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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Jinyun Tang, William J. Riley, Gianna L. Marschmann, and Eoin L. Brodie
EGUsphere, https://doi.org/10.5194/egusphere-2025-5448, https://doi.org/10.5194/egusphere-2025-5448, 2025
This preprint is open for discussion and under review for Biogeosciences (BG).
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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.
Fan Sun, Yu Cui, Jiayin Su, Mark W. Shephard, Shailesh K. Kharol, Yifan Zhang, Xuejing Shi, Junqing Zhang, Huili Liu, Qitao Xiao, Xiao Lu, Zhao-Cheng Zeng, Timothy J. Griffis, and Cheng Hu
Atmos. Chem. Phys., 25, 17907–17932, https://doi.org/10.5194/acp-25-17907-2025, https://doi.org/10.5194/acp-25-17907-2025, 2025
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This study used satellite data and models to track ammonia concentration and dry deposition across China from 2013 to 2023. Ammonia levels rose sharply, especially in urban and farming regions, with the North China Plain showing the highest values. Human activity was the main driver of change. These findings highlight growing environmental risks and provide key insights for managing air quality and nitrogen pollution in one of the world's major emission hotspots.
Zewei Ma, Kaiyu Guan, Bin Peng, Wang Zhou, Robert Grant, Jinyun Tang, Murugesu Sivapalan, Ming Pan, Li Li, and Zhenong Jin
Hydrol. Earth Syst. Sci., 29, 6393–6417, https://doi.org/10.5194/hess-29-6393-2025, https://doi.org/10.5194/hess-29-6393-2025, 2025
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By involving soil oxygen dynamics, we explore tile drainage impacts on the coupled hydrology–biogeochemistry–crop system. We find that soil oxygen dynamics is the key mediator of tile–system dynamics. Tile drainage lowers soil water content and improves soil oxygen levels, helping crops grow during wet springs. The developed roots also help mitigate drought stress in dry summers. Overall, tile drainage increases crop resilience to climate change, making it a valuable future agricultural practice.
Binghong Han, Jian Bi, Shengli Tao, Tong Yang, Yongli Tang, Mengshuai Ge, Hao Wang, Zhenong Jin, Jinwei Dong, Zhibiao Nan, and Jin-Sheng He
Earth Syst. Sci. Data, 17, 2933–2952, https://doi.org/10.5194/essd-17-2933-2025, https://doi.org/10.5194/essd-17-2933-2025, 2025
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The Tibetan Plateau is an important pastoral area where cultivated pastures play an increasingly important role. However, little is known about the spatial distribution of the cultivated pastures due to the difficulty in distinguishing them from natural grasslands with remote sensing. For the first time, we have mapped the cultivated pastures on the plateau at a resolution of 30 m with decent accuracy. This dataset is valuable to scientists, policymakers, conservationists, and pastoralists.
Lingbo Li, Hong-Yi Li, Guta Abeshu, Jinyun Tang, L. Ruby Leung, Chang Liao, Zeli Tan, Hanqin Tian, Peter Thornton, and Xiaojuan Yang
Earth Syst. Sci. Data, 17, 2713–2733, https://doi.org/10.5194/essd-17-2713-2025, https://doi.org/10.5194/essd-17-2713-2025, 2025
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We have developed new maps that reveal how organic carbon from soil leaches into headwater streams over the contiguous United States. We use advanced artificial intelligence techniques and a massive amount of data, including observations at over 2500 gauges and a wealth of climate and environmental information. The maps are a critical step in understanding and predicting how carbon moves through our environment, hence making them a useful tool for tackling climate challenges.
Julien Lamour, Shawn P. Serbin, Alistair Rogers, Kelvin T. Acebron, Elizabeth Ainsworth, Loren P. Albert, Michael Alonzo, Jeremiah Anderson, Owen K. Atkin, Nicolas Barbier, Mallory L. Barnes, Carl J. Bernacchi, Ninon Besson, Angela C. Burnett, Joshua S. Caplan, Jérôme Chave, Alexander W. Cheesman, Ilona Clocher, Onoriode Coast, Sabrina Coste, Holly Croft, Boya Cui, Clément Dauvissat, Kenneth J. Davidson, Christopher Doughty, Kim S. Ely, Jean-Baptiste Féret, Iolanda Filella, Claire Fortunel, Peng Fu, Maquelle Garcia, Bruno O. Gimenez, Kaiyu Guan, Zhengfei Guo, David Heckmann, Patrick Heuret, Marney Isaac, Shan Kothari, Etsushi Kumagai, Thu Ya Kyaw, Liangyun Liu, Lingli Liu, Shuwen Liu, Joan Llusià, Troy Magney, Isabelle Maréchaux, Adam R. Martin, Katherine Meacham-Hensold, Christopher M. Montes, Romà Ogaya, Joy Ojo, Regison Oliveira, Alain Paquette, Josep Peñuelas, Antonia Debora Placido, Juan M. Posada, Xiaojin Qian, Heidi J. Renninger, Milagros Rodriguez-Caton, Andrés Rojas-González, Urte Schlüter, Giacomo Sellan, Courtney M. Siegert, Guangqin Song, Charles D. Southwick, Daisy C. Souza, Clément Stahl, Yanjun Su, Leeladarshini Sujeeun, To-Chia Ting, Vicente Vasquez, Amrutha Vijayakumar, Marcelo Vilas-Boas, Diane R. Wang, Sheng Wang, Han Wang, Jing Wang, Xin Wang, Andreas P. M. Weber, Christopher Y. S. Wong, Jin Wu, Fengqi Wu, Shengbiao Wu, Zhengbing Yan, Dedi Yang, and Yingyi Zhao
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2025-213, https://doi.org/10.5194/essd-2025-213, 2025
Revised manuscript accepted for ESSD
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We present the Global Spectra-Trait Initiative (GSTI), a collaborative repository of paired leaf hyperspectral and gas exchange measurements from diverse ecosystems. This repository provides a unique source of information for creating hyperspectral models for predicting photosynthetic traits and associated leaf traits in terrestrial plants.
