Articles | Volume 9, issue 3
https://doi.org/10.5194/gmd-9-947-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/gmd-9-947-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Development and technical paper
| 
04 Mar 2016
Development and technical paper |
| 04 Mar 2016
Couplerlib: a metadata-driven library for the integration of multiple models of higher and lower trophic level marine systems with inexact functional group matching
Jonathan Beecham
CORRESPONDING AUTHOR
Cefas Lowestoft Laboratory, Pakefield Road, Lowestoft, Suffolk, NR33 0HT,
UK
Jorn Bruggeman
Bolding & Burchard ApS. Strandgyden 25, 5466 Asperup, Denmark
John Aldridge
Cefas Lowestoft Laboratory, Pakefield Road, Lowestoft, Suffolk, NR33 0HT,
UK
Steven Mackinson
Cefas Lowestoft Laboratory, Pakefield Road, Lowestoft, Suffolk, NR33 0HT,
UK
Related authors
No articles found.
Evgeniy V. Yakushev, Elizaveta A. Protsenko, Jorn Bruggeman, Philip Wallhead, Svetlana V. Pakhomova, Shamil Kh. Yakubov, Richard G. J. Bellerby, and Raoul-Marie Couture
Geosci. Model Dev., 10, 453–482, https://doi.org/10.5194/gmd-10-453-2017, https://doi.org/10.5194/gmd-10-453-2017, 2017
Short summary
Short summary
This paper presents a new benthic–pelagic biogeochemical model (BROM) that combines a relatively simple pelagic ecosystem model with a detailed biogeochemical model of the coupled cycles of N, P, Si, C, O, S, Mn, Fe in the water column, benthic boundary layer, and sediments, with a focus on oxygen and redox state. BROM should be of interest for the study of a range of environmental applications in addition to hypoxia, such as benthic nutrient recycling, redox biogeochemistry, and eutrophication.
Fenjuan Hu, Karsten Bolding, Jorn Bruggeman, Erik Jeppesen, Morgens R. Flindt, Luuk van Gerven, Jan H. Janse, Annette B. G. Janssen, Jan J. Kuiper, Wolf M. Mooij, and Dennis Trolle
Geosci. Model Dev., 9, 2271–2278, https://doi.org/10.5194/gmd-9-2271-2016, https://doi.org/10.5194/gmd-9-2271-2016, 2016
Short summary
Short summary
We present a redesign and further development of a complex and well-known aquatic ecosystem model (PCLake) into the Framework for Aquatic Biogeochemical Models (FABM). So PCLake can run in different hydrodynamic environments, ranging from 0-D to 3-D. We introduce the methods and technical details about how the model was re-designed into a modular structure and the new features of PCLake enabled by FABM. We further present a benchmark test case to verify the new model implementation.
Momme Butenschön, James Clark, John N. Aldridge, Julian Icarus Allen, Yuri Artioli, Jeremy Blackford, Jorn Bruggeman, Pierre Cazenave, Stefano Ciavatta, Susan Kay, Gennadi Lessin, Sonja van Leeuwen, Johan van der Molen, Lee de Mora, Luca Polimene, Sevrine Sailley, Nicholas Stephens, and Ricardo Torres
Geosci. Model Dev., 9, 1293–1339, https://doi.org/10.5194/gmd-9-1293-2016, https://doi.org/10.5194/gmd-9-1293-2016, 2016
Short summary
Short summary
ERSEM 15.06 is a model for marine biogeochemistry and the lower trophic levels of the marine food web. It comprises a pelagic and benthic sub-model including the microbial food web and the major biogeochemical cycles of carbon, nitrogen, phosphorus, silicate, and iron using dynamic stochiometry. Further features include modules for the carbonate system and calcification. We present full mathematical descriptions of all elements along with examples at various scales up to 3-D applications.
