Articles | Volume 21, issue 22
https://doi.org/10.5194/bg-21-5173-2024
© 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/bg-21-5173-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
19 Nov 2024
Research article |
| 19 Nov 2024
| 19 Nov 2024
Observational benchmarks inform representation of soil organic carbon dynamics in land surface models
Kamal Nyaupane
Department of Environmental Science and Engineering, Environmental Science and Engineering Program, The University of Texas at El Paso, El Paso, TX 79968, USA
Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA 94550, USA
Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
Kyongmin Yeo
IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10562, USA
William J. Riley
Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Forrest M. Hoffman
Climate Change Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
Sagar Gautam
Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA 94550, USA
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Elsa Abs, Christoph Keuschnig, Pierre Amato, Chris Bowler, Eric Capo, Alexander B. Chase, Luciana Chavez Rodriguez, Abraham N. Dabengwa, Thomas Dussarrat, Thomas Guzman, Linnea K. Hernandez, Jenni Hultman, Kirsten Küsel, Zhen Li, Anna Mankowski, William J. Riley, Scott R. Saleska, and Lisa Wingate
Biogeosciences, 23, 5205–5237, https://doi.org/10.5194/bg-23-5205-2026, https://doi.org/10.5194/bg-23-5205-2026, 2026
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Meta-omics technologies offer new tools to understand how microbial and plant functional diversity shape biogeochemical cycles across ecosystems. This perspective explores how integrating omics data with ecological and modeling approaches can improve our understanding of greenhouse gas fluxes and nutrient dynamics, from soils to clouds, and from the past to the future. We highlight challenges and opportunities for scaling omics insights from local processes to Earth system models.
Bin Wang, M. Luke McCormack, Daniel M. Ricciuto, Xiaojuan Yang, Min Xu, and Forrest M. Hoffman
EGUsphere, https://doi.org/10.5194/egusphere-2026-2759, https://doi.org/10.5194/egusphere-2026-2759, 2026
This preprint is open for discussion and under review for Geoscientific Model Development (GMD).
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Plants send about a third of their captured carbon below ground, to roots and soil fungi that take up water and nutrients. Most climate models still treat the entire root system as one uniform mass. We built a new land-model version that separates roots into three types: transport roots, absorptive roots, and fungal partners. Tested at twenty sites worldwide, it cut errors in simulated ecosystem carbon exchange by more than half, sharpening projections of how land will respond to climate change.
Haodi Xu, Joshua Fan, Feng Tao, Lifen Jiang, Fengqi You, Benjamin Houlton, Ying Sun, Carla P. Gomes, and Yiqi Luo
Geosci. Model Dev., 19, 6777–6795, https://doi.org/10.5194/gmd-19-6777-2026, https://doi.org/10.5194/gmd-19-6777-2026, 2026
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We developed the Biogeochemistry-Informed Neural Network (BINN) which embeds a process-based model inside an AI framework so the model’s parameters can be learned from empirical data. BINN could recover prescribed parameters in synthetic tests and retrieve key processes controlling the modeled soil organic carbon when applied to ~25 000 soil profiles in US. It operates more than 50 times faster than the traditional Bayesian approach for data-model integration.
Jinyun Tang, William J. Riley, Gianna L. Marschmann, and Eoin L. Brodie
Biogeosciences, 23, 3995–4010, https://doi.org/10.5194/bg-23-3995-2026, https://doi.org/10.5194/bg-23-3995-2026, 2026
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Carbon Use Efficiency (CUE) measures how biological organisms use carbon to synthesize new biomass, inferred to first increase and then decrease with specific growth rate. Our analysis of six biological growth models reveals that source-driven models fail to capture this relationship, while sink-driven models, using a reserve biomass pool, succeed. Existing biogeochemical models often depict a deterministic CUE-controlling factor relationship, which we find should be modeled dynamically instead.
