Articles | Volume 15, issue 7
https://doi.org/10.5194/gmd-15-2839-2022
© Author(s) 2022. 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-15-2839-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Development and technical paper
| 
07 Apr 2022
Development and technical paper |
| 07 Apr 2022
| 07 Apr 2022
KGML-ag: a modeling framework of knowledge-guided machine learning to simulate agroecosystems: a case study of estimating N2O emission using data from mesocosm experiments
Licheng Liu
Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
Shaoming Xu
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
Jinyun Tang
Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Kaiyu Guan
Agroecosystem Sustainability Center, Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Timothy J. Griffis
Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN 55108, USA
Matthew D. Erickson
Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN 55108, USA
Alexander L. Frie
Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN 55108, USA
Xiaowei Jia
Department of Computer Science, University of Pittsburgh, Pittsburgh, PA 15260, USA
Taegon Kim
Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
Department of Smart Farm, Jeonbuk National University, Jeonju, Jeollabuk-do, 54896, Republic of Korea
Lee T. Miller
Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN 55108, USA
Bin Peng
Agroecosystem Sustainability Center, Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Shaowei Wu
School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
Yufeng Yang
Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
Wang Zhou
Agroecosystem Sustainability Center, Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Vipin Kumar
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
Zhenong Jin
CORRESPONDING AUTHOR
Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
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Timothy J. Griffis, Jeffrey D. Wood, John M. Baker, Xuhui Lee, Ke Xiao, Zichong Chen, Lisa R. Welp, Natalie M. Schultz, Galen Gorski, Ming Chen, and John Nieber
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K. C. Wells, D. B. Millet, N. Bousserez, D. K. Henze, S. Chaliyakunnel, T. J. Griffis, Y. Luan, E. J. Dlugokencky, R. G. Prinn, S. O'Doherty, R. F. Weiss, G. S. Dutton, J. W. Elkins, P. B. Krummel, R. Langenfelds, L. P. Steele, E. A. Kort, S. C. Wofsy, and T. Umezawa
Geosci. Model Dev., 8, 3179–3198, https://doi.org/10.5194/gmd-8-3179-2015, https://doi.org/10.5194/gmd-8-3179-2015, 2015
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X. Zhang, X. Lee, T. J. Griffis, J. M. Baker, and W. Xiao
Atmos. Chem. Phys., 14, 10705–10719, https://doi.org/10.5194/acp-14-10705-2014, https://doi.org/10.5194/acp-14-10705-2014, 2014
L. Hu, D. B. Millet, S. Y. Kim, K. C. Wells, T. J. Griffis, E. V. Fischer, D. Helmig, J. Hueber, and A. J. Curtis
Atmos. Chem. Phys., 13, 3379–3392, https://doi.org/10.5194/acp-13-3379-2013, https://doi.org/10.5194/acp-13-3379-2013, 2013
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Using deep learning to integrate paleoclimate and global biogeochemistry over the Phanerozoic Eon
Modelling boreal forest's mineral soil and peat C dynamics with the Yasso07 model coupled with the Ricker moisture modifier
Dynamic ecosystem assembly and escaping the “fire trap” in the tropics: insights from FATES_15.0.0
NN-TOC v1: global prediction of total organic carbon in marine sediments using deep neural networks
In silico calculation of soil pH by SCEPTER v1.0
Simple process-led algorithms for simulating habitats (SPLASH v.2.0): robust calculations of water and energy fluxes
A global behavioural model of human fire use and management: WHAM! v1.0
Terrestrial Ecosystem Model in R (TEMIR) version 1.0: simulating ecophysiological responses of vegetation to atmospheric chemical and meteorological changes
biospheremetrics v1.0.2: an R package to calculate two complementary terrestrial biosphere integrity indicators – human colonization of the biosphere (BioCol) and risk of ecosystem destabilization (EcoRisk)
Modeling boreal forest soil dynamics with the microbially explicit soil model MIMICS+ (v1.0)
Optimal enzyme allocation leads to the constrained enzyme hypothesis: the Soil Enzyme Steady Allocation Model (SESAM; v3.1)
Implementing a dynamic representation of fire and harvest including subgrid-scale heterogeneity in the tile-based land surface model CLASSIC v1.45
Inferring the tree regeneration niche from inventory data using a dynamic forest model
Optimising CH4 simulations from the LPJ-GUESS model v4.1 using an adaptive Markov chain Monte Carlo algorithm
The XSO framework (v0.1) and Phydra library (v0.1) for a flexible, reproducible, and integrated plankton community modeling environment in Python
AgriCarbon-EO v1.0.1: large-scale and high-resolution simulation of carbon fluxes by assimilation of Sentinel-2 and Landsat-8 reflectances using a Bayesian approach
SAMM version 1.0: a numerical model for microbial- mediated soil aggregate formation
A model of the within-population variability of budburst in forest trees
Tatsuya Miyauchi, Makoto Saito, Hibiki M. Noda, Akihiko Ito, Tomomichi Kato, and Tsuneo Matsunaga
Geosci. Model Dev., 18, 2329–2347, https://doi.org/10.5194/gmd-18-2329-2025, https://doi.org/10.5194/gmd-18-2329-2025, 2025
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Solar-induced chlorophyll fluorescence (SIF) is an effective indicator for monitoring photosynthetic activity. This paper introduces VISIT-SIF, a biogeochemical model developed based on the Vegetation Integrative Simulator for Trace gases (VISIT) to represent satellite-observed SIF. Our simulations reproduced the global distribution and seasonal variations in observed SIF. VISIT-SIF helps to improve photosynthetic processes through a combination of biogeochemical modeling and observed SIF.
Mateus Dantas de Paula, Matthew Forrest, David Warlind, João Paulo Darela Filho, Katrin Fleischer, Anja Rammig, and Thomas Hickler
Geosci. Model Dev., 18, 2249–2274, https://doi.org/10.5194/gmd-18-2249-2025, https://doi.org/10.5194/gmd-18-2249-2025, 2025
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Our study maps global nitrogen (N) and phosphorus (P) availability and how they changed from 1901 to 2018. We find that tropical regions are mostly P-limited, while temperate and boreal areas face N limitations. Over time, P limitation increased, especially in the tropics, while N limitation decreased. These shifts are key to understanding global plant growth and carbon storage, highlighting the importance of including P dynamics in ecosystem models.
Wolfgang Knorr, Matthew Williams, Tea Thum, Thomas Kaminski, Michael Voßbeck, Marko Scholze, Tristan Quaife, T. Luke Smallman, Susan C. Steele-Dunne, Mariette Vreugdenhil, Tim Green, Sönke Zaehle, Mika Aurela, Alexandre Bouvet, Emanuel Bueechi, Wouter Dorigo, Tarek S. El-Madany, Mirco Migliavacca, Marika Honkanen, Yann H. Kerr, Anna Kontu, Juha Lemmetyinen, Hannakaisa Lindqvist, Arnaud Mialon, Tuuli Miinalainen, Gaétan Pique, Amanda Ojasalo, Shaun Quegan, Peter J. Rayner, Pablo Reyes-Muñoz, Nemesio Rodríguez-Fernández, Mike Schwank, Jochem Verrelst, Songyan Zhu, Dirk Schüttemeyer, and Matthias Drusch
Geosci. Model Dev., 18, 2137–2159, https://doi.org/10.5194/gmd-18-2137-2025, https://doi.org/10.5194/gmd-18-2137-2025, 2025
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When it comes to climate change, the land surface is where the vast majority of impacts happen. The task of monitoring those impacts across the globe is formidable and must necessarily rely on satellites – at a significant cost: the measurements are only indirect and require comprehensive physical understanding. We have created a comprehensive modelling system that we offer to the research community to explore how satellite data can be better exploited to help us capture the changes that happen on our lands.
