Articles | Volume 6, issue 5
Methods for assessment of models 16 Sep 2013
Methods for assessment of models | 16 Sep 2013
Assimilating water column and satellite data for marine export production estimation
X. Yao and R. Schlitzer
No articles found.
I. Borrione, O. Aumont, M. C. Nielsdóttir, and R. Schlitzer
Biogeosciences, 11, 1981–2001,
I. Borrione and R. Schlitzer
Biogeosciences, 10, 217–231,
Related subject area
BiogeosciencesCalibrating soybean parameters in JULES 5.0 from the US-Ne2/3 FLUXNET sites and the SoyFACE-O3 experimentModeling long-term fire impact on ecosystem characteristics and surface energy using a process-based vegetation–fire model SSiB4/TRIFFID-Fire v1.0Energy, water and carbon exchanges in managed forest ecosystems: description, sensitivity analysis and evaluation of the INRAE GO+ model, version 3.0Improving Yasso15 soil carbon model estimates with ensemble adjustment Kalman filter state data assimilationOceanic and atmospheric methane cycling in the cGENIE Earth system model – release v0.9.14Modeling the impacts of diffuse light fraction on photosynthesis in ORCHIDEE (v5453) land surface modelDescription and evaluation of the process-based forest model 4C v2.2 at four European forest sitesA multi-isotope model for simulating soil organic carbon cycling in eroding landscapes (WATEM_C v1.0)One-dimensional models of radiation transfer in heterogeneous canopies: a review, re-evaluation, and improved modelAn improved mechanistic model for ammonia volatilization in Earth system models: Flow of Agricultural Nitrogen version 2 (FANv2)Stoichiometrically coupled carbon and nitrogen cycling in the MIcrobial-MIneral Carbon Stabilization model version 1.0 (MIMICS-CN v1.0)Short-term forecasting of regional biospheric CO2 fluxes in Europe using a light-use-efficiency model (VPRM, MPI-BGC version 1.2)FLiES-SIF version 1.0: three-dimensional radiative transfer model for estimating solar induced fluorescenceThe importance of management information and soil moisture representation for simulating tillage effects on N2O emissions in LPJmL5.0-tillageEvaluation of CH4MODwetland and Terrestrial Ecosystem Model (TEM) used to estimate global CH4 emissions from natural wetlandsImproving the representation of cropland sites in the Community Land Model (CLM) version 5.0Simulating stable carbon isotopes in the ocean component of the FAMOUS general circulation model with MOSES1 (XOAVI)Quantitative assessment of fire and vegetation properties in simulations with fire-enabled vegetation models from the Fire Model Intercomparison ProjectMarine biogeochemical cycling and oceanic CO2 uptake simulated by the NUIST Earth System Model version 3 (NESM v3)CLASSIC v1.0: the open-source community successor to the Canadian Land Surface Scheme (CLASS) and the Canadian Terrestrial Ecosystem Model (CTEM) – Part 1: Model framework and site-level performanceIntegrated Modeling of Photosynthesis and Transfer of Energy, Mass and Momentum in the Soil-Plant-Atmosphere Continuum SystemConceptual Model to Simulate Long-term Soil Organic Carbon and Ground Ice Budget with Permafrost and Ice Sheets (SOC-ICE-v1.0)HR3DHG version 1: modeling the spatiotemporal dynamics of mercury in the Augusta Bay (southern Italy)CoupModel (v6.0): an ecosystem model for coupled phosphorus, nitrogen and carbon dynamics – evaluated against empirical data from a climatic and fertility gradient in SwedenBPOP-v1 model: exploring the impact of changes in the biological pump on the shelf sea and ocean nutrient and redox stateP-model v1.0: an optimality-based light use efficiency model for simulating ecosystem gross primary productionHETEROFOR 1.0: a spatially explicit model for exploring the response of structurally complex forests to uncertain future conditions – Part 2: Phenology and water cycleDynamic upscaling of decomposition kinetics for carbon cycling modelsCE-DYNAM (v1): a spatially explicit process-based carbon erosion scheme for use in Earth system modelsA coupled pelagic–benthic–sympagic biogeochemical model for the Bering Sea: documentation and validation of the BESTNPZ model (v2019.08.23) within a high-resolution regional ocean modelFORests and HYdrology under Climate Change in Switzerland v1.0: a spatially distributed model combining hydrology and forest dynamicsORCHIDEE MICT-LEAK (r5459), a global model for the production, transport, and transformation of dissolved organic carbon from Arctic permafrost regions – Part 2: Model evaluation over the Lena River basinGLOBAL-FATE (version 1.0.0): A geographical information system (GIS)-based model for assessing contaminants fate in the global river networkA comparative assessment of the uncertainties of global surface ocean CO2 estimates using a machine-learning ensemble (CSIR-ML6 version 2019a) – have we hit the wall?Improving the LPJmL4-SPITFIRE vegetation–fire model for South America using satellite dataAccounting for carbon and nitrogen interactions in the global terrestrial ecosystem model ORCHIDEE (trunk version, rev 4999): multi-scale evaluation of gross primary productionA new model of the coupled carbon, nitrogen, and phosphorus cycles in the terrestrial biosphere (QUINCY v1.0; revision 1996)Modelling biomass burning emissions and the effect of spatial resolution: a case study for Africa based on the Global Fire Emissions Database (GFED)A lattice-automaton bioturbation simulator with coupled physics, chemistry, and biology in marine sediments (eLABS v0.2)The biophysics, ecology, and biogeochemistry of functionally diverse, vertically and horizontally heterogeneous ecosystems: the Ecosystem Demography model, version 2.2 – Part 1: Model descriptionThe biophysics, ecology, and biogeochemistry of functionally diverse, vertically and horizontally heterogeneous ecosystems: the Ecosystem Demography model, version 2.2 – Part 2: Model evaluation for tropical South