highlighting the importance of multi-variate meteorological memory effects, our research pioneers unlock the secrets of vegetation phenology responses to climate change with deep learning techniques.
Martin Jung, Jacob Nelson, Mirco Migliavacca, Tarek El-Madany, Dario Papale, Markus Reichstein, Sophia Walther, and Thomas Wutzler
Biogeosciences, 21, 1827–1846, https://doi.org/10.5194/bg-21-1827-2024, https://doi.org/10.5194/bg-21-1827-2024, 2024
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We present a methodology to detect inconsistencies in perhaps the most important data source for measurements of ecosystem–atmosphere carbon, water, and energy fluxes. We expect that the derived consistency flags will be relevant for data users and will help in improving our understanding of and our ability to model ecosystem–climate interactions.
Richard Nair, Yunpeng Luo, Tarek El-Madany, Victor Rolo, Javier Pacheco-Labrador, Silvia Caldararu, Kendalynn A. Morris, Marion Schrumpf, Arnaud Carrara, Gerardo Moreno, Markus Reichstein, and Mirco Migliavacca
EGUsphere, https://doi.org/10.5194/egusphere-2023-2434, https://doi.org/10.5194/egusphere-2023-2434, 2023
Preprint archived
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We studied a Mediterranean ecosystem to understand carbon uptake efficiency and its controls. These ecosystems face potential nitrogen-phosphorus imbalances due to pollution. Analysing six years of carbon data, we assessed controls at different timeframes. This is crucial for predicting such vulnerable regions. Our findings revealed N limitation on C uptake, not N:P imbalance, and strong influence of water availability. whether drought or wetness promoted net C uptake depended on timescale.
Christine Fischer-Bedtke, Johanna Clara Metzger, Gökben Demir, Thomas Wutzler, and Anke Hildebrandt
Hydrol. Earth Syst. Sci., 27, 2899–2918, https://doi.org/10.5194/hess-27-2899-2023, https://doi.org/10.5194/hess-27-2899-2023, 2023
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Canopies change how rain reaches the soil: some spots receive more and others less water. It has long been debated whether this also leads to locally wetter and drier soil. We checked this using measurements of canopy drip and soil moisture. We found that the increase in soil water content after rain was aligned with canopy drip. Independently, the soil storage reaction was dampened in locations prone to drainage, like hig-macroporosity areas, suggesting that canopy drip enhances bypass flow.
Shane W. Stoner, Marion Schrumpf, Alison Hoyt, Carlos A. Sierra, Sebastian Doetterl, Valier Galy, and Susan Trumbore
Biogeosciences, 20, 3151–3163, https://doi.org/10.5194/bg-20-3151-2023, https://doi.org/10.5194/bg-20-3151-2023, 2023
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Soils store more carbon (C) than any other terrestrial C reservoir, but the processes that control how much C stays in soil, and for how long, are very complex. Here, we used a recent method that involves heating soil in the lab to measure the range of C ages in soil. We found that most C in soil is decades to centuries old, while some stays for much shorter times (days to months), and some is thousands of years old. Such detail helps us to estimate how soil C may react to changing climate.
Lin Yu, Silvia Caldararu, Bernhard Ahrens, Thomas Wutzler, Marion Schrumpf, Julian Helfenstein, Chiara Pistocchi, and Sönke Zaehle
Biogeosciences, 20, 57–73, https://doi.org/10.5194/bg-20-57-2023, https://doi.org/10.5194/bg-20-57-2023, 2023
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In this study, we addressed a key weakness in current ecosystem models regarding the phosphorus exchange in the soil and developed a new scheme to describe this process. We showed that the new scheme improved the model performance for plant productivity, soil organic carbon, and soil phosphorus content at five beech forest sites in Germany. We claim that this new model could be used as a better tool to study ecosystems under future climate change, particularly phosphorus-limited systems.
