Articles | Volume 15, issue 4
https://doi.org/10.5194/gmd-15-1735-2022
© 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-15-1735-2022
© 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
| 
02 Mar 2022
Development and technical paper |
| 02 Mar 2022
| 02 Mar 2022
Calibrating the soil organic carbon model Yasso20 with multiple datasets
Finnish Meteorological Institute, Helsinki, 00101, Finland
Janne Pusa
Finnish Meteorological Institute, Helsinki, 00101, Finland
Istem Fer
Finnish Meteorological Institute, Helsinki, 00101, Finland
Anna Repo
Natural Resource Center Finland, Helsinki, 00791, Finland
Julius Vira
Finnish Meteorological Institute, Helsinki, 00101, Finland
Jari Liski
Finnish Meteorological Institute, Helsinki, 00101, Finland
Related authors
Jarmo Mäkelä, Laura Arppe, Hannu Fritze, Jussi Heinonsalo, Kristiina Karhu, Jari Liski, Markku Oinonen, Petra Straková, and Toni Viskari
Biogeosciences, 19, 4305–4313, https://doi.org/10.5194/bg-19-4305-2022, https://doi.org/10.5194/bg-19-4305-2022, 2022
Short summary
Short summary
Soils account for the largest share of carbon found in terrestrial ecosystems, and accurate depiction of soil carbon decomposition is essential in understanding how permanent these carbon storages are. We present a straightforward way to include carbon isotope concentrations into soil decomposition and carbon storages for the Yasso model, which enables the model to use 13C as a natural tracer to track changes in the underlying soil organic matter decomposition.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490, https://doi.org/10.5194/bg-19-1469-2022, https://doi.org/10.5194/bg-19-1469-2022, 2022
Short summary
Short summary
This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Olli Nevalainen, Olli Niemitalo, Istem Fer, Antti Juntunen, Tuomas Mattila, Olli Koskela, Joni Kukkamäki, Layla Höckerstedt, Laura Mäkelä, Pieta Jarva, Laura Heimsch, Henriikka Vekuri, Liisa Kulmala, Åsa Stam, Otto Kuusela, Stephanie Gerin, Toni Viskari, Julius Vira, Jari Hyväluoma, Juha-Pekka Tuovinen, Annalea Lohila, Tuomas Laurila, Jussi Heinonsalo, Tuula Aalto, Iivari Kunttu, and Jari Liski
Geosci. Instrum. Method. Data Syst., 11, 93–109, https://doi.org/10.5194/gi-11-93-2022, https://doi.org/10.5194/gi-11-93-2022, 2022
Short summary
Short summary
Better monitoring of soil carbon sequestration is needed to understand the best carbon farming practices in different soils and climate conditions. We, the Field Observatory Network (FiON), have therefore established a methodology for monitoring and forecasting agricultural carbon sequestration by combining offline and near-real-time field measurements, weather data, satellite imagery, and modeling. To disseminate our work, we built a website called the Field Observatory (fieldobservatory.org).
Alexey N. Shiklomanov, Michael C. Dietze, Istem Fer, Toni Viskari, and Shawn P. Serbin
Geosci. Model Dev., 14, 2603–2633, https://doi.org/10.5194/gmd-14-2603-2021, https://doi.org/10.5194/gmd-14-2603-2021, 2021
Short summary
Short summary
Airborne and satellite images are a great resource for calibrating and evaluating computer models of ecosystems. Typically, researchers derive ecosystem properties from these images and then compare models against these derived properties. Here, we present an alternative approach where we modify a model to predict what the satellite would see more directly. We then show how this approach can be used to calibrate model parameters using airborne data from forest sites in the northeastern US.
Toni Viskari, Maisa Laine, Liisa Kulmala, Jarmo Mäkelä, Istem Fer, and Jari Liski
Geosci. Model Dev., 13, 5959–5971, https://doi.org/10.5194/gmd-13-5959-2020, https://doi.org/10.5194/gmd-13-5959-2020, 2020
Short summary
Short summary
The research here established whether a Bayesian statistical method called state data assimilation could be used to improve soil organic carbon (SOC) forecasts. Our test case was a fallow experiment where SOC content was measured over several decades from a plot where all vegetation was removed. Our results showed that state data assimilation improved projections and allowed for the detailed model state be updated with coarse total carbon measurements.
Jarmo Mäkelä, Jürgen Knauer, Mika Aurela, Andrew Black, Martin Heimann, Hideki Kobayashi, Annalea Lohila, Ivan Mammarella, Hank Margolis, Tiina Markkanen, Jouni Susiluoto, Tea Thum, Toni Viskari, Sönke Zaehle, and Tuula Aalto
Geosci. Model Dev., 12, 4075–4098, https://doi.org/10.5194/gmd-12-4075-2019, https://doi.org/10.5194/gmd-12-4075-2019, 2019
Short summary
Short summary
We assess the differences of six stomatal conductance formulations, embedded into a land–vegetation model JSBACH, on 10 boreal coniferous evergreen forest sites. We calibrate the model parameters using all six functions in a multi-year experiment, as well as for a separate drought event at one of the sites, using the adaptive population importance sampler. The analysis reveals weaknesses in the stomatal conductance formulation-dependent model behaviour that we are able to partially amend.
T. Viskari, E. Asmi, P. Kolmonen, H. Vuollekoski, T. Petäjä, and H. Järvinen
Atmos. Chem. Phys., 12, 11767–11779, https://doi.org/10.5194/acp-12-11767-2012, https://doi.org/10.5194/acp-12-11767-2012, 2012
T. Viskari, E. Asmi, A. Virkkula, P. Kolmonen, T. Petäjä, and H. Järvinen
Atmos. Chem. Phys., 12, 11781–11793, https://doi.org/10.5194/acp-12-11781-2012, https://doi.org/10.5194/acp-12-11781-2012, 2012
Natalie M. Mahowald, Longlei Li, Julius Vira, Marje Prank, Douglas S. Hamilton, Hitoshi Matsui, Ron L. Miller, Louis Lu, Ezgi Akyuz, Daphne Meidan, Peter G. Hess, Heikki Lihavainen, Christine Wiedinmyer, Jenny Hand, Maria Grazia Alaimo, Célia Alves, Andres Alastuey, Paulo Artaxo, Africa Barreto, Francisco Barraza, Silvia Becagli, Giulia Calzolai, Shankararaman Chellam, Ying Chen, Patrick Chuang, David D. Cohen, Cristina Colombi, Evangelia Diapouli, Gaetano Dongarra, Konstantinos Eleftheriadis, Johann Engelbrecht, Corinne Galy-Lacaux, Cassandra Gaston, Dario Gomez, Yenny González Ramos, Roy M. Harrison, Chris Heyes, Barak Herut, Philip Hopke, Christoph Hüglin, Maria Kanakidou, Zsofia Kertesz, Zbigniew Klimont, Katriina Kyllönen, Fabrice Lambert, Xiaohong Liu, Remi Losno, Franco Lucarelli, Willy Maenhaut, Beatrice Marticorena, Randall V. Martin, Nikolaos Mihalopoulos, Yasser Morera-Gomez, Adina Paytan, Joseph Prospero, Sergio Rodríguez, Patricia Smichowski, Daniela Varrica, Brenna Walsh, Crystal Weagle, and Xi Zhao
EGUsphere, https://doi.org/10.5194/egusphere-2024-1617, https://doi.org/10.5194/egusphere-2024-1617, 2024
This preprint is open for discussion and under review for Atmospheric Chemistry and Physics (ACP).