Luke Oberhagemann, Maik Billing, Werner von Bloh, Markus Drüke, Matthew Forrest, Simon P. K. Bowring, Jessica Hetzer, Jaime Ribalaygua Batalla, and Kirsten Thonicke
Geosci. Model Dev., 18, 2021–2050, https://doi.org/10.5194/gmd-18-2021-2025, https://doi.org/10.5194/gmd-18-2021-2025, 2025
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Under climate change, the conditions necessary for wildfires to form are occurring more frequently in many parts of the world. To help predict how wildfires will change in future, global fire models are being developed. We analyze and further develop one such model, SPITFIRE. Our work identifies and corrects sources of substantial bias in the model that are important to the global fire modelling field. With this analysis and these developments, we help to provide a basis for future improvements.
Trine Frisbæk Hansen, Donald Eugene Canfield, Ken Haste Andersen, and Christian Jannik Bjerrum
Geosci. Model Dev., 18, 1895–1916, https://doi.org/10.5194/gmd-18-1895-2025, https://doi.org/10.5194/gmd-18-1895-2025, 2025
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We describe and test the size-based Nutrient-Unicellular-Multicellular model, which defines unicellular plankton using a single set of parameters, on a eutrophic and oligotrophic ecosystem. The results demonstrate that both sites can be modeled with similar parameters and robust performance over a wide range of parameters. The study shows that the model is useful for non-experts and applicable for modeling ecosystems with limited data. It holds promise for evolutionary and deep-time climate models.
Ying Ye, Guy Munhoven, Peter Köhler, Martin Butzin, Judith Hauck, Özgür Gürses, and Christoph Völker
Geosci. Model Dev., 18, 977–1000, https://doi.org/10.5194/gmd-18-977-2025, https://doi.org/10.5194/gmd-18-977-2025, 2025
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Many biogeochemistry models assume all material reaching the seafloor is remineralized and returned to solution, which is sufficient for studies on short-term climate change. Under long-term climate change, the carbon storage in sediments slows down carbon cycling and influences feedbacks in the atmosphere–ocean–sediment system. This paper describes the coupling of a sediment model to an ocean biogeochemistry model and presents results under the pre-industrial climate and under CO2 perturbation.
Juliette Bernard, Elodie Salmon, Marielle Saunois, Shushi Peng, Penélope Serrano-Ortiz, Antoine Berchet, Palingamoorthy Gnanamoorthy, Joachim Jansen, and Philippe Ciais
Geosci. Model Dev., 18, 863–883, https://doi.org/10.5194/gmd-18-863-2025, https://doi.org/10.5194/gmd-18-863-2025, 2025
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Despite their importance, uncertainties remain in the evaluation of the drivers of temporal variability of methane emissions from wetlands on a global scale. Here, a simplified global model is developed, taking advantage of advances in remote-sensing data and in situ observations. The model reproduces the large spatial and temporal patterns of emissions, albeit with limitations in the tropics due to data scarcity. This model, while simple, can provide valuable insights into sensitivity analyses.
Christian Poppe Terán, Bibi S. Naz, Harry Vereecken, Roland Baatz, Rosie A. Fisher, and Harrie-Jan Hendricks Franssen
Geosci. Model Dev., 18, 287–317, https://doi.org/10.5194/gmd-18-287-2025, https://doi.org/10.5194/gmd-18-287-2025, 2025
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Carbon and water exchanges between the atmosphere and the land surface contribute to water resource availability and climate change mitigation. Land surface models, like the Community Land Model version 5 (CLM5), simulate these. This study finds that CLM5 and other data sets underestimate the magnitudes of and variability in carbon and water exchanges for the most abundant plant functional types compared to observations. It provides essential insights for further research into these processes.
Jianyong Ma, Almut Arneth, Benjamin Smith, Peter Anthoni, Xu-Ri, Peter Eliasson, David Wårlind, Martin Wittenbrink, and Stefan Olin
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-223, https://doi.org/10.5194/gmd-2024-223, 2024
Revised manuscript accepted for GMD
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Nitrous oxide (N2O) is a powerful greenhouse gas mainly released from natural and agricultural soils. This study examines how global soil N2O emissions have changed from 1961 to 2020 and identifies key factors driving these changes using an ecological model. The findings highlight croplands as the largest source, with factors like fertilizer use and climate change enhancing emissions. Rising CO2 levels, however, can partially mitigate N2O emissions through increased plant nitrogen uptake.
Katherine A. Muller, Peishi Jiang, Glenn Hammond, Tasneem Ahmadullah, Hyun-Seob Song, Ravi Kukkadapu, Nicholas Ward, Madison Bowe, Rosalie K. Chu, Qian Zhao, Vanessa A. Garayburu-Caruso, Alan Roebuck, and Xingyuan Chen
Geosci. Model Dev., 17, 8955–8968, https://doi.org/10.5194/gmd-17-8955-2024, https://doi.org/10.5194/gmd-17-8955-2024, 2024
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The new Lambda-PFLOTRAN workflow incorporates organic matter chemistry into reaction networks to simulate aerobic respiration and biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow in a Jupyter notebook interface that digests raw organic matter chemistry data via Fourier transform ion cyclotron resonance mass spectrometry, develops a representative reaction network, and completes a biogeochemical simulation with the open-source, parallel-reactive-flow, and transport code PFLOTRAN.
Ling Li, Peipei Wu, Peng Zhang, Shaojian Huang, and Yanxu Zhang
Geosci. Model Dev., 17, 8683–8695, https://doi.org/10.5194/gmd-17-8683-2024, https://doi.org/10.5194/gmd-17-8683-2024, 2024
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In this study, we incorporate sea surfactants and wave-breaking processes into MITgcm-ECCOv4-Hg. The updated model shows increased fluxes in high-wind-speed and high-wave regions and vice versa, enhancing spatial heterogeneity. It shows that elemental mercury (Hg0) transfer velocity is more sensitive to wind speed. These findings may elucidate the discrepancies in previous estimations and offer insights into global Hg cycling.
Jerome Guiet, Daniele Bianchi, Kim J. N. Scherrer, Ryan F. Heneghan, and Eric D. Galbraith
Geosci. Model Dev., 17, 8421–8454, https://doi.org/10.5194/gmd-17-8421-2024, https://doi.org/10.5194/gmd-17-8421-2024, 2024
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The BiOeconomic mArine Trophic Size-spectrum (BOATSv2) model dynamically simulates global commercial fish populations and their coupling with fishing activity, as emerging from environmental and economic drivers. New features, including separate pelagic and demersal populations, iron limitation, and spatial variation of fishing costs and management, improve the accuracy of high seas fisheries. The updated model code is available to simulate both historical and future scenarios.
Jize Jiang, David S. Stevenson, and Mark A. Sutton
Geosci. Model Dev., 17, 8181–8222, https://doi.org/10.5194/gmd-17-8181-2024, https://doi.org/10.5194/gmd-17-8181-2024, 2024
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A special model called AMmonia–CLIMate (AMCLIM) has been developed to understand and calculate NH3 emissions from fertilizer use and also taking into account how the environment influences these NH3 emissions. It is estimated that about 17 % of applied N in fertilizers was lost due to NH3 emissions. Hot and dry conditions and regions with high-pH soils can expect higher NH3 emissions.
Guillaume Marie, Jina Jeong, Hervé Jactel, Gunnar Petter, Maxime Cailleret, Matthew J. McGrath, Vladislav Bastrikov, Josefine Ghattas, Bertrand Guenet, Anne Sofie Lansø, Kim Naudts, Aude Valade, Chao Yue, and Sebastiaan Luyssaert
Geosci. Model Dev., 17, 8023–8047, https://doi.org/10.5194/gmd-17-8023-2024, https://doi.org/10.5194/gmd-17-8023-2024, 2024
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This research looks at how climate change influences forests, and particularly how altered wind and insect activities could make forests emit instead of absorb carbon. We have updated a land surface model called ORCHIDEE to better examine the effect of bark beetles on forest health. Our findings suggest that sudden events, such as insect outbreaks, can dramatically affect carbon storage, offering crucial insights into tackling climate change.