Mengze Li, Robert B. Jackson, Marielle Saunois, Philippe Ciais, Ben Poulter, Josep G. Canadell, Prabir K. Patra, Hanqin Tian, Zhen Zhang, Etienne Fluet-Chouinard, Zutao Ouyang, Ting Zhang, David J. Beerling, Dmitry A. Belikov, Philippe Bousquet, Danilo Custodio, Naveen Chandra, Xinyu Dou, Nicola Gedney, Peter O. Hopcroft, Alison M. Hoyt, Kazuhito Ichii, Akihito Ito, Atul K. Jain, Katherine Jensen, Fortunat Joos, Thomas Kleinen, Masayuki Kondo, Fa Li, Tingting Li, Xiangyu Liu, Shamil Maksyutov, Avni Malhotra, Adrien Martinez, Kyle McDonald, Joe R. Melton, Jurek Müller, Yosuke Niwa, Shufen Pan, Shushi Peng, Changhui Peng, Zhangcai Qin, Peter Raymond, William Riley, Arjo Segers, Rona L. Thompson, Aki Tsuruta, Yi Xi, Kunxiaojia Yuan, Wenxin Zhang, Bo Zheng, Qing Zhu, Qiuan Zhu, and Qianlai Zhuang
Earth Syst. Sci. Data, 18, 3507–3524, https://doi.org/10.5194/essd-18-3507-2026, https://doi.org/10.5194/essd-18-3507-2026, 2026
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We proposed a framework that combines machine-learning and climate data to predict global natural vegetated wetland methane emissions for 2000–2025. We found that although total global emissions remained stable in the post-2020s, Northern Hemisphere emissions surged whilst tropical emissions fell. This approach allows us to rapidly monitor emissions and provides early warnings for climate impacts.
Elias C. Massoud, Nathan Collier, Yaoping Wang, Jiafu Mao, Adrian Harpold, Steven A. Kannenberg, Gerbrand Koren, Mukesh Kumar, Pushpendra Raghav, Pallav Ray, Mingjie Shi, Jing Tao, Sreedevi P. Vasu, Huiqi Wang, Qing Zhu, and Forrest M. Hoffman
Geosci. Model Dev., 19, 3427–3453, https://doi.org/10.5194/gmd-19-3427-2026, https://doi.org/10.5194/gmd-19-3427-2026, 2026
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Soil moisture helps control how plants grow and how land exchanges water and energy with the atmosphere. We evaluated how well 16 Earth System Models represent soil moisture and its links to plant activity using a benchmarking system and observational data. Many models simulate surface soil moisture well but show larger errors deeper in the soil and in colder regions. Models that represent plant–soil water interactions more directly better capture how ecosystems respond to water availability.
Sagar Gautam, Chang Gyo Jung, Umakant Mishra, Rattan Lal, Klaus Lorenz, Jinyun Tang, DeAnn Ricks Presley, and Alan J. Franzluebbers
EGUsphere, https://doi.org/10.5194/egusphere-2026-1094, https://doi.org/10.5194/egusphere-2026-1094, 2026
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We developed an ensemble approach that combines three agroecosystem models to predict crop yields and changes in soil carbon across the United States. The ensemble results were more accurate and consistent compared to individual model. Ensemble result matched closely the observed yield data and soil carbon measurements while reducing the uncertainty from the individual models. This work improves our ability to track carbon change and supports carbon farming, climate action, and land management.
