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
Related authors
Marielle Saunois, Ann R. Stavert, Ben Poulter, Philippe Bousquet, Josep G. Canadell, Robert B. Jackson, Peter A. Raymond, Edward J. Dlugokencky, Sander Houweling, Prabir K. Patra, Philippe Ciais, Vivek K. Arora, David Bastviken, Peter Bergamaschi, Donald R. Blake, Gordon Brailsford, Lori Bruhwiler, Kimberly M. Carlson, Mark Carrol, Simona Castaldi, Naveen Chandra, Cyril Crevoisier, Patrick M. Crill, Kristofer Covey, Charles L. Curry, Giuseppe Etiope, Christian Frankenberg, Nicola Gedney, Michaela I. Hegglin, Lena Höglund-Isaksson, Gustaf Hugelius, Misa Ishizawa, Akihiko Ito, Greet Janssens-Maenhout, Katherine M. Jensen, Fortunat Joos, Thomas Kleinen, Paul B. Krummel, Ray L. Langenfelds, Goulven G. Laruelle, Licheng Liu, Toshinobu Machida, Shamil Maksyutov, Kyle C. McDonald, Joe McNorton, Paul A. Miller, Joe R. Melton, Isamu Morino, Jurek Müller, Fabiola Murguia-Flores, Vaishali Naik, Yosuke Niwa, Sergio Noce, Simon O'Doherty, Robert J. Parker, Changhui Peng, Shushi Peng, Glen P. Peters, Catherine Prigent, Ronald Prinn, Michel Ramonet, Pierre Regnier, William J. Riley, Judith A. Rosentreter, Arjo Segers, Isobel J. Simpson, Hao Shi, Steven J. Smith, L. Paul Steele, Brett F. Thornton, Hanqin Tian, Yasunori Tohjima, Francesco N. Tubiello, Aki Tsuruta, Nicolas Viovy, Apostolos Voulgarakis, Thomas S. Weber, Michiel van Weele, Guido R. van der Werf, Ray F. Weiss, Doug Worthy, Debra Wunch, Yi Yin, Yukio Yoshida, Wenxin Zhang, Zhen Zhang, Yuanhong Zhao, Bo Zheng, Qing Zhu, Qiuan Zhu, and Qianlai Zhuang
Earth Syst. Sci. Data, 12, 1561–1623, https://doi.org/10.5194/essd-12-1561-2020, https://doi.org/10.5194/essd-12-1561-2020, 2020
Short summary
Short summary
Understanding and quantifying the global methane (CH4) budget is important for assessing realistic pathways to mitigate climate change. We have established a consortium of multidisciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate new research aimed at improving and regularly updating the global methane budget. This is the second version of the review dedicated to the decadal methane budget, integrating results of top-down and bottom-up estimates.
Hanbo Yun, Qingbai Wu, Qianlai Zhuang, Anping Chen, Tong Yu, Zhou Lyu, Yuzhong Yang, Huijun Jin, Guojun Liu, Yang Qu, and Licheng Liu
The Cryosphere, 12, 2803–2819, https://doi.org/10.5194/tc-12-2803-2018, https://doi.org/10.5194/tc-12-2803-2018, 2018
Short summary
Short summary
Here we reported the QTP permafrost region was a CH4 sink of −0.86 ± 0.23 g CH4-C m−2 yr−1 over 2012–2016, soil temperature and soil water content were dominant factors controlling CH4 fluxes, and their correlations changed with soil depth due to cryoturbation dynamics. This region was a net CH4 sink in autumn, but a net source in spring, despite both seasons experiencing similar top soil thawing and freezing dynamics.
Licheng Liu, Qianlai Zhuang, Qing Zhu, Shaoqing Liu, Hella van Asperen, and Mari Pihlatie
Atmos. Chem. Phys., 18, 7913–7931, https://doi.org/10.5194/acp-18-7913-2018, https://doi.org/10.5194/acp-18-7913-2018, 2018
Short summary
Short summary
carbon monoxide (CO) plays an important role in atmosphere. We developed a model to quantify soil CO exchanges with the atmosphere. The simulation is conducted for various ecosystems on a global scale during the 20th and 21st centuries. We found that areas near the Equator, the eastern US, Europe and eastern Asia are the largest sinks due to optimum soil moisture and high temperature. This study will benefit the modeling of the global climate and atmospheric chemistry.
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 Discuss., https://doi.org/10.5194/essd-2024-43, https://doi.org/10.5194/essd-2024-43, 2024
Preprint under review for ESSD
Short summary
Short summary
We have developed a new map that reveals 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 2,500 gauges and a wealth of climate and environmental information. The map is a critical step in understanding and predicting how carbon moves through our environment, hence a useful tool for tackling climate challenges.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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.