Related subject area
Biogeosciences
The XSO framework (v0.1) and Phydra library (v0.1) for a flexible, reproducible, and integrated plankton community modeling environment in Python
AgriCarbon-EO v1.0.1: large-scale and high-resolution simulation of carbon fluxes by assimilation of Sentinel-2 and Landsat-8 reflectances using a Bayesian approach
SAMM version 1.0: a numerical model for microbial- mediated soil aggregate formation
A model of the within-population variability of budburst in forest trees
Computationally efficient parameter estimation for high-dimensional ocean biogeochemical models
The community-centered freshwater biogeochemistry model unified RIVE v1.0: a unified version for water column
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
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 of non-structural carbohydrate dynamics by the spatially explicit individual-based dynamic global vegetation model SEIB-DGVM (SEIB-DGVM-NSC version 1.0)
Terrestrial Ecosystem Model in R (TEMIR) version 1.0: Simulating ecophysiological responses of vegetation to atmospheric chemical and meteorological changes
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
Optimising CH4 simulations from the LPJ-GUESS model v4.1 using an adaptive MCMC algorithm
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)
Forest fluxes and mortality response to drought: model description (ORCHIDEE-CAN-NHA r7236) and evaluation at the Caxiuanã drought experiment
Matrix representation of lateral soil movements: scaling and calibrating CE-DYNAM (v2) at a continental level
CANOPS-GRB v1.0: a new Earth system model for simulating the evolution of ocean–atmosphere chemistry over geologic timescales
Low sensitivity of three terrestrial biosphere models to soil texture over the South American tropics
FESDIA (v1.0): exploring temporal variations of sediment biogeochemistry under the influence of flood events using numerical modelling
Impact of changes in climate and CO2 on the carbon storage potential of vegetation under limited water availability using SEIB-DGVM version 3.02
FORCCHN V2.0: an individual-based model for predicting multiscale forest carbon dynamics
Climate and parameter sensitivity and induced uncertainties in carbon stock projections for European forests (using LPJ-GUESS 4.0)
Use of genetic algorithms for ocean model parameter optimisation: a case study using PISCES-v2_RC for North Atlantic particulate organic carbon
SurEau-Ecos v2.0: a trait-based plant hydraulics model for simulations of plant water status and drought-induced mortality at the ecosystem level
Improved representation of plant physiology in the JULES-vn5.6 land surface model: photosynthesis, stomatal conductance and thermal acclimation
Representation of the phosphorus cycle in the Joint UK Land Environment Simulator (vn5.5_JULES-CNP)
CLM5-FruitTree: a new sub-model for deciduous fruit trees in the Community Land Model (CLM5)
The impact of hurricane disturbances on a tropical forest: implementing a palm plant functional type and hurricane disturbance module in ED2-HuDi V1.0
A validation standard for area of habitat maps for terrestrial birds and mammals
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.
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.
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.
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.
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.
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.
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.
Amos P. K. Tai, David H. Y. Yung, and Timothy Lam
EGUsphere, https://doi.org/10.5194/egusphere-2023-1287, https://doi.org/10.5194/egusphere-2023-1287, 2023
Short summary
Short summary
We have developed the Terrestrial Ecosystem Model in R (TEMIR), which simulates plant carbon and pollutant uptake and predict their response to varying atmospheric conditions. This model is designed to couple with an atmospheric chemistry model so that important questions related to plant-atmosphere interactions can be addressed, such as the effects of rising CO2 and ozone pollution on carbon uptake of the biosphere. The model has been well validated with both ground and satellite observations.
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.
Jalisha Theanutti Kallingal, Johan Lindström, Paul A Miller, Janne Rinne, Maarit Raivonen, and Marko Scholze
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2022-302, https://doi.org/10.5194/gmd-2022-302, 2023
Revised manuscript accepted for GMD
Short summary
Short summary
This manuscript describes the development of a Bayesian data assimilation framework around the wetland CH4 module in the LPJ-GUESS DGVM. The novel approach we developed combines the Rao-Blackwellised Adaptive Metropolis algorithm with the Global Adaptive Scaling (G-RB AM) for sampling the model parameters. Further, the manuscript demonstrates the application of the DA framework for optimising model process parameters by assimilating daily CH4 flux measurement data.