AmericaIdentification of key parameters controlling demographically structured vegetation dynamics in a land surface model: CLM4.5(FATES)Parameter calibration and stomatal conductance formulation comparison for boreal forests with adaptive population importance sampler in the land surface model JSBACHEvaluation of leaf-level optical properties employed in land surface modelsORCHIDEE MICT-LEAK (r5459), a global model for the production, transport, and transformation of dissolved organic carbon from Arctic permafrost regions – Part 1: Rationale, model description, and simulation protocolModelling northern peatland area and carbon dynamics since the Holocene with the ORCHIDEE-PEAT land surface model (SVN r5488)Simulating the effect of tillage practices with the global ecosystem model LPJmL (version 5.0-tillage)Description and validation of an intermediate complexity model for ecosystem photosynthesis and evapotranspiration: ACM-GPP-ETv1The quasi-equilibrium framework revisited: analyzing long-term CO2 enrichment responses in plant–soil modelsBayesian inference and predictive performance of soil respiration models in the presence of model discrepancy
Felix Leung, Karina Williams, Stephen Sitch, Amos P. K. Tai, Andy Wiltshire, Jemma Gornall, Elizabeth A. Ainsworth, Timothy Arkebauer, and David Scoby
Geosci. Model Dev., 13, 6201–6213,Short summary
Ground-level ozone (O3) is detrimental to plant productivity and crop yield. Currently, the Joint UK Land Environment Simulator (JULES) includes a representation of crops (JULES-crop). The parameters for O3 damage in soybean in JULES-crop were calibrated against photosynthesis measurements from the Soybean Free Air Concentration Enrichment (SoyFACE). The result shows good performance for yield, and it helps contribute to understanding of the impacts of climate and air pollution on food security.
Huilin Huang, Yongkang Xue, Fang Li, and Ye Liu
Geosci. Model Dev., 13, 6029–6050,Short summary
We developed a fire-coupled dynamic vegetation model that captures the spatial distribution, temporal variability, and especially the seasonal variability of fire regimes. The fire model is applied to assess the long-term fire impact on ecosystems and surface energy. We find that fire is an important determinant of the structure and function of the tropical savanna. By changing the vegetation composition and ecosystem characteristics, fire significantly alters surface energy balance.
Virginie Moreaux, Simon Martel, Alexandre Bosc, Delphine Picart, David Achat, Christophe Moisy, Raphael Aussenac, Christophe Chipeaux, Jean-Marc Bonnefond, Soisick Figuères, Pierre Trichet, Rémi Vezy, Vincent Badeau, Bernard Longdoz, André Granier, Olivier Roupsard, Manuel Nicolas, Kim Pilegaard, Giorgio Matteucci, Claudy Jolivet, Andrew T. Black, Olivier Picard, and Denis Loustau
Geosci. Model Dev., 13, 5973–6009,Short summary
The model GO+ describes the functioning of managed forests based upon biophysical and biogeochemical processes. It accounts for the impacts of forest operations on energy, water and carbon exchanges within the soil–vegetation–atmosphere continuum. It includes versatile descriptions of management operations. Its sensitivity and uncertainty are detailed and predictions are compared with observations about mass and energy exchanges, hydrological data, and tree growth variables from different sites.
Toni Viskari, Maisa Laine, Liisa Kulmala, Jarmo Mäkelä, Istem Fer, and Jari Liski
Geosci. Model Dev., 13, 5959–5971,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.
Christopher T. Reinhard, Stephanie L. Olson, Sandra Kirtland Turner, Cecily Pälike, Yoshiki Kanzaki, and Andy Ridgwell
Geosci. Model Dev., 13, 5687–5706,Short summary
We provide documentation and testing of new developments for the oceanic and atmospheric methane cycles in the cGENIE Earth system model. The model is designed to explore Earth's methane cycle across a wide range of timescales and scenarios, in particular assessing the mean climate state and climate perturbations in Earth's deep past. We further document the impact of atmospheric oxygen levels and ocean chemistry on fluxes of methane to the atmosphere from the ocean biosphere.
Yuan Zhang, Ana Bastos, Fabienne Maignan, Daniel Goll, Olivier Boucher, Laurent Li, Alessandro Cescatti, Nicolas Vuichard, Xiuzhi Chen, Christof Ammann, M. Altaf Arain, T. Andrew Black, Bogdan Chojnicki, Tomomichi Kato, Ivan Mammarella, Leonardo Montagnani, Olivier Roupsard, Maria J. Sanz, Lukas Siebicke, Marek Urbaniak, Francesco Primo Vaccari, Georg Wohlfahrt, Will Woodgate, and Philippe Ciais
Geosci. Model Dev., 13, 5401–5423,Short summary
We improved the ORCHIDEE LSM by distinguishing diffuse and direct light in canopy and evaluated the new model with observations from 159 sites. Compared with the old model, the new model has better sunny GPP and reproduced the diffuse light fertilization effect observed at flux sites. Our simulations also indicate different mechanisms causing the observed GPP enhancement under cloudy conditions at different times. The new model has the potential to study large-scale impacts of aerosol changes.
Petra Lasch-Born, Felicitas Suckow, Christopher P. O. Reyer, Martin Gutsch, Chris Kollas, Franz-Werner Badeck, Harald K. M. Bugmann, Rüdiger Grote, Cornelia Fürstenau, Marcus Lindner, and Jörg Schaber
Geosci. Model Dev., 13, 5311–5343,Short summary
The process-based model 4C has been developed to study climate impacts on forests and is now freely available as an open-source tool. This paper provides a comprehensive description of the 4C version (v2.2) for scientific users of the model and presents an evaluation of 4C. The evaluation focused on forest growth, carbon water, and heat fluxes. We conclude that 4C is widely applicable, reliable, and ready to be released to the scientific community to use and further develop the model.
