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Marcel Van Oijen
UK Centre for Ecology & Hydrology (CEH-Edinburgh), Penicuik, UK

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Article
Published: 09 July 2020 in Agroforestry Systems
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Coffee is often grown in production systems associated with shade trees that provide different ecosystem services. Management, weather and soil conditions are spatially variable production factors. CAF2007 is a dynamic model for coffee agroforestry systems that takes these factors as inputs and simulates the processes underlying berry production at the field scale. There remain, however, uncertainties about process rates that need to be reduced through calibration. Bayesian statistics using Markov chain Monte Carlo algorithms is increasingly used for calibration of parameter-rich models. However, very few studies have employed multi-site calibration, which aims to reduce parameter uncertainties using data from multiple sites simultaneously. The main objectives of this study were to calibrate the coffee agroforestry model using data gathered in long-term experiments in Costa Rica and Nicaragua, and to test the calibrated model against independent data from commercial coffee-growing farms. Two sub-models were improved: calculation of flowering date and the modelling of biennial production patterns. The modified model, referred to as CAF2014, can be downloaded at https://doi.org/10.5281/zenodo.3608877. Calibration improved model performance (higher R2, lower RMSE) for Turrialba (Costa Rica) and Masatepe (Nicaragua), including when all experiments were pooled together. Multi-site and single-site Bayesian calibration led to similar RMSE. Validation on new data from coffee-growing farms revealed that both calibration methods improved simulation of yield and its bienniality. The thus improved model was used to test the effect of N fertilizer and shade in different locations on coffee yield.

ACS Style

Oriana Ovalle-Rivera; Marcel Van Oijen; Peter Läderach; Olivier Roupsard; Elias De Melo Virginio Filho; Mirna Barrios; Bruno Rapidel. Assessing the accuracy and robustness of a process-based model for coffee agroforestry systems in Central America. Agroforestry Systems 2020, 94, 2033 -2051.

AMA Style

Oriana Ovalle-Rivera, Marcel Van Oijen, Peter Läderach, Olivier Roupsard, Elias De Melo Virginio Filho, Mirna Barrios, Bruno Rapidel. Assessing the accuracy and robustness of a process-based model for coffee agroforestry systems in Central America. Agroforestry Systems. 2020; 94 (5):2033-2051.

Chicago/Turabian Style

Oriana Ovalle-Rivera; Marcel Van Oijen; Peter Läderach; Olivier Roupsard; Elias De Melo Virginio Filho; Mirna Barrios; Bruno Rapidel. 2020. "Assessing the accuracy and robustness of a process-based model for coffee agroforestry systems in Central America." Agroforestry Systems 94, no. 5: 2033-2051.

Perspective
Published: 11 May 2020 in Nature Plants
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Plants and vegetation play a critical—but largely unpredictable—role in global environmental changes due to the multitude of contributing processes at widely different spatial and temporal scales. In this Perspective, we explore approaches to master this complexity and improve our ability to predict vegetation dynamics by explicitly taking account of principles that constrain plant and ecosystem behaviour: natural selection, self-organization and entropy maximization. These ideas are increasingly being used in vegetation models, but we argue that their full potential has yet to be realized. We demonstrate the power of natural selection-based optimality principles to predict photosynthetic and carbon allocation responses to multiple environmental drivers, as well as how individual plasticity leads to the predictable self-organization of forest canopies. We show how models of natural selection acting on a few key traits can generate realistic plant communities and how entropy maximization can identify the most probable outcomes of community dynamics in space- and time-varying environments. Finally, we present a roadmap indicating how these principles could be combined in a new generation of models with stronger theoretical foundations and an improved capacity to predict complex vegetation responses to environmental change.

ACS Style

Oskar Franklin; Sandy P. Harrison; Roderick Dewar; Caroline E. Farrior; Åke Brännström; Ulf Dieckmann; Stephan Pietsch; Daniel Falster; Wolfgang Cramer; Michel Loreau; Han Wang; Annikki Mäkelä; Karin T. Rebel; Ehud Meron; Stanislaus J. Schymanski; Elena Rovenskaya; Benjamin D. Stocker; Sönke Zaehle; Stefano Manzoni; Marcel Van Oijen; Ian J. Wright; Philippe Ciais; Peter M. Van Bodegom; Josep Peñuelas; Florian Hofhansl; Cesar Terrer; Nadejda A. Soudzilovskaia; Guy Midgley; I. Colin Prentice. Organizing principles for vegetation dynamics. Nature Plants 2020, 6, 444 -453.

AMA Style

Oskar Franklin, Sandy P. Harrison, Roderick Dewar, Caroline E. Farrior, Åke Brännström, Ulf Dieckmann, Stephan Pietsch, Daniel Falster, Wolfgang Cramer, Michel Loreau, Han Wang, Annikki Mäkelä, Karin T. Rebel, Ehud Meron, Stanislaus J. Schymanski, Elena Rovenskaya, Benjamin D. Stocker, Sönke Zaehle, Stefano Manzoni, Marcel Van Oijen, Ian J. Wright, Philippe Ciais, Peter M. Van Bodegom, Josep Peñuelas, Florian Hofhansl, Cesar Terrer, Nadejda A. Soudzilovskaia, Guy Midgley, I. Colin Prentice. Organizing principles for vegetation dynamics. Nature Plants. 2020; 6 (5):444-453.

Chicago/Turabian Style

Oskar Franklin; Sandy P. Harrison; Roderick Dewar; Caroline E. Farrior; Åke Brännström; Ulf Dieckmann; Stephan Pietsch; Daniel Falster; Wolfgang Cramer; Michel Loreau; Han Wang; Annikki Mäkelä; Karin T. Rebel; Ehud Meron; Stanislaus J. Schymanski; Elena Rovenskaya; Benjamin D. Stocker; Sönke Zaehle; Stefano Manzoni; Marcel Van Oijen; Ian J. Wright; Philippe Ciais; Peter M. Van Bodegom; Josep Peñuelas; Florian Hofhansl; Cesar Terrer; Nadejda A. Soudzilovskaia; Guy Midgley; I. Colin Prentice. 2020. "Organizing principles for vegetation dynamics." Nature Plants 6, no. 5: 444-453.

Journal article
Published: 26 March 2020 in Biogeosciences
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The impact of atmospheric reactive nitrogen (Nr) deposition on carbon (C) sequestration in soils and biomass of unfertilized, natural, semi-natural and forest ecosystems has been much debated. Many previous results of this dC∕dN response were based on changes in carbon stocks from periodical soil and ecosystem inventories, associated with estimates of Nr deposition obtained from large-scale chemical transport models. This study and a companion paper (Flechard et al., 2020) strive to reduce uncertainties of N effects on C sequestration by linking multi-annual gross and net ecosystem productivity estimates from 40 eddy covariance flux towers across Europe to local measurement-based estimates of dry and wet Nr deposition from a dedicated collocated monitoring network. To identify possible ecological drivers and processes affecting the interplay between C and Nr inputs and losses, these data were also combined with in situ flux measurements of NO, N2O and CH4 fluxes; soil NO3- leaching sampling; and results of soil incubation experiments for N and greenhouse gas (GHG) emissions, as well as surveys of available data from online databases and from the literature, together with forest ecosystem (BASFOR) modelling. Multi-year averages of net ecosystem productivity (NEP) in forests ranged from −70 to 826 g C m−2 yr−1 at total wet + dry inorganic Nr deposition rates (Ndep) of 0.3 to 4.3 g N m−2 yr−1 and from −4 to 361 g C m−2 yr−1 at Ndep rates of 0.1 to 3.1 g N m−2 yr−1 in short semi-natural vegetation (moorlands, wetlands and unfertilized extensively managed grasslands). The GHG budgets of the forests were strongly dominated by CO2 exchange, while CH4 and N2O exchange comprised a larger proportion of the GHG balance in short semi-natural vegetation. Uncertainties in elemental budgets were much larger for nitrogen than carbon, especially at sites with elevated Ndep where Nr leaching losses were also very large, and compounded by the lack of reliable data on organic nitrogen and N2 losses by denitrification. Nitrogen losses in the form of NO, N2O and especially NO3- were on average 27 % (range 6 %–54 %) of Ndep at sites with Ndep < 1 g N m−2 yr−1 versus 65 % (range 35 %–85 %) for Ndep > 3 g N m−2 yr−1. Such large levels of Nr loss likely indicate that different stages of N saturation occurred at a number of sites. The joint analysis of the C and N budgets provided further hints that N saturation could be detected in altered patterns of forest growth. Net ecosystem productivity increased with Nr deposition up to 2–2.5 g N m−2 yr−1, with large scatter associated with a wide range in carbon sequestration efficiency (CSE, defined as the NEP ∕ GPP ratio). At elevated Ndep levels (> 2.5 g N m−2 yr−1), where inorganic Nr losses were also increasingly large, NEP levelled off and then decreased. The apparent increase in NEP at low to intermediate Ndep levels was partly the result of geographical cross-correlations between Ndep and climate, indicating that the actual mean dC∕dN response at individual sites was significantly lower than would be suggested by a simple, straightforward regression of NEP vs. Ndep.