Short summary
Short summary
Aerosol particles are an important part of the Earth system, but their concentrations are spatially and temporally heterogeneous, as well as variable in size and composition. Here we present a new compilation of PM2.5 and PM10 aerosol observations, focusing on the spatial variability across different observational stations, including composition, and demonstrate a method for comparing the datasets to model output.
Natalie M. Mahowald, Longlei Li, Julius Vira, Marje Prank, Douglas S. Hamilton, Hitoshi Matsui, Ron L. Miller, Louis Lu, Ezgi Akyuz, Daphne Meidan, Peter Hess, Heikki Lihavainen, Christine Wiedinmyer, Jenny Hand, Maria Grazia Alaimo, Célia Alves, Andres Alastuey, Paulo Artaxo, Africa Barreto, Francisco Barraza, Silvia Becagli, Giulia Calzolai, Shankarararman Chellam, Ying Chen, Patrick Chuang, David D. Cohen, Cristina Colombi, Evangelia Diapouli, Gaetano Dongarra, Konstantinos Eleftheriadis, Corinne Galy-Lacaux, Cassandra Gaston, Dario Gomez, Yenny González Ramos, Hannele Hakola, Roy M. Harrison, Chris Heyes, Barak Herut, Philip Hopke, Christoph Hüglin, Maria Kanakidou, Zsofia Kertesz, Zbiginiw Klimont, Katriina Kyllönen, Fabrice Lambert, Xiaohong Liu, Remi Losno, Franco Lucarelli, Willy Maenhaut, Beatrice Marticorena, Randall V. Martin, Nikolaos Mihalopoulos, Yasser Morera-Gomez, Adina Paytan, Joseph Prospero, Sergio Rodríguez, Patricia Smichowski, Daniela Varrica, Brenna Walsh, Crystal Weagle, and Xi Zhao
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2024-1, https://doi.org/10.5194/essd-2024-1, 2024
Preprint withdrawn
Short summary
Short summary
Aerosol particles can interact with incoming solar radiation and outgoing long wave radiation, change cloud properties, affect photochemistry, impact surface air quality, and when deposited impact surface albedo of snow and ice, and modulate carbon dioxide uptake by the land and ocean. Here we present a new compilation of aerosol observations including composition, a methodology for comparing the datasets to model output, and show the implications of these results using one model.
Jarmo Mäkelä, Laura Arppe, Hannu Fritze, Jussi Heinonsalo, Kristiina Karhu, Jari Liski, Markku Oinonen, Petra Straková, and Toni Viskari
Biogeosciences, 19, 4305–4313, https://doi.org/10.5194/bg-19-4305-2022, https://doi.org/10.5194/bg-19-4305-2022, 2022
Short summary
Short summary
Soils account for the largest share of carbon found in terrestrial ecosystems, and accurate depiction of soil carbon decomposition is essential in understanding how permanent these carbon storages are. We present a straightforward way to include carbon isotope concentrations into soil decomposition and carbon storages for the Yasso model, which enables the model to use 13C as a natural tracer to track changes in the underlying soil organic matter decomposition.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490, https://doi.org/10.5194/bg-19-1469-2022, https://doi.org/10.5194/bg-19-1469-2022, 2022
Short summary
Short summary
This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Olli Nevalainen, Olli Niemitalo, Istem Fer, Antti Juntunen, Tuomas Mattila, Olli Koskela, Joni Kukkamäki, Layla Höckerstedt, Laura Mäkelä, Pieta Jarva, Laura Heimsch, Henriikka Vekuri, Liisa Kulmala, Åsa Stam, Otto Kuusela, Stephanie Gerin, Toni Viskari, Julius Vira, Jari Hyväluoma, Juha-Pekka Tuovinen, Annalea Lohila, Tuomas Laurila, Jussi Heinonsalo, Tuula Aalto, Iivari Kunttu, and Jari Liski
Geosci. Instrum. Method. Data Syst., 11, 93–109, https://doi.org/10.5194/gi-11-93-2022, https://doi.org/10.5194/gi-11-93-2022, 2022
Short summary
Short summary
Better monitoring of soil carbon sequestration is needed to understand the best carbon farming practices in different soils and climate conditions. We, the Field Observatory Network (FiON), have therefore established a methodology for monitoring and forecasting agricultural carbon sequestration by combining offline and near-real-time field measurements, weather data, satellite imagery, and modeling. To disseminate our work, we built a website called the Field Observatory (fieldobservatory.org).
Julius Vira, Peter Hess, Money Ossohou, and Corinne Galy-Lacaux
Atmos. Chem. Phys., 22, 1883–1904, https://doi.org/10.5194/acp-22-1883-2022, https://doi.org/10.5194/acp-22-1883-2022, 2022
Short summary
Short summary
Ammonia is one of the main components of nitrogen deposition. Here we use a new model to assess the ammonia emissions from agriculture, the largest anthropogenic source of ammonia. The model results are consistent with earlier estimates over industrialized regions in agreement with observations. However, the model predicts much higher emissions over sub-Saharan Africa compared to earlier estimates. Available observations from surface stations and satellites support these higher emissions.
Laura Heimsch, Annalea Lohila, Juha-Pekka Tuovinen, Henriikka Vekuri, Jussi Heinonsalo, Olli Nevalainen, Mika Korkiakoski, Jari Liski, Tuomas Laurila, and Liisa Kulmala
Biogeosciences, 18, 3467–3483, https://doi.org/10.5194/bg-18-3467-2021, https://doi.org/10.5194/bg-18-3467-2021, 2021
Short summary
Short summary
CO2 and H2O fluxes were measured at a newly established eddy covariance site in southern Finland for 2 years from 2018 to 2020. This agricultural grassland site focuses on the conversion from intensive towards more sustainable agricultural management. The first summer experienced prolonged dry periods, and notably larger fluxes were observed in the second summer. The field acted as a net carbon sink during both study years.