Jeffrey Beem-Miller, William J. Riley, Peter B. Reich, Michael W. I. Schmidt, Yuxuan Bai, Raimundo Bermudez Villanueva, Zach Brown, Abad Chabbi, Susan E. Crow, Wenxu Dong, Serita D. Frey, Paul J. Hanson, Kai Jensen, Melissa A. Knorr, Emma Lathrop, Avni Malhotra, Patrick Megonigal, Adrienne Nicotra, Andrew Nottingham, Genevieve L. Noyce, Roy L. Rich, Heidi Rodenhizer, Agustín Sarquis, Andreas Schindlbacher, Edward A. G. Schuur, Zheng Shi, Artur Stefanski, Viktoria Unger, Tana E. Wood, Yuanhe Yang, Zhijie Yang, Jizhong Zhou, Biao Zhu, and Margaret S. Torn
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2026-23, https://doi.org/10.5194/essd-2026-23, 2026
Revised manuscript has not been submitted
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The Soil Warming to Depth Data Integration Effort (SWEDDIE) synthesizes data from deep soil warming experiments around the world (n = 23), offering new insight into warming responses of both surface and subsoils. We demonstrate that variation in soil warming with depth is driven largely by warming methodology, while soil moisture changes due to warming differ by ecosystem. This work serves a foundation for future syntheses with SWEDDIE.
Ashley Brereton, Zelalem A. Mekonnen, Bhavna Arora, William J. Riley, Kunxiaojia Yuan, Yi Xu, Yu Zhang, Qing Zhu, Tyler L. Anthony, and Adina Paytan
Geosci. Model Dev., 18, 8157–8173, https://doi.org/10.5194/gmd-18-8157-2025, https://doi.org/10.5194/gmd-18-8157-2025, 2025
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Wetlands absorb carbon dioxide (CO2), helping slow climate change, but they also release methane, a potent warming gas. We developed a collection of AI-based models to estimate magnitudes of CO2 and methane exchanged between the land and the atmosphere, for wetlands on a regional scale. This approach helps to inform land-use planning, restoration, and greenhouse gas accounting, while also creating a foundation for future advancements in prediction accuracy.
Forrest M. Hoffman, Birgit Hassler, Ranjini Swaminathan, Jared Lewis, Bouwe Andela, Nathaniel Collier, Dóra Hegedűs, Jiwoo Lee, Charlotte Pascoe, Mika Pflüger, Martina Stockhause, Paul Ullrich, Min Xu, Lisa Bock, Felicity Chun, Bettina K. Gier, Douglas I. Kelley, Axel Lauer, Julien Lenhardt, Manuel Schlund, Mohanan G. Sreeush, Katja Weigel, Ed Blockley, Rebecca Beadling, Romain Beucher, Demiso D. Dugassa, Valerio Lembo, Jianhua Lu, Swen Brands, Jerry Tjiputra, Elizaveta Malinina, Brian Mederios, Enrico Scoccimarro, Jeremy Walton, Philip Kershaw, André L. Marquez, Malcolm J. Roberts, Eleanor O’Rourke, Elisabeth Dingley, Briony Turner, Helene Hewitt, and John P. Dunne
EGUsphere, https://doi.org/10.5194/egusphere-2025-2685, https://doi.org/10.5194/egusphere-2025-2685, 2025
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As Earth system models become more complex, rapid and comprehensive evaluation through comparison with observational data is necessary. The upcoming Assessment Fast Track for the Seventh Phase of the Coupled Model Intercomparison Project (CMIP7) will require fast analysis. This paper describes a new Rapid Evaluation Framework (REF) that was developed for the Assessment Fast Track that will be run at the Earth System Grid Federation (ESGF) to inform the community about the performance of models.