Stephen Björn Wirth, Johanna Braun, Jens Heinke, Sebastian Ostberg, Susanne Rolinski, Sibyll Schaphoff, Fabian Stenzel, Werner von Bloh, Friedhelm Taube, and Christoph Müller
Geosci. Model Dev., 17, 7889–7914, https://doi.org/10.5194/gmd-17-7889-2024, https://doi.org/10.5194/gmd-17-7889-2024, 2024
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We present a new approach to modelling biological nitrogen fixation (BNF) in the Lund–Potsdam–Jena managed Land dynamic global vegetation model. While in the original approach BNF depended on actual evapotranspiration, the new approach considers soil water content and temperature, vertical root distribution, the nitrogen (N) deficit and carbon (C) costs. The new approach improved simulated BNF compared to the scientific literature and the model ability to project future C and N cycle dynamics.
Saeed Harati-Asl, Liliana Perez, and Roberto Molowny-Horas
Geosci. Model Dev., 17, 7423–7443, https://doi.org/10.5194/gmd-17-7423-2024, https://doi.org/10.5194/gmd-17-7423-2024, 2024
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Social–ecological systems are the subject of many sustainability problems. Because of the complexity of these systems, we must be careful when intervening in them; otherwise we may cause irreversible damage. Using computer models, we can gain insight about these complex systems without harming them. In this paper we describe how we connected an ecological model of forest insect infestation with a social model of cooperation and simulated an intervention measure to save a forest from infestation.
Katarína Merganičová, Ján Merganič, Laura Dobor, Roland Hollós, Zoltán Barcza, Dóra Hidy, Zuzana Sitková, Pavel Pavlenda, Hrvoje Marjanovic, Daniel Kurjak, Michal Bošel'a, Doroteja Bitunjac, Maša Zorana Ostrogović Sever, Jiří Novák, Peter Fleischer, and Tomáš Hlásny
Geosci. Model Dev., 17, 7317–7346, https://doi.org/10.5194/gmd-17-7317-2024, https://doi.org/10.5194/gmd-17-7317-2024, 2024
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We developed a multi-objective calibration approach leading to robust parameter values aiming to strike a balance between their local precision and broad applicability. Using the Biome-BGCMuSo model, we tested the calibrated parameter sets for simulating European beech forest dynamics across large environmental gradients. Leveraging data from 87 plots and five European countries, the results demonstrated reasonable local accuracy and plausible large-scale productivity responses.
Hoa T. T. Nguyen, Ute Daewel, Neil Banas, and Corinna Schrum
EGUsphere, https://doi.org/10.5194/egusphere-2024-2710, https://doi.org/10.5194/egusphere-2024-2710, 2024
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Parameterisation is key in modeling to reproduce observations well but is often done manually. This study presents a Particle Swarm Optimizer-based toolbox for marine ecosystem models, compatible with the Framework for Aquatic Biogeochemical Models, thus enhancing its reusability. Applied to the Sylt ecosystem, the toolbox effectively (1) identified multiple parameter sets that matched observations well, thus providing different insights into ecosystem dynamics, (2) optimized model complexity.
Sylvain Schmitt, Fabian Fischer, James Ball, Nicolas Barbier, Marion Boisseaux, Damien Bonal, Benoit Burban, Xiuzhi Chen, Géraldine Derroire, Jeremy Lichstein, Daniela Nemetschek, Natalia Restrepo-Coupe, Scott Saleska, Giacomo Sellan, Philippe Verley, Grégoire Vincent, Camille Ziegler, Jérôme Chave, and Isabelle Maréchaux
EGUsphere, https://doi.org/10.5194/egusphere-2024-3106, https://doi.org/10.5194/egusphere-2024-3106, 2024
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We evaluate the capability of TROLL 4.0, a simulator of forest dynamics, to represent tropical forest structure, diversity and functioning in two Amazonian forests. Evaluation data include forest inventories, carbon and water fluxes between the forest and the atmosphere, and leaf area and canopy height from remote-sensing products. The model realistically predicts the structure and composition, and the seasonality of carbon and water fluxes at both sites.
Zhengyang Lin, Ling Huang, Hanqin Tian, Anping Chen, and Xuhui Wang
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-170, https://doi.org/10.5194/gmd-2024-170, 2024
Revised manuscript accepted for GMD
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Wildfires release large amounts of greenhouse gases, contributing to global warming. We developed a new model that provides near-real-time estimates of wildfire emissions in China. Our model improves the accuracy of burned area measurements and incorporates advanced data in fuel loads and emission factors. We found that most emissions come from agricultural fires, while emissions from forests and grasslands are decreasing. This model will help reduce the environmental impacts of wildfires.
Elchin E. Jafarov, Helene Genet, Velimir V. Vesselinov, Valeria Briones, Aiza Kabeer, Andrew L. Mullen, Benjamin Maglio, Tobey Carman, Ruth Rutter, Joy Clein, Chu-Chun Chang, Dogukan Teber, Trevor Smith, Joshua M. Rady, Christina Schädel, Jennifer D. Watts, Brendan M. Rogers, and Susan M. Natali
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-158, https://doi.org/10.5194/gmd-2024-158, 2024
Revised manuscript accepted for GMD
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Thawing permafrost could greatly impact global climate. Our study improves modeling of carbon cycling in Arctic ecosystems. We developed an automated method to fine-tune a model that simulates carbon and nitrogen flows, using computer-generated data. Using computer-generated data, we tested our method and found it enhances accuracy and reduces the time needed for calibration. This work helps make climate predictions more reliable in sensitive permafrost regions.
Zavud Baghirov, Martin Jung, Markus Reichstein, Marco Körner, and Basil Kraft
EGUsphere, https://doi.org/10.5194/egusphere-2024-2044, https://doi.org/10.5194/egusphere-2024-2044, 2024
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We use an innovative approach to study the Earth's water cycle by blending advanced computer learning techniques with a traditional water cycle model. We developed a model that learns from meteorological data, with a special focus on understanding how vegetation influences water movement. Our model closely aligns with real-world observations, yet there are areas that need improvement. This study opens up new possibilities to better understand the water cycle and its interactions with vegetation.
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.
Thi Lan Anh Dinh, Daniel Goll, Philippe Ciais, and Ronny Lauerwald
Geosci. Model Dev., 17, 6725–6744, https://doi.org/10.5194/gmd-17-6725-2024, https://doi.org/10.5194/gmd-17-6725-2024, 2024
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The study assesses the performance of the dynamic global vegetation model (DGVM) ORCHIDEE in capturing the impact of land-use change on carbon stocks across Europe. Comparisons with observations reveal that the model accurately represents carbon fluxes and stocks. Despite the underestimations in certain land-use conversions, the model describes general trends in soil carbon response to land-use change, aligning with the site observations.
Nathaelle Bouttes, Lester Kwiatkowski, Manon Berger, Victor Brovkin, and Guy Munhoven
Geosci. Model Dev., 17, 6513–6528, https://doi.org/10.5194/gmd-17-6513-2024, https://doi.org/10.5194/gmd-17-6513-2024, 2024
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Coral reefs are crucial for biodiversity, but they also play a role in the carbon cycle on long time scales of a few thousand years. To better simulate the future and past evolution of coral reefs and their effect on the global carbon cycle, hence on atmospheric CO2 concentration, it is necessary to include coral reefs within a climate model. Here we describe the inclusion of coral reef carbonate production in a carbon–climate model and its validation in comparison to existing modern data.