Sinikka Jasmin Paulus, Tarek Sebastian El-Madany, René Orth, Anke Hildebrandt, Thomas Wutzler, Arnaud Carrara, Gerardo Moreno, Oscar Perez-Priego, Olaf Kolle, Markus Reichstein, and Mirco Migliavacca
Hydrol. Earth Syst. Sci., 26, 6263–6287, https://doi.org/10.5194/hess-26-6263-2022, https://doi.org/10.5194/hess-26-6263-2022, 2022
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In this study, we analyze small inputs of water to ecosystems such as fog, dew, and adsorption of vapor. To measure them, we use a scaling system and later test our attribution of different water fluxes to weight changes. We found that they occur frequently during 1 year in a dry summer ecosystem. In each season, a different flux seems dominant, but they all mainly occur during the night. Therefore, they could be important for the biosphere because rain is unevenly distributed over the year.
Thomas Wutzler, Lin Yu, Marion Schrumpf, and Sönke Zaehle
Geosci. Model Dev., 15, 8377–8393, https://doi.org/10.5194/gmd-15-8377-2022, https://doi.org/10.5194/gmd-15-8377-2022, 2022
Short summary
Short summary
Soil microbes process soil organic matter and affect carbon storage and plant nutrition at the ecosystem scale. We hypothesized that decadal dynamics is constrained by the ratios of elements in litter inputs, microbes, and matter and that microbial community optimizes growth. This allowed the SESAM model to descibe decadal-term carbon sequestration in soils and other biogeochemical processes explicitly accounting for microbial processes but without its problematic fine-scale parameterization.
Jeffrey Prescott Beem-Miller, Craig Rasmussen, Alison May Hoyt, Marion Schrumpf, Georg Guggenberger, and Susan Trumbore
EGUsphere, https://doi.org/10.5194/egusphere-2022-1083, https://doi.org/10.5194/egusphere-2022-1083, 2022
Preprint withdrawn
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We compared the age of persistent soil organic matter as well as active emissions of carbon dioxide from soils across a gradient of climate and geology. We found that clay minerals are more important than mean annual temperature for both persistent and actively cycling soil carbon, and that they may attenuate the sensitivity of soil organic matter decomposition to temperature. Accounting for geology and soil development could therefore improve estimates of soil carbon stocks and changes.
Rachael Akinyede, Martin Taubert, Marion Schrumpf, Susan Trumbore, and Kirsten Küsel
Biogeosciences, 19, 4011–4028, https://doi.org/10.5194/bg-19-4011-2022, https://doi.org/10.5194/bg-19-4011-2022, 2022
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Soils will likely become warmer in the future, and this can increase the release of carbon dioxide (CO2) into the atmosphere. As microbes can take up soil CO2 and prevent further escape into the atmosphere, this study compares the rate of uptake and release of CO2 at two different temperatures. With warming, the rate of CO2 uptake increases less than the rate of release, indicating that the capacity to modulate soil CO2 release into the atmosphere will decrease under future warming.
Marion Schrumpf, Klaus Kaiser, Allegra Mayer, Günter Hempel, and Susan Trumbore
Biogeosciences, 18, 1241–1257, https://doi.org/10.5194/bg-18-1241-2021, https://doi.org/10.5194/bg-18-1241-2021, 2021
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A large amount of organic carbon (OC) in soil is protected against decay by bonding to minerals. We studied the release of mineral-bonded OC by NaF–NaOH extraction and H2O2 oxidation. Unexpectedly, extraction and oxidation removed mineral-bonded OC at roughly constant portions and of similar age distributions, irrespective of mineral composition, land use, and soil depth. The results suggest uniform modes of interactions between OC and minerals across soils in quasi-steady state with inputs.
Naixin Fan, Sujan Koirala, Markus Reichstein, Martin Thurner, Valerio Avitabile, Maurizio Santoro, Bernhard Ahrens, Ulrich Weber, and Nuno Carvalhais
Earth Syst. Sci. Data, 12, 2517–2536, https://doi.org/10.5194/essd-12-2517-2020, https://doi.org/10.5194/essd-12-2517-2020, 2020
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The turnover time of terrestrial carbon (τ) controls the global carbon cycle–climate feedback. In this study, we provide a new, updated ensemble of diagnostic terrestrial carbon turnover times and associated uncertainties on a global scale. Despite the large variation in both magnitude and spatial patterns of τ, we identified robust features in the spatial patterns of τ which could contribute to uncertainty reductions in future projections of the carbon cycle–climate feedback.