ACS Style

Chris R. Flechard; Andreas Ibrom; Ute M. Skiba; Wim De Vries; Marcel Van Oijen; David R. Cameron; Nancy B. Dise; Janne F. J. Korhonen; Nina Buchmann; Arnaud Legout; David Simpson; Maria J. Sanz; Marc Aubinet; Denis Loustau; Leonardo Montagnani; Johan Neirynck; Ivan A. Janssens; Mari Pihlatie; Ralf Kiese; Jan Siemens; André-Jean Francez; Jürgen Augustin; Andrej Varlagin; Janusz Olejnik; Radosław Juszczak; Mika Aurela; Daniel Berveiller; Bogdan H. Chojnicki; Ulrich Dämmgen; Nicolas Delpierre; Vesna Djuricic; Julia Drewer; Eric Dufrêne; Werner Eugster; Yannick Fauvel; David Fowler; Arnoud Frumau; André Granier; Patrick Gross; Yannick Hamon; Carole Helfter; Arjan Hensen; László Horváth; Barbara Kitzler; Bart Kruijt; Werner L. Kutsch; Raquel Lobo-Do-Vale; Annalea Lohila; Bernard Longdoz; Michal V. Marek; Giorgio Matteucci; Marta Mitosinkova; Virginie Moreaux; Albrecht Neftel; Jean-Marc Ourcival; Kim Pilegaard; Gabriel Pita; Francisco Sanz; Jan K. Schjoerring; Maria-Teresa Sebastià; Y. Sim Tang; Hilde Uggerud; Marek Urbaniak; Netty Van Dijk; Timo Vesala; Sonja Vidic; Caroline Vincke; Tamás Weidinger; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Eiko Nemitz; Mark A. Sutton. Carbon–nitrogen interactions in European forests and semi-natural vegetation – Part 1: Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling. Biogeosciences 2020, 17, 1583 -1620.

AMA Style

Chris R. Flechard, Andreas Ibrom, Ute M. Skiba, Wim De Vries, Marcel Van Oijen, David R. Cameron, Nancy B. Dise, Janne F. J. Korhonen, Nina Buchmann, Arnaud Legout, David Simpson, Maria J. Sanz, Marc Aubinet, Denis Loustau, Leonardo Montagnani, Johan Neirynck, Ivan A. Janssens, Mari Pihlatie, Ralf Kiese, Jan Siemens, André-Jean Francez, Jürgen Augustin, Andrej Varlagin, Janusz Olejnik, Radosław Juszczak, Mika Aurela, Daniel Berveiller, Bogdan H. Chojnicki, Ulrich Dämmgen, Nicolas Delpierre, Vesna Djuricic, Julia Drewer, Eric Dufrêne, Werner Eugster, Yannick Fauvel, David Fowler, Arnoud Frumau, André Granier, Patrick Gross, Yannick Hamon, Carole Helfter, Arjan Hensen, László Horváth, Barbara Kitzler, Bart Kruijt, Werner L. Kutsch, Raquel Lobo-Do-Vale, Annalea Lohila, Bernard Longdoz, Michal V. Marek, Giorgio Matteucci, Marta Mitosinkova, Virginie Moreaux, Albrecht Neftel, Jean-Marc Ourcival, Kim Pilegaard, Gabriel Pita, Francisco Sanz, Jan K. Schjoerring, Maria-Teresa Sebastià, Y. Sim Tang, Hilde Uggerud, Marek Urbaniak, Netty Van Dijk, Timo Vesala, Sonja Vidic, Caroline Vincke, Tamás Weidinger, Sophie Zechmeister-Boltenstern, Klaus Butterbach-Bahl, Eiko Nemitz, Mark A. Sutton. Carbon–nitrogen interactions in European forests and semi-natural vegetation – Part 1: Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling. Biogeosciences. 2020; 17 (6):1583-1620.

Chicago/Turabian Style

Chris R. Flechard; Andreas Ibrom; Ute M. Skiba; Wim De Vries; Marcel Van Oijen; David R. Cameron; Nancy B. Dise; Janne F. J. Korhonen; Nina Buchmann; Arnaud Legout; David Simpson; Maria J. Sanz; Marc Aubinet; Denis Loustau; Leonardo Montagnani; Johan Neirynck; Ivan A. Janssens; Mari Pihlatie; Ralf Kiese; Jan Siemens; André-Jean Francez; Jürgen Augustin; Andrej Varlagin; Janusz Olejnik; Radosław Juszczak; Mika Aurela; Daniel Berveiller; Bogdan H. Chojnicki; Ulrich Dämmgen; Nicolas Delpierre; Vesna Djuricic; Julia Drewer; Eric Dufrêne; Werner Eugster; Yannick Fauvel; David Fowler; Arnoud Frumau; André Granier; Patrick Gross; Yannick Hamon; Carole Helfter; Arjan Hensen; László Horváth; Barbara Kitzler; Bart Kruijt; Werner L. Kutsch; Raquel Lobo-Do-Vale; Annalea Lohila; Bernard Longdoz; Michal V. Marek; Giorgio Matteucci; Marta Mitosinkova; Virginie Moreaux; Albrecht Neftel; Jean-Marc Ourcival; Kim Pilegaard; Gabriel Pita; Francisco Sanz; Jan K. Schjoerring; Maria-Teresa Sebastià; Y. Sim Tang; Hilde Uggerud; Marek Urbaniak; Netty Van Dijk; Timo Vesala; Sonja Vidic; Caroline Vincke; Tamás Weidinger; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Eiko Nemitz; Mark A. Sutton. 2020. "Carbon–nitrogen interactions in European forests and semi-natural vegetation – Part 1: Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling." Biogeosciences 17, no. 6: 1583-1620.

Journal article
Published: 26 March 2020 in Biogeosciences
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The effects of atmospheric nitrogen deposition (Ndep) on carbon (C) sequestration in forests have often been assessed by relating differences in productivity to spatial variations of Ndep across a large geographic domain. These correlations generally suffer from covariation of other confounding variables related to climate and other growth-limiting factors, as well as large uncertainties in total (dry + wet) reactive nitrogen (Nr) deposition. We propose a methodology for untangling the effects of Ndep from those of meteorological variables, soil water retention capacity and stand age, using a mechanistic forest growth model in combination with eddy covariance CO2 exchange fluxes from a Europe-wide network of 22 forest flux towers. Total Nr deposition rates were estimated from local measurements as far as possible. The forest data were compared with data from natural or semi-natural, non-woody vegetation sites. The response of forest net ecosystem productivity to nitrogen deposition (dNEP ∕ dNdep) was estimated after accounting for the effects on gross primary productivity (GPP) of the co-correlates by means of a meta-modelling standardization procedure, which resulted in a reduction by a factor of about 2 of the uncorrected, apparent dGPP ∕ dNdep value. This model-enhanced analysis of the C and Ndep flux observations at the scale of the European network suggests a mean overall dNEP ∕ dNdep response of forest lifetime C sequestration to Ndep of the order of 40–50 g C per g N, which is slightly larger but not significantly different from the range of estimates published in the most recent reviews. Importantly, patterns of gross primary and net ecosystem productivity versus Ndep were non-linear, with no further growth responses at high Ndep levels (Ndep > 2.5–3 g N m−2 yr−1) but accompanied by increasingly large ecosystem N losses by leaching and gaseous emissions. The reduced increase in productivity per unit N deposited at high Ndep levels implies that the forecast increased Nr emissions and increased Ndep levels in large areas of Asia may not positively impact the continent's forest CO2 sink. The large level of unexplained variability in observed carbon sequestration efficiency (CSE) across sites further adds to the uncertainty in the dC∕dN response.