Alexey N. Shiklomanov, Michael C. Dietze, Istem Fer, Toni Viskari, and Shawn P. Serbin
Geosci. Model Dev., 14, 2603–2633, https://doi.org/10.5194/gmd-14-2603-2021, https://doi.org/10.5194/gmd-14-2603-2021, 2021
Short summary
Short summary
Airborne and satellite images are a great resource for calibrating and evaluating computer models of ecosystems. Typically, researchers derive ecosystem properties from these images and then compare models against these derived properties. Here, we present an alternative approach where we modify a model to predict what the satellite would see more directly. We then show how this approach can be used to calibrate model parameters using airborne data from forest sites in the northeastern US.
Toni Viskari, Maisa Laine, Liisa Kulmala, Jarmo Mäkelä, Istem Fer, and Jari Liski
Geosci. Model Dev., 13, 5959–5971, https://doi.org/10.5194/gmd-13-5959-2020, https://doi.org/10.5194/gmd-13-5959-2020, 2020
Short summary
Short summary
The research here established whether a Bayesian statistical method called state data assimilation could be used to improve soil organic carbon (SOC) forecasts. Our test case was a fallow experiment where SOC content was measured over several decades from a plot where all vegetation was removed. Our results showed that state data assimilation improved projections and allowed for the detailed model state be updated with coarse total carbon measurements.
Tea Thum, Julia E. M. S. Nabel, Aki Tsuruta, Tuula Aalto, Edward J. Dlugokencky, Jari Liski, Ingrid T. Luijkx, Tiina Markkanen, Julia Pongratz, Yukio Yoshida, and Sönke Zaehle
Biogeosciences, 17, 5721–5743, https://doi.org/10.5194/bg-17-5721-2020, https://doi.org/10.5194/bg-17-5721-2020, 2020
Short summary
Short summary
Global vegetation models are important tools in estimating the impacts of global climate change. The fate of soil carbon is of the upmost importance as its emissions will enhance the atmospheric carbon dioxide concentration. To evaluate the skill of global vegetation models to model the soil carbon and its responses to environmental factors, it is important to use different data sources. We evaluated two different soil carbon models by using atmospheric carbon dioxide concentrations.
Julius Vira, Peter Hess, Jeff Melkonian, and William R. Wieder
Geosci. Model Dev., 13, 4459–4490, https://doi.org/10.5194/gmd-13-4459-2020, https://doi.org/10.5194/gmd-13-4459-2020, 2020
Short summary
Short summary
Mostly emitted by the agricultural sector, ammonia has an important role in atmospheric chemistry. We developed a model to simulate how ammonia emissions respond to changes in temperature and soil moisture, and we evaluated agricultural ammonia emissions globally. The simulated emissions agree with earlier estimates over many regions, but the results highlight the variability of ammonia emissions and suggest that emissions in warm climates may be higher than previously thought.
Rostislav Kouznetsov, Mikhail Sofiev, Julius Vira, and Gabriele Stiller
Atmos. Chem. Phys., 20, 5837–5859, https://doi.org/10.5194/acp-20-5837-2020, https://doi.org/10.5194/acp-20-5837-2020, 2020
Short summary
Short summary
Estimates of the age of stratospheric air (AoA), its distribution, and trends, obtained by different experimental methods, differ among each other. AoA derived form MIPAS satellite observations, the richest observational dataset on sulfur hexafluoride (SF6) in the stratosphere, are a clear outlier. With multi-decade simulations of AoA and SF6 in the stratosphere, we show that the origin of the discrepancy is in a methodology of deriving AoA from observations rather than in observational data.
Susanna Salminen-Paatero, Julius Vira, and Jussi Paatero
Atmos. Chem. Phys., 20, 5759–5769, https://doi.org/10.5194/acp-20-5759-2020, https://doi.org/10.5194/acp-20-5759-2020, 2020
Short summary
Short summary
We measured concentrations and isotope ratios of plutonium in air filters collected in Finnish Lapland in 1965–2011. Radioactive-contamination sources were global nuclear-testing fallout and the Fukushima and SNAP-9A accidents. Both real and hypothetical nuclear accidents were studied with atmospheric-dispersion modeling. The radioactive-contamination effect on Finnish Lapland would be minor from an intended nuclear power plant and negligible from a floating nuclear reactor in the Barents Sea.
Anne-Marlene Blechschmidt, Joaquim Arteta, Adriana Coman, Lyana Curier, Henk Eskes, Gilles Foret, Clio Gielen, Francois Hendrick, Virginie Marécal, Frédérik Meleux, Jonathan Parmentier, Enno Peters, Gaia Pinardi, Ankie J. M. Piters, Matthieu Plu, Andreas Richter, Arjo Segers, Mikhail Sofiev, Álvaro M. Valdebenito, Michel Van Roozendael, Julius Vira, Tim Vlemmix, and John P. Burrows
Atmos. Chem. Phys., 20, 2795–2823, https://doi.org/10.5194/acp-20-2795-2020, https://doi.org/10.5194/acp-20-2795-2020, 2020
Short summary
Short summary
MAX-DOAS tropospheric NO2 vertical column retrievals from a set of European measurement stations are compared to regional air quality models which contribute to the operational Copernicus Atmosphere Monitoring Service (CAMS). Correlations are on the order of 35 %–75 %; large differences occur for individual pollution plumes. The results demonstrate that future model development needs to concentrate on improving representation of diurnal cycles and associated temporal scalings.
Jarmo Mäkelä, Jürgen Knauer, Mika Aurela, Andrew Black, Martin Heimann, Hideki Kobayashi, Annalea Lohila, Ivan Mammarella, Hank Margolis, Tiina Markkanen, Jouni Susiluoto, Tea Thum, Toni Viskari, Sönke Zaehle, and Tuula Aalto
Geosci. Model Dev., 12, 4075–4098, https://doi.org/10.5194/gmd-12-4075-2019, https://doi.org/10.5194/gmd-12-4075-2019, 2019
Short summary
Short summary
We assess the differences of six stomatal conductance formulations, embedded into a land–vegetation model JSBACH, on 10 boreal coniferous evergreen forest sites. We calibrate the model parameters using all six functions in a multi-year experiment, as well as for a separate drought event at one of the sites, using the adaptive population importance sampler. The analysis reveals weaknesses in the stomatal conductance formulation-dependent model behaviour that we are able to partially amend.