Cited articles
Ahrens, B., Braakhekke, M. C., Guggenberger, G., Schrumpf, M., and Reichstein, M.: Contribution of sorption, DOC transport and microbial interactions to the 14C age of a soil organic carbon profile: Insights from a calibrated process model, Soil Biol. Biochem., 88, 390–402, https://doi.org/10.1016/j.soilbio.2015.06.008, 2015. a
Arrieta, J. M., Mayol, E., Hansman, R. L., Herndl, G. J., Dittmar, T., and Duarte, C. M.: Dilution limits dissolved organic carbon utilization in the deep ocean, Science, 348, 331–333, https://doi.org/10.1126/science.1258955, 2015. a
Calabrese, S., Mohanty, B. P., and Malik, A. A.: Soil microorganisms regulate extracellular enzyme production to maximize their growth rate, Biogeochemistry, 158, 303–312, https://doi.org/10.1007/s10533-022-00899-8, 2022. a
Carvalhais, L. C., Dennis, P. G., Tyson, G. W., and Schenk, P. M.: Application of metatranscriptomics to soil environments, J. Microb. Meth., 91, 246–251, https://doi.org/10.1016/j.mimet.2012.08.011, 2012. a
Cheng, W., Parton, W. J., Gonzalez-Meler, M. A., Phillips, R., Asao, S., McNickle, G. G., Brzostek, E., and Jastrow, J. D.: Synthesis and modeling perspectives of rhizosphere priming, New Phytol., 201, 31–44, https://doi.org/10.1111/nph.12440, 2014. a
Dewar, R. C.: Maximum entropy production and plant optimization theories, Philos. T. Roy. Soc. B, 365, 1429–1435, https://doi.org/10.1098/rstb.2009.0293, 2010. a, b
Dungait, J. A. J., Hopkins, D. W., Gregory, A. S., and Whitmore, A. P.: Soil organic matter turnover is governed by accessibility not recalcitrance, Global Change Biol., 18, 1781–1796, https://doi.org/10.1111/j.1365-2486.2012.02665.x, 2012. a
Ekschmitt, K., Liu, M. Q., Vetter, S., Fox, O., and Wolters, V.: Strategies used by soil biota to overcome soil organic matter stability – why is dead organic matter left over in the soil?, Geoderma, 128, 167–176, 2005. a
Ekschmitt, K., Kandeler, E., Poll, C., Brune, A., Buscot, F., Friedrich, M., Gleixner, G., Hartmann, A., Kästner, M., Marhan, S., Miltner, A., Scheu, S., and Wolters, V.: Soil-carbon preservation through habitat constraints and biological limitations on decomposer activity, J. Plant Nutr. Soil Sci., 171, 27–35, https://doi.org/10.1002/jpln.200700051, 2008. a
Feng, X., Lu, Y., Jiang, M., Katul, G., Manzoni, S., Mrad, A., and Vico, G.: Instantaneous stomatal optimization results in suboptimal carbon gain due to legacy effects, Plant Cell Environ., 45, 3189–3204, https://doi.org/10.1111/pce.14427, 2022. a
Harvey, O. R., Myers-Pigg, A. N., Kuo, L.-J., Singh, B. P., Kuehn, K. A., and Louchouarn, P.: Discrimination in Degradability of Soil Pyrogenic Organic Matter Follows a Return-On-Energy-Investment Principle, Environ. Sci. Technol., 50, 8578–8585, https://doi.org/10.1021/acs.est.6b01010, 2016. a
Heitkötter, J. and Marschner, B.: Soil zymography as a powerful tool for exploring hotspots and substrate limitation in undisturbed subsoil, Soil Biol. Biochem., 124, 210–217, https://doi.org/10.1016/j.soilbio.2018.06.021, 2018. a
Henneron, L., Balesdent, J., Alvarez, G., Barré, P., Baudin, F., Basile-Doelsch, I., Cécillon, L., Fernandez-Martinez, A., Hatté, C., and Fontaine, S.: Bioenergetic control of soil carbon dynamics across depth, Nat. Commun., 13, 7676, https://doi.org/10.1038/s41467-022-34951-w, 2022. a