Zhengang Wang, Jianxiu Qiu, and Kristof Van Oost
Geosci. Model Dev., 13, 4977–4992,Short summary
This study developed a spatially distributed carbon cycling model applicable in an eroding landscape. It includes all three carbon isotopes so that it is able to represent the carbon isotopic compositions. The model is able to represent the observations that eroding area is enriched in 13C and depleted of 14C compared to depositional area. Our simulations show that the spatial variability of carbon isotopic properties in an eroding landscape is mainly caused by the soil redistribution.
Brian N. Bailey, María A. Ponce de León, and E. Scott Krayenhoff
Geosci. Model Dev., 13, 4789–4808,Short summary
Numerous models of plant radiation interception based on a range of assumptions are available in the literature, but the importance of each assumption is not well understood. In this work, we evaluate several assumptions common in simple models of radiation interception in canopies with widely spaced plants by comparing against a detailed 3-D model. This yielded a simple model based on readily measurable parameters that could accurately predict interception for a wide range of architectures.
Julius Vira, Peter Hess, Jeff Melkonian, and William R. Wieder
Geosci. Model Dev., 13, 4459–4490,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.
Emily Kyker-Snowman, William R. Wieder, Serita D. Frey, and A. Stuart Grandy
Geosci. Model Dev., 13, 4413–4434,Short summary
Microbes drive carbon (C) and nitrogen (N) transformations in soil, and soil models have started to include explicit microbial physiology and functioning to try to reduce uncertainty in soil–climate feedbacks. Here, we add N cycling to a microbially explicit soil C model and reproduce C and N dynamics in soil during litter decomposition across a range of sites. We discuss model-generated hypotheses about soil C and N cycling and highlight the need for landscape-scale model evaluation data.
Jinxuan Chen, Christoph Gerbig, Julia Marshall, and Kai Uwe Totsche
Geosci. Model Dev., 13, 4091–4106,Short summary
One of the essential challenge for atmospheric CO2 forecasting is predicting CO2 flux variation on synoptic timescale. For CAMS CO2 forecast, a process-based vegetation model is used. In this research we evaluate another type of model (i.e., the light-use-efficiency model VPRM), which is a data-driven approach and thus ideal for realistic estimation, on its ability of flux prediction. Errors from different sources are assessed, and overall the model is capable of CO2 flux prediction.
Yuma Sakai, Hideki Kobayashi, and Tomomichi Kato
Geosci. Model Dev., 13, 4041–4066,Short summary
Chlorophyll fluorescence is one of the energy release pathways of excess incident light in the photosynthetic process. The canopy-scale Sun-induced chlorophyll fluorescence (SIF), which potentially provides a direct pathway to link leaf-level photosynthesis to global GPP, can be observed from satellites. We develop the three-dimensional Monte Carlo plant canopy radiative transfer model to understand the biological and physical mechanisms behind SIF emission from complex forest canopies.
Femke Lutz, Stephen Del Grosso, Stephen Ogle, Stephen Williams, Sara Minoli, Susanne Rolinski, Jens Heinke, Jetse J. Stoorvogel, and Christoph Müller
Geosci. Model Dev., 13, 3905–3923,Short summary
Previous findings have shown deviations between the LPJmL5.0-tillage model and results from meta-analyses on global estimates of tillage effects on N2O emissions. By comparing model results with observational data of four experimental sites and outputs from field-scale DayCent model simulations, we show that advancing information on agricultural management, as well as the representation of soil moisture dynamics, improves LPJmL5.0-tillage and the estimates of tillage effects on N2O emissions.
Tingting Li, Yanyu Lu, Lingfei Yu, Wenjuan Sun, Qing Zhang, Wen Zhang, Guocheng Wang, Zhangcai Qin, Lijun Yu, Hailing Li, and Ran Zhang
Geosci. Model Dev., 13, 3769–3788,Short summary
Reliable models are required to estimate global wetland CH4 emissions, which are the largest and most uncertain source of atmospheric CH4. This paper evaluated CH4MODwetland and TEM models against CH4 measurements from different continents and wetland types. Based on best-model performance, we estimated 117–125 Tg yr−1 of global CH4 emissions from wetlands for the period 2000–2010. Efforts should be made to reduce estimate uncertainties for different wetland types and regions.
Theresa Boas, Heye Bogena, Thomas Grünwald, Bernard Heinesch, Dongryeol Ryu, Marius Schmidt, Harry Vereecken, Andrew Western, and Harrie-Jan Hendricks-Franssen
Geosci. Model Dev. Discuss.,
Revised manuscript accepted for GMDShort summary
In this study we were able to significantly improve the CLM5 model performance for European cropland sites by adding a winter wheat representation, specific plant parameters for important cash crops and a cover cropping subroutine to its crop module. We anticipate that our findings and modifications can help to improve regional scale yield predictions, and offer the possibility to study the effects of large-scale cover cropping on energy fluxes, CN pools and the terrestrial water cycle.
Jennifer E. Dentith, Ruza F. Ivanovic, Lauren J. Gregoire, Julia C. Tindall, and Laura F. Robinson
Geosci. Model Dev., 13, 3529–3552,Short summary
We have added a new tracer (13C) into the ocean of the FAMOUS climate model to study large-scale circulation and the marine carbon cycle. The model captures the large-scale spatial pattern of observations but the simulated values are consistently higher than observed. In the first instance, our new tracer is therefore useful for recalibrating the physical and biogeochemical components of the model.