Huajie Zhu, Mousong Wu, Fei Jiang, Michael Vossbeck, Thomas Kaminski, Xiuli Xing, Jun Wang, Weimin Ju, and Jing M. Chen
Geosci. Model Dev., 17, 6337–6363, https://doi.org/10.5194/gmd-17-6337-2024, https://doi.org/10.5194/gmd-17-6337-2024, 2024
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In this work, we developed the Nanjing University Carbon Assimilation System (NUCAS v1.0). Data assimilation experiments were conducted to demonstrate the robustness and investigate the feasibility and applicability of NUCAS. The assimilation of ecosystem carbonyl sulfide (COS) fluxes improved the model performance in gross primary productivity, evapotranspiration, and sensible heat, showing that COS provides constraints on parameters relevant to carbon-, water-, and energy-related processes.
Ye Liu, Huilin Huang, Sing-Chun Wang, Tao Zhang, Donghui Xu, and Yang Chen
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-151, https://doi.org/10.5194/gmd-2024-151, 2024
Revised manuscript accepted for GMD
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This study integrates machine learning with a land surface model to improve wildfire predictions in North America. Traditional models struggle with accurately simulating burned areas due to simplified processes. By combining the predictive power of machine learning with a land model, our hybrid framework better captures fire dynamics. This approach enhances our understanding of wildfire behavior and aids in developing more effective climate and fire management strategies.
Sergi Molins, Benjamin Andre, Jeffrey Johnson, Glenn Hammond, Benjamin Sulman, Konstantin Lipnikov, Marcus Day, James Beisman, Daniil Svyatsky, Hang Deng, Peter Lichtner, Carl Steefel, and David Moulton
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-108, https://doi.org/10.5194/gmd-2024-108, 2024
Revised manuscript accepted for GMD
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Developing scientific software and making sure it functions properly requires a significant effort. As we advance our understanding of natural systems, however, there is the need to develop yet more complex models and codes. In this work, we present a piece of software that facilitates this work, specifically with regard to reactive processes. Existing tried-and-true codes are made available via this new interface, freeing up resources to focus on the new aspects of the problems at hand.
Fang Li, Zhimin Zhou, Samuel Levis, Stephen Sitch, Felicity Hayes, Zhaozhong Feng, Peter B. Reich, Zhiyi Zhao, and Yanqing Zhou
Geosci. Model Dev., 17, 6173–6193, https://doi.org/10.5194/gmd-17-6173-2024, https://doi.org/10.5194/gmd-17-6173-2024, 2024
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A new scheme is developed to model the surface ozone damage to vegetation in regional and global process-based models. Based on 4210 data points from ozone experiments, it accurately reproduces statistically significant linear or nonlinear photosynthetic and stomatal responses to ozone in observations for all vegetation types. It also enables models to implicitly capture the variability in plant ozone tolerance and the shift among species within a vegetation type.
Alexander S. Brunmayr, Frank Hagedorn, Margaux Moreno Duborgel, Luisa I. Minich, and Heather D. Graven
Geosci. Model Dev., 17, 5961–5985, https://doi.org/10.5194/gmd-17-5961-2024, https://doi.org/10.5194/gmd-17-5961-2024, 2024
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A new generation of soil models promises to more accurately predict the carbon cycle in soils under climate change. However, measurements of 14C (the radioactive carbon isotope) in soils reveal that the new soil models face similar problems to the traditional models: they underestimate the residence time of carbon in soils and may therefore overestimate the net uptake of CO2 by the land ecosystem. Proposed solutions include restructuring the models and calibrating model parameters with 14C data.
Nina Raoult, Simon Beylat, James M. Salter, Frédéric Hourdin, Vladislav Bastrikov, Catherine Ottlé, and Philippe Peylin
Geosci. Model Dev., 17, 5779–5801, https://doi.org/10.5194/gmd-17-5779-2024, https://doi.org/10.5194/gmd-17-5779-2024, 2024
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We use computer models to predict how the land surface will respond to climate change. However, these complex models do not always simulate what we observe in real life, limiting their effectiveness. To improve their accuracy, we use sophisticated statistical and computational techniques. We test a technique called history matching against more common approaches. This method adapts well to these models, helping us better understand how they work and therefore how to make them more realistic.
Jorn Bruggeman, Karsten Bolding, Lars Nerger, Anna Teruzzi, Simone Spada, Jozef Skákala, and Stefano Ciavatta
Geosci. Model Dev., 17, 5619–5639, https://doi.org/10.5194/gmd-17-5619-2024, https://doi.org/10.5194/gmd-17-5619-2024, 2024
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To understand and predict the ocean’s capacity for carbon sequestration, its ability to supply food, and its response to climate change, we need the best possible estimate of its physical and biogeochemical properties. This is obtained through data assimilation which blends numerical models and observations. We present the Ensemble and Assimilation Tool (EAT), a flexible and efficient test bed that allows any scientist to explore and further develop the state of the art in data assimilation.
Dongyu Zheng, Andrew S. Merdith, Yves Goddéris, Yannick Donnadieu, Khushboo Gurung, and Benjamin J. W. Mills
Geosci. Model Dev., 17, 5413–5429, https://doi.org/10.5194/gmd-17-5413-2024, https://doi.org/10.5194/gmd-17-5413-2024, 2024
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This study uses a deep learning method to upscale the time resolution of paleoclimate simulations to 1 million years. This improved resolution allows a climate-biogeochemical model to more accurately predict climate shifts. The method may be critical in developing new fully continuous methods that are able to be applied over a moving continental surface in deep time with high resolution at reasonable computational expense.
Boris Ťupek, Aleksi Lehtonen, Alla Yurova, Rose Abramoff, Bertrand Guenet, Elisa Bruni, Samuli Launiainen, Mikko Peltoniemi, Shoji Hashimoto, Xianglin Tian, Juha Heikkinen, Kari Minkkinen, and Raisa Mäkipää
Geosci. Model Dev., 17, 5349–5367, https://doi.org/10.5194/gmd-17-5349-2024, https://doi.org/10.5194/gmd-17-5349-2024, 2024
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Updating the Yasso07 soil C model's dependency on decomposition with a hump-shaped Ricker moisture function improved modelled soil organic C (SOC) stocks in a catena of mineral and organic soils in boreal forest. The Ricker function, set to peak at a rate of 1 and calibrated against SOC and CO2 data using a Bayesian approach, showed a maximum in well-drained soils. Using SOC and CO2 data together with the moisture only from the topsoil humus was crucial for accurate model estimates.
Jacquelyn K. Shuman, Rosie A. Fisher, Charles Koven, Ryan Knox, Lara Kueppers, and Chonggang Xu
Geosci. Model Dev., 17, 4643–4671, https://doi.org/10.5194/gmd-17-4643-2024, https://doi.org/10.5194/gmd-17-4643-2024, 2024
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We adapt a fire behavior and effects module for use in a size-structured vegetation demographic model to test how climate, fire regime, and fire-tolerance plant traits interact to determine the distribution of tropical forests and grasslands. Our model captures the connection between fire disturbance and plant fire-tolerance strategies in determining plant distribution and provides a useful tool for understanding the vulnerability of these areas under changing conditions across the tropics.
Naveenkumar Parameswaran, Everardo González, Ewa Burwicz-Galerne, Malte Braack, and Klaus Wallmann
EGUsphere, https://doi.org/10.5194/egusphere-2024-1360, https://doi.org/10.5194/egusphere-2024-1360, 2024
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Our research uses deep learning to predict organic carbon stocks in ocean sediments, crucial for understanding their role in the global carbon cycle. By analyzing over 22,000 samples and various seafloor characteristics, our model gives more accurate results than traditional methods. We estimate the top 10 cm of ocean sediments hold about 171 petagrams of carbon. This work enhances carbon stock estimates and helps plan future sampling strategies to better understand oceanic carbon burial.