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.
Yitong Yao, Emilie Joetzjer, Philippe Ciais, Nicolas Viovy, Fabio Cresto Aleina, Jerome Chave, Lawren Sack, Megan Bartlett, Patrick Meir, Rosie Fisher, and Sebastiaan Luyssaert
Geosci. Model Dev., 15, 7809–7833, https://doi.org/10.5194/gmd-15-7809-2022, https://doi.org/10.5194/gmd-15-7809-2022, 2022
Short summary
Short summary
To facilitate more mechanistic modeling of drought effects on forest dynamics, our study implements a hydraulic module to simulate the vertical water flow, change in water storage and percentage loss of stem conductance (PLC). With the relationship between PLC and tree mortality, our model can successfully reproduce the large biomass drop observed under throughfall exclusion. Our hydraulic module provides promising avenues benefiting the prediction for mortality under future drought events.
Arthur Nicolaus Fendrich, Philippe Ciais, Emanuele Lugato, Marco Carozzi, Bertrand Guenet, Pasquale Borrelli, Victoria Naipal, Matthew McGrath, Philippe Martin, and Panos Panagos
Geosci. Model Dev., 15, 7835–7857, https://doi.org/10.5194/gmd-15-7835-2022, https://doi.org/10.5194/gmd-15-7835-2022, 2022
Short summary
Short summary
Currently, spatially explicit models for soil carbon stock can simulate the impacts of several changes. However, they do not incorporate the erosion, lateral transport, and deposition (ETD) of soil material. The present work developed ETD formulation, illustrated model calibration and validation for Europe, and presented the results for a depositional site. We expect that our work advances ETD models' description and facilitates their reproduction and incorporation in land surface models.
Kazumi Ozaki, Devon B. Cole, Christopher T. Reinhard, and Eiichi Tajika
Geosci. Model Dev., 15, 7593–7639, https://doi.org/10.5194/gmd-15-7593-2022, https://doi.org/10.5194/gmd-15-7593-2022, 2022
Short summary
Short summary
A new biogeochemical model (CANOPS-GRB v1.0) for assessing the redox stability and dynamics of the ocean–atmosphere system on geologic timescales has been developed. In this paper, we present a full description of the model and its performance. CANOPS-GRB is a useful tool for understanding the factors regulating atmospheric O2 level and has the potential to greatly refine our current understanding of Earth's oxygenation history.
Félicien Meunier, Wim Verbruggen, Hans Verbeeck, and Marc Peaucelle
Geosci. Model Dev., 15, 7573–7591, https://doi.org/10.5194/gmd-15-7573-2022, https://doi.org/10.5194/gmd-15-7573-2022, 2022
Short summary
Short summary
Drought stress occurs in plants when water supply (i.e. root water uptake) is lower than the water demand (i.e. atmospheric demand). It is strongly related to soil properties and expected to increase in intensity and frequency in the tropics due to climate change. In this study, we show that contrary to the expectations, state-of-the-art terrestrial biosphere models are mostly insensitive to soil texture and hence probably inadequate to reproduce in silico the plant water status in drying soils.
Stanley I. Nmor, Eric Viollier, Lucie Pastor, Bruno Lansard, Christophe Rabouille, and Karline Soetaert
Geosci. Model Dev., 15, 7325–7351, https://doi.org/10.5194/gmd-15-7325-2022, https://doi.org/10.5194/gmd-15-7325-2022, 2022
Short summary
Short summary
The coastal marine environment serves as a transition zone in the land–ocean continuum and is susceptible to episodic phenomena such as flash floods, which cause massive organic matter deposition. Here, we present a model of sediment early diagenesis that explicitly describes this type of deposition while also incorporating unique flood deposit characteristics. This model can be used to investigate the temporal evolution of marine sediments following abrupt changes in environmental conditions.