Stijn Hantson, Douglas I. Kelley, Almut Arneth, Sandy P. Harrison, Sally Archibald, Dominique Bachelet, Matthew Forrest, Thomas Hickler, Gitta Lasslop, Fang Li, Stephane Mangeon, Joe R. Melton, Lars Nieradzik, Sam S. Rabin, I. Colin Prentice, Tim Sheehan, Stephen Sitch, Lina Teckentrup, Apostolos Voulgarakis, and Chao Yue
Geosci. Model Dev., 13, 3299–3318,Short summary
Global fire–vegetation models are widely used, but there has been limited evaluation of how well they represent various aspects of fire regimes. Here we perform a systematic evaluation of simulations made by nine FireMIP models in order to quantify their ability to reproduce a range of fire and vegetation benchmarks. While some FireMIP models are better at representing certain aspects of the fire regime, no model clearly outperforms all other models across the full range of variables assessed.
Yifei Dai, Long Cao, and Bin Wang
Geosci. Model Dev., 13, 3119–3144,Short summary
NESM v3 is one of the CMIP6 registered Earth system models. We evaluate its ocean carbon cycle component and present its present-day and future oceanic CO2 uptake based on the CMIP6 historical and SSP5–8.5 scenarios. We hope that this paper can serve as a documentation of the marine biogeochemical cycle in NESM v3. Also, the model defects found and their underlying causes analyzed in this paper could help users and further model development.
Joe R. Melton, Vivek K. Arora, Eduard Wisernig-Cojoc, Christian Seiler, Matthew Fortier, Ed Chan, and Lina Teckentrup
Geosci. Model Dev., 13, 2825–2850,Short summary
We transitioned the CLASS-CTEM land surface model to an open-source community model format by modernizing the code base to make the model easier to use and understand, providing a complete software environment to run the model within, developing a benchmarking suite for model evaluation, and creating an infrastructure to support community involvement. The new model, the Canadian Land Surface Scheme including Biogeochemical Cycles (CLASSIC), is now available for the community to use and develop.
Yunfei Wang, Yijian Zeng, Lianyu Yu, Peiqi Yang, Christiaan Van de Tol, Huanjie Cai, and Zhongbo Su
Geosci. Model Dev. Discuss.,
Revised manuscript accepted for GMDShort summary
This study integrates photosynthesis and transfer of energy, mass, and momentum in the soil-plant-atmosphere continuum system, via a simplified 1D root growth model. The results indicated that the simulation of land surface fluxes was significantly improved due to considering the root water uptake, especially when vegetation is experiencing severe water stress. This finding highlights the importance of enhanced soil heat and moisture transfer on simulating ecosystem functioning.
Kazuyuki Saito, Hirokazu Machiya, Go Iwahana, Tokuta Yokohata, and Hiroshi Ohno
Geosci. Model Dev. Discuss.,
Revised manuscript accepted for GMDShort summary
The circum-Arctic distribution of soil organic carbon (SOC) and ground ice (ICE) is essential to assess the impacts of permafrost degradation, but uncertainties remain. A new conceptual numerical model for long-term SOC and ICE budget with frozen ground, ice sheets and coastlines changes was run for north of 50° N for the last 125 thousand years, and compared well with observation data for reproducibility. The simulated timeseries can produce maps of SOC and ICE for past, present and future.
Giovanni Denaro, Daniela Salvagio Manta, Alessandro Borri, Maria Bonsignore, Davide Valenti, Enza Quinci, Andrea Cucco, Bernardo Spagnolo, Mario Sprovieri, and Andrea De Gaetano
Geosci. Model Dev., 13, 2073–2093,Short summary
The HR3DHG (high-resolution 3D mercury model) investigates the spatiotemporal behavior, in seawater and marine sediments, of three mercury species (elemental, inorganic, and organic mercury) in a highly polluted marine environment (Augusta Bay, southern Italy). The model shows fair agreement with the experimental data collected during six different oceanographic cruises and can possibly be used for a detailed exploration of the effects of climate change on mercury distribution.
Hongxing He, Per-Erik Jansson, and Annemieke Gärdenäs
Geosci. Model Dev. Discuss.,
Revised manuscript accepted for GMDShort summary
We present the integration of the phosphorus (P) cycle into CoupModel (Coup-CNP). The extended Coup-CNP enables simulations of coupled C, N and P dynamics for terrestrial ecosystems which explicitly consider mycorrhizal interactions. The development and evaluation of the new Coup-CNP model demonstrate that P fluxes need to be further considered in studies of how climate change will influence C turnover and ecosystem responses.
Elisa Lovecchio and Timothy M. Lenton
Geosci. Model Dev., 13, 1865–1883,Short summary
We present here the newly developed BPOP box model. BPOP is aimed at studying the impact of large-scale changes in the biological pump, i.e. the cycle of production, export and remineralization of the marine organic matter, on the nutrient and oxygen concentrations in the shelf and open ocean. This model has been developed to investigate the global consequences of the evolution of larger and heavier phytoplankton cells but can be applied to a variety of past and future case studies.
Benjamin D. Stocker, Han Wang, Nicholas G. Smith, Sandy P. Harrison, Trevor F. Keenan, David Sandoval, Tyler Davis, and I. Colin Prentice
Geosci. Model Dev., 13, 1545–1581,Short summary
Estimating terrestrial photosynthesis relies on satellite data of vegetation cover and models simulating the efficiency by which light absorbed by vegetation is used for CO2 assimilation. This paper presents the P-model, a light use efficiency model derived from a carbon–water optimality principle, and evaluates its predictions of ecosystem-level photosynthesis against globally distributed observations. The model is implemented and openly accessible as an R package (rpmodel).