Susan J. Cheng, Peter G. Hess, William R. Wieder, R. Quinn Thomas, Knute J. Nadelhoffer, Julius Vira, Danica L. Lombardozzi, Per Gundersen, Ivan J. Fernandez, Patrick Schleppi, Marie-Cécile Gruselle, Filip Moldan, and Christine L. Goodale
Biogeosciences, 16, 2771–2793, https://doi.org/10.5194/bg-16-2771-2019, https://doi.org/10.5194/bg-16-2771-2019, 2019
Short summary
Short summary
Nitrogen deposition and fertilizer can change how much carbon is stored in plants and soils. Understanding how much added nitrogen is recovered in plants or soils is critical to estimating the size of the future land carbon sink. We compared how nitrogen additions are recovered in modeled soil and plant stocks against data from long-term nitrogen addition experiments. We found that the model simulates recovery of added nitrogen into soils through a different process than found in the field.
Zhun Mao, Delphine Derrien, Markus Didion, Jari Liski, Thomas Eglin, Manuel Nicolas, Mathieu Jonard, and Laurent Saint-André
Biogeosciences, 16, 1955–1973, https://doi.org/10.5194/bg-16-1955-2019, https://doi.org/10.5194/bg-16-1955-2019, 2019
Short summary
Short summary
In a context of global changes, modeling and predicting the dynamics of soil carbon stocks in forest ecosystems are vital but challenging. Yasso07 is considered to be one of the most promising models for such a purpose. We examine the accuracy of its prediction of soil carbon dynamics over the whole French metropolitan territory at a decennial timescale. We revealed how the bottleneck in soil carbon modeling is linked with the lack of knowledge on soil carbon quality and fine-root litter.
Mikhail Sofiev, Olga Ritenberga, Roberto Albertini, Joaquim Arteta, Jordina Belmonte, Carmi Geller Bernstein, Maira Bonini, Sevcan Celenk, Athanasios Damialis, John Douros, Hendrik Elbern, Elmar Friese, Carmen Galan, Gilles Oliver, Ivana Hrga, Rostislav Kouznetsov, Kai Krajsek, Donat Magyar, Jonathan Parmentier, Matthieu Plu, Marje Prank, Lennart Robertson, Birthe Marie Steensen, Michel Thibaudon, Arjo Segers, Barbara Stepanovich, Alvaro M. Valdebenito, Julius Vira, and Despoina Vokou
Atmos. Chem. Phys., 17, 12341–12360, https://doi.org/10.5194/acp-17-12341-2017, https://doi.org/10.5194/acp-17-12341-2017, 2017
Short summary
Short summary
This work presents the features and evaluates the quality of the Copernicus Atmospheric Monitoring Service forecasts of olive pollen distribution in Europe. It is shown that the models can predict the main features of the observed pollen distribution but have more difficulties in capturing the season start and end, which appeared shifted by a few days. We also demonstrated that the combined use of model predictions with up-to-date measurements (data fusion) can strongly improve the results.
Julius Vira, Elisa Carboni, Roy G. Grainger, and Mikhail Sofiev
Geosci. Model Dev., 10, 1985–2008, https://doi.org/10.5194/gmd-10-1985-2017, https://doi.org/10.5194/gmd-10-1985-2017, 2017
Short summary
Short summary
The vertical and temporal distributions of sulfur dioxide emissions during the 2010 eruption of Eyjafjallajökull were reconstructed by combining data from the IASI satellite instrument with a dispersion model. Unlike in previous studies, both column density (the total amount above a given point) and the plume height were derived from the satellite data. This resulted in more accurate simulated vertical distributions for the times when the emission was not constrained by the column densities.
M. Sofiev, J. Vira, R. Kouznetsov, M. Prank, J. Soares, and E. Genikhovich
Geosci. Model Dev., 8, 3497–3522, https://doi.org/10.5194/gmd-8-3497-2015, https://doi.org/10.5194/gmd-8-3497-2015, 2015
Short summary
Short summary
The paper presents a transport mechanism of SILAM CTM based on an algorithm of M. Galperin. We describe the original scheme and its updates needed for applications to long-living species, complex atmospheric flows, etc. The scheme is connected to vertical diffusion, chemical transformation and deposition algorithms. Quality of the advection routine is evaluated with a large set of tests, which showed performance fully comparable with state-of-the-art algorithms at much lower computational costs.
V. Marécal, V.-H. Peuch, C. Andersson, S. Andersson, J. Arteta, M. Beekmann, A. Benedictow, R. Bergström, B. Bessagnet, A. Cansado, F. Chéroux, A. Colette, A. Coman, R. L. Curier, H. A. C. Denier van der Gon, A. Drouin, H. Elbern, E. Emili, R. J. Engelen, H. J. Eskes, G. Foret, E. Friese, M. Gauss, C. Giannaros, J. Guth, M. Joly, E. Jaumouillé, B. Josse, N. Kadygrov, J. W. Kaiser, K. Krajsek, J. Kuenen, U. Kumar, N. Liora, E. Lopez, L. Malherbe, I. Martinez, D. Melas, F. Meleux, L. Menut, P. Moinat, T. Morales, J. Parmentier, A. Piacentini, M. Plu, A. Poupkou, S. Queguiner, L. Robertson, L. Rouïl, M. Schaap, A. Segers, M. Sofiev, L. Tarasson, M. Thomas, R. Timmermans, Á. Valdebenito, P. van Velthoven, R. van Versendaal, J. Vira, and A. Ung
Geosci. Model Dev., 8, 2777–2813, https://doi.org/10.5194/gmd-8-2777-2015, https://doi.org/10.5194/gmd-8-2777-2015, 2015
Short summary
Short summary
This paper describes the air quality forecasting system over Europe put in place in the Monitoring Atmospheric Composition and Climate projects. It provides daily and 4-day forecasts and analyses for the previous day for major gas and particulate pollutants and their main precursors. These products are based on a multi-model approach using seven state-of-the-art models developed in Europe. An evaluation of the performance of the system is discussed in the paper.
M. Sofiev, U. Berger, M. Prank, J. Vira, J. Arteta, J. Belmonte, K.-C. Bergmann, F. Chéroux, H. Elbern, E. Friese, C. Galan, R. Gehrig, D. Khvorostyanov, R. Kranenburg, U. Kumar, V. Marécal, F. Meleux, L. Menut, A.-M. Pessi, L. Robertson, O. Ritenberga, V. Rodinkova, A. Saarto, A. Segers, E. Severova, I. Sauliene, P. Siljamo, B. M. Steensen, E. Teinemaa, M. Thibaudon, and V.-H. Peuch
Atmos. Chem. Phys., 15, 8115–8130, https://doi.org/10.5194/acp-15-8115-2015, https://doi.org/10.5194/acp-15-8115-2015, 2015
Short summary
Short summary
The paper presents the first ensemble modelling experiment for forecasting the atmospheric dispersion of birch pollen in Europe. The study included 7 models of MACC-ENS tested over the season of 2010 and applied for 2013 in forecasting and reanalysis modes. The results were compared with observations in 11 countries, members of European Aeroallergen Network. The models successfully reproduced the timing of the unusually late season of 2013 but had more difficulties with absolute concentration.