Yoshiki Kanzaki, Isabella Chiaravalloti, Shuang Zhang, Noah J. Planavsky, and Christopher T. Reinhard
Geosci. Model Dev., 17, 4515–4532, https://doi.org/10.5194/gmd-17-4515-2024, https://doi.org/10.5194/gmd-17-4515-2024, 2024
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Soil pH is one of the most commonly measured agronomical and biogeochemical indices, mostly reflecting exchangeable acidity. Explicit simulation of both porewater and bulk soil pH is thus crucial to the accurate evaluation of alkalinity required to counteract soil acidification and the resulting capture of anthropogenic carbon dioxide through the enhanced weathering technique. This has been enabled by the updated reactive–transport SCEPTER code and newly developed framework to simulate soil pH.
David Sandoval, Iain Colin Prentice, and Rodolfo L. B. Nóbrega
Geosci. Model Dev., 17, 4229–4309, https://doi.org/10.5194/gmd-17-4229-2024, https://doi.org/10.5194/gmd-17-4229-2024, 2024
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Numerous estimates of water and energy balances depend on empirical equations requiring site-specific calibration, posing risks of "the right answers for the wrong reasons". We introduce novel first-principles formulations to calculate key quantities without requiring local calibration, matching predictions from complex land surface models.
Oliver Perkins, Matthew Kasoar, Apostolos Voulgarakis, Cathy Smith, Jay Mistry, and James D. A. Millington
Geosci. Model Dev., 17, 3993–4016, https://doi.org/10.5194/gmd-17-3993-2024, https://doi.org/10.5194/gmd-17-3993-2024, 2024
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Wildfire is often presented in the media as a danger to human life. Yet globally, millions of people’s livelihoods depend on using fire as a tool. So, patterns of fire emerge from interactions between humans, land use, and climate. This complexity means scientists cannot yet reliably say how fire will be impacted by climate change. So, we developed a new model that represents globally how people use and manage fire. The model reveals the extent and diversity of how humans live with and use fire.
Amos P. K. Tai, David H. Y. Yung, and Timothy Lam
Geosci. Model Dev., 17, 3733–3764, https://doi.org/10.5194/gmd-17-3733-2024, https://doi.org/10.5194/gmd-17-3733-2024, 2024
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We have developed the Terrestrial Ecosystem Model in R (TEMIR), which simulates plant carbon and pollutant uptake and predicts their response to varying atmospheric conditions. This model is designed to couple with an atmospheric chemistry model so that questions related to plant–atmosphere interactions, such as the effects of climate change, rising CO2, and ozone pollution on forest carbon uptake, can be addressed. The model has been well validated with both ground and satellite observations.
Fabian Stenzel, Johanna Braun, Jannes Breier, Karlheinz Erb, Dieter Gerten, Jens Heinke, Sarah Matej, Sebastian Ostberg, Sibyll Schaphoff, and Wolfgang Lucht
Geosci. Model Dev., 17, 3235–3258, https://doi.org/10.5194/gmd-17-3235-2024, https://doi.org/10.5194/gmd-17-3235-2024, 2024
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We provide an R package to compute two biosphere integrity metrics that can be applied to simulations of vegetation growth from the dynamic global vegetation model LPJmL. The pressure metric BioCol indicates that we humans modify and extract > 20 % of the potential preindustrial natural biomass production. The ecosystems state metric EcoRisk shows a high risk of ecosystem destabilization in many regions as a result of climate change and land, water, and fertilizer use.
Elin Ristorp Aas, Heleen A. de Wit, and Terje K. Berntsen
Geosci. Model Dev., 17, 2929–2959, https://doi.org/10.5194/gmd-17-2929-2024, https://doi.org/10.5194/gmd-17-2929-2024, 2024
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By including microbial processes in soil models, we learn how the soil system interacts with its environment and responds to climate change. We present a soil process model, MIMICS+, which is able to reproduce carbon stocks found in boreal forest soils better than a conventional land model. With the model we also find that when adding nitrogen, the relationship between soil microbes changes notably. Coupling the model to a vegetation model will allow for further study of these mechanisms.
Thomas Wutzler, Christian Reimers, Bernhard Ahrens, and Marion Schrumpf
Geosci. Model Dev., 17, 2705–2725, https://doi.org/10.5194/gmd-17-2705-2024, https://doi.org/10.5194/gmd-17-2705-2024, 2024
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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.
Salvatore R. Curasi, Joe R. Melton, Elyn R. Humphreys, Txomin Hermosilla, and Michael A. Wulder
Geosci. Model Dev., 17, 2683–2704, https://doi.org/10.5194/gmd-17-2683-2024, https://doi.org/10.5194/gmd-17-2683-2024, 2024
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Canadian forests are responding to fire, harvest, and climate change. Models need to quantify these processes and their carbon and energy cycling impacts. We develop a scheme that, based on satellite records, represents fire, harvest, and the sparsely vegetated areas that these processes generate. We evaluate model performance and demonstrate the impacts of disturbance on carbon and energy cycling. This work has implications for land surface modeling and assessing Canada’s terrestrial C cycle.
Yannek Käber, Florian Hartig, and Harald Bugmann
Geosci. Model Dev., 17, 2727–2753, https://doi.org/10.5194/gmd-17-2727-2024, https://doi.org/10.5194/gmd-17-2727-2024, 2024
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Many forest models include detailed mechanisms of forest growth and mortality, but regeneration is often simplified. Testing and improving forest regeneration models is challenging. We address this issue by exploring how forest inventories from unmanaged European forests can be used to improve such models. We find that competition for light among trees is captured by the model, unknown model components can be informed by forest inventory data, and climatic effects are challenging to capture.
Jalisha T. Kallingal, Johan Lindström, Paul A. Miller, Janne Rinne, Maarit Raivonen, and Marko Scholze
Geosci. Model Dev., 17, 2299–2324, https://doi.org/10.5194/gmd-17-2299-2024, https://doi.org/10.5194/gmd-17-2299-2024, 2024
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By unlocking the mysteries of CH4 emissions from wetlands, our work improved the accuracy of the LPJ-GUESS vegetation model using Bayesian statistics. Via assimilation of long-term real data from a wetland, we significantly enhanced CH4 emission predictions. This advancement helps us better understand wetland contributions to atmospheric CH4, which are crucial for addressing climate change. Our method offers a promising tool for refining global climate models and guiding conservation efforts
Benjamin Post, Esteban Acevedo-Trejos, Andrew D. Barton, and Agostino Merico
Geosci. Model Dev., 17, 1175–1195, https://doi.org/10.5194/gmd-17-1175-2024, https://doi.org/10.5194/gmd-17-1175-2024, 2024
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Creating computational models of how phytoplankton grows in the ocean is a technical challenge. We developed a new tool set (Xarray-simlab-ODE) for building such models using the programming language Python. We demonstrate the tool set in a library of plankton models (Phydra). Our goal was to allow scientists to develop models quickly, while also allowing the model structures to be changed easily. This allows us to test many different structures of our models to find the most appropriate one.
Taeken Wijmer, Ahmad Al Bitar, Ludovic Arnaud, Remy Fieuzal, and Eric Ceschia
Geosci. Model Dev., 17, 997–1021, https://doi.org/10.5194/gmd-17-997-2024, https://doi.org/10.5194/gmd-17-997-2024, 2024
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Quantification of carbon fluxes of crops is an essential building block for the construction of a monitoring, reporting, and verification approach. We developed an end-to-end platform (AgriCarbon-EO) that assimilates, through a Bayesian approach, high-resolution (10 m) optical remote sensing data into radiative transfer and crop modelling at regional scale (100 x 100 km). Large-scale estimates of carbon flux are validated against in situ flux towers and yield maps and analysed at regional scale.