Marielle Saunois, Ann R. Stavert, Ben Poulter, Philippe Bousquet, Josep G. Canadell, Robert B. Jackson, Peter A. Raymond, Edward J. Dlugokencky, Sander Houweling, Prabir K. Patra, Philippe Ciais, Vivek K. Arora, David Bastviken, Peter Bergamaschi, Donald R. Blake, Gordon Brailsford, Lori Bruhwiler, Kimberly M. Carlson, Mark Carrol, Simona Castaldi, Naveen Chandra, Cyril Crevoisier, Patrick M. Crill, Kristofer Covey, Charles L. Curry, Giuseppe Etiope, Christian Frankenberg, Nicola Gedney, Michaela I. Hegglin, Lena Höglund-Isaksson, Gustaf Hugelius, Misa Ishizawa, Akihiko Ito, Greet Janssens-Maenhout, Katherine M. Jensen, Fortunat Joos, Thomas Kleinen, Paul B. Krummel, Ray L. Langenfelds, Goulven G. Laruelle, Licheng Liu, Toshinobu Machida, Shamil Maksyutov, Kyle C. McDonald, Joe McNorton, Paul A. Miller, Joe R. Melton, Isamu Morino, Jurek Müller, Fabiola Murguia-Flores, Vaishali Naik, Yosuke Niwa, Sergio Noce, Simon O'Doherty, Robert J. Parker, Changhui Peng, Shushi Peng, Glen P. Peters, Catherine Prigent, Ronald Prinn, Michel Ramonet, Pierre Regnier, William J. Riley, Judith A. Rosentreter, Arjo Segers, Isobel J. Simpson, Hao Shi, Steven J. Smith, L. Paul Steele, Brett F. Thornton, Hanqin Tian, Yasunori Tohjima, Francesco N. Tubiello, Aki Tsuruta, Nicolas Viovy, Apostolos Voulgarakis, Thomas S. Weber, Michiel van Weele, Guido R. van der Werf, Ray F. Weiss, Doug Worthy, Debra Wunch, Yi Yin, Yukio Yoshida, Wenxin Zhang, Zhen Zhang, Yuanhong Zhao, Bo Zheng, Qing Zhu, Qiuan Zhu, and Qianlai Zhuang
Earth Syst. Sci. Data, 12, 1561–1623, https://doi.org/10.5194/essd-12-1561-2020, https://doi.org/10.5194/essd-12-1561-2020, 2020
Short summary
Short summary
Understanding and quantifying the global methane (CH4) budget is important for assessing realistic pathways to mitigate climate change. We have established a consortium of multidisciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate new research aimed at improving and regularly updating the global methane budget. This is the second version of the review dedicated to the decadal methane budget, integrating results of top-down and bottom-up estimates.
Riccardo Tortini, Nina Noujdina, Samantha Yeo, Martina Ricko, Charon M. Birkett, Ankush Khandelwal, Vipin Kumar, Miriam E. Marlier, and Dennis P. Lettenmaier
Earth Syst. Sci. Data, 12, 1141–1151, https://doi.org/10.5194/essd-12-1141-2020, https://doi.org/10.5194/essd-12-1141-2020, 2020
Short summary
Short summary
We present a global collection of satellite-derived time series of surface water volume changes for 347 lakes and reservoirs for 1992–2018. These changes were estimated using a statistical relationship between water surface elevation and area measured from satellite, even during periods when either elevation or area was not available. These records represent the most complete global surface water time series, and they are of fundamental importance to baseline future satellite missions.
Chongya Jiang, Kaiyu Guan, Ming Pan, Youngryel Ryu, Bin Peng, and Sibo Wang
Hydrol. Earth Syst. Sci., 24, 1251–1273, https://doi.org/10.5194/hess-24-1251-2020, https://doi.org/10.5194/hess-24-1251-2020, 2020
Short summary
Short summary
Quantifying crop water use at each field every day is challenging because of the complexity of the evapotranspiration (ET) process and the unavailability of data at high spatiotemporal resolutions. We fuse multi-satellite data and employ a sophisticated model to estimate ET at 30 m resolution and a daily interval. With validation against 86 site years of ground truth in the US Corn Belt, we are confident that our ET estimation is accurate and a reliable tool for water resource management.
Fushan Wang, Guangheng Ni, William J. Riley, Jinyun Tang, Dejun Zhu, and Ting Sun
Geosci. Model Dev., 12, 2119–2138, https://doi.org/10.5194/gmd-12-2119-2019, https://doi.org/10.5194/gmd-12-2119-2019, 2019
Short summary
Short summary
The current lake model in the Weather Research and Forecasting system was reported to be insufficient in simulating deep lakes and reservoirs. We thus revised the lake model by improving its spatial discretization scheme, surface property parameterization, diffusivity parameterization, and convection scheme. The revised model was evaluated at a deep reservoir in southwestern China and the results were in good agreement with measurements.
Hanbo Yun, Qingbai Wu, Qianlai Zhuang, Anping Chen, Tong Yu, Zhou Lyu, Yuzhong Yang, Huijun Jin, Guojun Liu, Yang Qu, and Licheng Liu
The Cryosphere, 12, 2803–2819, https://doi.org/10.5194/tc-12-2803-2018, https://doi.org/10.5194/tc-12-2803-2018, 2018
Short summary
Short summary
Here we reported the QTP permafrost region was a CH4 sink of −0.86 ± 0.23 g CH4-C m−2 yr−1 over 2012–2016, soil temperature and soil water content were dominant factors controlling CH4 fluxes, and their correlations changed with soil depth due to cryoturbation dynamics. This region was a net CH4 sink in autumn, but a net source in spring, despite both seasons experiencing similar top soil thawing and freezing dynamics.
Licheng Liu, Qianlai Zhuang, Qing Zhu, Shaoqing Liu, Hella van Asperen, and Mari Pihlatie
Atmos. Chem. Phys., 18, 7913–7931, https://doi.org/10.5194/acp-18-7913-2018, https://doi.org/10.5194/acp-18-7913-2018, 2018
Short summary
Short summary
carbon monoxide (CO) plays an important role in atmosphere. We developed a model to quantify soil CO exchanges with the atmosphere. The simulation is conducted for various ecosystems on a global scale during the 20th and 21st centuries. We found that areas near the Equator, the eastern US, Europe and eastern Asia are the largest sinks due to optimum soil moisture and high temperature. This study will benefit the modeling of the global climate and atmospheric chemistry.