Shanlin Tong, Weiguang Wang, Jie Chen, Chong-Yu Xu, Hisashi Sato, and Guoqing Wang
Geosci. Model Dev., 15, 7075–7098, https://doi.org/10.5194/gmd-15-7075-2022, https://doi.org/10.5194/gmd-15-7075-2022, 2022
Short summary
Short summary
Plant carbon storage potential is central to moderate atmospheric CO2 concentration buildup and mitigation of climate change. There is an ongoing debate about the main driver of carbon storage. To reconcile this discrepancy, we use SEIB-DGVM to investigate the trend and response mechanism of carbon stock fractions among water limitation regions. Results show that the impact of CO2 and temperature on carbon stock depends on water limitation, offering a new perspective on carbon–water coupling.
Jing Fang, Herman H. Shugart, Feng Liu, Xiaodong Yan, Yunkun Song, and Fucheng Lv
Geosci. Model Dev., 15, 6863–6872, https://doi.org/10.5194/gmd-15-6863-2022, https://doi.org/10.5194/gmd-15-6863-2022, 2022
Short summary
Short summary
Our study provided a detailed description and a package of an individual tree-based carbon model, FORCCHN2. This model used non-structural carbohydrate (NSC) pools to couple tree growth and phenology. The model could reproduce daily carbon fluxes across Northern Hemisphere forests. Given the potential importance of the application of this model, there is substantial scope for using FORCCHN2 in fields as diverse as forest ecology, climate change, and carbon estimation.
Johannes Oberpriller, Christine Herschlein, Peter Anthoni, Almut Arneth, Andreas Krause, Anja Rammig, Mats Lindeskog, Stefan Olin, and Florian Hartig
Geosci. Model Dev., 15, 6495–6519, https://doi.org/10.5194/gmd-15-6495-2022, https://doi.org/10.5194/gmd-15-6495-2022, 2022
Short summary
Short summary
Understanding uncertainties of projected ecosystem dynamics under environmental change is of immense value for research and climate change policy. Here, we analyzed these across European forests. We find that uncertainties are dominantly induced by parameters related to water, mortality, and climate, with an increasing importance of climate from north to south. These results highlight that climate not only contributes uncertainty but also modifies uncertainties in other ecosystem processes.
Marcus Falls, Raffaele Bernardello, Miguel Castrillo, Mario Acosta, Joan Llort, and Martí Galí
Geosci. Model Dev., 15, 5713–5737, https://doi.org/10.5194/gmd-15-5713-2022, https://doi.org/10.5194/gmd-15-5713-2022, 2022
Short summary
Short summary
This paper describes and tests a method which uses a genetic algorithm (GA), a type of optimisation algorithm, on an ocean biogeochemical model. The aim is to produce a set of numerical parameters that best reflect the observed data of particulate organic carbon in a specific region of the ocean. We show that the GA can provide optimised model parameters in a robust and efficient manner and can also help detect model limitations, ultimately leading to a reduction in the model uncertainties.
Julien Ruffault, François Pimont, Hervé Cochard, Jean-Luc Dupuy, and Nicolas Martin-StPaul
Geosci. Model Dev., 15, 5593–5626, https://doi.org/10.5194/gmd-15-5593-2022, https://doi.org/10.5194/gmd-15-5593-2022, 2022
Short summary
Short summary
A widespread increase in tree mortality has been observed around the globe, and this trend is likely to continue because of ongoing climate change. Here we present SurEau-Ecos, a trait-based plant hydraulic model to predict tree desiccation and mortality. SurEau-Ecos can help determine the areas and ecosystems that are most vulnerable to drying conditions.
Rebecca J. Oliver, Lina M. Mercado, Doug B. Clark, Chris Huntingford, Christopher M. Taylor, Pier Luigi Vidale, Patrick C. McGuire, Markus Todt, Sonja Folwell, Valiyaveetil Shamsudheen Semeena, and Belinda E. Medlyn
Geosci. Model Dev., 15, 5567–5592, https://doi.org/10.5194/gmd-15-5567-2022, https://doi.org/10.5194/gmd-15-5567-2022, 2022
Short summary
Short summary
We introduce new representations of plant physiological processes into a land surface model. Including new biological understanding improves modelled carbon and water fluxes for the present in tropical and northern-latitude forests. Future climate simulations demonstrate the sensitivity of photosynthesis to temperature is important for modelling carbon cycle dynamics in a warming world. Accurate representation of these processes in models is necessary for robust predictions of climate change.