M. Bocquet, H. Elbern, H. Eskes, M. Hirtl, R. Žabkar, G. R. Carmichael, J. Flemming, A. Inness, M. Pagowski, J. L. Pérez Camaño, P. E. Saide, R. San Jose, M. Sofiev, J. Vira, A. Baklanov, C. Carnevale, G. Grell, and C. Seigneur
Atmos. Chem. Phys., 15, 5325–5358, https://doi.org/10.5194/acp-15-5325-2015, https://doi.org/10.5194/acp-15-5325-2015, 2015
Short summary
Short summary
Data assimilation is used in atmospheric chemistry models to improve air quality forecasts, construct re-analyses of concentrations, and perform inverse modeling. Coupled chemistry meteorology models (CCMM) are atmospheric chemistry models that simulate meteorological processes and chemical transformations jointly. We review here the current status of data assimilation in atmospheric chemistry models, with a particular focus on future prospects for data assimilation in CCMM.
J. Vira and M. Sofiev
Geosci. Model Dev., 8, 191–203, https://doi.org/10.5194/gmd-8-191-2015, https://doi.org/10.5194/gmd-8-191-2015, 2015
T. Viskari, E. Asmi, P. Kolmonen, H. Vuollekoski, T. Petäjä, and H. Järvinen
Atmos. Chem. Phys., 12, 11767–11779, https://doi.org/10.5194/acp-12-11767-2012, https://doi.org/10.5194/acp-12-11767-2012, 2012
T. Viskari, E. Asmi, A. Virkkula, P. Kolmonen, T. Petäjä, and H. Järvinen
Atmos. Chem. Phys., 12, 11781–11793, https://doi.org/10.5194/acp-12-11781-2012, https://doi.org/10.5194/acp-12-11781-2012, 2012
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
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)
Modeling demographic-driven vegetation dynamics and ecosystem biogeochemical cycling in NASA GISS's Earth system model (ModelE-BiomeE v.1.0)
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.
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.
Ensheng Weng, Igor Aleinov, Ram Singh, Michael J. Puma, Sonali S. McDermid, Nancy Y. Kiang, Maxwell Kelley, Kevin Wilcox, Ray Dybzinski, Caroline E. Farrior, Stephen W. Pacala, and Benjamin I. Cook
Geosci. Model Dev., 15, 8153–8180, https://doi.org/10.5194/gmd-15-8153-2022, https://doi.org/10.5194/gmd-15-8153-2022, 2022
Short summary
Short summary
We develop a demographic vegetation model to improve the representation of terrestrial vegetation dynamics and ecosystem biogeochemical cycles in the Goddard Institute for Space Studies ModelE. The individual-based competition for light and soil resources makes the modeling of eco-evolutionary optimality possible. This model will enable ModelE to simulate long-term biogeophysical and biogeochemical feedbacks between the climate system and land ecosystems at decadal to centurial temporal scales.
Cited articles
Abramoff, R., Xiaofeng, X., Hartmann, M., O'Brien, S., Feng, W., Davidson,
E., Finzi, A., Moorhead, D., Schimel, J., Torn, M., and Mayes, M. A.: The
Millennial model: in search of measurable pools and transformations for
modeling soil carbon in the new century, Biogeochemistry, 137, 51–71, 2018.
Beer, C., Reichstein, M., Tomelleri, E., Ciais, P., Jung, M., Carvalhais,
N., Rödenbeck, C., Arain, M. A., Baldocchi, D., Bonan, G. B., Bondeau, A.,
Cescatti, A., Lasslop, G., Lindroth, A., Lomas, M., Luyssaert, S., Margolis,
H., Oleson, K. W., Roupsard, O., Veenendaal, E., Viovy, N., Williams, C.,
Woodward, F. I., and Papale, D.: Terrestrial Gross Carbon Dioxide Uptake:
Global Distribution and Covariation with Climate, Science, 329, 834–838, 2010.
Berg, B., Hannus, K., Popoff, T., and Theander, P.: Changes in organic
components of litter during decomposition. Long term decomposition in a
Scots pine forest, I. Can. J. Bot., 60, 1310–1319, 1982.
Berg, B., Booltink, H., Breymeyer, A., Ewertsson, A., Gallardo, A., Holm,
B., Johansson, M. B., Koivuoja, S., Meentemeyer, V., Nyman, P., Olofsson, J.,
Pettersson, A.-S., Reurslag, A., Staaf, H., Staaf, I., Uba, L., Berg,
B., Booltink, H., Breymeyer, A., Ewertsson, A., Gallardo, A., Holm, B.,
Johansson, M. B., Koivuoja, S., Meentemeyer, V., Nyman, P., Olofsson, J.,
Pettersson, A.-S., Reurslag, A., Staaf, H., Staaf, I., and Uba, L.: Data on
Needle Litter Decomposition and Soil Climate as Well as Site Characteristics
for Some Coniferous Forest Sites, Part I, Site Characteristics. Report 41,
Swedish University of Agricultural Sciences, Department of Ecology and
Environmental Research, Uppsala, 1991a.
Berg, B., Booltink, H., Breymeyer, A., Ewertsson, A., Gallardo, A., Holm,
B., Johansson, M. B., Koivuoja, S., Meentemeyer, V., Nyman, P., Olofsson, J.,
Pettersson, A. S., Reurslag, A., Staaf, H., Staaf, I., and Uba, L.: Data on
Needle Litter Decomposition and Soil Climate as Well as Site Characteristics
for Some Coniferous Forest Sites, Part II, Decomposition Data. Report 42,
Swedish University of Agricultural Sciences, Department of Ecology and
Environmental Research, Uppsala, 1991b.
Cailleret, M., Bircher, N., Hartig, F., Hulsmann, L., and Bugmann, H.:
Bayesian calibration of a growth-dependent tree mortality model to simulate
the dynamics of European temperate forests, Ecol. Appl., 30, e02021, https://doi.org/10.1002/eap.2021, 2020.
Camino-Serrano, M., Guenet, B., Luyssaert, S., Ciais, P., Bastrikov, V., De Vos, B., Gielen, B., Gleixner, G., Jornet-Puig, A., Kaiser, K., Kothawala, D., Lauerwald, R., Peñuelas, J., Schrumpf, M., Vicca, S., Vuichard, N., Walmsley, D., and Janssens, I. A.: ORCHIDEE-SOM: modeling soil organic carbon (SOC) and dissolved organic carbon (DOC) dynamics along vertical soil profiles in Europe, Geosci. Model Dev., 11, 937–957, https://doi.org/10.5194/gmd-11-937-2018, 2018.