Moritz Laub, Sergey Blagodatsky, Marijn Van de Broek, Samuel Schlichenmaier, Benjapon Kunlanit, Johan Six, Patma Vityakon, and Georg Cadisch
Geosci. Model Dev., 17, 931–956, https://doi.org/10.5194/gmd-17-931-2024, https://doi.org/10.5194/gmd-17-931-2024, 2024
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To manage soil organic matter (SOM) sustainably, we need a better understanding of the role that soil microbes play in aggregate protection. Here, we propose the SAMM model, which connects soil aggregate formation to microbial growth. We tested it against data from a tropical long-term experiment and show that SAMM effectively represents the microbial growth, SOM, and aggregate dynamics and that it can be used to explore the importance of aggregate formation in SOM stabilization.
Jianhong Lin, Daniel Berveiller, Christophe François, Heikki Hänninen, Alexandre Morfin, Gaëlle Vincent, Rui Zhang, Cyrille Rathgeber, and Nicolas Delpierre
Geosci. Model Dev., 17, 865–879, https://doi.org/10.5194/gmd-17-865-2024, https://doi.org/10.5194/gmd-17-865-2024, 2024
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Currently, the high variability of budburst between individual trees is overlooked. The consequences of this neglect when projecting the dynamics and functioning of tree communities are unknown. Here we develop the first process-oriented model to describe the difference in budburst dates between individual trees in plant populations. Beyond budburst, the model framework provides a basis for studying the dynamics of phenological traits under climate change, from the individual to the community.
Cited articles
Barton, L., Wolf, B., Rowlings, D., Scheer, C., Kiese, R., Grace, P., Grace, P., Stefanova, K., and Butterbach-Bahl, K.: Sampling frequency affects estimates of annual nitrous oxide fluxes, Scientific Reports, 5, 15912, https://doi.org/10.1038/srep15912, 2015.
Bauer, P., Dueben, P. D., Hoefler, T., Quintino, T., Schulthess, T. C., and Wedi, N. P.: The digital revolution of Earth-system science, Nature Computational Science, 1, 104–113, https://doi.org/10.1038/s43588-021-00023-0, 2021.
Beucler, T., Rasp, S., Pritchard, M., and Gentine, P.: Achieving conservation of energy in neural network emulators for climate modeling, arXiv [preprint], arXiv:1906.06622, 2019.
Beucler, T., Pritchard, M., Rasp, S., Ott, J., Baldi, P., and Gentine, P.: Enforcing analytic constraints in neural networks emulating physical systems, Phys. Rev. Lett., 126, 098302, https://doi.org/10.1103/PhysRevLett.126.098302, 2021.
Butterbach-Bahl, K., Baggs, E. M., Dannenmann, M., Kiese, R., and Zechmeister-Boltenstern, S.: Nitrous oxide emissions from soils: how well do we understand the processes and their controls?, Philos. T. Roy. Soc. B, 368, 20130122, https://doi.org/10.1098/rstb.2013.0122, 2013.
Cho, K., Van Merriënboer, B., Bahdanau, D., and Bengio, Y.: On the properties of neural machine translation: Encoder-decoder approaches, arXiv [preprint], arXiv:1409.1259, 2014.
Chung, J., Gulcehre, C., Cho, K. H., and Bengio, Y.: Empirical evaluation of gated recurrent neural networks on sequence modeling, arXiv [preprint], arXiv:1412.3555, 2014.
Davidson, E. A., Keller, M., Erickson, H. E., Verchot, L. V., and Veldkamp, E.: Testing a conceptual model of soil emissions of nitrous and nitric oxides: using two functions based on soil nitrogen availability and soil water content, the hole-in-the-pipe model characterizes a large fraction of the observed variation of nitric oxide and nitrous oxide emissions from soils, Bioscience, 50, 667–680, https://doi.org/10.1641/0006-3568(2000)050[0667:TACMOS]2.0.CO;2, 2000.
Del Grosso, S. J., Parton, W. J., Mosier, A. R., Ojima, D. S., Kulmala, A. E., and Phongpan, S.: General model for N2O and N2 gas emissions from soils due to dentrification, Global Biogeochem. Cy., 14, 1045–1060, https://doi.org/10.1029/1999GB001225, 2020.
Fassbinder, J. J., Griffis, T. J., and Baker, J. M.: Evaluation of carbon isotope flux partitioning theory under simplified and controlled environmental conditions, Agr. Forest Meteorol., 153, 154–164, https://doi.org/10.1016/j.agrformet.2011.09.020, 2012.
Fassbinder, J. J., Schultz, N. M., Baker, J. M., and Griffis, T. J.: Automated, Low-Power Chamber System for Measuring Nitrous Oxide Emissions, J. Environ. Qual., 42, 606, https://doi.org/10.2134/jeq2012.0283, 2013.
Forster, P., Storelvmo, T., Armour, K., Collins, W., Dufresne, J.-L., Frame, D., Lunt, D., Mauritsen, T., Palmer, M., Watanabe, M., Wild, M., and Zhang, H.: The Earth's Energy Budget, Climate Feedbacks, and Climate Sensitivity, in: Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change, Open Access Te Herenga Waka-Victoria University of Wellington, https://doi.org/10.25455/wgtn.16869671.v1 (last access: 26 October 2021), 2021.
Grant, R. F.: A review of the Canadian ecosystem model ecosys: Modeling Carbon and Nitrogen Dynamics for Soil Management, 1st edn., CRC Press, Boca Raton, FL, USA, 173–264, ISBN 1566705290, 2001.
Grant, R. F. and Pattey, E.: Mathematical modeling of nitrous oxide emissions from an agricultural field during spring thaw, Global Biogeochem. Cy., 13, 679–694, https://doi.org/10.1029/1998GB900018, 1999.
Grant, R. F. and Pattey, E.: Modelling variability in N2O emissions from fertilized agricultural fields, Soil Biol. Biochem., 35, 225–243, https://doi.org/10.1016/S0038-0717(02)00256-0, 2003.
Grant, R. F. and Pattey, E.: Temperature sensitivity of N2O emissions from fertilized agricultural soils: Mathematical modeling in ecosys, Global Biogeochem. Cy., 22, GB4019, https://doi.org/10.1029/2008GB003273, 2008.
Grant, R. F., Pattey, E., Goddard, T. W., Kryzanowski, L. M., and Puurveen, H.: Modeling the effects of fertilizer application rate on nitrous oxide emissions, Soil Sci. Soc. Am. J., 70, 235–248, https://doi.org/10.2136/sssaj2005.0104, 2006.
Grant, R. F., Black, T. A., Jassal, R. S., and Bruemmer, C.: Changes in net ecosystem productivity and greenhouse gas exchange with fertilization of Douglas fir: Mathematical modeling in ecosys, J. Geophys. Res.-Biogeo., 115, G04009, https://doi.org/10.1029/2009JG001094, 2010.
Grant, R. F., Neftel, A., and Calanca, P.: Ecological controls on N2O emission in surface litter and near-surface soil of a managed grassland: modelling and measurements, Biogeosciences, 13, 3549–3571, https://doi.org/10.5194/bg-13-3549-2016, 2016.
Hamrani, A., Akbarzadeh, A., and Madramootoo, C. A.: Machine learning for predicting greenhouse gas emissions from agricultural soils, Sci. Total Environ., 741, 140338, https://doi.org/10.1016/j.scitotenv.2020.140338, 2020.
Hanson, P. C., Stillman, A. B., Jia, X., Karpatne, A., Dugan, H. A., Carey, C. C., Stachelek, J., Ward, N. K., Zhang, Y., Read, J. S., and Kumar, V.: Predicting lake surface water phosphorus dynamics using process-guided machine learning, Ecol. Model., 430, 109136, https://doi.org/10.1016/j.ecolmodel.2020.109136, 2020.