Louis de Wergifosse, Frédéric André, Nicolas Beudez, François de Coligny, Hugues Goosse, François Jonard, Quentin Ponette, Hugues Titeux, Caroline Vincke, and Mathieu Jonard
Geosci. Model Dev., 13, 1459–1498,Short summary
Given their key role in the simulation of climate impacts on tree growth, phenological and water balance processes must be integrated in models simulating forest dynamics under a changing environment. Here, we describe these processes integrated in HETEROFOR, a model accounting simultaneously for the functional, structural and spatial complexity to explore the forest response to forestry practices. The model evaluation using phenological and soil water content observations is quite promising.
Arjun Chakrawal, Anke M. Herrmann, John Koestel, Jerker Jarsjö, Naoise Nunan, Thomas Kätterer, and Stefano Manzoni
Geosci. Model Dev., 13, 1399–1429,Short summary
Soils are heterogeneous, which results in a nonuniform spatial distribution of substrates and the microorganisms feeding on them. Our results show that the variability in the spatial distribution of substrates and microorganisms at the pore scale is crucial because it affects how fast substrates are used by microorganisms and thus the decomposition rate observed at the soil core scale. This work provides a methodology to include microscale heterogeneity in soil carbon cycling models.
Victoria Naipal, Ronny Lauerwald, Philippe Ciais, Bertrand Guenet, and Yilong Wang
Geosci. Model Dev., 13, 1201–1222,Short summary
In this study we present the Carbon Erosion DYNAMics model (CE-DYNAM) that links sediment dynamics resulting from water erosion with the soil carbon cycle along a cascade of hillslopes, floodplains, and rivers. The model can simulate the removal of soil and carbon from eroding areas and their destination at regional scale. We calibrated and validated the model for the Rhine catchment, and we show that soil erosion is a potential large net carbon sink over the period 1850–2005.
Kelly Kearney, Albert Hermann, Wei Cheng, Ivonne Ortiz, and Kerim Aydin
Geosci. Model Dev., 13, 597–650,Short summary
We describe an ecosystem model for the Bering Sea. Biological components in the Bering Sea can be found in the water column, on and within the bottom sediments, and within the porous lower layer of seasonal sea ice. This model simulates the exchange of material between nutrients and plankton within all three environments. Here, we thoroughly document the model and assess its skill in capturing key biophysical features across the Bering Sea.
Matthias J. R. Speich, Massimiliano Zappa, Marc Scherstjanoi, and Heike Lischke
Geosci. Model Dev., 13, 537–564,Short summary
Climate change is expected to substantially affect natural processes, and simulation models are a valuable tool to anticipate these changes. In this study, we combine two existing models that each describe one aspect of the environment: forest dynamics and the terrestrial water cycle. The coupled model better described observed patterns in vegetation structure. We also found that including the effect of water availability on tree height and rooting depth improved the model.
Simon P. K. Bowring, Ronny Lauerwald, Bertrand Guenet, Dan Zhu, Matthieu Guimberteau, Pierre Regnier, Ardalan Tootchi, Agnès Ducharne, and Philippe Ciais
Geosci. Model Dev., 13, 507–520,Short summary
In this second part of the study, we performed simulations of the carbon and water budget of the Lena catchment with the land surface model ORCHIDEE MICT-LEAK, enabled to simulate dissolved organic carbon (DOC) production in soils and its transport and fate in high-latitude inland waters. We compare simulations using this model to existing data sources to show that it is capable of reproducing dissolved carbon fluxes of potentially great importance for the future of the global permafrost.
Carme Font, Francesco Bregoli, Vicenç Acuña, Sergi Sabater, and Rafael Marcé
Geosci. Model Dev., 12, 5213–5228,Short summary
GLOBAL-FATE is an open-source, multiplatform, and flexible model that simulates the fate of pharmaceutical-like compounds in the global river network. The model considers the consumption of pharmaceuticals by humans, differentiates between pharmaceutical load treated in wastewater treatment plants from that directly delivered to streams and rivers, and integrates lakes and reservoirs in calculations. GLOBAL-FATE is a powerful tool for pollutant impact studies at the global scale.
Luke Gregor, Alice D. Lebehot, Schalk Kok, and Pedro M. Scheel Monteiro
Geosci. Model Dev., 12, 5113–5136,Short summary
The ocean plays a vital role in mitigating climate change by taking up atmospheric carbon dioxide (CO2). Historically sparse ship-based measurements of surface ocean CO2 make direct estimates of CO2 exchange changes unreliable. We introduce a machine-learning ensemble approach to fill these observational gaps. Our method performs incrementally better relative to past methods, leading to our hypothesis that we are perhaps reaching the limitation of machine-learning algorithms' capability.
Markus Drüke, Matthias Forkel, Werner von Bloh, Boris Sakschewski, Manoel Cardoso, Mercedes Bustamante, Jürgen Kurths, and Kirsten Thonicke
Geosci. Model Dev., 12, 5029–5054,Short summary
This work shows the successful application of a systematic model–data integration setup, as well as the implementation of a new fire danger formulation, in order to optimize a process-based fire-enabled dynamic global vegetation model. We have demonstrated a major improvement in the fire representation within LPJmL4-SPITFIRE in terms of the spatial pattern and the interannual variability of burned area in South America as well as in the modelling of biomass and the distribution of plant types.