Marielle Saunois, Adrien Martinez, Benjamin Poulter, Zhen Zhang, Peter A. Raymond, Pierre Regnier, Josep G. Canadell, Robert B. Jackson, Prabir K. Patra, Philippe Bousquet, Philippe Ciais, Edward J. Dlugokencky, Xin Lan, George H. Allen, David Bastviken, David J. Beerling, Dmitry A. Belikov, Donald R. Blake, Simona Castaldi, Monica Crippa, Bridget R. Deemer, Fraser Dennison, Giuseppe Etiope, Nicola Gedney, Lena Höglund-Isaksson, Meredith A. Holgerson, Peter O. Hopcroft, Gustaf Hugelius, Akihiko Ito, Atul K. Jain, Rajesh Janardanan, Matthew S. Johnson, Thomas Kleinen, Paul B. Krummel, Ronny Lauerwald, Tingting Li, Xiangyu Liu, Kyle C. McDonald, Joe R. Melton, Jens Mühle, Jurek Müller, Fabiola Murguia-Flores, Yosuke Niwa, Sergio Noce, Shufen Pan, Robert J. Parker, Changhui Peng, Michel Ramonet, William J. Riley, Gerard Rocher-Ros, Judith A. Rosentreter, Motoki Sasakawa, Arjo Segers, Steven J. Smith, Emily H. Stanley, Joël Thanwerdas, Hanqin Tian, Aki Tsuruta, Francesco N. Tubiello, Thomas S. Weber, Guido R. van der Werf, Douglas E. J. Worthy, Yi Xi, Yukio Yoshida, Wenxin Zhang, Bo Zheng, Qing Zhu, Qiuan Zhu, and Qianlai Zhuang
Earth Syst. Sci. Data, 17, 1873–1958, https://doi.org/10.5194/essd-17-1873-2025, https://doi.org/10.5194/essd-17-1873-2025, 2025
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Methane (CH4) is the second most important human-influenced greenhouse gas in terms of climate forcing after carbon dioxide (CO2). A consortium of multi-disciplinary scientists synthesise and update the budget of the sources and sinks of CH4. This edition benefits from important progress in estimating emissions from lakes and ponds, reservoirs, and streams and rivers. For the 2010s decade, global CH4 emissions are estimated at 575 Tg CH4 yr-1, including ~65 % from anthropogenic sources.
Jinyun Tang and William J. Riley
Biogeosciences, 22, 1809–1819, https://doi.org/10.5194/bg-22-1809-2025, https://doi.org/10.5194/bg-22-1809-2025, 2025
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A new mathematical formulation of the dynamic energy budget model is presented for the growth of biological organisms. This new formulation combines mass conservation law and chemical kinetics theory and is computationally faster than the standard formulation of dynamic energy budget models. In simulating the growth of Thalassiosira weissflogii in a nitrogen-limiting chemostat, the new model is as good as the standard dynamic energy budget model using almost the same parameter values.
Zhen Zhang, Benjamin Poulter, Joe R. Melton, William J. Riley, George H. Allen, David J. Beerling, Philippe Bousquet, Josep G. Canadell, Etienne Fluet-Chouinard, Philippe Ciais, Nicola Gedney, Peter O. Hopcroft, Akihiko Ito, Robert B. Jackson, Atul K. Jain, Katherine Jensen, Fortunat Joos, Thomas Kleinen, Sara H. Knox, Tingting Li, Xin Li, Xiangyu Liu, Kyle McDonald, Gavin McNicol, Paul A. Miller, Jurek Müller, Prabir K. Patra, Changhui Peng, Shushi Peng, Zhangcai Qin, Ryan M. Riggs, Marielle Saunois, Qing Sun, Hanqin Tian, Xiaoming Xu, Yuanzhi Yao, Yi Xi, Wenxin Zhang, Qing Zhu, Qiuan Zhu, and Qianlai Zhuang
Biogeosciences, 22, 305–321, https://doi.org/10.5194/bg-22-305-2025, https://doi.org/10.5194/bg-22-305-2025, 2025
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This study assesses global methane emissions from wetlands between 2000 and 2020 using multiple models. We found that wetland emissions increased by 6–7 Tg CH4 yr-1 in the 2010s compared to the 2000s. Rising temperatures primarily drove this increase, while changes in precipitation and CO2 levels also played roles. Our findings highlight the importance of wetlands in the global methane budget and the need for continuous monitoring to understand their impact on climate change.
Jinyun Tang and William J. Riley
Biogeosciences, 21, 1061–1070, https://doi.org/10.5194/bg-21-1061-2024, https://doi.org/10.5194/bg-21-1061-2024, 2024
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A chemical kinetics theory is proposed to explain the non-monotonic relationship between temperature and biochemical rates. It incorporates the observed thermally reversible enzyme denaturation that is ensured by the ceaseless thermal motion of molecules and ions in an enzyme solution and three well-established theories: (1) law of mass action, (2) diffusion-limited chemical reaction theory, and (3) transition state theory.