Hochreiter, S. and Schmidhuber, J.: Long short-term memory, Neural Comput., 9, 1735–1780, https://doi.org/10.1162/neco.1997.9.8.1735, 1997.
Holzworth, D. P., Huth, N. I., deVoil, P. G., Zurcher, E. J., Herrmann, N. I., McLean, G., Chenu, K., van Oosterom, E. J., Snow, V., Murphy, C., Moore, A. D., Brown, H., Whish, J. P. M., Verrall, S., Fainges, J., Bell, L. W., Peake, A. S., Poulton, P. L., Hochman, Z., Thorburn, P. J., Gaydon, D. S., Dalgliesh, N. P., Rodriguez, D., Cox, H., Chapman, S., Doherty, A., Teixeira, E., Sharp, J., Cichota, R., Vogeler, I., Li, F. Y., Wang, E., Hammer, G. L., Robertson, M. J., Dimes, J. P., Whitbread, A. M., Hunt, J., van Rees, H., McClelland, T., Carberry, P. S., Hargreaves, J. N. G., MacLeod, N., McDonald, C., Harsdorf, J., Wedgwood, S., and Keating, B. A.: APSIM – evolution towards a new generation of agricultural systems simulation, Environ. Modell. Softw., 62, 327–350, https://doi.org/10.1016/j.envsoft.2014.07.009, 2014.
Irrgang, C., Boers, N., Sonnewald, M., Barnes, E. A., Kadow, C., Staneva, J., and Saynisch-Wagner, J.: Towards neural Earth system modelling by integrating artificial intelligence in Earth system science, Nature Machine Intelligence, 3, 667–674, https://doi.org/10.1038/s42256-021-00374-3, 2021.
Jia, X., Willard, J., Karpatne, A., Read, J., Zwart, J., Steinbach, M., and Kumar, V.: Physics guided RNNs for modeling dynamical systems: A case study in simulating lake temperature profiles, in: Proceedings of the 2019 SIAM International Conference on Data Mining, Society for Industrial and Applied Mathematics, Calgary, Alberta, Canada, 2–4 May 2019, 558–566, https://doi.org/10.1137/1.9781611975673.58, 2019.
Jia, X., Willard, J., Karpatne, A., Read, J. S., Zwart, J. A., Steinbach, M., and Kumar, V.: Physics-guided machine learning for scientific discovery: An application in simulating lake temperature profiles, ACM/IMS Transactions on Data Science, 2, 20, https://doi.org/10.1145/3447814, 2021.
Karpatne, A., Atluri, G., Faghmous, J. H., Steinbach, M., Banerjee, A., Ganguly, A., Shekhar, S., Samatova, N., and Kumar, V.: Theory-guided data science: A new paradigm for scientific discovery from data, IEEE T. Knowl. Data En., 29, 2318–2331, 2017.
Keating, B. A., Carberry, P. S., Hammer, G. L., Probert, M. E., Robertson, M. J., Holzworth, D., Huth, N. I., Hargreaves, J. N., Meinke, H., Hochman, Z., and McLean, G.: An overview of APSIM, a model designed for farming systems simulation, Eur. J. Agron., 18, 267–288, https://doi.org/10.1016/s1161-0301(02)00108-9, 2003.
Khandelwal, A., Xu, S., Li, X., Jia, X., Stienbach, M., Duffy, C., Nieber, J. and Kumar, V.: Physics guided machine learning methods for hydrology, arXiv [preprint], arXiv:2012.02854, 2020.
Kim, T., Jin, Z., Smith, T. M., Liu, L., Yang, Y., Yang, Y., Peng, B., Phillips, K., Guan, K., Hunter, L. C., and Zhou, W.: Quantifying nitrogen loss hotspots and mitigation potential for individual fields in the US Corn Belt with a metamodeling approach, Environ. Res. Lett., 16, 075008, https://doi.org/10.1088/1748-9326/ac0d21, 2021.
Kraft, B., Jung, M., Körner, M., Koirala, S., and Reichstein, M.: Towards hybrid modeling of the global hydrological cycle, Hydrol. Earth Syst. Sci., 26, 1579–1614, https://doi.org/10.5194/hess-26-1579-2022, 2022.
Liu, L. and Jin, Z.: Code and data for “KGML-ag: A Modeling Framework of Knowledge-Guided Machine Learning to Simulate Agroecosystems: A Case Study of Estimating N2O Emission using Data from Mesocosm Experiments” (v1.0), Zenodo [code and data set], https://doi.org/10.5281/zenodo.5504533, 2021.
Metivier, K. A., Pattey, E., and Grant, R. F.: Using the ecosys mathematical model to simulate temporal variability of nitrous oxide emissions from a fertilized agricultural soil, Soil Biol. Biochem., 41, 2370–2386, https://doi.org/10.1016/j.soilbio.2009.03.007, 2009.
Miller, L. T.: Assessing Agricultural Nitrous Oxide Emissions and Hot Moments Using Mesocosm Simulations, Master Thesis, University of Minnesota, University of Minnesota Digital Conservancy, https://hdl.handle.net/11299/219276, last access: 15 September 2021.
Miller, L. T., Griffis, T. J., Erickson, M. D., Turner, P. A., Deventer, M. J., Chen, Z., Yu, Z., Venterea, R. T., Baker, J. M., and Frie, A. L.: Response of nitrous oxide emissions to future changes in precipitation and individual rain events, J. Environ. Qual., https://doi.org/https://doi.org/10.1002/jeq2.20348, accepted, 2022.
Necpálová, M., Anex, R. P., Fienen, M. N., Del Grosso, S. J., Castellano, M. J., Sawyer, J. E., Iqbal, J., Pantoja, J. L., and Barker, D. W.: Understanding the DayCent model: Calibration, sensitivity, and identifiability through inverse modeling, Environ. Modell. Softw., 66, 110–130, https://doi.org/10.1016/j.envsoft.2014.12.011, 2015.
Oord, A. van den, Dieleman, S., Zen, H., Simonyan, K., Vinyals, O., Graves, A., Kalchbrenner, N., Senior, A., and Kavukcuoglu, K.: Wavenet: A generative model for raw audio, arXiv [preprint], arXiv:1609.03499, 2016.
Pachauri, R. K., Allen, M. R., Barros, V. R., Broome, J., Cramer, W., Christ, R., Church, J. A., Clarke, L., Dahe, Q., Dasgupta, P., Dubash, N. K., Edenhofer, O., Elgizouli, I., Field, C. B., Forster, P., Friedlingstein, P., Fuglestvedt, J., Gomez-Echeverri, L., Hallegatte, S., Hegerl, G., Howden, M., Jiang, K., Jimenez Cisneroz, B., Kattsov, V., Lee, H., Mach, K. J., Marotzke, J., Mastrandrea, M. D., Meyer, L., Minx, J., Mulugetta, Y., O'Brien, K., Oppenheimer, M., Pereira, J. J., Pichs-Madruga, R., Plattner, G. K., Pörtner, H. O., Power, S. B., Preston, B., Ravindranath, N. H., Reisinger, A., Riahi, K., Rusticucci, M., Scholes, R., Seyboth, K., Sokona, Y., Stavins, R., Stocker, T. F., Tschakert, P., van Vuuren, D. and van Ypserle, J. P.: Climate change 2014: synthesis report. Contribution of Working Groups I, II and III to the fifth assessment report of the Intergovernmental Panel on Climate Change, IPCC, 151, ISBN 978-92-9169-143-2, 2014.
