G. Abramowitz, Towards a benchmark for land surface models, Geophys. Res. Lett, vol.32, p.22702, 2005.

G. Abramowitz and A. Pitman, Systematic bias in land surface models, J. Hydrometeorol, vol.8, pp.989-1001, 2007.

G. Abramowitz and H. Gupta, Toward a model space and model independence metric, Geophys. Res. Lett, vol.35, p.5705, 2008.

M. Aubinet, A. Grelle, A. Ibrom, U. Rannik, J. Moncrieff et al., Estimates of the annual net carbon and water exchange of forests: the EUROFLUX methodology, Adv. Ecol. Res, vol.30, pp.113-175, 2000.

D. Baldocchi, E. Falge, L. H. Gu, R. Olson, D. Hollinger et al., FLUXNET: A new tool to study the temporal and spatial variability of ecosystem-scale carbon dioxide, water vapor, and energy flux densities, B. Am. Meteor. Soc, vol.82, pp.2415-2434, 2001.

D. D. Baldocchi, C. Beer, M. Reichstein, P. Ciais, G. D. Farquhar et al., Assessing the eddy covariance technique for evaluating carbon dioxide exchange rates of ecosystems: past, present and future, Geophys. Res. Lett, vol.9, p.5401, 2003.

K. Beven and J. Freer, Equifinality, data assimilation, and uncertainty estimation in mechanistic modelling of complex environmental systems using the GLUE methodology, J. Hydrol, vol.249, pp.11-29, 2001.

G. B. Bonan, Land atmosphere CO 2 exchange simulated by a land-surface process model coupled to an atmospheric generalcirculation model, J. Geophys. Res.-Atmos, vol.100, pp.2817-2831, 1995.

G. B. Bonan, Forests and Climate Change: Forcings, Feedbacks, and the Climate Benefits of Forests, Science, vol.320, pp.1444-1449, 2008.

A. Bondeau, P. C. Smith, S. Zaehle, S. Schaphoff, W. Lucht et al., Modelling the role of agriculture for the 20th century global terrestrial carbon balance, Glob. Change Biol, vol.13, pp.679-706, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01757164

B. H. Braswell, W. J. Sacks, E. Linder, and D. S. Schimel, Estimating diurnal to annual ecosystem parameters by synthesis of a carbon flux model with eddy covariance net ecosystem exchange observations, Glob. Change Biol, vol.11, pp.335-355, 2005.

N. Carvalhais, M. Reichstein, S. , G. J. , C. Santos-pereira et al., Implications of Carbon Cycle Steady State Assumptions for Biogeochemical Modeling Performance and Inverse Parameter Retrieval, Global Biogeochem. Cy, vol.22, p.2007, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02668520

G. Churkina, J. Tenhunen, P. Thornton, E. M. Falge, J. A. Elbers et al., Analyzing the ecosystem carbon dynamics of four European coniferous forests using a biogeochemistry model, Ecosystems, vol.6, pp.68-184, 2003.

P. Courtier, J. Thépaut, and A. Hollingsworth, A strategy for operational implementation of 4D-VAR, using an incremental approach, Q. J. Roy. Meteor. Soc, vol.120, pp.1367-1387, 1994.

J. Demarty, F. Chevallier, A. D. Friend, N. Viovy, S. Piao et al., Assimilation of global MODIS leaf area index retrievals within a terrestrial biosphere model, Geophys. Res. Lett, vol.34, p.15402, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01863533

E. Falge, D. Baldocchi, and R. J. Olson, Gap Filling Strategies for Defensible Annual Sums of Net Ecosystem Exchange, Ag. For. Meteorol, vol.107, pp.43-69, 2001.

L. Feng, P. I. Palmer, H. Bösch, and S. Dance, Estimating surface CO 2 fluxes from space-borne CO 2 dry air mole fraction observations using an ensemble Kalman Filter, Atmos. Chem. Phys, vol.9, pp.2619-2633, 2009.

T. Foken and B. Wichura, Tools for quality assessment of surfacebased flux measurements, Ag. For. Meteorol, vol.78, pp.83-105, 1996.

J. A. Foley, I. C. Prentice, N. Ramunkutty, S. Levis, D. Pollard et al., The REFLEX project: comparing different algorithms and implementations for the inversion of a terrestrial ecosystem model against eddy covariance data, Global Biogeochem. Cy, vol.10, pp.603-628, 1996.

P. Friedlingstein, P. Cox, R. Betts, L. Bopp, W. Von-bloh et al., Climate-carbon cycle feedback analysis: Results from the (CMIP)-M-4 model intercomparison, vol.19, pp.3337-3353, 2006.

A. J. Gillespie, Rationale for a National Annual Forest Inventory Program, J. Forestry, vol.97, pp.16-20, 1999.

M. L. Goulden, J. W. Munger, S. Fan, B. C. Daube, and S. C. Wofsy, Measurements of carbon storage by long-term eddy correlation: Methods and a critical evaluation of accuracy, Global Change Biol, vol.2, pp.169-182, 1996.

J. H. Gove and D. Y. Hollinger, Application of a dual unscented Kalman filter for simultaneous state and parameter estimation in problems of surface-atmosphere exchange, J. Geophys. Res, vol.111, pp.8-15, 2006.

A. Grinsted, J. C. Moore, and S. Jevrejeva, Application of the cross wavelet transform and wavelet coherence to geophysical time series, Nonlin. Processes Geophys, vol.11, pp.561-566, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00302394

W. Hargrove, F. Hoffman, and B. Law, New analysis reveals representativeness of the AmeriFlux network, Eos Trans. AGU, vol.82, p.525, 2003.