Kelley C. Wells, Dylan B. Millet, Nicolas Bousserez, Daven K. Henze, Timothy J. Griffis, Sreelekha Chaliyakunnel, Edward J. Dlugokencky, Eri Saikawa, Gao Xiang, Ronald G. Prinn, Simon O'Doherty, Dickon Young, Ray F. Weiss, Geoff S. Dutton, James W. Elkins, Paul B. Krummel, Ray Langenfelds, and L. Paul Steele
Atmos. Chem. Phys., 18, 735–756, https://doi.org/10.5194/acp-18-735-2018, https://doi.org/10.5194/acp-18-735-2018, 2018
Short summary
Short summary
This paper uses three different frameworks to derive nitrous oxide (N2O) emissions based on global surface observations. One of these frameworks employs a new approach that allows for fast computation and explores a larger solution space than other methods. Our results point to a few conclusions about the global N2O budget, including a larger contribution from tropical sources, an overestimate of natural soil emissions, and an underestimate of agricultural sources particularly in springtime.
Jin-Yun Tang and William J. Riley
Geosci. Model Dev., 10, 3277–3295, https://doi.org/10.5194/gmd-10-3277-2017, https://doi.org/10.5194/gmd-10-3277-2017, 2017
Short summary
Short summary
We proposed the SUPECA kinetics to scale from single biogeochemical reactions to a network of mixed substrates and consumers. The framework for the first time represents single-substrate reactions, two-substrate reactions, and mineral surface sorption reactions in a scaling consistent manner. This new theory is theoretically solid and outperforms existing theories, particularly for substrate-limiting systems. The test with aerobic soil respiration showed its strengths for pragmatic application.
Congsheng Fu, Xuhui Lee, Timothy J. Griffis, Edward J. Dlugokencky, and Arlyn E. Andrews
Atmos. Chem. Phys. Discuss., https://doi.org/10.5194/acp-2016-761, https://doi.org/10.5194/acp-2016-761, 2016
Revised manuscript not accepted
Short summary
Short summary
To the best of our knowledge, no modeling studies have been published on the relationship between the spatial characteristics of agricultural N2O emissions and the atmospheric N2O mixing ratio at the regional scale. To fill this gap, we proposed a simple inverse analysis method based on tower measurements and an Eulerian model. According to our study, the N2O emissions from the U. S. Corn Belt is clearly estimated by IPCC, and such underestimate is not dependent on tower measurement location.
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
Atmos. Chem. Phys., 16, 5139–5157, https://doi.org/10.5194/acp-16-5139-2016, https://doi.org/10.5194/acp-16-5139-2016, 2016
Short summary
Short summary
Increasing atmospheric humidity and convective precipitation over land provide evidence of intensification of the hydrologic cycle. We present the first multi-annual isotope (oxygen and deuterium) water vapor observations from a very tall tower (185 m) in the upper Midwest, United States, to diagnose the sources, transport, and fractionation of water vapor in the atmosphere. The results show a relatively high degree of summertime water recycling within the region (~30 % mean and ~60 % maximum).
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
Short summary
Short summary
This paper introduces a new inversion framework for N2O using GEOS-Chem and its adjoint, which we employed in a series of observing system simulation experiments to evaluate the source and sink constraints provided by surface and aircraft-based N2O measurements. We also applied a new approach for estimating a posteriori uncertainty for high-dimensional inversions, and used it to quantify the spatial and temporal resolution of N2O emission constraints achieved with the current observing network.
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
Related subject area
Biogeosciences
Dynamic ecosystem assembly and escaping the “fire trap” in the tropics: insights from FATES_15.0.0
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
Quantifying the role of ozone-caused damage to vegetation in the Earth system: A new parameterization scheme for photosynthetic and stomatal responses
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
Exploring the Potential of History Matching for Land Surface Model Calibration
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
Using Deep Learning to integrate paleoclimate and global biogeochemistry over Phanerozoic time
A model of the within-population variability of budburst in forest trees
Computationally efficient parameter estimation for high-dimensional ocean biogeochemical models
Radiocarbon analysis reveals underestimation of soil organic carbon persistence in new-generation soil models
The community-centered freshwater biogeochemistry model unified RIVE v1.0: a unified version for water column
EAT v0.9.6: a 1D testbed for physical-biogeochemical data assimilation in natural waters
Observation-based sowing dates and cultivars significantly affect yield and irrigation for some crops in the Community Land Model (CLM5)
The statistical emulators of GGCMI phase 2: responses of year-to-year variation of crop yield to CO2, temperature, water, and nitrogen perturbations
A novel Eulerian model based on central moments to simulate age and reactivity continua interacting with mixing processes
AdaScape 1.0: a coupled modelling tool to investigate the links between tectonics, climate, and biodiversity
An along-track Biogeochemical Argo modelling framework: a case study of model improvements for the Nordic seas
Peatland-VU-NUCOM (PVN 1.0): using dynamic plant functional types to model peatland vegetation, CH4, and CO2 emissions
Quantification of hydraulic trait control on plant hydrodynamics and risk of hydraulic failure within a demographic structured vegetation model in a tropical forest (FATES–HYDRO V1.0)
SedTrace 1.0: a Julia-based framework for generating and running reactive-transport models of marine sediment diagenesis specializing in trace elements and isotopes
A high-resolution marine mercury model MITgcm-ECCO2-Hg with online biogeochemistry
Improving nitrogen cycling in a land surface model (CLM5) to quantify soil N2O, NO, and NH3 emissions from enhanced rock weathering with croplands
Assimilation of Carbonyl Sulfide (COS) fluxes within the adjoint-based data assimilation system–Nanjing University Carbon Assimilation System (NUCAS v1.0)