Nicolas Vuichard, Palmira Messina, Sebastiaan Luyssaert, Bertrand Guenet, Sönke Zaehle, Josefine Ghattas, Vladislav Bastrikov, and Philippe Peylin
Geosci. Model Dev., 12, 4751–4779,Short summary
In this research, we present a new version of the global terrestrial ecosystem model ORCHIDEE in which carbon and nitrogen cycles are coupled. We evaluate its skills at simulating primary production at 78 sites and at a global scale. Based on a set of additional simulations in which carbon and nitrogen cycles are coupled and uncoupled, we show that the functional responses of the model with carbon–nitrogen interactions better agree with our current understanding of photosynthesis.
Tea Thum, Silvia Caldararu, Jan Engel, Melanie Kern, Marleen Pallandt, Reiner Schnur, Lin Yu, and Sönke Zaehle
Geosci. Model Dev., 12, 4781–4802,Short summary
To predict the response of the vegetation to climate change, we need global models that describe the relevant processes taking place in the vegetation. Recently, we have obtained more in-depth understanding of vegetation processes and the role of nutrients in the biogeochemical cycles. We have developed a new global vegetation model that includes carbon, water, nitrogen, and phosphorus cycles. We show that the model is successful in evaluation against a wide range of observations.
Dave van Wees and Guido R. van der Werf
Geosci. Model Dev., 12, 4681–4703,Short summary
For this paper, a novel high spatial-resolution fire emission model based on the Global Fire Emissions Database (GFED) modelling framework was developed and compared to a coarser-resolution version of the same model. Our findings highlight the importance of fine spatial resolution when modelling global-scale fire emissions, especially considering the comparison of model pixels to individual field measurements and the model representation of heterogeneity in the landscape.
Yoshiki Kanzaki, Bernard P. Boudreau, Sandra Kirtland Turner, and Andy Ridgwell
Geosci. Model Dev., 12, 4469–4496,Short summary
This paper provides eLABS, an extension of the lattice-automaton bioturbation simulator LABS. In our new model, the benthic animal behavior interacts and changes dynamically with oxygen and organic matter concentrations and the water flows caused by benthic animals themselves, in a 2-D marine-sediment grid. The model can address the mechanisms behind empirical observations of bioturbation based on the interactions between physical, chemical and biological aspects of marine sediment.
Marcos Longo, Ryan G. Knox, David M. Medvigy, Naomi M. Levine, Michael C. Dietze, Yeonjoo Kim, Abigail L. S. Swann, Ke Zhang, Christine R. Rollinson, Rafael L. Bras, Steven C. Wofsy, and Paul R. Moorcroft
Geosci. Model Dev., 12, 4309–4346,Short summary
Our paper describes the Ecosystem Demography model. This computer program calculates how plants and ground exchange heat, water, and carbon with the air, and how plants grow, reproduce and die in different climates. Most models simplify forests to an average big tree. We consider that tall, deep-rooted trees get more light and water than small plants, and that some plants can with shade and drought. This diversity helps us to better explain how plants live and interact with the atmosphere.
Marcos Longo, Ryan G. Knox, Naomi M. Levine, Abigail L. S. Swann, David M. Medvigy, Michael C. Dietze, Yeonjoo Kim, Ke Zhang, Damien Bonal, Benoit Burban, Plínio B. Camargo, Matthew N. Hayek, Scott R. Saleska, Rodrigo da Silva, Rafael L. Bras, Steven C. Wofsy, and Paul R. Moorcroft
Geosci. Model Dev., 12, 4347–4374,Short summary
The Ecosystem Demography model calculates the fluxes of heat, water, and carbon between plants and ground and the air, and the life cycle of plants in different climates. To test if our calculations were reasonable, we compared our results with field and satellite measurements. Our model predicts well the extent of the Amazon forest, how much light forests absorb, and how much water forests release to the air. However, it must improve the tree growth rates and how fast dead plants decompose.
Elias C. Massoud, Chonggang Xu, Rosie A. Fisher, Ryan G. Knox, Anthony P. Walker, Shawn P. Serbin, Bradley O. Christoffersen, Jennifer A. Holm, Lara M. Kueppers, Daniel M. Ricciuto, Liang Wei, Daniel J. Johnson, Jeffrey Q. Chambers, Charlie D. Koven, Nate G. McDowell, and Jasper A. Vrugt
Geosci. Model Dev., 12, 4133–4164,Short summary
We conducted a comprehensive sensitivity analysis to understand behaviors of a demographic vegetation model within a land surface model. By running the model 5000 times with changing input parameter values, we found that (1) the photosynthetic capacity controls carbon fluxes, (2) the allometry is important for tree growth, and (3) the targeted carbon storage is important for tree survival. These results can provide guidance on improved model parameterization for a better fit to observations.
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,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.
Titta Majasalmi and Ryan M. Bright
Geosci. Model Dev., 12, 3923–3938,Short summary
Many land surface models rely on solutions derived from two-stream approximations utilizing leaf-level optical properties, many of which have not been formally reviewed or published. Using plant functional type groupings of the Community Land Model (CLM), we found large deviations between measured and CLM default near-infrared optical properties, implying that the modeled shortwave radiation budget including surface albedo may be expected to change after updating the biased parameters.
Simon P. K. Bowring, Ronny Lauerwald, Bertrand Guenet, Dan Zhu, Matthieu Guimberteau, Ardalan Tootchi, Agnès Ducharne, and Philippe Ciais
Geosci. Model Dev., 12, 3503–3521,Short summary
Few Earth system models represent permafrost soil biogeochemistry, contributing to uncertainty in estimating its response and that of the planet to warming. Because the permafrost contains over double the carbon in the present atmosphere, its fate as it is
unlockedby warming is globally significant. One way it can be mobilised is into rivers, the sea, or the atmosphere: a vector previously ignored in climate modelling. We present a model scheme for resolving this vector at a global scale.