ACS Style

Chris R. Flechard; Marcel van Oijen; David R. Cameron; Wim de Vries; Andreas Ibrom; Nina Buchmann; Nancy B. Dise; Ivan A. Janssens; Johan Neirynck; Leonardo Montagnani; Andrej Varlagin; Denis Loustau; Arnaud Legout; Klaudia Ziemblińska; Marc Aubinet; Mika Aurela; Bogdan H. Chojnicki; Julia Drewer; Werner Eugster; André-Jean Francez; Radosław Juszczak; Barbara Kitzler; Werner L. Kutsch; Annalea Lohila; Bernard Longdoz; Giorgio Matteucci; Virginie Moreaux; Albrecht Neftel; Janusz Olejnik; Maria J. Sanz; Jan Siemens; Timo Vesala; Caroline Vincke; Eiko Nemitz; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Ute M. Skiba; Mark A. Sutton. Carbon–nitrogen interactions in European forests and semi-natural vegetation – Part 2: Untangling climatic, edaphic, management and nitrogen deposition effects on carbon sequestration potentials. Biogeosciences 2020, 17, 1621 -1654.

AMA Style

Chris R. Flechard, Marcel van Oijen, David R. Cameron, Wim de Vries, Andreas Ibrom, Nina Buchmann, Nancy B. Dise, Ivan A. Janssens, Johan Neirynck, Leonardo Montagnani, Andrej Varlagin, Denis Loustau, Arnaud Legout, Klaudia Ziemblińska, Marc Aubinet, Mika Aurela, Bogdan H. Chojnicki, Julia Drewer, Werner Eugster, André-Jean Francez, Radosław Juszczak, Barbara Kitzler, Werner L. Kutsch, Annalea Lohila, Bernard Longdoz, Giorgio Matteucci, Virginie Moreaux, Albrecht Neftel, Janusz Olejnik, Maria J. Sanz, Jan Siemens, Timo Vesala, Caroline Vincke, Eiko Nemitz, Sophie Zechmeister-Boltenstern, Klaus Butterbach-Bahl, Ute M. Skiba, Mark A. Sutton. Carbon–nitrogen interactions in European forests and semi-natural vegetation – Part 2: Untangling climatic, edaphic, management and nitrogen deposition effects on carbon sequestration potentials. Biogeosciences. 2020; 17 (6):1621-1654.

Chicago/Turabian Style

Chris R. Flechard; Marcel van Oijen; David R. Cameron; Wim de Vries; Andreas Ibrom; Nina Buchmann; Nancy B. Dise; Ivan A. Janssens; Johan Neirynck; Leonardo Montagnani; Andrej Varlagin; Denis Loustau; Arnaud Legout; Klaudia Ziemblińska; Marc Aubinet; Mika Aurela; Bogdan H. Chojnicki; Julia Drewer; Werner Eugster; André-Jean Francez; Radosław Juszczak; Barbara Kitzler; Werner L. Kutsch; Annalea Lohila; Bernard Longdoz; Giorgio Matteucci; Virginie Moreaux; Albrecht Neftel; Janusz Olejnik; Maria J. Sanz; Jan Siemens; Timo Vesala; Caroline Vincke; Eiko Nemitz; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Ute M. Skiba; Mark A. Sutton. 2020. "Carbon–nitrogen interactions in European forests and semi-natural vegetation – Part 2: Untangling climatic, edaphic, management and nitrogen deposition effects on carbon sequestration potentials." Biogeosciences 17, no. 6: 1621-1654.

Review
Published: 12 February 2020 in Agronomy
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Multi-species grasslands are reservoirs of biodiversity and provide multiple ecosystem services, including fodder production and carbon sequestration. The provision of these services depends on the control exerted on the biogeochemistry and plant diversity of the system by the interplay of biotic and abiotic factors, e.g., grazing or mowing intensity. Biogeochemical models incorporate a mechanistic view of the functioning of grasslands and provide a sound basis for studying the underlying processes. However, in these models, the simulation of biogeochemical cycles is generally not coupled to simulation of plant species dynamics, which leads to considerable uncertainty about the quality of predictions. Ecological models, on the other hand, do account for biodiversity with approaches adopted from plant demography, but without linking the dynamics of plant species to the biogeochemical processes occurring at the community level, and this hampers the models’ capacity to assess resilience against abiotic stresses such as drought and nutrient limitation. While setting out the state-of-the-art developments of biogeochemical and ecological modelling, we explore and highlight the role of plant diversity in the regulation of the ecosystem processes underlying the ecosystems services provided by multi-species grasslands. An extensive literature and model survey was carried out with an emphasis on technically advanced models reconciling biogeochemistry and biodiversity, which are readily applicable to managed grasslands in temperate latitudes. We propose a roadmap of promising developments in modelling.

ACS Style

Marcel Van Oijen; Zoltán Barcza; Roberto Confalonieri; Panu Korhonen; György Kröel-Dulay; Eszter Lellei-Kovács; Gaëtan Louarn; Frédérique Louault; Raphaël Martin; Thibault Moulin; Ermes Movedi; Catherine Picon-Cochard; Susanne Rolinski; Nicolas Viovy; Stephen Björn Wirth; Gianni Bellocchi. Incorporating Biodiversity into Biogeochemistry Models to Improve Prediction of Ecosystem Services in Temperate Grasslands: Review and Roadmap. Agronomy 2020, 10, 259 .

AMA Style

Marcel Van Oijen, Zoltán Barcza, Roberto Confalonieri, Panu Korhonen, György Kröel-Dulay, Eszter Lellei-Kovács, Gaëtan Louarn, Frédérique Louault, Raphaël Martin, Thibault Moulin, Ermes Movedi, Catherine Picon-Cochard, Susanne Rolinski, Nicolas Viovy, Stephen Björn Wirth, Gianni Bellocchi. Incorporating Biodiversity into Biogeochemistry Models to Improve Prediction of Ecosystem Services in Temperate Grasslands: Review and Roadmap. Agronomy. 2020; 10 (2):259.

Chicago/Turabian Style

Marcel Van Oijen; Zoltán Barcza; Roberto Confalonieri; Panu Korhonen; György Kröel-Dulay; Eszter Lellei-Kovács; Gaëtan Louarn; Frédérique Louault; Raphaël Martin; Thibault Moulin; Ermes Movedi; Catherine Picon-Cochard; Susanne Rolinski; Nicolas Viovy; Stephen Björn Wirth; Gianni Bellocchi. 2020. "Incorporating Biodiversity into Biogeochemistry Models to Improve Prediction of Ecosystem Services in Temperate Grasslands: Review and Roadmap." Agronomy 10, no. 2: 259.

Original article
Published: 16 January 2020 in Grass and Forage Science
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Recent years have seen a decline in herbage production and tiller populations in New Zealand's perennial ryegrass (Lolium perenne) dairy pastures. One hypothesis is that modern genotypes are less suited to the warmer, drier weather experienced under changing climate patterns. In this study, a combination of long‐term trial data (2011–2017) and a process‐based pasture model (BASGRA) was used to explore the causes and possible mitigation of the observed production and population loss at three sites (dryland sites in Northland and Waikato and an irrigated site in Canterbury). Bayesian calibration was used to identify the model parameter sets that were consistent with the trial data and to identify differences in plant morphology and responses between sites. The model successfully simulated the observed differences in tiller numbers between the dryland sites, where populations and production declined rapidly after the second year and the irrigated site where populations and production were maintained. Analysis of the model calibrations along with preliminary scenario simulations suggests that increased tiller mortality associated with drought was the main cause of persistence failure at the dryland sites and that decreasing grazing pressure or breeding for tolerance to higher temperatures may not be successful in preventing this.