Clemmensen, K. E, Bahr, A., Ovaskainen, O., Dahlberg, A., Ekblad, A.,
Wallander, H., Stenlid, J., Finlay, R. D., Wardle, D. A., and Lindahl, B. D.:
Roots and associated fungi drive long-term carbon sequestration in boreal
forest, Science, 339, 1615–1618, 2013.
Davidson, E. A. and Janssens, I. A.: Temperature sensitivity of soil carbon
decomposition and feedbacks to climate change, Nature, 440, 165–173, 2006.
Davies, J. A. C., Tipping, E., Rowe, E. C., Boyle, J. F., Graf Pannatier, E.,
and Martinsen, V.: Long-term P weathering and recent N deposition control
plant-soil C, N and P, Glob. Biochem. Cycles., 30, 231–249, https://doi.org/10.1002/2015GB005167, 2016.
Fer, I., Shiklomanov, A., Novick, K. A., Gough, C. M., Arain, M. A., Chen, J.,
Murphy, B., Desai, A. R., and Dietze, M. C.: Capturing site-to-site variability
through Hierarchical Bayesian calibration of a process-based dynamic
vegetation model, bioRxiv, 04.28.441243, https://doi.org/10.1101/2021.04.28.441243, 2021.
Gelman, A. G. and Rubin, D. B.: Inference from iterative simulation using
multiple sequences, Stat. Sci., 7, 457e472, https://doi.org/10.1214/ss/1177011136, 1992.
Gholz, H. L., Wedin, D. A., Smitherman, S. M., Harmon, M. E., and Parton, W. J.:
Long- term dynamics of pine and hardwood litter in contrasting environments:
toward a global model of decomposition, Glob. Change Biol., 6, 751e765, https://doi.org/10.1046/j.1365-2486.2000.00349.x, 2000
Goll, D. S., Vuichard, N., Maignan, F., Jornet-Puig, A., Sardans, J., Violette, A., Peng, S., Sun, Y., Kvakic, M., Guimberteau, M., Guenet, B., Zaehle, S., Penuelas, J., Janssens, I., and Ciais, P.: A representation of the phosphorus cycle for ORCHIDEE (revision 4520), Geosci. Model Dev., 10, 3745–3770, https://doi.org/10.5194/gmd-10-3745-2017, 2017.
Haario, H., Saksman, E., and Tamminen, J.: Anadaptive Metropolis algorithm,
Bernoulli, 7, 223–242, https://doi.org/10.2307/3318737,
2001.
Harmon, M. E., Krankina, O. N., and Sexton, J.: Decomposition vectors: a new
approach to estimating woody detritus decomposition dynamics, Can. J. For. Res., 30, 76–84,
2000.
Harmon, M. E., Silver, W. L., Fasth, B., Chen, H., Burke, I. C., Parton, W. J.,
Hart, S. C., Currie, W. S., and the LIDET team: Long-term patterns in of mass
loss in during decomposition of leaf and fine root litter: an intersite
comparison, Global Chang. Biol., 15, 1320–1338, 2009.
Hartig, F., Minunno, F., and Paul, S.: BayesianTools: General-Purpose MCMC
and SMC Samples and Tools for Bayesian Statistics. R package version 0.1.7,
https://CRAN.R-project.org/package=BayesianTools (last access: 28 January 2022), 2019.
Hobbie, S. E.: Contrasting Effects of Substrate and Fertilizer Nitrogen on
the Early Stages of Litter Decomposition, Ecosystems, 8, 644–656, 2005.
Jackson, R. B., Lajtha, K., Crow, S. E., Hugelius, G., Kramer, M. G., and
Pineiro, G.: The ecology of soil carbon: pools, vulnerabilities, and biotic
and abiotic controls. Annual Review of Ecology, Evolution, and Systematics,
48, 419–445, 2017.
Jandl, R., Rodeghiero, M., Martinez, C., Cotrufo, C. M., Bampa, F., van
Wesemael, B., Harrison, R. B., Guerrini, I. A., deB Richter, D., Rustad, L.,
Lorenz, K., Chabbi, A., and Miglietta, F.: Current status, uncertainty and
future needs in soil organic carbon monitoring, Sci. Total Environ., 468–469, 376–383, 2014.
Karhu, K., Fritzen, H., Hämäläinen, K., Vanhala, P., Jungner,
P., Oinonen, M., Sonninen, E., Tuomi, M., Spetz, P., Kitunen, V., and Liski,
J.: Temperature sensitivity of soil carbon fractions in boreal forest soil,
Ecology, 91, 370–376, 2010.
Keiluweit, M., Wanzek, T., Kleber, M., Nico, P., and Fendorf, S.: Anaerobic
microsites have an unaccounted role in soil carbon stabilization, Nat. Commun., 8, 1771, https://doi.org/10.1038/s41467-017-01406-6,
2017.
Kyker-Snowman, E., Wieder, W. R., Frey, S. D., and Grandy, A. S.: Stoichiometrically coupled carbon and nitrogen cycling in the MIcrobial-MIneral Carbon Stabilization model version 1.0 (MIMICS-CN v1.0), Geosci. Model Dev., 13, 4413–4434, https://doi.org/10.5194/gmd-13-4413-2020, 2020.
Laloy, E. and Vrugt, J. A.: High-dimensional posterior exploration of
hydrologic models using multiple-try DREAM (ZS) and high-performance
computing, Water Resour. Res., 48, W01526. https://doi.org/10.1029/2011WR010608, 2012.
Liang, C., Schimel, J. P., and Jastrow, J. D.: The importance of anabolism in
microbial control over soil carbon storage, Nat. Microbiol., 2, 17105, https://doi.org/10.1038/nmicrobiol.2017.105, 2017.
Liski, J. and Westman, C. J.: Density of organic carbon in soil at
coniferous forest sites in southern Finland, Biogeochemistry, 29, 183–197, 1995.
Liski, J., Ilvesniemi, H., Mäkelä, A., and Starr, M.: Model analysis
of the effects of soil age, fires and harvesting on the carbon storage of
boreal forest soils, Eur. J. Soil Sci., 49, 407–416, 1998.
Liski, J., Nissinen, A., Erhard, M., and Taskinen, O.: Climate effects on
litter decomposition from arctic tundra to tropical rainforest, Global
Change Biol., 9, 1–10, 2003.