Mahdi André Nakhavali, Lina M. Mercado, Iain P. Hartley, Stephen Sitch, Fernanda V. Cunha, Raffaello di Ponzio, Laynara F. Lugli, Carlos A. Quesada, Kelly M. Andersen, Sarah E. Chadburn, Andy J. Wiltshire, Douglas B. Clark, Gyovanni Ribeiro, Lara Siebert, Anna C. M. Moraes, Jéssica Schmeisk Rosa, Rafael Assis, and José L. Camargo
Geosci. Model Dev., 15, 5241–5269, https://doi.org/10.5194/gmd-15-5241-2022, https://doi.org/10.5194/gmd-15-5241-2022, 2022
Short summary
Short summary
In tropical ecosystems, the availability of rock-derived elements such as P can be very low. Thus, without a representation of P cycling, tropical forest responses to rising atmospheric CO2 conditions in areas such as Amazonia remain highly uncertain. We introduced P dynamics and its interactions with the N and P cycles into the JULES model. Our results highlight the potential for high P limitation and therefore lower CO2 fertilization capacity in the Amazon forest with low-fertility soils.
Olga Dombrowski, Cosimo Brogi, Harrie-Jan Hendricks Franssen, Damiano Zanotelli, and Heye Bogena
Geosci. Model Dev., 15, 5167–5193, https://doi.org/10.5194/gmd-15-5167-2022, https://doi.org/10.5194/gmd-15-5167-2022, 2022
Short summary
Short summary
Soil carbon storage and food production of fruit orchards will be influenced by climate change. However, they lack representation in models that study such processes. We developed and tested a new sub-model, CLM5-FruitTree, that describes growth, biomass distribution, and management practices in orchards. The model satisfactorily predicted yield and exchange of carbon, energy, and water in an apple orchard and can be used to study land surface processes in fruit orchards at different scales.
Jiaying Zhang, Rafael L. Bras, Marcos Longo, and Tamara Heartsill Scalley
Geosci. Model Dev., 15, 5107–5126, https://doi.org/10.5194/gmd-15-5107-2022, https://doi.org/10.5194/gmd-15-5107-2022, 2022
Short summary
Short summary
We implemented hurricane disturbance in a vegetation dynamics model and calibrated the model with observations of a tropical forest. We used the model to study forest recovery from hurricane disturbance and found that a single hurricane disturbance enhances AGB and BA in the long term compared with a no-hurricane situation. The model developed and results presented in this study can be utilized to understand the impact of hurricane disturbances on forest recovery under the changing climate.
Prabhat Raj Dahal, Maria Lumbierres, Stuart H. M. Butchart, Paul F. Donald, and Carlo Rondinini
Geosci. Model Dev., 15, 5093–5105, https://doi.org/10.5194/gmd-15-5093-2022, https://doi.org/10.5194/gmd-15-5093-2022, 2022
Short summary
Short summary
This paper describes the validation of area of habitat (AOH) maps produced for terrestrial birds and mammals. The main objective was to assess the accuracy of the maps based on independent data. We used open access data from repositories, such as ebird and gbif to check if our maps were a better reflection of species' distribution than random. When points were not available we used logistic models to validate the AOH maps. The majority of AOH maps were found to have a high accuracy.
Cited articles
Althauser, L. L.: An Ecopath/Ecosim analysis of an estuarine food web:
Seasonal energy flow and response to River-flow related perturbations, MSC
Thesis Louisiana State University and Agricultural and Mechanical College,
2003.