Xiaojuan Yang, Peter Thornton, Daniel Ricciuto, Yilong Wang, and Forrest Hoffman
Biogeosciences, 20, 2813–2836, https://doi.org/10.5194/bg-20-2813-2023, https://doi.org/10.5194/bg-20-2813-2023, 2023
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We evaluated the performance of a land surface model (ELMv1-CNP) that includes both nitrogen (N) and phosphorus (P) limitation on carbon cycle processes. We show that ELMv1-CNP produces realistic estimates of present-day carbon pools and fluxes. We show that global C sources and sinks are significantly affected by P limitation. Our study suggests that introduction of P limitation in land surface models is likely to have substantial consequences for projections of future carbon uptake.
Doaa Aboelyazeed, Chonggang Xu, Forrest M. Hoffman, Jiangtao Liu, Alex W. Jones, Chris Rackauckas, Kathryn Lawson, and Chaopeng Shen
Biogeosciences, 20, 2671–2692, https://doi.org/10.5194/bg-20-2671-2023, https://doi.org/10.5194/bg-20-2671-2023, 2023
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Photosynthesis is critical for life and has been affected by the changing climate. Many parameters come into play while modeling, but traditional calibration approaches face many issues. Our framework trains coupled neural networks to provide parameters to a photosynthesis model. Using big data, we independently found parameter values that were correlated with those in the literature while giving higher correlation and reduced biases in photosynthesis rates.
Bharat Sharma, Jitendra Kumar, Auroop R. Ganguly, and Forrest M. Hoffman
Biogeosciences, 20, 1829–1841, https://doi.org/10.5194/bg-20-1829-2023, https://doi.org/10.5194/bg-20-1829-2023, 2023
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Rising atmospheric carbon dioxide increases vegetation growth and causes more heatwaves and droughts. The impact of such climate extremes is detrimental to terrestrial carbon uptake capacity. We found that due to overall climate warming, about 88 % of the world's regions towards the end of 2100 will show anomalous losses in net biospheric productivity (NBP) rather than gains. More than 50 % of all negative NBP extremes were driven by the compound effect of dry, hot, and fire conditions.
Fa Li, Qing Zhu, William J. Riley, Lei Zhao, Li Xu, Kunxiaojia Yuan, Min Chen, Huayi Wu, Zhipeng Gui, Jianya Gong, and James T. Randerson
Geosci. Model Dev., 16, 869–884, https://doi.org/10.5194/gmd-16-869-2023, https://doi.org/10.5194/gmd-16-869-2023, 2023
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We developed an interpretable machine learning model to predict sub-seasonal and near-future wildfire-burned area over African and South American regions. We found strong time-lagged controls (up to 6–8 months) of local climate wetness on burned areas. A skillful use of such time-lagged controls in machine learning models results in highly accurate predictions of wildfire-burned areas; this will also help develop relevant early-warning and management systems for tropical wildfires.
Ziqi Lin, Yongjiu Dai, Umakant Mishra, Guocheng Wang, Wei Shangguan, Wen Zhang, and Zhangcai Qin
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2022-232, https://doi.org/10.5194/essd-2022-232, 2022
Manuscript not accepted for further review
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Spatial soil organic carbon (SOC) data is critical for predictions in carbon climate feedbacks and future climate trends, but no conclusion has yet been reached on which dataset to be used for specific purposes. We evaluated the SOC estimates from five widely used global soil datasets and a regional permafrost dataset, and identify uncertainties of SOC estimates by region, biome, and data sources, hoping to help improve SOC/soil data in the future.