Liski, J., Palosuo, T., Peltoniemi, M., and Sievänen, R.: Carbon and
decomposition model Yasso for forest soils, Ecol. Modell., 189, 168–182, https://doi.org/10.1016/j.ecolmodel.2005.03.005, 2005.
Lu, D., Ricciuto, D., Walker, A., Safta, C., and Munger, W.: Bayesian calibration of terrestrial ecosystem models: a study of advanced Markov chain Monte Carlo methods, Biogeosciences, 14, 4295–4314, https://doi.org/10.5194/bg-14-4295-2017, 2017.
MacBean, N., Peylin, P., Chevallier, F., Scholze, M., and Schürmann, G.: Consistent assimilation of multiple data streams in a carbon cycle data assimilation system, Geosci. Model Dev., 9, 3569–3588, https://doi.org/10.5194/gmd-9-3569-2016, 2016.
Malhotra, A., Todd-Brown, K., Nave, L. E., Batjes, N. H., Holmquist, J. R.,
Hoyt, A. M., Iversen, C. M., Jackson, R. B., Lajtha, K., Lawrence, C.,
Vinduskova, O., Wieder, W., Williams, M., Hugelius, G., and Harden, J.: The
landscape of soil carbon data: Emerging questions, synergies and questions,
Prog. Phys. Geogr., 43, 707–719, 2019.
Manzoni, S. P. and Porporato, A.: Soil carbon and nitrogen mineralization:
Theory and models across scales, Soil Biol. Biochem., 41, 1355–1379, 2009.
Mayer, M., Prescott, C. E., Abaker, W. E. A., Augusto, L., Cecillon, L.,
Ferreira, G. W. D., James, J., Jandl, R., Katzensteiner, K., Laclau, J.-P.,
Laganiere, J., Nouvellon, Y., Pare, D., Stanturf, J. A., Vanguelova, E. I.,
and Vesterdal, L.: Tamm Review: Influence of forest management activities on
soil organic carbon stocks: A knowledge synthesis, For. Ecol. Manag., 466,
118–127, https://doi.org/10.1016/j.foreco.2020.118127, 2020.
Meentemeyer, V.: Macroclimate and lignin control of litter decomposition
rates, Ecology, 59, 465–472, 1978.
Menichetti, L., Ågren, G. I., Barre, P., Moyano, B., and Kätterer,
T.: Generic parameters of first-order kinetics accurately describe soil
organic matter decay in bare fallow soils over a wide edaphic and climatic
range, Sci. Rep.-UK, 9, 20319, https://doi.org/10.1038/s41598-019-55058-1, 2019.
Mäkinen, H., Hynynen, J., Siitonen, J., and Sievänen, R.: Predicting
the decomposition of scots pine, norway spruce, and birch stems in Finland,
Ecol. Appl., 16, 1865–1879, 2006.
Mäkipää, R., Häkkinen, M., Muukkonen, P., and Peltoniemi,
M.: The costs of monitoring changes in forest soil carbon stocks, Boreal Environ. Res., 13,
120–130, 2008.
Moore, T., Trofymow, J. A., Prescott, C., Titus, B. D., and the CIDET working
group: Can short-term litter-bag measurements predict long-term
decomposition in northern forests, Plant Soil, 416, 419–426, 2017.
Oades, J. M.: The retention of organic matter in soils, Biogeochemistry, 5, 35–70,
1988.
Oberpriller, J., Cameron, D. R., Dietze, M. C., and Hartig, F.: Towards robust
statistical inference for complex computer models, Ecol. Lett., 24, 1251–1261, 2021.
Olson, J. S.: Energy storage and the balance of producers and decomposers in
ecological systems, Ecology, 44, 322–331, 1963.
Olson, D. M., Dinerstein, E., Wikramanayake, E. D., Burgess, N. D., Powell,
G. V. N., Underwood, E. C., D'Amico, J. A., Itoua, I., Strand, H. E., Morrison,
J. C., Loucks, C. J., Allnut, T. F., Ricketts, T. H., Kura, Y., Lamoreux, J. F.,
Wettengel, W. W., Hedao, P., and Kassem, K. R.: Terrestrial Ecoregions of the
World: A New Map of Life on Earth: A new global map of terrestrial
ecoregions provides an innovative tool for conserving biodiversity,
BioScience, 51, 933–938, 2001.
Palosuo, T., Foereid, B., Svensson, M., Shurpali, N., Lehtonen, A., Herbst,
M., Linkosalo, T., Ortiz, C., Rampazzo Todorovic, G., Marcinkonis, S., Li,
C., and Jandl, R.: A multi-model comparison of soil carbon assessment of a
coniferous forest stand, Environ. Modell. Softw., 35, 38–49, 2012.
Parton, W. J.: The CENTURY model, in: Evaluation of Soil Organic Matter Models, edited by: Powlson, D. S., Smith, P., and Smith,
J. U., NATO ASI Series (Series
I: Global Environmental Change), vol. 38, Springer, Berlin, Heidelberg, https://doi.org/10.2307/1932179, 1996.
Peng, Y., Thomas, S. C., and Tian, D.: For management and soil respiration:
Implications for carbon sequestration, Environ. Rev., 16, 93–111, https://doi.org/10.1139/A08-003, 2008.
Rasmussen, C., Heckman, S., Wieder, W. R., Keiluweit, M., Lawrence, C. R.,
Berhe, A. A., Blankinship, J. C., Crow, S. E., Druhan, J. L., Hicks Pries, C. E.,
Marin-Spiotta, E., Plante, A. F., Schädel, C., Schimel, J. P., Sierra,
C. A., Thompson, A., and Wagai, R.: Beyond Clay: towards an improved set of
variables for predicting soil organic matter content, Biogeochem. Lett., 137, 297–306, 2018.
Schmidt, M. W. I., Torn, M. S., Abiven, S., Dittmar, T., Guggenberger, G.,
Janssens, I., Kleber, M., Kögel-Knabner, I., Lehmann, J., Manning,
D. A. C., Nannipier, P., Rasse, D. P., Weiner, S., and Trumbore, S. E.:
Persistence of soil organic matter as an ecosystem property, Nature, 478,
49–56, 2011.
Stevenson, F. J.: Humus Chemistry: Genesis, Composition, Reactions, John
Wiley & Sons, New York, 1982.
Sulman, B. N., Moore, J. A. M., Abramoff, R., Averill, C., Kivlin, S.,
Georgiou, K., Sridhar, B., Hartmann, M. D., Wang, G., Wieder, W., Bradford,
M. A., Luo, Y., Mayer, M. A., Morrison, E., Riley, W. J., Salazar, A., Schimel,
J. P., Tang, J., and Classen, A. T.: Multiple models and experiments underscore
large uncertainty in soil carbon dynamics, Biogeochemistry, 141, 109–123, 2018.