Anderson, T. R. and Mitra, A.: Dysfunctionality in ecosystem models: an
underrated pitfall?, Prog. Oceanogr., 84, 66–68, 2009.
Aumont, O., Maier-Reimer, E., Blain, S., and Pondaven, P.: An ecosystem model
of the global ocean including Fe, Si, P co-limitations, Global Biogeochem.
Cy., 17, 1060, https://doi.org/10.1029/2001GB001745, 2003.
Baretta, J. W., Ebanhoh, W., and Ruardij, P.: The European Regional Seas
Ecosystem Model (ERSEM) II, J. Sea Res., 38, 229–483, 1997.
Berners-Lee, T., Fielding, R. T., and Masinter, L.: Uniform Resource
Identifier (URI): Generic Syntax 2005, Internet Society, available at:
https://www.rfc-editor.org/rfc/rfc3986.txt (last access: 1 March 2016),
2005.
Blackford, J. C., Allen, J. I., and Gilbert, F. J.: Ecosystem dynamics at six
contrasting sites: a generic modelling study, J. Marine Syst., 52, 191–215,
2004.
Blaxter, J. H. S. and Hunter, J. R.: The biology of Clupeoid fishes, Adv.
Mar. Biol., 20, 1–223, 1982.
Borja, A., Fontán, A., Sáenz, J., and Valencia, V.: Climate,
oceanography, and recruitment: the case of the Bay of Biscay Anchovy
(Engraulis sicolus), Fish. Oceanogr., 17, 477–493, 2008.
Broekhuizen, N., Heath, M. R., Hay, S. J., and Gurney, W. S. C.: Modelling
the dynamics of the North Sea's Mesozooplankton. Netherlands, J. Sea Res.,
33, 381–406, 1995.
Bruggeman, J. and Bolding, K.: GOTM Graphical User Interface, available at:
http://www.gotm.net/index.php?go=software&page=gui/index, 2007.
Bruggeman, J. and Bolding, K.: A general framework for aquatic biogeochemical
models, Environ. Model. Softw., 61, 249–265, 2014.
Burchard, H., Bolding, K., and Villarreal, M. R.: GOTM – a general ocean
turbulence model. Theory, applications and test cases, Tech. Rep. EUR 18745
EN, European Commission, 1999.
Burchard, H., Bolding, K., Kuhn, W., Meister, A., Neumann, T., and Umlauf,
L.: Description of a flexible and extendable physical-biogeochemical model
system for the water column, J. Marine Syst., 61, 180–211, 2006.
Chavez, F. P., Ryan, J., Lluch-Cota, S. E., and Ñiquen, M.: From
anchovies to sardines and back: multidecadal change in the Pacific Ocean,
Science, 299, 217–221, 2003.
Christensen, V., Walters, C. J., and Pauly, D.: Ecosim with Ecopath: a user's
guide, November 2005 Edn., Report Fisheries Centre, University of British
Columbia, Vancouver, Canada, 2005.
Clark, A. and Johnson, N. M.: Scaling of metabolic rate with body mass and
temperature in teleost fish, J. Anim. Ecol., 68, 893–905, 1999.
Corten, A.: A possible adaptation of herring feeding migrations to a change
in timing of the Calanus finmarchicus season in the eastern North
Sea, ICES J. Mar. Sci., 57, 1261–1270, 2000.
Cushing, D. H.: Towards a science of recruitment in fish populations, in:
Excellence in Ecology, edited by: Kinne, O., 7, 175 pp., Ecology Institute,
Luhe, Germany, 1996.
Daewel, U., Sætre Hjøllo, S., Huret, M., Ji, R., Maar, M., Niiranen,
S., Travers-Trolet, M., Peck, M. A., and van de Wolfshaar, K. E.: Predation
control of zooplankton dynamics: a review of observations and models ICES J.
Mar. Sci., 71, 254–271, 2014.
Engelhard, G. H., van der Koij, J., Bell, E. D., Pinnegar, J. K., Blanchard,
J. L., Mackinson, S., and Righton, D.: Fishing mortality versus natural
predation on diurnally migrating sandeels, Ammodytes marinus, Mar.