Chunjing Qiu, Dan Zhu, Philippe Ciais, Bertrand Guenet, Shushi Peng, Gerhard Krinner, Ardalan Tootchi, Agnès Ducharne, and Adam Hastie
Geosci. Model Dev., 12, 2961–2982,Short summary
We present a model that can simulate the dynamics of peatland area extent and the vertical buildup of peat. The model is validated across a range of northern peatland sites and over the Northern Hemisphere (> 30° N). It is able to reproduce the spatial extent of northern peatlands and peat carbon accumulation over the Holocene.
Femke Lutz, Tobias Herzfeld, Jens Heinke, Susanne Rolinski, Sibyll Schaphoff, Werner von Bloh, Jetse J. Stoorvogel, and Christoph Müller
Geosci. Model Dev., 12, 2419–2440,Short summary
Tillage practices are under-represented in global biogeochemical models so that assessments of agricultural greenhouse gas emissions and climate mitigation options are hampered. We describe the implementation of tillage modules into the model LPJmL5.0, including multiple feedbacks between soil water, nitrogen, and productivity. By comparing simulation results with observational data, we show that the model can reproduce reported tillage effects on carbon and water dynamics and crop yields.
Thomas Luke Smallman and Mathew Williams
Geosci. Model Dev., 12, 2227–2253,Short summary
Photosynthesis and evapotranspiration are processes with global significance for climate, carbon and water cycling. Process-orientated simulation of these processes and their interactions have till now come at high computational cost. Here we present a new coupled model of intermediate complexity operating at orders of magnitude greater speed. Independent evaluation at FLUXNET sites for a single, global parameterization shows good agreement, with a typical R2 value of ~ 0.60.
Mingkai Jiang, Sönke Zaehle, Martin G. De Kauwe, Anthony P. Walker, Silvia Caldararu, David S. Ellsworth, and Belinda E. Medlyn
Geosci. Model Dev., 12, 2069–2089,Short summary
Here we used a simple analytical framework developed by Comins and McMurtrie (1993) to investigate how different model assumptions affected plant responses to elevated CO2. This framework is useful in revealing both the consequences and the mechanisms through which different assumptions affect predictions. We therefore recommend the use of this framework to analyze the likely outcomes of new assumptions before introducing them to complex model structures.
Ahmed S. Elshall, Ming Ye, Guo-Yue Niu, and Greg A. Barron-Gafford
Geosci. Model Dev., 12, 2009–2032,Short summary
The assumptions that the residuals are independent, identically distributed, and have constant variance tend to simplify the underlying mathematics of data models for Bayesian inference. We relax these three assumptions step-wise, resulting in eight data models. Using three mechanistic soil respiration models with different levels of model discrepancy, we discuss the impacts of data models on parameter estimation and predictive performance, and provide recommendations for data model selection.
Anderson, L. A. and Sarmiento, J. L.: Redfield ratios of remineralization determined by nutrient data analysis, Global Biogeochem. Cy., 8, 65–80, 1994.
Archer, D., Kheshgi, H., and Maier-Reimer, E.: Dynamics of fossil fuel CO2 neutralization by marine CaCO3, Global Biogeochem. Cy., 12, 259–276, 1998.
Aumont, O., Maier-Reimer, E., Blain, S., and Monfray, P.: An ecosystem model of the global ocean including Fe, Si, P colimitations, Global Biogeochem. Cy., 17, 1060, https://doi.org/10.1029/2001GB001745, 2003.
Balch, W., Gordon, H., Bowler, B., Drapeau, D., and Booth, E.: Calcium carbonate measurements in the surface global ocean based on Moderate-Resolution Imaging Spectroradiometer data, J. Geophys. Res, 110, C07001, https://doi.org/10.1029/2004JC002560, 2005.
Behrenfeld, M. J. and Falkowski, P. G.: Photosynthetic rates derived from satellite-based chlorophyll concentration, Limnol. Oceanogr., 42, 1–20, 1997.
Bishop, J. K. B. and Wood, T. J.: Year-round observations of carbon biomass and flux variability in the Southern Ocean, Global Biogeochem. Cy., 23, GB2019, https://doi.org/10.1029/2008GB003206, 2009.
Buesseler, K., Pike, S., Maiti, K., Lamborg, C., Siegel, D., and Trull, T.: Thorium-234 as a tracer of spatial, temporal and vertical variability in particle flux in the North Pacific, Deep Sea Res. Pt I, 56, 1143–1167, 2009.
Eppley, R.: Temperature and phytoplankton growth in the sea, Fishery Bulletin, 70, 1063–1085 1972.
Eppley, R. and Peterson, B.: Particulate organic matter flux and planktonic new production in the deep ocean, Nature, 282, 677–680, 1979.
Garcia, H. E., Locarnini, R. A., Boyer, T. P., Antonov, J. I., Zweng, M. M., Baranova, O. K., and Johnson, D. R.: World Ocean Atlas 2009, Volume 4: Nutrients (phosphate, nitrate, silicate), edited by: Levitus, S., NOAA Atlas NESDIS 71, US Government Printing Office, Washington, DC, 398 pp., 2010.
Gardner, W.: Sediment trap sampling in surface waters, Cambridge University Press, Cambridge, 2000.
Giering, R. and Kaminski, T.: Recipes for adjoint code construction, ACM Transactions on Mathematical Software (TOMS), 24, 437–474, 1998.
Giering, R. and Kaminski, T.: On the performance of derivative code generated by TAMC, 2000.
Giering, R., Kaminski, T., and Slawig, T.: Generating efficient derivative code with TAF:: Adjoint and tangent linear Euler flow around an airfoil, Future Gen. Comput. Syst., 21, 1345–1355, 2005.