ACS Style

Simon J. R. Woodward; Marcel Van Oijen; Wendy M. Griffiths; Pierre C. Beukes; David F. Chapman. Identifying causes of low persistence of perennial ryegrass (Lolium perenne) dairy pasture using the Basic Grassland model (BASGRA). Grass and Forage Science 2020, 75, 45 -63.

AMA Style

Simon J. R. Woodward, Marcel Van Oijen, Wendy M. Griffiths, Pierre C. Beukes, David F. Chapman. Identifying causes of low persistence of perennial ryegrass (Lolium perenne) dairy pasture using the Basic Grassland model (BASGRA). Grass and Forage Science. 2020; 75 (1):45-63.

Chicago/Turabian Style

Simon J. R. Woodward; Marcel Van Oijen; Wendy M. Griffiths; Pierre C. Beukes; David F. Chapman. 2020. "Identifying causes of low persistence of perennial ryegrass (Lolium perenne) dairy pasture using the Basic Grassland model (BASGRA)." Grass and Forage Science 75, no. 1: 45-63.

Journal article
Published: 07 January 2020 in Ecological Modelling
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The main objective of this paper is to present the new model BASGRA_N, to show how it was parameterized for grass swards in Scandinavia, and to evaluate its performance in predicting above-ground biomass, crude protein, cell wall content and dry matter digestibility. The model was developed to allow simulation of: (1) the impact of N-supply on the plants and their environment, (2) the dynamics of greenhouse gas emissions from grasslands, (3) the dynamics of cell-wall content and digestibility of leaves and stems, which could not be simulated with its predecessor, the BASGRA-model. To calibrate and test the model, we used field experimental data. One dataset included observations of biomass (DM) and crude protein content (CP) under different N fertilizer regimes from five sites in central and southern Sweden. The other dataset included observations of DM, and sward components as well as CP, cell wall content (NDF) and DM digestibility as affected by harvesting regime from one site in southwestern Norway. The total number of experiments was nine, of which three were used for model testing. When BASGRA_N was run with the maximum a-posteriori (MAP) parameter vector from the Bayesian calibration for the Swedish test sites, DM and CP were both simulated to an overall Pearson correlation coefficient (Rb) of minimum 0.58, Willmott's index of agreement (d) of minimum 0.69 and normalized root mean squared error (NRMSE) of maximum 0.30. Corresponding metrics for Norwegian test sites were 0.93, 0.96 and 0.27 for DM and >0.73, >0.61, <0.18 for DM digestibility, NDF and CP content, respectively. We conclude that BASGRA_N can be used to simulate yield and CP responses to N with satisfactory precision, while maintaining key features from its predecessor. The results also suggest that DM digestibility and NDF can be simulated satisfactorily, which is supported by results from a recent model comparison study. Further testing of the model is needed for a few variables for which we currently do not have enough data, notably leaching and emission of N-containing compounds. Further work will include application of the model to investigate greenhouse gas mitigation options, and evaluation against independent data for the conditions for which it will be applied.

ACS Style

Mats Höglind; David Cameron; Tomas Persson; Xiao Huang; Marcel van Oijen. BASGRA_N: A model for grassland productivity, quality and greenhouse gas balance. Ecological Modelling 2020, 417, 108925 .

AMA Style

Mats Höglind, David Cameron, Tomas Persson, Xiao Huang, Marcel van Oijen. BASGRA_N: A model for grassland productivity, quality and greenhouse gas balance. Ecological Modelling. 2020; 417 ():108925.

Chicago/Turabian Style

Mats Höglind; David Cameron; Tomas Persson; Xiao Huang; Marcel van Oijen. 2020. "BASGRA_N: A model for grassland productivity, quality and greenhouse gas balance." Ecological Modelling 417, no. : 108925.

Journal article
Published: 11 October 2019 in Agricultural and Forest Meteorology
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Horizontal heterogeneity causes difficulties in the eddy covariance technique for measuring surface fluxes, related to both advection and the confounding of temporal and spatial variability. Our aim here was to address this problem, using statistical modelling and footprint analysis, applied to a case study of fluxes of sensible heat and methane in a subarctic mire. We applied a new method to infer the spatial heterogeneity in fluxes of sensible heat and methane from a subarctic ecosystem in northern Sweden, where there were clear differences in surface types within the landscape. We inferred the flux from each of these surface types, using a Bayesian approach to estimate the parameters of a hierarchical model which includes coefficients for the different surface types. The approach is based on the variation in the flux observed at a single eddy covariance tower as the footprint changes over time. The method has applications wherever spatial heterogeneity is a concern in the interpretation of eddy covariance fluxes.

ACS Style

Peter Levy; Julia Drewer; Mathilde Jammet; Sarah Leeson; Thomas Friborg; Ute Skiba; Marcel Van Oijen. Inference of spatial heterogeneity in surface fluxes from eddy covariance data: A case study from a subarctic mire ecosystem. Agricultural and Forest Meteorology 2019, 280, 107783 .

AMA Style

Peter Levy, Julia Drewer, Mathilde Jammet, Sarah Leeson, Thomas Friborg, Ute Skiba, Marcel Van Oijen. Inference of spatial heterogeneity in surface fluxes from eddy covariance data: A case study from a subarctic mire ecosystem. Agricultural and Forest Meteorology. 2019; 280 ():107783.

Chicago/Turabian Style

Peter Levy; Julia Drewer; Mathilde Jammet; Sarah Leeson; Thomas Friborg; Ute Skiba; Marcel Van Oijen. 2019. "Inference of spatial heterogeneity in surface fluxes from eddy covariance data: A case study from a subarctic mire ecosystem." Agricultural and Forest Meteorology 280, no. : 107783.

Preprint content
Published: 11 September 2019
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ACS Style

Chris R. Flechard; Marcel Van Oijen; David R. Cameron; Wim De Vries; Andreas Ibrom; Nina Buchmann; Nancy B. Dise; Ivan A. Janssens; Johan Neirynck; Leonardo Montagnani; Andrej Varlagin; Denis Loustau; Arnaud Legout; Klaudia Ziemblińska; Marc Aubinet; Mika Aurela; Bogdan H. Chojnicki; Julia Drewer; Werner Eugster; André-Jean Francez; Radosław Juszczak; Barbara Kitzler; Werner L. Kutsch; Annalea Lohila; Bernard Longdoz; Giorgio Matteucci; Virginie Moreaux; Albrecht Neftel; Janusz Olejnik; Maria J. Sanz; Jan Siemens; Timo Vesala; Caroline Vincke; Eiko Nemitz; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Ute M. Skiba; Mark A. Sutton. Supplementary material to "Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part II: Untangling climatic, edaphic, management and nitrogen deposition effects on carbon sequestration potentials". 2019, 1 .

AMA Style

Chris R. Flechard, Marcel Van Oijen, David R. Cameron, Wim De Vries, Andreas Ibrom, Nina Buchmann, Nancy B. Dise, Ivan A. Janssens, Johan Neirynck, Leonardo Montagnani, Andrej Varlagin, Denis Loustau, Arnaud Legout, Klaudia Ziemblińska, Marc Aubinet, Mika Aurela, Bogdan H. Chojnicki, Julia Drewer, Werner Eugster, André-Jean Francez, Radosław Juszczak, Barbara Kitzler, Werner L. Kutsch, Annalea Lohila, Bernard Longdoz, Giorgio Matteucci, Virginie Moreaux, Albrecht Neftel, Janusz Olejnik, Maria J. Sanz, Jan Siemens, Timo Vesala, Caroline Vincke, Eiko Nemitz, Sophie Zechmeister-Boltenstern, Klaus Butterbach-Bahl, Ute M. Skiba, Mark A. Sutton. Supplementary material to "Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part II: Untangling climatic, edaphic, management and nitrogen deposition effects on carbon sequestration potentials". . 2019; ():1.