Ecol. Prog. Ser., 369, 213–227, 2008.
Frigstad, H., Andersen, T., Hessen, D. O., Naustvoll, L.-J., Johnsen, T. M.,
and Bellerby, R. G. J.: Seasonal variation in marine C : N : P
stoichiometry: can the composition of seston explain stable Redfield ratios?,
Biogeosciences, 8, 2917–2933, https://doi.org/10.5194/bg-8-2917-2011, 2011.
Fulton, E. A.: Approaches to end to end ecosystem models, J. Marine Syst.,
81, 171–183, 2010.
Fulton, E. A., Smith, A. D. M., and Johnson, C. R.: Effect of complexity on
marine ecosystem models, Marine Ecol. Prog. Ser., 253, 1–6, 2003.
Kearney, K. A.: An analysis of marine ecosystem dynamics through development
of a coupled physical-biogeochemical-fisheries food web model, PhD Thesis,
University of Princetown, 2012.
Le Hégaret, P., Whitmer, R., and Wood, L.: Document Object Model,
available at: http://www.w3c.org/DOM (last access: 1 March 2016), 2009.
Levins, R.: The Strategy of Model Building in Population Biology, Am. Sci.,
54, 421–431, 1966.
Lewis, K. and Allen, J. I.: Validation of a hydrodynamic-ecosystem model
simulation with time-series data collected in the western English Channel, J.
Marine Syst., 3, 296–311, 2009.
Libralato, S. and Solidoro, C.: Bridging biogeochemical and food web models
for an End-to-End representation of marine ecosystem dynamics: The Venice
lagoon case study, Ecol. Model., 220, 2960–2971, 2009.
Lotze, H. K. H. S., Lenihan, B. J., Bourque, R. H., Bradbury, R. G., Cooke,
M. C., Kay, S. M., Kidwell, M., Kirby, C. H., Peterson, J. B., and Jackson,
C.: Depletion, Degradation, and Recovery Potential of Estuaries and Coastal
Seas, Science, 312, 1806–1809, 2006.
Machuo, E., Ettahiri, O., Kifani, S., Benazzouz, A., Makaoui, A., and
Demarcq, H.: Environmental control of the recruitment of sardines
(Sardina pilchardus) over the western Saharan shelf between 1995 and
2002: a coupled physical ∕ biogeochemical modelling experiment, Fish.
Oceanogr., 18, 287–300, 2009.
Mackinson, S. and Daskalov, G.: An ecosystem model of the North Sea to
support an ecosystem approach to fisheries management: description and
parameterisation, Sci Ser. Tech. Rep., Cefas Lowestoft, 142, 196 pp., 2007.
Madec, G., Chartier, M., Delecluse, P., and Crépon, M.: A
three-dimensional numerical study of deep water formation in the Northwestern
Mediterranean Sea, J. Phys. Oceanogr., 21, 1349–1371, 1991.
Minto, C., Myers, R. A., and Blanchard, W.: Survival variability and
population density in fish populations, Nature, 452, 344–347, 2008.
Nakicenovic, N., Alcamo, J., Davis, G., de Vries, B., Fenhann, J., Gaffin,
S., Gregory, K., Grubler, A., Jung, T. Y., Kram, T., La Rovere, E. L.,
Michaelis, L., Mori, S., Morita, T., Pepper, W., Pitcher, H. M., Price, L.,
Riahi, K., Roehrl, A., Rogner, H.-H., Sankovski, A., Schlesinger, M., Shukla,
P., Smith, S. J., Swart, R., van Rooijen, S., Victor, N., and Dadi, Z.:
Special Report on Emissions Scenarios : a special report of Working Group III
of the Intergovernmental Panel on Climate Change. Cambridge University Press,
New York, NY (US), 2000.
Officer, C. B. and Ryther, J. H.: The importance of silicon in marine
eutrophication, Mar. Ecol. Prog. Ser., 3, 83–91, 1980.