Gordon, H., Boynton, G., Balch, W., Groom, S., Harbour, D., and Smyth, T.: Retrieval of coccolithophore calcite concentration from SeaWiFS imagery, Geophys. Res. Lett., 28, 1587–1590, 2001.
Gust, G., Michaels, A., Johnson, R., Deuser, W., and Bowles, W.: Mooring line motions and sediment trap hydromechanics: in situ intercomparison of three common deployment designs, Deep Sea Res. Pt. I, 41, 831–857, 1994.
Honjo, S., Manganini, S. J., Krishfield, R. A., and Francois, R.: Particulate organic carbon fluxes to the ocean interior and factors controlling the biological pump: a synthesis of global sediment trap programs since 1983, Progress Oceanogr., 76, 217–285, 2008.
Kahler, P. and Bauerfeind, E.: Organic particles in a shallow sediment trap: Substantial loss to the dissolved phase, Limnol. Oceanogr., 46, 719–723, 2001.
Laws, E., Falkowski, P., Smith, W., Ducklow, H., and McCarthy, J.: Temperature effects on export production in the open ocean, Global Biogeochem. Cy., 14, 1231–1246, 2000.
Locarnini, R. A., Mishonov, A. V., Antonov, J. I., Boyer, T. P., Garcia, H. E., Baranova, O. K., Zweng, M. M., and Johnson, D. R.: World Ocean Atlas 2009, Volume 1: Temperature, edited by: Levitus, S., NOAA Atlas NESDIS 68, 184 pp., 2010.
Martin, J. H., Knauer, G. A., Karl, D. M., and Broenkow, W. W.: VERTEX: Carbon cycling in the Northeast Pacific, Deep-Sea Res., 34, 267–285, 1987.
Monterey, G. and Levitus, S.: Seasonal Variability of Mixed Layer Depth for the World Ocean, US Gov. Printing Office, Wash., DC, 96 pp., 87 figs, 1997.
Navon, I. M.: Practical and theoretical aspects of adjoint parameter estimation and identifiability in meteorology and oceanography, Dynam. Atmos. Ocean., 27, 55–79, 1998.
Navon, I. M., Zou, X., Derber, J., and Sela, J.: Variational data assimilation with an adiabatic version of the NMC spectral model, Mon. Weather Rev., 120, 1433–1446, 1992.
Oschlies, A. and Kähler, P.: Biotic contribution to air-sea fluxes of CO2 and O2 and its relation to new production, export production, and net community production, Global Biogeochem. Cy., 18, GB1015, https://doi.org/10.1029/2003GB002094, 2004.
Palmer, J. and Totterdell, I.: Production and export in a global ocean ecosystem model, Deep Sea Res. Pt. I, 48, 1169–1198, 2001.
Redfield, A. C., Ketchum, B. H., and Richards, F. A.: The influence of organisms on the composition of sea-water, in: The sea: Ideas and observations on progress in the study of the seas, edited by: Hill, M. N., Interscience, New York, 26–27, 1963.
Rutgers v. d. Loeff, M., Cai, P., Stimac, I., Bracher, A., Middag, R., Klunder, M., and Van Heuven, S.: 234Th in surface waters: distribution of particle export flux across the Antarctic Circumpolar Current and in the Weddell Sea during the GEOTRACES expedition ZERO and DRAKE, Deep-Sea Res. Pt. II, 58, 2749–2766, 2011.
Sarmiento, J. and Sundquist, E.: Revised budget for the oceanic uptake of anthropogenic carbon dioxide, Nature, 356, 589–593, 1992.
Schartau, M. and Oschlies, A.: Simultaneous data-based optimization of a 1D-ecosystem model at three locations in the North Atlantic: Part I-Method and parameter estimates, J. Marine Res., 61, 765–793, 2003.
Schlitzer, R.: Determining the Mean, Large-Scale Cirulation of the Atlantic with the Adjoint Method, J. Phys. Oceanogr., 23, 1935–1952, 1993.
Schlitzer, R.: An adjoint model for the determination of the mean oceanic circulation, air-sea fluxes and mixing coefficients, Alfred-Wegener-Inst. für Polar-und Meeresforschung, Bremerhaven, 1995.
Schlitzer, R.: Applying the adjoint method for biogeochemical modeling: export of particulate organic matter in the world ocean, Inverse methods in global biogeochemical cycles, edited by: Kasibhatla, P., Heimann, M., Hartley, D., Mahowald, N., Prinn, R., and Rayner, P., AGU Geophys. Monograph Series, 114, 107–124, 2000.
Schlitzer, R.: Carbon export fluxes in the Southern Ocean: Results from inverse modeling and comparison with satellite-based estimates, Deep-Sea Res. Pt. II, 49, 1623–1644, 2002.
Schlitzer, R.: Assimilation of radiocarbon and chlorofluorocarbon data to constrain deep and bottom water transports in the world ocean, J. Phys. Oceanogr., 37, 259–276, 2007.
Stramski, D., Reynolds, R. A., Babin, M., Kaczmarek, S., Lewis, M. R., Röttgers, R., Sciandra, A., Stramska, M., Twardowski, M. S., Franz, B. A., and Claustre, H.: Relationships between the surface concentration of particulate organic carbon and optical properties in the eastern South Pacific and eastern Atlantic Oceans, Biogeosciences, 5, 171–201, https://doi.org/10.5194/bg-5-171-2008, 2008.
Volk, T. and Hoffert, M. I.: Ocean carbon pumps: Analysis of relative strengths and efficiencies in ocean-driven atmospheric CO2 changes, The Carbon Cycle and Atmospheric CO2: Natural Variations Archean to Present, Geophys. Monogr. Ser, 32, 99–110, 1985.