Chicago/Turabian Style

Chris R. Flechard; Marcel Van Oijen; David R. Cameron; Wim De Vries; Andreas Ibrom; Nina Buchmann; Nancy B. Dise; Ivan A. Janssens; Johan Neirynck; Leonardo Montagnani; Andrej Varlagin; Denis Loustau; Arnaud Legout; Klaudia Ziemblińska; Marc Aubinet; Mika Aurela; Bogdan H. Chojnicki; Julia Drewer; Werner Eugster; André-Jean Francez; Radosław Juszczak; Barbara Kitzler; Werner L. Kutsch; Annalea Lohila; Bernard Longdoz; Giorgio Matteucci; Virginie Moreaux; Albrecht Neftel; Janusz Olejnik; Maria J. Sanz; Jan Siemens; Timo Vesala; Caroline Vincke; Eiko Nemitz; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Ute M. Skiba; Mark A. Sutton. 2019. "Supplementary material to "Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part II: Untangling climatic, edaphic, management and nitrogen deposition effects on carbon sequestration potentials"." , no. : 1.

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Published: 11 September 2019
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The effects of atmospheric nitrogen deposition (Ndep) on carbon (C) sequestration in forests have often been assessed by relating differences in productivity to spatial variations of Ndep across a large geographic domain. These correlations generally suffer from covariation of other confounding variables related to climate and other growth-limiting factors, as well as large uncertainties in total (dry + wet) reactive nitrogen (Nr) deposition. We propose a methodology for untangling the effects of Ndep from those of meteorological variables, soil water retention capacity and stand age, using a mechanistic forest growth model in combination with eddy covariance CO2 exchange fluxes from a Europe-wide network of forest flux towers. Total Nr deposition rates were estimated from local measurements as far as possible. The forest data were compared with data from natural or semi-natural, non-woody vegetation sites. The carbon sequestration response of forests to nitrogen deposition (dC / dN) was estimated after accounting for the effects of the co-correlates by means of a meta-modelling standardization procedure, which resulted in a reduction by a factor of about 2 of the uncorrected, apparent dC / dN value. This model-enhanced analysis of the C and Ndep flux observations at the scale of the European network suggests a mean overall dC / dN response of forest lifetime C sequestration to Ndep of the order of 40–50 g (C) g−1 (N), which is slightly larger but not significantly different from the range of estimates published in the most recent reviews. Importantly, patterns of gross primary and net ecosystem productivity versus Ndep were non-linear, with no further responses at high Ndep levels (Ndep > 2.5–3 g (N) m−2 yr−1) partly due to large ecosystem N losses by leaching and gaseous emissions. The reduced increase in productivity per unit N deposited at high Ndep levels implies that the forecast increased Nr emissions and increased Ndep levels in large areas of Asia may not positively impact the continent's forest CO2 sink. The large level of unexplained variability in observed carbon sequestration efficiency (CSE) across sites further adds to the uncertainty in the dC / dN response.

ACS Style

Chris R. Flechard; Marcel Van Oijen; David R. Cameron; Wim De Vries; Andreas Ibrom; Nina Buchmann; Nancy B. Dise; Ivan A. Janssens; Johan Neirynck; Leonardo Montagnani; Andrej Varlagin; Denis Loustau; Arnaud Legout; Klaudia Ziemblińska; Marc Aubinet; Mika Aurela; Bogdan H. Chojnicki; Julia Drewer; Werner Eugster; André-Jean Francez; Radosław Juszczak; Barbara Kitzler; Werner L. Kutsch; Annalea Lohila; Bernard Longdoz; Giorgio Matteucci; Virginie Moreaux; Albrecht Neftel; Janusz Olejnik; Maria J. Sanz; Jan Siemens; Timo Vesala; Caroline Vincke; Eiko Nemitz; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Ute M. Skiba; Mark A. Sutton. Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part II: Untangling climatic, edaphic, management and nitrogen deposition effects on carbon sequestration potentials. 2019, 2019, 1 -38.

AMA Style

Chris R. Flechard, Marcel Van Oijen, David R. Cameron, Wim De Vries, Andreas Ibrom, Nina Buchmann, Nancy B. Dise, Ivan A. Janssens, Johan Neirynck, Leonardo Montagnani, Andrej Varlagin, Denis Loustau, Arnaud Legout, Klaudia Ziemblińska, Marc Aubinet, Mika Aurela, Bogdan H. Chojnicki, Julia Drewer, Werner Eugster, André-Jean Francez, Radosław Juszczak, Barbara Kitzler, Werner L. Kutsch, Annalea Lohila, Bernard Longdoz, Giorgio Matteucci, Virginie Moreaux, Albrecht Neftel, Janusz Olejnik, Maria J. Sanz, Jan Siemens, Timo Vesala, Caroline Vincke, Eiko Nemitz, Sophie Zechmeister-Boltenstern, Klaus Butterbach-Bahl, Ute M. Skiba, Mark A. Sutton. Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part II: Untangling climatic, edaphic, management and nitrogen deposition effects on carbon sequestration potentials. . 2019; 2019 ():1-38.

Chicago/Turabian Style

Chris R. Flechard; Marcel Van Oijen; David R. Cameron; Wim De Vries; Andreas Ibrom; Nina Buchmann; Nancy B. Dise; Ivan A. Janssens; Johan Neirynck; Leonardo Montagnani; Andrej Varlagin; Denis Loustau; Arnaud Legout; Klaudia Ziemblińska; Marc Aubinet; Mika Aurela; Bogdan H. Chojnicki; Julia Drewer; Werner Eugster; André-Jean Francez; Radosław Juszczak; Barbara Kitzler; Werner L. Kutsch; Annalea Lohila; Bernard Longdoz; Giorgio Matteucci; Virginie Moreaux; Albrecht Neftel; Janusz Olejnik; Maria J. Sanz; Jan Siemens; Timo Vesala; Caroline Vincke; Eiko Nemitz; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Ute M. Skiba; Mark A. Sutton. 2019. "Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part II: Untangling climatic, edaphic, management and nitrogen deposition effects on carbon sequestration potentials." 2019, no. : 1-38.

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Published: 11 September 2019
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The impact of atmospheric reactive nitrogen (Nr) deposition on carbon (C) sequestration in soils and biomass of unfertilised, natural, semi-natural and forest ecosystems has been much debated. Many previous results of this dC / dN response were based on changes in carbon stocks from periodical soil and ecosystem inventories, associated with estimates of Nr deposition obtained from large-scale chemical transport models. This study and a companion paper (Flechard et al., 2019) strive to reduce uncertainties of N effects on C sequestration by linking multi-annual gross and net ecosystem productivity estimates from 40 eddy covariance flux towers across Europe to local measurement-based estimates of dry and wet Nr deposition from a dedicated collocated monitoring network. To identify possible ecological drivers and processes affecting the interplay between C and Nr inputs and losses, these data were also combined with in situ flux measurements of NO, N2O and CH4 fluxes, soil NO3− leaching sampling, as well as results of soil incubation experiments for N and greenhouse gas (GHG) emissions, surveys of available data from online databases and from the literature, together with forest ecosystem (BASFOR) modelling. Multi-year averages of net ecosystem productivity (NEP) in forests ranged from −70 to 826 g (C) m−2 yr−1 at total wet + dry inorganic Nr deposition rates (Ndep) of 0.3 to 4.3 g (N) m−2 yr−1; and from −4 to 361 g (C) m−2 yr−1 at Ndep rates of 0.1 to 3.1 g (N) m−2 yr−1 in short semi-natural vegetation (moorlands, wetlands and unfertilised extensively managed grasslands). The GHG budgets of the forests were strongly dominated by CO2 exchange, while CH4 and N2O exchange comprised a larger proportion of the GHG balance in short semi-natural vegetation. Nitrogen losses in the form of NO, N2O and especially NO3− were of the order of 10–20 % of Ndep at sites with Ndep 3 g (N) m−2 yr−1, indicating that perhaps one third of the sites were in a state of early to advanced N saturation. Net ecosystem productivity increased with Nr deposition up to 2–2.5 g (N) m−2 yr−1, with large scatter associated with a wide range in carbon sequestration efficiency (CSE, defined as the NEP / GPP ratio). At elevated Ndep levels (> 2.5 g (N) m−2 yr−1), where inorganic Nr losses were also increasingly large, NEP levelled off and then decreased. The apparent increase in NEP at low to intermediate Ndep levels was partly the result of geographical cross-correlations between Ndep and climate, indicating that the actual mean dC / dN response at individual sites was significantly lower than would be suggested by a simple, straightforward regression of NEP vs. Ndep.