Pätsch, J. and Kühn, W.: Nitrogen and carbon cycling in the North Sea
and exchange with the North Atlantic – a model study, Part I. Nitrogen
budget and fluxes, Cont. Shelf Res., 28, 767–787, 2008.
Peterson, P.: F2Py: Fortran to Python Interface Generator, available at:
http://cens.ioc.ee/projects/f2py2e/ (last access: 1 March 2016), 2007.
Richardson, A. J. and Schoeman, D. S.: Climate impact on plankton ecosystems
in the Northeast Atlantic, Science, 305, 1609–1612, 2004.
Rose, K. A.: End-to end models for marine ecosystems: Are we on the precipice
of a significant advance or just putting lipstick on a pig?, Scientia Marina,
76, 195–201, 2012.
Rose, K. A., Werner, F. E., Megrey, B. A., Noguchi-Aita, M., Yamanaka, Y.,
Hay, D. E., Schweigert, J. F., and Foster, M. B.: Simulated herring growth
responses in the Northeastern Pacific to historic temperature and zooplankton
conditions generated by the 3-dimensional NEMURO
nutrient-phytoplankton-zooplankton model, Ecol. Model., 202, 184–195, 2007.
Rose, K. A., Allen, J. I., Artioli, Y., Barange, M., Blackford, J., Carlotti,
F., Cropp, R., Daewel, U., Edwards, K., Flynn, K., Hill, S. L.,
HilleRisLambers, R., Huse, G., Mackinson, S., Megrey, B., Moll, A., Rivkin,
R., Salihoglu, B., Schrum, C., Shannon, L., Shin, Y.-J., Smith, S. L., Smith
C., Solidoro, C., St. John, M., and Zhou, M.: End-To-End Models for the
Analysis of Marine Ecosystems: Challenges, Issues, and Next Steps, Marine and
Coastal Fisheries: Dynamics, Management, and Ecosystem Science, 2, 115–130,
2010.
Rossberg, A. G.: Food webs and biodiversity: Foundations, models, data,
Wiley, Chichester, West Sussex, UK, 2013.
Schrum, C., Alekseeva, I., and Stjohn, M.: Development of a coupled
physical–biological ecosystem model ECOSMOPart I: Model description and
validation for the North Sea, J. Marine Syst., 61, 79–99, 2006.
Travers, M., Shin, Y.-J., Jennings, S., and Cury, P.: Towards end-to-end
models for investigating the effects of climate and fishing in marine
ecosystems, Prog. Oceanogr., 75, 751–770, 2007.
Travers, M., Shin, Y.-J., Jennings, S., Machu, E., Huggett, J. A., Field, J.
G., and Cury, P. M.: Two-way coupling versus one-way forcing of plankton and
fish models to predict ecosystem changes in the Benguela, Ecol. Model., 220,
3089–3099, 2009.
Urban, H. J.: Modeling growth of different developmental stages in bivalves,
Mar. Ecol. Prog. Ser., 238, 109–114, 2002.
van der Molen, J., Aldridge, J. N., Coughlan, C., Parker, E. R., Stephens,
D., and Ruardij, P.: Modelling marine ecosystem response to climate change
and trawling in the North Sea, Biogeochemistry, 113, 213–236, 2012.
Vichi, M., Oddo, P., Zavatarelli, M., Coluccelli, A., Coppini, G., Celio, M.,
Fonda Umani, S., and Pinardi, N.: Calibration and validation of a
one-dimensional complex marine biogeochemical flux model in different areas
of the northern Adriatic shelf, Ann. Geophys., 21, 413–436,
https://doi.org/10.5194/angeo-21-413-2003, 2003.
Short summary
This paper is a description of how very different higher and lower trophic level models (Ecopath with Ecosim) and ERSEM, respectively, can be coupled together using a metadata coupling system together with a number of examples of short- and long-range projections for end to end modelling.
This paper is a description of how very different higher and lower trophic level models (Ecopath...