Ocean biogeochemistry in the coupled ocean–sea ice–biogeochemistry model FESOM2.1–REcoM3
Forcing the Global Fire Emissions Database burned-area dataset into the Community Land Model version 5.0: impacts on carbon and water fluxes at high latitudes
Modeling boreal forest’s mineral soil and peat C stock dynamics with Yasso07 model coupled with updated moisture modifier
Modeling of non-structural carbohydrate dynamics by the spatially explicit individual-based dynamic global vegetation model SEIB-DGVM (SEIB-DGVM-NSC version 1.0)
MEDFATE 2.9.3: a trait-enabled model to simulate Mediterranean forest function and dynamics at regional scales
Modelling the role of livestock grazing in C and N cycling in grasslands with LPJmL5.0-grazing
Implementation of trait-based ozone plant sensitivity in the Yale Interactive terrestrial Biosphere model v1.0 to assess global vegetation damage
The Permafrost and Organic LayEr module for Forest Models (POLE-FM) 1.0
CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics
Validation of a new spatially explicit process-based model (HETEROFOR) to simulate structurally and compositionally complex forest stands in eastern North America
Global agricultural ammonia emissions simulated with the ORCHIDEE land surface model
ForamEcoGEnIE 2.0: incorporating symbiosis and spine traits into a trait-based global planktic foraminiferal model
FABM-NflexPD 2.0: testing an instantaneous acclimation approach for modeling the implications of phytoplankton eco-physiology for the carbon and nutrient cycles
Evaluating the vegetation–atmosphere coupling strength of ORCHIDEE land surface model (v7266)
Non-Redfieldian carbon model for the Baltic Sea (ERGOM version 1.2) – implementation and budget estimates
Implementation of a new crop phenology and irrigation scheme in the ISBA land surface model using SURFEX_v8.1
Simulating long-term responses of soil organic matter turnover to substrate stoichiometry by abstracting fast and small-scale microbial processes: the Soil Enzyme Steady Allocation Model (SESAM; v3.0)
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
Short summary
Short summary
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.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
Soil microbes provide a strong link for elemental fluxes in the earth system. The SESAM model applies an optimality assumption to model those linkages and their adaptation. We found that a previous heuristic description was a special case of a newly developed more rigorous description. The finding of new behaviour at low microbial biomass led us to formulate the constrained enzyme hypothesis. We now can better describe how microbially mediated linkages of elemental fluxes adapt across decades.
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
Short summary
Short summary
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
Short summary
Short summary
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.
Fang Li, Zhimin Zhou, Samuel Levis, Stephen Sitch, Felicity Hayes, Zhaozhong Feng, Peter Reich, Zhiyi Zhao, and Yanqing Zhou
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-6, https://doi.org/10.5194/gmd-2024-6, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
This study introduces a new scheme to simulate 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 response 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.
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
Short summary
Short summary
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
Short summary
Short summary
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.
Nina Raoult, Simon Beylat, James M. Salter, Frédéric Hourdin, Vladislav Bastrikov, Catherine Ottlé, and Philippe Peylin
EGUsphere, https://doi.org/10.5194/egusphere-2023-2996, https://doi.org/10.5194/egusphere-2023-2996, 2024
Short summary
Short summary
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. Here we test a technique called “History matching” against more common approaches. This method adapts well to these models, helping better understand how they work and therefore how to make them more realistic.
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
Short summary
Short summary
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
Short summary
Short summary
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.
Dongyu Zheng, Andrew Merdith, Yves Goddéris, Yannick Donnadieu, Khushboo Gurung, and Benjamin J. W. Mills
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2023-230, https://doi.org/10.5194/gmd-2023-230, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
This study uses a deep learning method to enhance the time resolution of paleoclimate simulations to 1 million years. This improved resolution allows a climate-biogeochemical model for more accurate predictions of climate shifts. The method may be critical in developing new fully-continuous methods that are able to translate over a moving continental surface in deep time with high-resolution at a reasonable computational expense.
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
Short summary
Short summary
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.
Skyler Kern, Mary E. McGuinn, Katherine M. Smith, Nadia Pinardi, Kyle E. Niemeyer, Nicole S. Lovenduski, and Peter E. Hamlington
Geosci. Model Dev., 17, 621–649, https://doi.org/10.5194/gmd-17-621-2024, https://doi.org/10.5194/gmd-17-621-2024, 2024
Short summary
Short summary
Computational models are used to simulate the behavior of marine ecosystems. The models often have unknown parameters that need to be calibrated to accurately represent observational data. Here, we propose a novel approach to simultaneously determine a large set of parameters for a one-dimensional model of a marine ecosystem in the surface ocean at two contrasting sites. By utilizing global and local optimization techniques, we estimate many parameters in a computationally efficient manner.
Alexander S. Brunmayr, Frank Hagedorn, Margaux Moreno Duborgel, Luisa I. Minich, and Heather D. Graven
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2023-242, https://doi.org/10.5194/gmd-2023-242, 2024
Revised manuscript accepted for GMD
Short summary
Short summary
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 as 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.