Peng, B., Guan, K., Tang, J., Ainsworth, E. A., Asseng, S., Bernacchi, C. J., Cooper, M., Delucia, E. H., Elliott, J. W., Ewert, F., Grant, R. F., Gustafson, D. I., Hammer, G. L., Jin, Z., Jones, J. W., Kimm, H., Lawrence, D. M., Li, Y., Lombardozzi, D. L., Marshall-Colon, A., Messina, C. D., Ort, D. R., Schnable, J. C., Vallejos, C. E., Wu, A., Yin, X., and Zhou, W.: Towards a multiscale crop modelling framework for climate change adaptation assessment, Nat. Plants, 6, 338–348, https://doi.org/10.1038/s41477-020-0625-3, 2020.
Read, J. S., Jia, X., Willard, J., Appling, A. P., Zwart, J. A., Oliver, S. K., Karpatne, A., Hansen, G. J. A., Hanson, P. C., Watkins, W., Steinbach, M., and Kumar, V.: Process-guided deep learning predictions of lake water temperature, Water Resour. Res., 55, 9173–9190, https://doi.org/10.1029/2019WR024922, 2019.
Reichstein, M., Camps-Valls, G., Stevens, B., Jung, M., Denzler, J., and Carvalhais, N.: Deep learning and process understanding for data-driven Earth system science, Nature, 566, 195–204, https://doi.org/10.1038/s41586-019-0912-1, 2019.
Robertson, M., BenDor, T. K., Lave, R., Riggsbee, A., Ruhl, J. B., and Doyle, M.: Stacking ecosystem services, Front. Ecol. Environ., 12, 186–193, https://doi.org/10.1890/110292, 2014.
Rohe, L., Apelt, B., Vogel, H.-J., Well, R., Wu, G.-M., and Schlüter, S.: Denitrification in soil as a function of oxygen availability at the microscale, Biogeosciences, 18, 1185–1201, https://doi.org/10.5194/bg-18-1185-2021, 2021.
Saha, D., Basso, B., and Robertson, G. P.: Machine learning improves predictions of agricultural nitrous oxide (N2O) emissions from intensively managed cropping systems, Environ. Res. Lett., 16, 024004, https://doi.org/10.1088/1748-9326/abd2f3, 2021.
Soil Survey Staff: Gridded soil survey geographic (gSSURGO)
database for the United States of America and the
Territories, Commonwealths, and Island Nations served by
the USDA-NRCS United States Department of Agriculture,
Natural Resources Conservation Service, https://gdg.sc.egov.usda.gov/, last access: 15 September 2021.
Solazzo, E., Crippa, M., Guizzardi, D., Muntean, M.,
Choulga, M., and Janssens-Maenhout, G.: Uncertainties in the
Emissions Database for Global Atmospheric Research (EDGAR) emission
inventory of greenhouse gases, Atmos. Chem. Phys., 21, 5655–5683,
https://doi.org/10.5194/acp-21-5655-2021,
2021.
Syakila, A. and Kroeze, C.: The global nitrous oxide budget revisited, Greenhouse Gas Measurement and Management, 1, 17–26, https://doi.org/10.3763/ghgmm.2010.0007, 2011.
Thompson, R. L., Lassaletta, L., Patra, P. K., Wilson, C., Wells, K. C., Gressent, A., Koffi, E. N., Chipperfield, M. P., Winiwarter, W., Davidson, E. A., Tian, H., and Canadell, J. G.: Acceleration of global N2O emissions seen from two decades of atmospheric inversion, Nature Clim. Change, 9, 993–998, https://doi.org/10.1038/s41558-019-0613-7, 2019.
Thornley, J. H. and France, J.: Mathematical models in agriculture: quantitative methods for the plant, animal and ecological sciences, Cabi, ISBN 9780851990101, 2007.
Tian, H., Xu, R., Canadell, J. G., Thompson, R. L., Winiwarter, W., Suntharalingam, P., Davidson, E. A., Ciais, P., Jackson, R. B., Janssens-Maenhout, G., Prather, M. J., Regnier, P., Pan, N., Pan, S., Peters, G. P., Shi, H., Tubiello, F. N., Zaehle, S., Zhou, F., Arneth, A., Battaglia, G., Berthet, S., Bopp, L., Bouwman, A. F., Buitenhuis, E. T., Chang, J., Chipperfield, M. P., Dangal, S. R. S., Dlugokencky, E., Elkins, J. W., Eyre, B. D., Fu, B., Hall, B., Ito, A., Joos, F., Krummel, P. B., Landolfi, A., Laruelle, G. G., Lauerwald, R., Li, W., Lienert, S., Maavara, T., MacLeod, M., Millet, D. B., Olin, S., Patra, P. K., Prinn, R. G., Raymond, P. A., Ruiz, D. J., van der Werf, G. R., Vuichard, N., Wang, J., Weiss, R. F., Wells, K. C., Wilson, C., Yang, J., and Yao, Y.: A comprehensive quantification of global nitrous oxide sources and sinks, Nature, 586, 248–256, https://doi.org/10.1038/s41586-020-2780-0, 2020.
Venterea, R. T., Maharjan, B., and Dolan, M. S.: Fertilizer source and tillage effects on yield-scaled nitrous oxide emissions in a corn cropping system, J. Environ. Qual., 40, 1521–1531, https://doi.org/10.2134/jeq2011.0039, 2011.
Wagner-Riddle, C., Congreves, K. A., Abalos, D., Berg, A. A., Brown, S. E., Ambadan, J. T., Gao, X., and Tenuta, M.: Globally important nitrous oxide emissions from croplands induced by freeze–thaw cycles, Nat. Geosci., 10, 279–283, https://doi.org/10.1038/ngeo2907, 2017.
Willard, J., Jia, X., Xu, S., Steinbach, M., and Kumar, V.: Integrating Scientific Knowledge with Machine Learning for Engineering and Environmental Systems, arXiv [preprint], arXiv:2003.04919, 2020.
Xia, Y., Mitchell, K., Ek, M., Sheffield, J., Cosgrove, B., Wood, E., Luo, L., Alonge, C., Wei, H., Meng, J., Livneh, B., Lettenmaier, D., Koren, V., Duan, Q., Mo, K., Fan, Y., and Mocko, D.: Continental‐scale water and energy flux analysis and validation for the North American Land Data Assimilation System project phase 2 (NLDAS‐2): 1. Intercomparison and application of model products, J. Geophys. Res.-Atmos., 117, D03109, https://doi.org/10.1029/2011jd016048, 2012.
Zhang, Y. and Niu, H.: The development of the DNDC plant growth sub-model and the application of DNDC in agriculture: a review, Agr. Ecosyst. Environ., 230, 271–282, https://doi.org/10.1016/j.agee.2016.06.017, 2016.
Zhang, Y., Li, C., Zhou, X., and Moore III, B.: A simulation model linking crop growth and soil biogeochemistry for sustainable agriculture, Ecol. Model., 151, 75–108, https://doi.org/10.1016/S0304-3800(01)00527-0, 2002.
Zhou, W., Guan, K., Peng, B., Tang, J., Jin, Z., Jiang, C., Grant, R., and Mezbahuddin, S.: Quantifying carbon budget, crop yields and their responses to environmental variability using the ecosys model for US Midwestern agroecosystems, Agr. Forest Meteorol., 307, 108521, https://doi.org/10.1016/j.agrformet.2021.108521, 2021.
Short summary
By incorporating the domain knowledge into a machine learning model, KGML-ag overcomes the well-known limitations of process-based models due to insufficient representations and constraints, and unlocks the “black box” of machine learning models. Therefore, KGML-ag can outperform existing approaches on capturing the hot moment and complex dynamics of N2O flux. This study will be a critical reference for the new generation of modeling paradigm for biogeochemistry and other geoscience processes.
By incorporating the domain knowledge into a machine learning model, KGML-ag overcomes the...