Hungate, B. A., Mau, R. L., Schwartz, E., Caporaso, J. G., Dijkstra, P., van Gestel, N., Koch, B. J., Liu, C. M., McHugh, T. A., Marks, J. C., Morrissey, E. M., and Price, L. B.: Quantitative Microbial Ecology through Stable Isotope Probing, Appl. Environ. Microbiol., 81, 7570–7581, https://doi.org/10.1128/aem.02280-15, 2015. a
Jannasch, H. W.: Growth of marine bacteria at limiting concentration of organic carbon in seawater, Limnol. Oceanogr., 12, 264–271, https://doi.org/10.4319/lo.1967.12.2.0264, 1967. a
Jiao, N., Herndl, G. J., Hansell, D. A., Benner, R., Kattner, G., Wilhelm, S. W., Kirchman, D. L., Weinbauer, M. G., Luo, T., Chen, F., and Azam, F.: Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean, Nat. Rev. Microbiol., 8, 593–599, https://doi.org/10.1038/nrmicro2386, 2010. a
Kaiser, C., Franklin, O., Dieckmann, U., and Richter, A.: Microbial community dynamics alleviate stoichiometric constraints during litter decay, Ecol. Lett., 17, 680–690, https://doi.org/10.1111/ele.12269, 2014. a, b
Keiluweit, M., Bougoure, J. J., Nico, P. S., Pett-Ridge, J., Weber, P. K., and Kleber, M.: Mineral protection of soil carbon counteracted by root exudates, Nat. Clim. Change, 5, 588–595, 2015. a
Keiluweit, M., Wanzek, T., Kleber, M., Nico, P., and Fendorf, S.: Anaerobic microsites have an unaccounted role in soil carbon stabilization, Nat. Commun., 8, 1771, https://doi.org/10.1038/s41467-017-01406-6, 2017. a
Kondepudi, D.: Modern Thermodynamics: From Heat Engines to Dissipative Structures, John Wiley & Sons, ISBN 0471973947, 1998. a
Kozjek, K., Manoharan, L., Urich, T., Ahrén, D., and Hedlund, K.: Microbial gene activity in straw residue amendments reveals carbon sequestration mechanisms in agricultural soils, Soil Biol. Biochem., 179, 108994, https://doi.org/10.1016/j.soilbio.2023.108994, 2023. a
Kuzyakov, Y., Friedel, J. K., and Stahr, K.: Review of mechanisms and quantification of priming effects, Soil Biol. Biochem., 32, 1485–1498, 2000. a
Kögel-Knabner, I.: The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter: Fourteen years on, Soil Biol. Biochem., 105, A3–A8, https://doi.org/10.1016/j.soilbio.2016.08.011, 2017. a
Lehmann, J., Kinyangi, J., and Solomon, D.: Organic matter stabilization in soil microaggregates: implications from spatial heterogeneity of organic carbon contents and carbon forms, Biogeochemistry, 85, 45–57, https://doi.org/10.1007/s10533-007-9105-3, 2007. a
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. a
Manzoni, S.: Flexible Carbon-Use Efficiency across Litter Types and during Decomposition Partly Compensates Nutrient Imbalances – Results from Analytical Stoichiometric Models, Front. Microbiol., 8, 661, https://doi.org/10.3389/fmicb.2017.00661, 2017. a
Manzoni, S., Čapek, P., Mooshammer, M., Lindahl, B. D., Richter, A., and Šantrůčková, H.: Optimal metabolic regulation along resource stoichiometry gradients, Ecol. Lett., 20, 1182–1191, https://doi.org/10.1111/ele.12815, 2017. a
Manzoni, S., Chakrawal, A., Spohn, M., and Lindahl, B. D.: Modeling Microbial Adaptations to Nutrient Limitation During Litter Decomposition, Front. Forests Glob. Change, 4, 686945, https://doi.org/10.3389/ffgc.2021.686945, 2021. a
Manzoni, S., Chakrawal, A., and Ledder, G.: Decomposition rate as an emergent property of optimal microbial foraging, Front. Ecol. Evol., 11, 1094269, https://doi.org/10.3389/fevo.2023.1094269, 2023. a
Marx, M.-C., Wood, M., and Jarvis, S.: A microplate fluorimetric assay for the study of enzyme diversity in soils, Soil Biol. Biochem., 33, 1633–1640, https://doi.org/10.1016/s0038-0717(01)00079-7, 2001. a