Shuaitao Wang, Vincent Thieu, Gilles Billen, Josette Garnier, Marie Silvestre, Audrey Marescaux, Xingcheng Yan, and Nicolas Flipo
Geosci. Model Dev., 17, 449–476, https://doi.org/10.5194/gmd-17-449-2024, https://doi.org/10.5194/gmd-17-449-2024, 2024
Short summary
Short summary
This paper presents unified RIVE v1.0, a unified version of the freshwater biogeochemistry model RIVE. It harmonizes different RIVE implementations, providing the referenced formalisms for microorganism activities to describe full biogeochemical cycles in the water column (e.g., carbon, nutrients, oxygen). Implemented as open-source projects in Python 3 (pyRIVE 1.0) and ANSI C (C-RIVE 0.32), unified RIVE v1.0 promotes and enhances collaboration among research teams and public services.
Jorn Bruggeman, Karsten Bolding, Lars Nerger, Anna Teruzzi, Simone Spada, Jozef Skákala, and Stefano Ciavatta
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2023-238, https://doi.org/10.5194/gmd-2023-238, 2023
Revised manuscript accepted for GMD
Short summary
Short summary
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. Here, we present EAT, a flexible and efficient testbed that allows any scientist to explore and further develop the state-of-the-art in data assimilation.
Sam S. Rabin, William J. Sacks, Danica L. Lombardozzi, Lili Xia, and Alan Robock
Geosci. Model Dev., 16, 7253–7273, https://doi.org/10.5194/gmd-16-7253-2023, https://doi.org/10.5194/gmd-16-7253-2023, 2023
Short summary
Short summary
Climate models can help us simulate how the agricultural system will be affected by and respond to environmental change, but to be trustworthy they must realistically reproduce historical patterns. When farmers plant their crops and what varieties they choose will be important aspects of future adaptation. Here, we improve the crop component of a global model to better simulate observed growing seasons and examine the impacts on simulated crop yields and irrigation demand.
Weihang Liu, Tao Ye, Christoph Müller, Jonas Jägermeyr, James A. Franke, Haynes Stephens, and Shuo Chen
Geosci. Model Dev., 16, 7203–7221, https://doi.org/10.5194/gmd-16-7203-2023, https://doi.org/10.5194/gmd-16-7203-2023, 2023
Short summary
Short summary
We develop a machine-learning-based crop model emulator with the inputs and outputs of multiple global gridded crop model ensemble simulations to capture the year-to-year variation of crop yield under future climate change. The emulator can reproduce the year-to-year variation of simulated yield given by the crop models under CO2, temperature, water, and nitrogen perturbations. Developing this emulator can provide a tool to project future climate change impact in a simple way.
Jurjen Rooze, Heewon Jung, and Hagen Radtke
Geosci. Model Dev., 16, 7107–7121, https://doi.org/10.5194/gmd-16-7107-2023, https://doi.org/10.5194/gmd-16-7107-2023, 2023
Short summary
Short summary
Chemical particles in nature have properties such as age or reactivity. Distributions can describe the properties of chemical concentrations. In nature, they are affected by mixing processes, such as chemical diffusion, burrowing animals, and bottom trawling. We derive equations for simulating the effect of mixing on central moments that describe the distributions. We then demonstrate applications in which these equations are used to model continua in disturbed natural environments.
Esteban Acevedo-Trejos, Jean Braun, Katherine Kravitz, N. Alexia Raharinirina, and Benoît Bovy
Geosci. Model Dev., 16, 6921–6941, https://doi.org/10.5194/gmd-16-6921-2023, https://doi.org/10.5194/gmd-16-6921-2023, 2023
Short summary
Short summary
The interplay of tectonics and climate influences the evolution of life and the patterns of biodiversity we observe on earth's surface. Here we present an adaptive speciation component coupled with a landscape evolution model that captures the essential earth-surface, ecological, and evolutionary processes that lead to the diversification of taxa. We can illustrate with our tool how life and landforms co-evolve to produce distinct biodiversity patterns on geological timescales.
Veli Çağlar Yumruktepe, Erik Askov Mousing, Jerry Tjiputra, and Annette Samuelsen
Geosci. Model Dev., 16, 6875–6897, https://doi.org/10.5194/gmd-16-6875-2023, https://doi.org/10.5194/gmd-16-6875-2023, 2023
Short summary
Short summary
We present an along BGC-Argo track 1D modelling framework. The model physics is constrained by the BGC-Argo temperature and salinity profiles to reduce the uncertainties related to mixed layer dynamics, allowing the evaluation of the biogeochemical formulation and parameterization. We objectively analyse the model with BGC-Argo and satellite data and improve the model biogeochemical dynamics. We present the framework, example cases and routines for model improvement and implementations.
Tanya J. R. Lippmann, Ype van der Velde, Monique M. P. D. Heijmans, Han Dolman, Dimmie M. D. Hendriks, and Ko van Huissteden
Geosci. Model Dev., 16, 6773–6804, https://doi.org/10.5194/gmd-16-6773-2023, https://doi.org/10.5194/gmd-16-6773-2023, 2023
Short summary
Short summary
Vegetation is a critical component of carbon storage in peatlands but an often-overlooked concept in many peatland models. We developed a new model capable of simulating the response of vegetation to changing environments and management regimes. We evaluated the model against observed chamber data collected at two peatland sites. We found that daily air temperature, water level, harvest frequency and height, and vegetation composition drive methane and carbon dioxide emissions.