ACS Style

Chris R. Flechard; Andreas Ibrom; Ute M. Skiba; Wim De Vries; Marcel Van Oijen; David R. Cameron; Nancy B. Dise; Janne F. J. Korhonen; Nina Buchmann; Arnaud Legout; David Simpson; Maria J. Sanz; Marc Aubinet; Denis Loustau; Leonardo Montagnani; Johan Neirynck; Ivan A. Janssens; Mari Pihlatie; Ralf Kiese; Jan Siemens; André-Jean Francez; Jürgen Augustin; Andrej Varlagin; Janusz Olejnik; Radosław Juszczak; Mika Aurela; Bogdan H. Chojnicki; Ulrich Dämmgen; Vesna Djuricic; Julia Drewer; Werner Eugster; Yannick Fauvel; David Fowler; Arnoud Frumau; André Granier; Patrick Gross; Yannick Hamon; Carole Helfter; Arjan Hensen; László Horváth; Barbara Kitzler; Bart Kruijt; Werner L. Kutsch; Raquel Lobo-Do-Vale; Annalea Lohila; Bernard Longdoz; Michal V. Marek; Giorgio Matteucci; Marta Mitosinkova; Virginie Moreaux; Albrecht Neftel; Jean-Marc Ourcival; Kim Pilegaard; Gabriel Pita; Francisco Sanz; Jan K. Schjoerring; Maria-Teresa Sebastià; Y. Sim Tang; Hilde Uggerud; Marek Urbaniak; Netty Van Dijk; Timo Vesala; Sonja Vidic; Caroline Vincke; Tamás Weidinger; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Eiko Nemitz; Mark A. Sutton. Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part I: Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling. 2019, 2019, 1 -50.

AMA Style

Chris R. Flechard, Andreas Ibrom, Ute M. Skiba, Wim De Vries, Marcel Van Oijen, David R. Cameron, Nancy B. Dise, Janne F. J. Korhonen, Nina Buchmann, Arnaud Legout, David Simpson, Maria J. Sanz, Marc Aubinet, Denis Loustau, Leonardo Montagnani, Johan Neirynck, Ivan A. Janssens, Mari Pihlatie, Ralf Kiese, Jan Siemens, André-Jean Francez, Jürgen Augustin, Andrej Varlagin, Janusz Olejnik, Radosław Juszczak, Mika Aurela, Bogdan H. Chojnicki, Ulrich Dämmgen, Vesna Djuricic, Julia Drewer, Werner Eugster, Yannick Fauvel, David Fowler, Arnoud Frumau, André Granier, Patrick Gross, Yannick Hamon, Carole Helfter, Arjan Hensen, László Horváth, Barbara Kitzler, Bart Kruijt, Werner L. Kutsch, Raquel Lobo-Do-Vale, Annalea Lohila, Bernard Longdoz, Michal V. Marek, Giorgio Matteucci, Marta Mitosinkova, Virginie Moreaux, Albrecht Neftel, Jean-Marc Ourcival, Kim Pilegaard, Gabriel Pita, Francisco Sanz, Jan K. Schjoerring, Maria-Teresa Sebastià, Y. Sim Tang, Hilde Uggerud, Marek Urbaniak, Netty Van Dijk, Timo Vesala, Sonja Vidic, Caroline Vincke, Tamás Weidinger, Sophie Zechmeister-Boltenstern, Klaus Butterbach-Bahl, Eiko Nemitz, Mark A. Sutton. Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part I: Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling. . 2019; 2019 ():1-50.

Chicago/Turabian Style

Chris R. Flechard; Andreas Ibrom; Ute M. Skiba; Wim De Vries; Marcel Van Oijen; David R. Cameron; Nancy B. Dise; Janne F. J. Korhonen; Nina Buchmann; Arnaud Legout; David Simpson; Maria J. Sanz; Marc Aubinet; Denis Loustau; Leonardo Montagnani; Johan Neirynck; Ivan A. Janssens; Mari Pihlatie; Ralf Kiese; Jan Siemens; André-Jean Francez; Jürgen Augustin; Andrej Varlagin; Janusz Olejnik; Radosław Juszczak; Mika Aurela; Bogdan H. Chojnicki; Ulrich Dämmgen; Vesna Djuricic; Julia Drewer; Werner Eugster; Yannick Fauvel; David Fowler; Arnoud Frumau; André Granier; Patrick Gross; Yannick Hamon; Carole Helfter; Arjan Hensen; László Horváth; Barbara Kitzler; Bart Kruijt; Werner L. Kutsch; Raquel Lobo-Do-Vale; Annalea Lohila; Bernard Longdoz; Michal V. Marek; Giorgio Matteucci; Marta Mitosinkova; Virginie Moreaux; Albrecht Neftel; Jean-Marc Ourcival; Kim Pilegaard; Gabriel Pita; Francisco Sanz; Jan K. Schjoerring; Maria-Teresa Sebastià; Y. Sim Tang; Hilde Uggerud; Marek Urbaniak; Netty Van Dijk; Timo Vesala; Sonja Vidic; Caroline Vincke; Tamás Weidinger; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Eiko Nemitz; Mark A. Sutton. 2019. "Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part I: Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling." 2019, no. : 1-50.

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Published: 11 September 2019
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ACS Style

Chris R. Flechard; Andreas Ibrom; Ute M. Skiba; Wim De Vries; Marcel Van Oijen; David R. Cameron; Nancy B. Dise; Janne F. J. Korhonen; Nina Buchmann; Arnaud Legout; David Simpson; Maria J. Sanz; Marc Aubinet; Denis Loustau; Leonardo Montagnani; Johan Neirynck; Ivan A. Janssens; Mari Pihlatie; Ralf Kiese; Jan Siemens; André-Jean Francez; Jürgen Augustin; Andrej Varlagin; Janusz Olejnik; Radosław Juszczak; Mika Aurela; Bogdan H. Chojnicki; Ulrich Dämmgen; Vesna Djuricic; Julia Drewer; Werner Eugster; Yannick Fauvel; David Fowler; Arnoud Frumau; André Granier; Patrick Gross; Yannick Hamon; Carole Helfter; Arjan Hensen; László Horváth; Barbara Kitzler; Bart Kruijt; Werner L. Kutsch; Raquel Lobo-Do-Vale; Annalea Lohila; Bernard Longdoz; Michal V. Marek; Giorgio Matteucci; Marta Mitosinkova; Virginie Moreaux; Albrecht Neftel; Jean-Marc Ourcival; Kim Pilegaard; Gabriel Pita; Francisco Sanz; Jan K. Schjoerring; Maria-Teresa Sebastià; Y. Sim Tang; Hilde Uggerud; Marek Urbaniak; Netty Van Dijk; Timo Vesala; Sonja Vidic; Caroline Vincke; Tamás Weidinger; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Eiko Nemitz; Mark A. Sutton. Supplementary material to "Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part I: Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling". 2019, 1 .

AMA Style

Chris R. Flechard, Andreas Ibrom, Ute M. Skiba, Wim De Vries, Marcel Van Oijen, David R. Cameron, Nancy B. Dise, Janne F. J. Korhonen, Nina Buchmann, Arnaud Legout, David Simpson, Maria J. Sanz, Marc Aubinet, Denis Loustau, Leonardo Montagnani, Johan Neirynck, Ivan A. Janssens, Mari Pihlatie, Ralf Kiese, Jan Siemens, André-Jean Francez, Jürgen Augustin, Andrej Varlagin, Janusz Olejnik, Radosław Juszczak, Mika Aurela, Bogdan H. Chojnicki, Ulrich Dämmgen, Vesna Djuricic, Julia Drewer, Werner Eugster, Yannick Fauvel, David Fowler, Arnoud Frumau, André Granier, Patrick Gross, Yannick Hamon, Carole Helfter, Arjan Hensen, László Horváth, Barbara Kitzler, Bart Kruijt, Werner L. Kutsch, Raquel Lobo-Do-Vale, Annalea Lohila, Bernard Longdoz, Michal V. Marek, Giorgio Matteucci, Marta Mitosinkova, Virginie Moreaux, Albrecht Neftel, Jean-Marc Ourcival, Kim Pilegaard, Gabriel Pita, Francisco Sanz, Jan K. Schjoerring, Maria-Teresa Sebastià, Y. Sim Tang, Hilde Uggerud, Marek Urbaniak, Netty Van Dijk, Timo Vesala, Sonja Vidic, Caroline Vincke, Tamás Weidinger, Sophie Zechmeister-Boltenstern, Klaus Butterbach-Bahl, Eiko Nemitz, Mark A. Sutton. Supplementary material to "Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part I: Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling". . 2019; ():1.