Mathieu, J. A., Hatté, C., Balesdent, J., and Parent, É.: Deep soil carbon dynamics are driven more by soil type than by climate: a worldwide meta-analysis of radiocarbon profiles, Global Change Biol., 21, 4278–4292, https://doi.org/10.1111/gcb.13012, 2015. a
Mooshammer, M., Wanek, W., Hämmerle, I., Fuchslueger, L., Hofhansl, F., Knoltsch, A., Schnecker, J., Takriti, M., Watzka, M., Wild, B., Keiblinger, K. M., Zechmeister-Boltenstern, S., and Richter, A.: Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling, Nat. Commun., 5, 3694, https://doi.org/10.1038/ncomms4694, 2014a. a
Mooshammer, M., Wanek, W., Zechmeister-Boltenstern, S., and Richter, A.: Stoichiometric imbalances between terrestrial decomposer communities and their resources: mechanisms and implications of microbial adaptations to their resources, Front. Microbiol., 5, 22, https://doi.org/10.3389/fmicb.2014.00022, 2014b. a
Nielsen, S., Müller, F., Marques, J., Bastianoni, S., and Jørgensen, S.: Thermodynamics in Ecology – An Introductory Review, Entropy, 22, 820, https://doi.org/10.3390/e22080820, 2020. a
Or, D., Smets, B., Wraith, J., Dechesne, A., and Friedman, S.: Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review, Adv. Water Resour., 30, 1505–1527, https://doi.org/10.1016/j.advwatres.2006.05.025, 2007. a
Perveen, N., Barot, S., Alvarez, G., Klumpp, K., Martin, R., Rapaport, A., Herfurth, D., Louault, F., and Fontaine, S.: Priming effect and microbial diversity in ecosystem functioning and response to global change: a modeling approach using the SYMPHONY model, Global Change Biol., 20, 1174–1190, https://doi.org/10.1111/gcb.12493, 2014. a
Richter, A.: What controls carbon and nutrient cycling in soil? Microbial growth as the fundamental driver of soil biogeochemistry, EGU General Assembly 2023, Vienna, Austria, 24–28 April 2023, EGU23-10907, https://doi.org/10.5194/egusphere-egu23-10907, 2023. a
Robert W. Sterner, J. J. E.: Ecological stoichiometry: the biology of elements from molecules to the biosphere, Princeton University Press, ISBN 9780691074917, 2002. a
Salome, C., Nunan, N., Pouteau, V., Lerch, T., and Chenu, C.: Carbon dynamics in topsoil and in subsoil may be controlled by different regulatory mechanisms, Global Change Biol., 16, 416–426, https://doi.org/10.1111/j.1365-2486.2009.01884.x, 2009. a
Schmidt, M. W. I., Torn, M. S., Abiven, S., Dittmar, T., Guggenberger, G., Janssens, I. A., Kleber, M., Kögel-Knabner, I., Lehmann, J., Manning, D. A. C., Nannipieri, P., Rasse, D. P., Weiner, S., and Trumbore, S. E.: Persistence of soil organic matter as an ecosystem property, Nature, 478, 49–56, https://doi.org/10.1038/nature10386, 2011. a
Schrumpf, M., Kaiser, K., Guggenberger, G., Persson, T., Kögel-Knabner, I., and Schulze, E.-D.: Storage and stability of organic carbon in soils as related to depth, occlusion within aggregates, and attachment to minerals, Biogeosciences, 10, 1675–1691, https://doi.org/10.5194/bg-10-1675-2013, 2013. a, b
Six, J., Elliott, E. T., and Paustian, K.: Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under no-tillage agriculture, Soil Biol. Biochem., 32, 2099–2103, 2000. a
Spohn, M., Carminati, A., and Kuzyakov, Y.: Soil zymography – A novel in situ method for mapping distribution of enzyme activity in soil, Soil Biol. Biochem., 58, 275–280, https://doi.org/10.1016/j.soilbio.2012.12.004, 2013. a