Chonggang Xu, Bradley Christoffersen, Zachary Robbins, Ryan Knox, Rosie A. Fisher, Rutuja Chitra-Tarak, Martijn Slot, Kurt Solander, Lara Kueppers, Charles Koven, and Nate McDowell
Geosci. Model Dev., 16, 6267–6283, https://doi.org/10.5194/gmd-16-6267-2023, https://doi.org/10.5194/gmd-16-6267-2023, 2023
Short summary
Short summary
We introduce a plant hydrodynamic model for the U.S. Department of Energy (DOE)-sponsored model, the Functionally Assembled Terrestrial Ecosystem Simulator (FATES). To better understand this new model system and its functionality in tropical forest ecosystems, we conducted a global parameter sensitivity analysis at Barro Colorado Island, Panama. We identified the key parameters that affect the simulated plant hydrodynamics to guide both modeling and field campaign studies.
Jianghui Du
Geosci. Model Dev., 16, 5865–5894, https://doi.org/10.5194/gmd-16-5865-2023, https://doi.org/10.5194/gmd-16-5865-2023, 2023
Short summary
Short summary
Trace elements and isotopes (TEIs) are important tools to study the changes in the ocean environment both today and in the past. However, the behaviors of TEIs in marine sediments are poorly known, limiting our ability to use them in oceanography. Here we present a modeling framework that can be used to generate and run models of the sedimentary cycling of TEIs assisted with advanced numerical tools in the Julia language, lowering the coding barrier for the general user to study marine TEIs.
Siyu Zhu, Peipei Wu, Siyi Zhang, Oliver Jahn, Shu Li, and Yanxu Zhang
Geosci. Model Dev., 16, 5915–5929, https://doi.org/10.5194/gmd-16-5915-2023, https://doi.org/10.5194/gmd-16-5915-2023, 2023
Short summary
Short summary
In this study, we estimate the global biogeochemical cycling of Hg in a state-of-the-art physical-ecosystem ocean model (high-resolution-MITgcm/Hg), providing a more accurate portrayal of surface Hg concentrations in estuarine and coastal areas, strong western boundary flow and upwelling areas, and concentration diffusion as vortex shapes. The high-resolution model can help us better predict the transport and fate of Hg in the ocean and its impact on the global Hg cycle.
Maria Val Martin, Elena Blanc-Betes, Ka Ming Fung, Euripides P. Kantzas, Ilsa B. Kantola, Isabella Chiaravalloti, Lyla L. Taylor, Louisa K. Emmons, William R. Wieder, Noah J. Planavsky, Michael D. Masters, Evan H. DeLucia, Amos P. K. Tai, and David J. Beerling
Geosci. Model Dev., 16, 5783–5801, https://doi.org/10.5194/gmd-16-5783-2023, https://doi.org/10.5194/gmd-16-5783-2023, 2023
Short summary
Short summary
Enhanced rock weathering (ERW) is a CO2 removal strategy that involves applying crushed rocks (e.g., basalt) to agricultural soils. However, unintended processes within the N cycle due to soil pH changes may affect the climate benefits of C sequestration. ERW could drive changes in soil emissions of non-CO2 GHGs (N2O) and trace gases (NO and NH3) that may affect air quality. We present a new improved N cycling scheme for the land model (CLM5) to evaluate ERW effects on soil gas N emissions.
Huajie Zhu, Mousong Wu, Fei Jiang, Michael Vossbeck, Thomas Kaminski, Xiuli Xing, Jun Wang, Weimin Ju, and Jing M. Chen
EGUsphere, https://doi.org/10.5194/egusphere-2023-1955, https://doi.org/10.5194/egusphere-2023-1955, 2023
Short summary
Short summary
In this work, Nanjing University Carbon Assimilation System (NUCAS) was developed. Data assimilation experiments were conducted to demonstrate the robustness and to investigate the feasibility and applicability of NUCAS. The assimilation of COS significantly improved the model performance in gross primary productivity, sensible heat, latent heat and even soil moisture, demonstrating that COS can provide strong constraints on parameters relevant to water, energy and carbon processes.
Özgür Gürses, Laurent Oziel, Onur Karakuş, Dmitry Sidorenko, Christoph Völker, Ying Ye, Moritz Zeising, Martin Butzin, and Judith Hauck
Geosci. Model Dev., 16, 4883–4936, https://doi.org/10.5194/gmd-16-4883-2023, https://doi.org/10.5194/gmd-16-4883-2023, 2023
Short summary
Short summary
This paper assesses the biogeochemical model REcoM3 coupled to the ocean–sea ice model FESOM2.1. The model can be used to simulate the carbon uptake or release of the ocean on timescales of several hundred years. A detailed analysis of the nutrients, ocean productivity, and ecosystem is followed by the carbon cycle. The main conclusion is that the model performs well when simulating the observed mean biogeochemical state and variability and is comparable to other ocean–biogeochemical models.
Hocheol Seo and Yeonjoo Kim
Geosci. Model Dev., 16, 4699–4713, https://doi.org/10.5194/gmd-16-4699-2023, https://doi.org/10.5194/gmd-16-4699-2023, 2023
Short summary
Short summary
Wildfire is a crucial factor in carbon and water fluxes on the Earth system. About 2.1 Pg of carbon is released into the atmosphere by wildfires annually. Because the fire processes are still limitedly represented in land surface models, we forced the daily GFED4 burned area into the land surface model over Alaska and Siberia. The results with the GFED4 burned area significantly improved the simulated carbon emissions and net ecosystem exchange compared to the default simulation.