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.
Zitong Li, Kang Sun, Kaiyu Guan, Sheng Wang, Bin Peng, Lieven Clarisse, Martin Van Damme, Pierre-François Coheur, Karen Cady-Pereira, Mark W. Shephard, Mark Zondlo, and Daniel Moore
EGUsphere, https://doi.org/10.5194/egusphere-2025-725, https://doi.org/10.5194/egusphere-2025-725, 2025
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We estimate ammonia fluxes over the contiguous U.S. from 2008 to 2022 using a directional derivative approach applied to satellite observations from IASI and CrIS. Satellite-based flux estimates reveal that ammonia emissions deposit in nearby vegetation, with pronounced seasonal and spatial variability driven by agricultural activities, underscoring the need for improved monitoring and management strategies.
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.
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.
Bharat Rastogi, John B. Miller, Micheal Trudeau, Arlyn E. Andrews, Lei Hu, Marikate Mountain, Thomas Nehrkorn, Bianca Baier, Kathryn McKain, John Mund, Kaiyu Guan, and Caroline B. Alden
Atmos. Chem. Phys., 21, 14385–14401, https://doi.org/10.5194/acp-21-14385-2021, https://doi.org/10.5194/acp-21-14385-2021, 2021
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Predicting Earth's climate is difficult, partly due to uncertainty in forecasting how much CO2 can be removed by oceans and plants, because we cannot measure these exchanges directly on large scales. Satellites such as NASA's OCO-2 can provide part of the needed information, but data need to be highly precise and accurate. We evaluate these data and find small biases in certain months that are similar to the signals of interest. We argue that continued improvement of these data is necessary.
Cheng Hu, Jiaping Xu, Cheng Liu, Yan Chen, Dong Yang, Wenjing Huang, Lichen Deng, Shoudong Liu, Timothy J. Griffis, and Xuhui Lee
Atmos. Chem. Phys., 21, 10015–10037, https://doi.org/10.5194/acp-21-10015-2021, https://doi.org/10.5194/acp-21-10015-2021, 2021
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Seventy percent of global CO2 emissions were emitted from urban landscapes. The Yangtze River delta (YRD) ranks as one of the most densely populated regions in the world and is an anthropogenic CO2 hotspot. Besides anthropogenic factors, natural ecosystems and croplands act as significant CO2 sinks and sources. Independent quantification of the fossil and cement CO2 emission and assessment of their impact on atmospheric δ13C-CO2 have potential to improve our understanding of urban CO2 cycling.
Chongya Jiang, Kaiyu Guan, Genghong Wu, Bin Peng, and Sheng Wang
Earth Syst. Sci. Data, 13, 281–298, https://doi.org/10.5194/essd-13-281-2021, https://doi.org/10.5194/essd-13-281-2021, 2021
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Photosynthesis, quantified by gross primary production (GPP), is a key Earth system process. To date, there is a lack of a high-spatiotemporal-resolution, real-time and observation-based GPP dataset. This work addresses this gap by developing a SatelLite Only Photosynthesis Estimation (SLOPE) model and generating a new GPP product, which is advanced in spatial and temporal resolutions, instantaneity, and quantitative uncertainty. The dataset will benefit a range of research and applications.
Xueying Yu, Dylan B. Millet, Kelley C. Wells, Daven K. Henze, Hansen Cao, Timothy J. Griffis, Eric A. Kort, Genevieve Plant, Malte J. Deventer, Randall K. Kolka, D. Tyler Roman, Kenneth J. Davis, Ankur R. Desai, Bianca C. Baier, Kathryn McKain, Alan C. Czarnetzki, and A. Anthony Bloom
Atmos. Chem. Phys., 21, 951–971, https://doi.org/10.5194/acp-21-951-2021, https://doi.org/10.5194/acp-21-951-2021, 2021
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Methane concentrations have doubled since 1750. The US Upper Midwest is a key region contributing to such trends, but sources are poorly understood. We collected and analyzed aircraft data to resolve spatial and timing biases in wetland and livestock emission estimates and uncover errors in inventory treatment of manure management. We highlight the importance of intensive agriculture for the regional and US methane budgets and the potential for methane mitigation through improved management.
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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...