Strogatz, S. H.: Nonlinear dynamics and chaos: with applications to physics, Studies in Nonlinearity, Westview, Perseus books publishing, 1994. a
Tang, J. and Riley, W. J.: Competitor and substrate sizes and diffusion together define enzymatic depolymerization and microbial substrate uptake rates, Soil Biol. Biochem., 139, 107624, https://doi.org/10.1016/j.soilbio.2019.107624, 2019. a
Ulanowicz, R. E.: The balance between adaptability and adaptation, Biosystems, 64, 13–22, https://doi.org/10.1016/s0303-2647(01)00170-8, 2002. a
Ulanowicz, R. E.: The dual nature of ecosystem dynamics, Ecol. Model., 220, 1886–1892, https://doi.org/10.1016/j.ecolmodel.2009.04.015, 2009. a
von Lützow, M., Kögel-Knabner, I., Ekschmitt, K., Matzner, E., Guggenberger, G., Marschner, B., and Flessa, H.: Stabilization of organic matter in temperate soils: mechanisms and their relevance under different soil conditions – a review, Eur. J. Soil Sci., 57, 426–445, 2006. a
von Lützow, M., Kögel-Knabner, I., Ludwig, B., Matzner, E., Flessa, H., Ekschmitt, K., Guggenberger, G., Marschner, B., and Kalbitz, K.: Stabilization mechanisms of organic matter in four temperate soils: Development and application of a conceptual model, J. Plant Nutr. Soil Sci., 171, 111–124, https://doi.org/10.1002/jpln.200700047, 2008. a
Weverka, J. R., Moeller, H. V., and Schimel, J. P.: Chemodiversity controls microbial assimilation of soil organic carbon: A theoretical model, Soil Biol. Biochem., 187, 109161, https://doi.org/10.1016/j.soilbio.2023.109161, 2023. a, b, c
Woolf, D. and Lehmann, J.: Microbial models with minimal mineral protection can explain long-term soil organic carbon persistence, Sci. Rep.-UK, 9, 6522, https://doi.org/10.1038/s41598-019-43026-8, 2019. a
Wutzler, T. and Reichstein, M.: Colimitation of decomposition by substrate and decomposers – a comparison of model formulations, Biogeosciences, 5, 749–759, https://doi.org/10.5194/bg-5-749-2008, 2008. a
Wutzler, T., Zaehle, S., Schrumpf, M., Ahrens, B., and Reichstein, M.: Adaptation of microbial resource allocation affects modelled long term soil organic matter and nutrient cycling, Soil Biol. Biochem., 115, 322–336, https://doi.org/10.1016/j.soilbio.2017.08.031, 2017. a, b
Wutzler, T., Yu, L., Schrumpf, M., and Zaehle, S.: Simulating long-term responses of soil organic matter turnover to substrate stoichiometry by abstracting fast and small-scale microbial processes: the Soil Enzyme Steady Allocation Model (SESAM; v3.0), Geosci. Model Dev., 15, 8377–8393, https://doi.org/10.5194/gmd-15-8377-2022, 2022. a, b, c, d, e, f, g, h
Wutzler, T.: bgctw/sesam: Wutzler23_optimAlloc (gmd_Wutzler23), Zenodo [code], https://doi.org/10.5281/zenodo.8026318, 2023a. a
Wutzler, T.: bgctw/Sesam.jl: GMD_Wutzler23_discussion (gmd_wutzler23), Zenodo [code], https://doi.org/10.5281/zenodo.8026366, 2023b. a
Short summary
Soil microbes provide a strong link for elemental fluxes in the earth system. The SESAM model applies an optimality assumption to model those linkages and their adaptation. We found that a previous heuristic description was a special case of a newly developed more rigorous description. The finding of new behaviour at low microbial biomass led us to formulate the constrained enzyme hypothesis. We now can better describe how microbially mediated linkages of elemental fluxes adapt across decades.
Soil microbes provide a strong link for elemental fluxes in the earth system. The SESAM model...