Boris Ťupek, Aleksi Lehtonen, Alla Yurova, Rose Abramoff, Stefano Manzoni, Bertrand Guenet, Elisa Bruni, Samuli Launiainen, Mikko Peltoniemi, Shoji Hashimoto, Xianglin Tian, Juha Heikkinen, Kari Minkkinen, and Raisa Mäkipää
EGUsphere, https://doi.org/10.5194/egusphere-2023-1523, https://doi.org/10.5194/egusphere-2023-1523, 2023
Short summary
Short summary
Improving representation of peatlands in Earth system models (ESMs) (e.g., in Yasso soil C model coupled with JSBACH model) is rare. We updated Yasso07 moisture dependency for applications on both the mineral soils and peatlands of boreal forest. Our moisture function improved the simulated peatland C stocks and CO2 dynamics. However, due to nature of the measurements used for Bayesian MCMC data assimilation, it contrasts with functions in other ESMs (see graphical abstract).
Hideki Ninomiya, Tomomichi Kato, Lea Végh, and Lan Wu
Geosci. Model Dev., 16, 4155–4170, https://doi.org/10.5194/gmd-16-4155-2023, https://doi.org/10.5194/gmd-16-4155-2023, 2023
Short summary
Short summary
Non-structural carbohydrates (NSCs) play a crucial role in plants to counteract the effects of climate change. We added a new NSC module into the SEIB-DGVM, an individual-based ecosystem model. The simulated NSC levels and their seasonal patterns show a strong agreement with observed NSC data at both point and global scales. The model can be used to simulate the biotic effects resulting from insufficient NSCs, which are otherwise difficult to measure in terrestrial ecosystems globally.
Miquel De Cáceres, Roberto Molowny-Horas, Antoine Cabon, Jordi Martínez-Vilalta, Maurizio Mencuccini, Raúl García-Valdés, Daniel Nadal-Sala, Santiago Sabaté, Nicolas Martin-StPaul, Xavier Morin, Francesco D'Adamo, Enric Batllori, and Aitor Améztegui
Geosci. Model Dev., 16, 3165–3201, https://doi.org/10.5194/gmd-16-3165-2023, https://doi.org/10.5194/gmd-16-3165-2023, 2023
Short summary
Short summary
Regional-level applications of dynamic vegetation models are challenging because they need to accommodate the variation in plant functional diversity. This can be done by estimating parameters from available plant trait databases while adopting alternative solutions for missing data. Here we present the design, parameterization and evaluation of MEDFATE (version 2.9.3), a novel model of forest dynamics for its application over a region in the western Mediterranean Basin.
Jens Heinke, Susanne Rolinski, and Christoph Müller
Geosci. Model Dev., 16, 2455–2475, https://doi.org/10.5194/gmd-16-2455-2023, https://doi.org/10.5194/gmd-16-2455-2023, 2023
Short summary
Short summary
We develop a livestock module for the global vegetation model LPJmL5.0 to simulate the impact of grazing dairy cattle on carbon and nitrogen cycles in grasslands. A novelty of the approach is that it accounts for the effect of feed quality on feed uptake and feed utilization by animals. The portioning of dietary nitrogen into milk, feces, and urine shows very good agreement with estimates obtained from animal trials.
Yimian Ma, Xu Yue, Stephen Sitch, Nadine Unger, Johan Uddling, Lina M. Mercado, Cheng Gong, Zhaozhong Feng, Huiyi Yang, Hao Zhou, Chenguang Tian, Yang Cao, Yadong Lei, Alexander W. Cheesman, Yansen Xu, and Maria Carolina Duran Rojas
Geosci. Model Dev., 16, 2261–2276, https://doi.org/10.5194/gmd-16-2261-2023, https://doi.org/10.5194/gmd-16-2261-2023, 2023
Short summary
Short summary
Plants have been found to respond differently to O3, but the variations in the sensitivities have rarely been explained nor fully implemented in large-scale assessment. This study proposes a new O3 damage scheme with leaf mass per area to unify varied sensitivities for all plant species. Our assessment reveals an O3-induced reduction of 4.8 % in global GPP, with the highest reduction of >10 % for cropland, suggesting an emerging risk of crop yield loss under the threat of O3 pollution.
Winslow D. Hansen, Adrianna Foster, Benjamin Gaglioti, Rupert Seidl, and Werner Rammer
Geosci. Model Dev., 16, 2011–2036, https://doi.org/10.5194/gmd-16-2011-2023, https://doi.org/10.5194/gmd-16-2011-2023, 2023
Short summary
Short summary
Permafrost and the thick soil-surface organic layers that insulate permafrost are important controls of boreal forest dynamics and carbon cycling. However, both are rarely included in process-based vegetation models used to simulate future ecosystem trajectories. To address this challenge, we developed a computationally efficient permafrost and soil organic layer module that operates at fine spatial (1 ha) and temporal (daily) resolutions.
Heewon Jung, Hyun-Seob Song, and Christof Meile
Geosci. Model Dev., 16, 1683–1696, https://doi.org/10.5194/gmd-16-1683-2023, https://doi.org/10.5194/gmd-16-1683-2023, 2023
Short summary
Short summary
Microbial activity responsible for many chemical transformations depends on environmental conditions. These can vary locally, e.g., between poorly connected pores in porous media. We present a modeling framework that resolves such small spatial scales explicitly, accounts for feedback between transport and biogeochemical conditions, and can integrate state-of-the-art representations of microbes in a computationally efficient way, making it broadly applicable in science and engineering use cases.