Qing Zhu, Fa Li, William J. Riley, Li Xu, Lei Zhao, Kunxiaojia Yuan, Huayi Wu, Jianya Gong, and James Randerson
Geosci. Model Dev., 15, 1899–1911, https://doi.org/10.5194/gmd-15-1899-2022, https://doi.org/10.5194/gmd-15-1899-2022, 2022
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Wildfire is a devastating Earth system process that burns about 500 million hectares of land each year. It wipes out vegetation including trees, shrubs, and grasses and causes large losses of economic assets. However, modeling the spatial distribution and temporal changes of wildfire activities at a global scale is challenging. This study built a machine-learning-based wildfire surrogate model within an existing Earth system model and achieved high accuracy.
Jinyun Tang, William J. Riley, and Qing Zhu
Geosci. Model Dev., 15, 1619–1632, https://doi.org/10.5194/gmd-15-1619-2022, https://doi.org/10.5194/gmd-15-1619-2022, 2022
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We here describe version 2 of BeTR, a reactive transport model created to help ease the development of biogeochemical capability in Earth system models that are used for quantifying ecosystem–climate feedbacks. We then coupled BeTR-v2 to the Energy Exascale Earth System Model to quantify how different numerical couplings of plants and soils affect simulated ecosystem biogeochemistry. We found that different couplings lead to significant uncertainty that is not correctable by tuning parameters.
Martijn M. T. A. Pallandt, Jitendra Kumar, Marguerite Mauritz, Edward A. G. Schuur, Anna-Maria Virkkala, Gerardo Celis, Forrest M. Hoffman, and Mathias Göckede
Biogeosciences, 19, 559–583, https://doi.org/10.5194/bg-19-559-2022, https://doi.org/10.5194/bg-19-559-2022, 2022
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Thawing of Arctic permafrost soils could trigger the release of vast amounts of carbon to the atmosphere, thus enhancing climate change. Our study investigated how well the current network of eddy covariance sites to monitor greenhouse gas exchange at local scales captures pan-Arctic flux patterns. We identified large coverage gaps, e.g., in Siberia, but also demonstrated that a targeted addition of relatively few sites can significantly improve network performance.
Jing Tao, Qing Zhu, William J. Riley, and Rebecca B. Neumann
The Cryosphere, 15, 5281–5307, https://doi.org/10.5194/tc-15-5281-2021, https://doi.org/10.5194/tc-15-5281-2021, 2021
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We improved the DOE's E3SM land model (ELMv1-ECA) simulations of soil temperature, zero-curtain period durations, cold-season CH4, and CO2 emissions at several Alaskan Arctic tundra sites. We demonstrated that simulated CH4 emissions during zero-curtain periods accounted for more than 50 % of total emissions throughout the entire cold season (Sep to May). We also found that cold-season CO2 emissions largely offset warm-season net uptake currently and showed increasing trends from 1950 to 2017.
Yaoping Wang, Jiafu Mao, Mingzhou Jin, Forrest M. Hoffman, Xiaoying Shi, Stan D. Wullschleger, and Yongjiu Dai
Earth Syst. Sci. Data, 13, 4385–4405, https://doi.org/10.5194/essd-13-4385-2021, https://doi.org/10.5194/essd-13-4385-2021, 2021
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We developed seven global soil moisture datasets (1970–2016, monthly, half-degree, and multilayer) by merging a wide range of data sources, including in situ and satellite observations, reanalysis, offline land surface model simulations, and Earth system model simulations. Given the great value of long-term, multilayer, gap-free soil moisture products to climate research and applications, we believe this paper and the presented datasets would be of interest to many different communities.
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Short summary
Representing soil organic carbon (SOC) dynamics in Earth system models (ESMs) is a key source of uncertainty in predicting carbon–climate feedbacks. Using machine learning, we develop and compare predictive relationships in observations (Obs) and ESMs. We find different relationships between environmental factors and SOC stocks in Obs and ESMs. SOC prediction in ESMs may be improved by representing the functional relationships of environmental controllers in a way consistent with observations.
Representing soil organic carbon (SOC) dynamics in Earth system models (ESMs) is a key source of...
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