Swift, M. J.: The ecology of wood decomposition, Sci. Prog. Oxf., 64, 175–199,
1977.
Tang, J. and Riley, W. J.: Linear two-pool models are insufficient to infer
soil organic matter decomposition temperature sensitivity from incubations,
Biochemistry, 149, 251–261, 2020.
ter Braak, C. J. F. and Vrugt, J. A.: Differential evolution Markov chain with
snooker updater and fewer chains, Stat. Comput., 18, 435e446,
https://doi.org/10.1007/s11222-008-9104-9, 2008.
Thum, T., Caldararu, S., Engel, J., Kern, M., Pallandt, M., Schnur, R., Yu, L., and Zaehle, S.: A new model of the coupled carbon, nitrogen, and phosphorus cycles in the terrestrial biosphere (QUINCY v1.0; revision 1996), Geosci. Model Dev., 12, 4781–4802, https://doi.org/10.5194/gmd-12-4781-2019, 2019.
Tian, X., Minunno, F., Cao, T., Peltoniemi, M., Kalliokoski, T., and
Mäkelä, A.: Extending the range of applicability of the
semi-empirical ecosystem flux model PRELES for varying forest types and
climate, Glob. Change Biol., 26, 2923–2943, 2020.
Trofymow, J. A. and the CIDET Working Group: The Canadian Intersite
Decomposition Experiment (CIDET): Project and Site Establishment Report,
Information Report BC-X-378, Pacific Forestry Centre, Victoria, Canada, 1998.
Tuomi, M., Vanhala, P., Karhu, K., Fritze, H., and Liski, J.: Heterotrophic
soil respiration – comparison of different models describing its
temperature dependence, Ecol. Modell., 211, 182–190, 2008.
Tuomi, M., Thum, T., Järvinen, H., Fronzek, S., Berg, B., Harmon, M.,
Trofymow, J.A., Sevanto, S., and Liski, J.: Leaf litter decomposition –
Estimates of global variability based on Yasso07 model, Ecol. Modell., 220,
3362–3371, https://doi.org/10.1016/j.ecolmodel.2009.05.016,
2009.
Tuomi, M., Laiho, R., Repo, A., and Liski, J.: Wood decomposition model for
boreal forests, Ecol. Modell., 222, 709–718, 2011a.
Tuomi, M., Rasinmäki, J., Repo, A., Vanhala, P. and Liski, J.: Soil
carbon model Yasso07 graphical user interface, Environ. Model. Softw., 26, 1358–1362, 2011b.
Viskari, T., Pusa, J., Fer, I., Repo, A., Vira, J., and Liski, J.: The impact of calibrating soil organic carbon model Yasso with multiple datasets, Zenodo [code/data set], https://doi.org/10.5281/zenodo.5059909, 2021.
Vrugt, J. A.: Markov chain Monte Carlo simulation using theDREAM software
package: Theory, concepts, and MATLAB im-plementation, Environ. Model.
Softw., 75, 273–316, https://doi.org/10.1016/j.envsoft.2015.08.013, 2016.
Vrugt, J. A., ter Braak, C. J. F., Diks, C. G. H., Higdon, D., Robinson, B. A., and
Hyman, J. M.: Accelerating Markov chain Monte Carlo simulation by
differential evolution with self-adaptive randomized subspace sampling, Int.
J. Nonlinear Sci. Numer. Simul., 10, 273e290, https://doi.org/10.1515/IJNSNS.2009.10.3.273, 2009.
Wiesmeier, M., Urbanski, L., Hobley, E., Lang, B., von Lützow, M.,
Marin-Spiotta, E., van Wesemael, B., Rabot, E., Liess, Mareike,
Garcia-Franco, N., Wollschläger, U., Vogel, H.-J., and
Kögel-Krabner, I.: Soil organic carbon storage as key function of soils
– A review of drivers and indicators at various scales, Geoderma, 333,
149–162, https://doi.org/10.1016/j.geoderma.2018.07.026, 2019.
Wutzler, T. and Reichstein, M.: Soils apart from equilibrium – consequences for soil carbon balance modelling, Biogeosciences, 4, 125–136, https://doi.org/10.5194/bg-4-125-2007, 2007.
Zaehle, S. and Friend, A. D.: Carbon and nitrogen cycle dynamics in the O-CN
land surface model: 1. Model description, site-scale evaluation, and
sensitivity to parameter estimates, Global Biogeochem. Cy., 24,
GB1005, https://doi.org/10.1029/2009GB003521,
2010.
Zaehle, S., Medlyn, B. E., De Kauwe, M. G., Walker A. P., Dietze, M. C.,
Hickler, T., Luo, Y., Wang, Y.-P., El-Masri, B., Thornton, P., Jain, A.,
Wang, S., Warlind, D., Weng, E., Parton, W., Iverson, C. M., Gallet-Budynek,
A., McCarthy, H., Finzi, A., Hanson, P. J., Prentice, C. I., Oren, R., and
Norby, R. J.: Evaluation of 11 terrestrial carbon–nitrogen cycle models
against observations from two temperate Free-Air CO2 Enrichment studies, N.
Phytol., 202, 803–822, 2014.
Zhang, H., Goll, D. S., Wang, P.-S., Ciais, P., Wieder, W. R., Abramoff, R.,
Huang, Y., Guenet, B., Prescher, A.-K., Viscarra Rossel, R. A., Barre, P.,
Chenu, C., Zhou, G., and Tang, X.: Microbial dynamics and soil
physicochemical properties explain large-scale variations in in soil organic
carbon, Glob. Change Biol., 26, 2668–2685, 2020.
Zinke, P. J., Stangenberger, A. G., Post, W. M., Emanuel, W. R., and Olson,
J. S.: Worldwide organic soil carbon and nitrogen data. NDP-018, Carbon
Dioxide Information Center, Oak Ridge National Laboratory, Oak Ridge,
Tennessee, 1986.
Zobitz, J. M., Desai, A. R., Moore, D. J. P., and Chadwick, M. A.: A primer for
data assimilation with ecological models using Markov Chain Monte Carlo
(MCMC), Oceologia, 167, 599–611, 2011.
Short summary
We wanted to examine how the chosen measurement data and calibration process affect soil organic carbon model calibration. In our results we found that there is a benefit in using data from multiple litter-bag decomposition experiments simultaneously, even with the required assumptions. Additionally, due to the amount of noise and uncertainties in the system, more advanced calibration methods should be used to parameterize the models.
We wanted to examine how the chosen measurement data and calibration process affect soil organic...