Arthur Guignabert, Quentin Ponette, Frédéric André, Christian Messier, Philippe Nolet, and Mathieu Jonard
Geosci. Model Dev., 16, 1661–1682, https://doi.org/10.5194/gmd-16-1661-2023, https://doi.org/10.5194/gmd-16-1661-2023, 2023
Short summary
Short summary
Spatially explicit and process-based models are useful to test innovative forestry practices under changing and uncertain conditions. However, their larger use is often limited by the restricted range of species and stand structures they can reliably account for. We therefore calibrated and evaluated such a model, HETEROFOR, for 23 species across southern Québec. Our results showed that the model is robust and can predict accurately both individual tree growth and stand dynamics in this region.
Maureen Beaudor, Nicolas Vuichard, Juliette Lathière, Nikolaos Evangeliou, Martin Van Damme, Lieven Clarisse, and Didier Hauglustaine
Geosci. Model Dev., 16, 1053–1081, https://doi.org/10.5194/gmd-16-1053-2023, https://doi.org/10.5194/gmd-16-1053-2023, 2023
Short summary
Short summary
Ammonia mainly comes from the agricultural sector, and its volatilization relies on environmental variables. Our approach aims at benefiting from an Earth system model framework to estimate it. By doing so, we represent a consistent spatial distribution of the emissions' response to environmental changes.
We greatly improved the seasonal cycle of emissions compared with previous work. In addition, our model includes natural soil emissions (that are rarely represented in modeling approaches).
Rui Ying, Fanny M. Monteiro, Jamie D. Wilson, and Daniela N. Schmidt
Geosci. Model Dev., 16, 813–832, https://doi.org/10.5194/gmd-16-813-2023, https://doi.org/10.5194/gmd-16-813-2023, 2023
Short summary
Short summary
Planktic foraminifera are marine-calcifying zooplankton; their shells are widely used to measure past temperature and productivity. We developed ForamEcoGEnIE 2.0 to simulate the four subgroups of this organism. We found that the relative abundance distribution agrees with marine sediment core-top data and that carbon export and biomass are close to sediment trap and plankton net observations respectively. This model provides the opportunity to study foraminiferal ecology in any geological era.
Onur Kerimoglu, Markus Pahlow, Prima Anugerahanti, and Sherwood Lan Smith
Geosci. Model Dev., 16, 95–108, https://doi.org/10.5194/gmd-16-95-2023, https://doi.org/10.5194/gmd-16-95-2023, 2023
Short summary
Short summary
In classical models that track the changes in the elemental composition of phytoplankton, additional state variables are required for each element resolved. In this study, we show how the behavior of such an explicit model can be approximated using an
instantaneous acclimationapproach, in which the elemental composition of the phytoplankton is assumed to adjust to an optimal value instantaneously. Through rigorous tests, we evaluate the consistency of this scheme.
Yuan Zhang, Devaraju Narayanappa, Philippe Ciais, Wei Li, Daniel Goll, Nicolas Vuichard, Martin G. De Kauwe, Laurent Li, and Fabienne Maignan
Geosci. Model Dev., 15, 9111–9125, https://doi.org/10.5194/gmd-15-9111-2022, https://doi.org/10.5194/gmd-15-9111-2022, 2022
Short summary
Short summary
There are a few studies to examine if current models correctly represented the complex processes of transpiration. Here, we use a coefficient Ω, which indicates if transpiration is mainly controlled by vegetation processes or by turbulence, to evaluate the ORCHIDEE model. We found a good performance of ORCHIDEE, but due to compensation of biases in different processes, we also identified how different factors control Ω and where the model is wrong. Our method is generic to evaluate other models.
Thomas Neumann, Hagen Radtke, Bronwyn Cahill, Martin Schmidt, and Gregor Rehder
Geosci. Model Dev., 15, 8473–8540, https://doi.org/10.5194/gmd-15-8473-2022, https://doi.org/10.5194/gmd-15-8473-2022, 2022
Short summary
Short summary
Marine ecosystem models are usually constrained by the elements nitrogen and phosphorus and consider carbon in organic matter in a fixed ratio. Recent observations show a substantial deviation from the simulated carbon cycle variables. In this study, we present a marine ecosystem model for the Baltic Sea which allows for a flexible uptake ratio for carbon, nitrogen, and phosphorus. With this extension, the model reflects much more reasonable variables of the marine carbon cycle.
Arsène Druel, Simon Munier, Anthony Mucia, Clément Albergel, and Jean-Christophe Calvet
Geosci. Model Dev., 15, 8453–8471, https://doi.org/10.5194/gmd-15-8453-2022, https://doi.org/10.5194/gmd-15-8453-2022, 2022
Short summary
Short summary
Crop phenology and irrigation is implemented into a land surface model able to work at a global scale. A case study is presented over Nebraska (USA). Simulations with and without the new scheme are compared to different satellite-based observations. The model is able to produce a realistic yearly irrigation water amount. The irrigation scheme improves the simulated leaf area index, gross primary productivity, evapotransipiration, and land surface temperature.
Thomas Wutzler, Lin Yu, Marion Schrumpf, and Sönke Zaehle
Geosci. Model Dev., 15, 8377–8393, https://doi.org/10.5194/gmd-15-8377-2022, https://doi.org/10.5194/gmd-15-8377-2022, 2022
Short summary
Short summary
Soil microbes process soil organic matter and affect carbon storage and plant nutrition at the ecosystem scale. We hypothesized that decadal dynamics is constrained by the ratios of elements in litter inputs, microbes, and matter and that microbial community optimizes growth. This allowed the SESAM model to descibe decadal-term carbon sequestration in soils and other biogeochemical processes explicitly accounting for microbial processes but without its problematic fine-scale parameterization.
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...