Chicago/Turabian Style

Chris R. Flechard; Andreas Ibrom; Ute M. Skiba; Wim De Vries; Marcel Van Oijen; David R. Cameron; Nancy B. Dise; Janne F. J. Korhonen; Nina Buchmann; Arnaud Legout; David Simpson; Maria J. Sanz; Marc Aubinet; Denis Loustau; Leonardo Montagnani; Johan Neirynck; Ivan A. Janssens; Mari Pihlatie; Ralf Kiese; Jan Siemens; André-Jean Francez; Jürgen Augustin; Andrej Varlagin; Janusz Olejnik; Radosław Juszczak; Mika Aurela; Bogdan H. Chojnicki; Ulrich Dämmgen; Vesna Djuricic; Julia Drewer; Werner Eugster; Yannick Fauvel; David Fowler; Arnoud Frumau; André Granier; Patrick Gross; Yannick Hamon; Carole Helfter; Arjan Hensen; László Horváth; Barbara Kitzler; Bart Kruijt; Werner L. Kutsch; Raquel Lobo-Do-Vale; Annalea Lohila; Bernard Longdoz; Michal V. Marek; Giorgio Matteucci; Marta Mitosinkova; Virginie Moreaux; Albrecht Neftel; Jean-Marc Ourcival; Kim Pilegaard; Gabriel Pita; Francisco Sanz; Jan K. Schjoerring; Maria-Teresa Sebastià; Y. Sim Tang; Hilde Uggerud; Marek Urbaniak; Netty Van Dijk; Timo Vesala; Sonja Vidic; Caroline Vincke; Tamás Weidinger; Sophie Zechmeister-Boltenstern; Klaus Butterbach-Bahl; Eiko Nemitz; Mark A. Sutton. 2019. "Supplementary material to "Carbon / nitrogen interactions in European forests and semi-natural vegetation. Part I: Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling"." , no. : 1.

Journal article
Published: 01 July 2018 in Field Crops Research
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During the past few years, several studies have compared the performance of crop simulation models to assess the uncertainties in model-based climate change impact assessments and other modelling studies. Many of these studies have concentrated on cereal crops, while fewer model comparisons have been conducted for grasses. We compared the predictions for timothy grass (Phleum pratense L.) yields for first and second cuts along with the dynamics of above-ground biomass for the grass simulation models BASGRA and CATIMO, and the soil-crop model STICS. The models were calibrated and evaluated using field data from seven sites across Northern Europe and Canada with different climates, soil conditions and management practices. Altogether the models were compared using data on timothy grass from 33 combinations of sites, cultivars and management regimes. Model performances with two calibration approaches, cultivar-specific and generic calibrations, were compared. All the models studied estimated the dynamics of above-ground biomass and the leaf area index satisfactorily, but tended to underestimate the first cut yield. Cultivar-specific calibration resulted in more accurate first cut yield predictions than the generic calibration achieving root mean square errors approximately one third lower for the cultivar-specific calibration. For the second cut, the difference between the calibration methods was small. The results indicate that detailed soil process descriptions improved the overall model performance and the model responses to management, such as nitrogen applications. The results also suggest that taking the genetic variability into account between cultivars of timothy grass also improves the yield estimates. Calibrations using both spring and summer growth data simultaneously revealed that processes determining the growth in these two periods require further attention in model development.

ACS Style

Panu Korhonen; Taru Palosuo; Tomas Persson; Mats Höglind; Guillaume Jégo; Marcel Van Oijen; Anne-Maj Gustavsson; Gilles Bélanger; Perttu Virkajarvi. Modelling grass yields in northern climates – a comparison of three growth models for timothy. Field Crops Research 2018, 224, 37 -47.

AMA Style

Panu Korhonen, Taru Palosuo, Tomas Persson, Mats Höglind, Guillaume Jégo, Marcel Van Oijen, Anne-Maj Gustavsson, Gilles Bélanger, Perttu Virkajarvi. Modelling grass yields in northern climates – a comparison of three growth models for timothy. Field Crops Research. 2018; 224 ():37-47.

Chicago/Turabian Style

Panu Korhonen; Taru Palosuo; Tomas Persson; Mats Höglind; Guillaume Jégo; Marcel Van Oijen; Anne-Maj Gustavsson; Gilles Bélanger; Perttu Virkajarvi. 2018. "Modelling grass yields in northern climates – a comparison of three growth models for timothy." Field Crops Research 224, no. : 37-47.

Journal article
Published: 27 April 2018 in Geoscientific Model Development
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Atmospheric chemistry transport models (ACTMs) are widely used to underpin policy decisions associated with the impact of potential changes in emissions on future pollutant concentrations and deposition. It is therefore essential to have a quantitative understanding of the uncertainty in model output arising from uncertainties in the input pollutant emissions. ACTMs incorporate complex and non-linear descriptions of chemical and physical processes which means that interactions and non-linearities in input–output relationships may not be revealed through the local one-at-a-time sensitivity analysis typically used. The aim of this work is to demonstrate a global sensitivity and uncertainty analysis approach for an ACTM, using as an example the FRAME model, which is extensively employed in the UK to generate source–receptor matrices for the UK Integrated Assessment Model and to estimate critical load exceedances. An optimised Latin hypercube sampling design was used to construct model runs within ±40 % variation range for the UK emissions of SO2, NOx, and NH3, from which regression coefficients for each input–output combination and each model grid ( > 10 000 across the UK) were calculated. Surface concentrations of SO2, NOx, and NH3 (and of deposition of S and N) were found to be predominantly sensitive to the emissions of the respective pollutant, while sensitivities of secondary species such as HNO3 and particulate SO42−, NO3−, and NH4+ to pollutant emissions were more complex and geographically variable. The uncertainties in model output variables were propagated from the uncertainty ranges reported by the UK National Atmospheric Emissions Inventory for the emissions of SO2, NOx, and NH3 (±4, ±10, and ±20 % respectively). The uncertainties in the surface concentrations of NH3 and NOx and the depositions of NHx and NOy were dominated by the uncertainties in emissions of NH3, and NOx respectively, whilst concentrations of SO2 and deposition of SOy were affected by the uncertainties in both SO2 and NH3 emissions. Likewise, the relative uncertainties in the modelled surface concentrations of each of the secondary pollutant variables (NH4+, NO3−, SO42−, and HNO3) were due to uncertainties in at least two input variables. In all cases the spatial distribution of relative uncertainty was found to be geographically heterogeneous. The global methods used here can be applied to conduct sensitivity and uncertainty analyses of other ACTMs.

ACS Style

Ksenia Aleksankina; Mathew R. Heal; Anthony J. Dore; Marcel Van Oijen; Stefan Reis. Global sensitivity and uncertainty analysis of an atmospheric chemistry transport model: the FRAME model (version 9.15.0) as a case study. Geoscientific Model Development 2018, 11, 1653 -1664.

AMA Style

Ksenia Aleksankina, Mathew R. Heal, Anthony J. Dore, Marcel Van Oijen, Stefan Reis. Global sensitivity and uncertainty analysis of an atmospheric chemistry transport model: the FRAME model (version 9.15.0) as a case study. Geoscientific Model Development. 2018; 11 (4):1653-1664.

Chicago/Turabian Style

Ksenia Aleksankina; Mathew R. Heal; Anthony J. Dore; Marcel Van Oijen; Stefan Reis. 2018. "Global sensitivity and uncertainty analysis of an atmospheric chemistry transport model: the FRAME model (version 9.15.0) as a case study." Geoscientific Model Development 11, no. 4: 1653-1664.

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Published: 20 April 2018
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David Cameron; Christophe Flechard; Marcel Van Oijen. Supplementary material to "Calibrating a process-based forest model with a rich observational dataset at 22 European forest sites". 2018, 1 .

AMA Style

David Cameron, Christophe Flechard, Marcel Van Oijen. Supplementary material to "Calibrating a process-based forest model with a rich observational dataset at 22 European forest sites". . 2018; ():1.

Chicago/Turabian Style

David Cameron; Christophe Flechard; Marcel Van Oijen. 2018. "Supplementary material to "Calibrating a process-based forest model with a rich observational dataset at 22 European forest sites"." , no. : 1.

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Published: 20 April 2018 in Biogeosciences Discussions
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In recent years model-data interaction has improved through use of probabilistic techniques to inform and reduce the uncertainty of model parameters, while also taking into account observational uncertainty. This study builds on previous work, through access to a richer representation of the plant-soil ecosystem at multiple European forest sites, than was previously available. Given this rich dataset, we asked which observational datasets were most effective in reducing uncertainty in model predictions and model-data differences. Also, since there is a lack of consensus about whether it is more beneficial to calibrate forest sites separately or together we revisited this question with a particular emphasis on which is most effective in reducing model-data differences and uncertainty. We performed single dataset Bayesian calibrations (BC) and compared the results with a calibration with all the observations included. We also compared calibrations where each pine forest site was calibrated separately with a calibration where all the pine sites were calibrated together. While measurements of plant and soil carbon stocks were more sparse, their inclusion in the BC were more important for reducing model-data differences and uncertainty in the above and belowground carbon pools than the greater numbers of carbon and water flux data. Our results suggest that use of calibration data representing just a few aspects of the ecosystem could be problematic, since improved model-data fits for the parts of the system represented by the data could be at the expense of other part of the system, where the model-data fit worsened. The single dataset calibrations helped to diagnose where there may be inconsistencies between different datasets or between the model and data or both. These inconsistencies hampered the reduction in model-data differences in the calibration with all the observations present. As expected, we found a strong relationship between the quantity of data included in the calibration and the uncertainty reduction after BC, finding the largest reduction in uncertainty when all the observations were included. For some ecosystem variables uncertainty reduced after calibration but model-data differences increased. This would suggest that there were deficiencies in the model or systematic errors in the data or both. These results advocate the use of calibration datasets which represent the rich diversity of the ecosystem under investigation but where model discrepancies and data systematic errors are explicitly represented in the BC. While separate calibrations at each forest site generally reduced model-data differences more than calibrating at all the sites together, parts of the ecosystem that were sparsely observed benefited more from the multi-site calibration. Multi-site calibration led to larger and more consistent reductions in uncertainty than separate calibrations at each site, especially for ecosystem variables with fewer observations. These results support the use of Bayesian hierarchical calibration which allows variation in model parameters between different sites while allowing information to be shared across sites for sparsely observed ecosystem variables.

ACS Style

David Cameron; Christophe Flechard; Marcel Van Oijen. Calibrating a process-based forest model with a rich observational dataset at 22 European forest sites. Biogeosciences Discussions 2018, 2018, 1 -42.

AMA Style

David Cameron, Christophe Flechard, Marcel Van Oijen. Calibrating a process-based forest model with a rich observational dataset at 22 European forest sites. Biogeosciences Discussions. 2018; 2018 ():1-42.

Chicago/Turabian Style

David Cameron; Christophe Flechard; Marcel Van Oijen. 2018. "Calibrating a process-based forest model with a rich observational dataset at 22 European forest sites." Biogeosciences Discussions 2018, no. : 1-42.

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Published: 19 March 2018
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Marcel Van Oijen. Fer et al.: "Linking big models to big data: efficient ecosystem model calibration through Bayesian model emulation". 2018, 1 .

AMA Style

Marcel Van Oijen. Fer et al.: "Linking big models to big data: efficient ecosystem model calibration through Bayesian model emulation". . 2018; ():1.

Chicago/Turabian Style

Marcel Van Oijen. 2018. "Fer et al.: "Linking big models to big data: efficient ecosystem model calibration through Bayesian model emulation"." , no. : 1.

Journal article
Published: 14 March 2018 in Biogeosciences
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We present a method for estimating land-use change using a Bayesian data assimilation approach. The approach provides a general framework for combining multiple disparate data sources with a simple model. This allows us to constrain estimates of gross land-use change with reliable national-scale census data, whilst retaining the detailed information available from several other sources. Eight different data sources, with three different data structures, were combined in our posterior estimate of land use and land-use change, and other data sources could easily be added in future. The tendency for observations to underestimate gross land-use change is accounted for by allowing for a skewed distribution in the likelihood function. The data structure produced has high temporal and spatial resolution, and is appropriate for dynamic process-based modelling. Uncertainty is propagated appropriately into the output, so we have a full posterior distribution of output and parameters. The data are available in the widely used netCDF file format from http://eidc.ceh.ac.uk/.

ACS Style

Peter Levy; Marcel Van Oijen; Gwen Buys; Sam Tomlinson. Estimation of gross land-use change and its uncertainty using a Bayesian data assimilation approach. Biogeosciences 2018, 15, 1497 -1513.

AMA Style

Peter Levy, Marcel Van Oijen, Gwen Buys, Sam Tomlinson. Estimation of gross land-use change and its uncertainty using a Bayesian data assimilation approach. Biogeosciences. 2018; 15 (5):1497-1513.

Chicago/Turabian Style

Peter Levy; Marcel Van Oijen; Gwen Buys; Sam Tomlinson. 2018. "Estimation of gross land-use change and its uncertainty using a Bayesian data assimilation approach." Biogeosciences 15, no. 5: 1497-1513.

Journal article
Published: 01 March 2018 in Ecological Modelling
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ACS Style

Maurizio Bagnara; Marcel Van Oijen; David Cameron; Damiano Gianelle; Federico Magnani; Matteo Sottocornola. Bayesian calibration of simple forest models with multiplicative mathematical structure: A case study with two Light Use Efficiency models in an alpine forest. Ecological Modelling 2018, 371, 90 -100.

AMA Style

Maurizio Bagnara, Marcel Van Oijen, David Cameron, Damiano Gianelle, Federico Magnani, Matteo Sottocornola. Bayesian calibration of simple forest models with multiplicative mathematical structure: A case study with two Light Use Efficiency models in an alpine forest. Ecological Modelling. 2018; 371 ():90-100.

Chicago/Turabian Style

Maurizio Bagnara; Marcel Van Oijen; David Cameron; Damiano Gianelle; Federico Magnani; Matteo Sottocornola. 2018. "Bayesian calibration of simple forest models with multiplicative mathematical structure: A case study with two Light Use Efficiency models in an alpine forest." Ecological Modelling 371, no. : 90-100.

Review
Published: 02 February 2018 in Agronomy
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There is increasing evidence that the impact of climate change on the productivity of grasslands will at least partly depend on their biodiversity. A high level of biodiversity may confer stability to grassland ecosystems against environmental change, but there are also direct effects of biodiversity on the quantity and quality of grassland productivity. To explain the manifold interactions, and to predict future climatic responses, models may be used. However, models designed for studying the interaction between biodiversity and productivity tend to be structurally different from models for studying the effects of climatic impacts. Here we review the literature on the impacts of climate change on biodiversity and productivity of grasslands. We first discuss the availability of data for model development. Then we analyse strengths and weaknesses of three types of model: ecological, process-based and integrated. We discuss the merits of this model diversity and the scope for merging different model types.

ACS Style

Marcel Van Oijen; Gianni Bellocchi; Mats Höglind. Effects of Climate Change on Grassland Biodiversity and Productivity: The Need for a Diversity of Models. Agronomy 2018, 8, 14 .

AMA Style

Marcel Van Oijen, Gianni Bellocchi, Mats Höglind. Effects of Climate Change on Grassland Biodiversity and Productivity: The Need for a Diversity of Models. Agronomy. 2018; 8 (2):14.

Chicago/Turabian Style

Marcel Van Oijen; Gianni Bellocchi; Mats Höglind. 2018. "Effects of Climate Change on Grassland Biodiversity and Productivity: The Need for a Diversity of Models." Agronomy 8, no. 2: 14.