V. Haverd, R. Leuning, D. W. Griffith, E. Van-gorsel, and M. Cuntz, The Lagrangian time scale for turbulent transport in forest canopies, determined from measured fluxes and concentrations and modelled source distributions, Bound.-Lay. Meteorol, vol.130, pp.209-228, 2009.

B. R. Helliker, J. A. Berry, A. K. Betts, P. S. Bakwin, K. J. Davis et al., Estimates of net CO2 flux by application of equilibrium boundary layer concepts to CO 2 and water vapor measurements from a tall tower, J. Geophys. Res.-Atmos, vol.109, p.20106, 2004.

D. Y. Hollinger and A. D. Richardson, Uncertainty in eddy covariance measurements and its application to physiological models, Tree Phys, vol.25, pp.873-885, 2005.

D. Hui, Y. Luo, G. Katul, A. Ibrom, P. G. Jarvis et al., Partitioning interannual variability in net ecosystem exchange between climatic variability and function changes, Synthesis Report, vol.23, pp.845-864, 1009.

M. Jung, M. Vetter, M. Herold, G. Churkina, M. Reichstein et al., Uncertainties of modeling gross primary productivity over Europe: A systematic study on the effects of using different drivers and terrestrial biosphere models, Global Biogeochem. Cy, vol.21, p.4021, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01788252

E. A. Kowalczyk, Y. P. Wang, R. M. Davies, J. L. Mcgregor, A. et al., The CSIRO Atmosphere Biosphere Land Exchange (CABLE) model for use in climate models and as an offline model, CSIRO Mar. Atmos. Res, vol.13, p.13, 2006.

G. Krinner, N. Viovy, N. De-noblet-ducoudre, J. Ogee, J. Polcher et al., A dynamic global vegetation model for studies of the coupled atmosphere-biosphere system, Global Biogeochem. Cy, vol.19, p.1015, 2005.
URL : https://hal.archives-ouvertes.fr/insu-00374606

G. Lasslop, M. Reichstein, J. Kattge, and D. Papale, Influences of observation errors in eddy flux data on inverse model parameter estimation, Biogeosciences, vol.5, pp.1311-1324, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00297973

X. Lee, On micrometeorological observations of surface-air exchange over tall vegetation, Agr. Forest Meteorol, vol.91, pp.39-49, 1998.

R. Leuning, H. A. Cleugh, S. J. Zegelin, and D. Hughes, Carbon and water fluxes over a temperate Eucalyptus forest and a tropical wet/dry savanna in Australia: measurements and comparison with MODIS remote sensing estimates, Ag. Forest Meteorol, vol.129, pp.151-173, 2005.

Y. Liu and H. V. Gupta, Uncertainty in hydrologic modeling: Toward an integrated data assimilation framework, Water. Resour

. Res, , vol.43, p.7401, 2007.

A. C. Lorenc, Atmospheric Data Assimilation, UK Meteorological Office, 1995.

Y. Q. Luo, L. H. Wu, J. A. Andrews, L. White, R. Matamala et al., Elevated CO 2 differentiates ecosystem carbon processes: Deconvolution analysis of Duke Forest FACE data, Ecol. Monogr, vol.71, pp.357-376, 2001.

Y. Q. Luo, L. W. White, J. G. Canadell, E. H. Delucia, D. S. Ellsworth et al., Sustainability of terrestrial carbon sequestration: A case study in Duke Forest with inversion approach, Global Biogeochem. Cy, vol.17, p.1021, 2003.

S. Luyssaert, I. Inglima, M. Jung, A. D. Richardson, M. Reichsteins et al., CO 2 balance of boreal, temperate, and tropical forests derived from a global database, MEA: Ecosystems and Human Well-Being, Millennium Ecosystem Assessment, vol.13, pp.2509-2537, 2005.
URL : https://hal.archives-ouvertes.fr/hal-01080954

B. E. Medlyn, A. P. Robinson, R. Clement, and R. E. Mcmurtrie, On the validation of models of forest CO 2 exchange using eddy covariance data: some perils and pitfalls, Tree Physiol, vol.25, pp.839-857, 2005.

D. G. Meyer and D. G. Butler, Statistical validation, Ecol. Mod, vol.68, pp.21-32, 1993.

A. M. Moffat, D. Papale, M. Reichstein, D. Y. Hollinger, A. D. Richardson et al., Comprehensive comparison of gap-filling techniques for eddy covariance net carbon fluxes, Ag. Forest Meteorol, vol.147, pp.209-232, 2007.

J. Moncrieff, Y. Malhi, and R. Leuning, The propagation of errors in long-term measurements of land-atmosphere fluxes of carbon and water, Global Change Biol, vol.2, pp.231-240, 1996.

P. Morales, M. T. Sykes, I. C. Prentice, P. Smith, B. Smith et al., Comparing and evaluating process-based ecosystem model predictions of carbon and water fluxes in major European forest biomes, Global Change Biol, vol.11, pp.2211-2233, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02681252

D. Papale and A. Valentini, A new assessment of European forests carbon exchanges by eddy fluxes and artificial neural network spatialization, Global Change Biol, vol.9, pp.525-535, 2003.

D. Papale, M. Reichstein, M. Aubinet, E. Canfora, C. Bernhofer et al., Towards a standardized processing of Net Ecosystem Exchange measured with eddy covariance technique: algorithms and uncertainty estimation, Biogeosciences, vol.3, pp.571-583, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02658214

S. A. Pietsch and H. Hasenauer, Evaluating the self-initialization procedure for large-scale ecosystem models, Glob. Ch. Biol, vol.12, pp.1658-1669, 2006.

I. C. Prentice, W. Cramer, S. P. Harrison, R. Leemans, R. A. Monserude et al., A global biome model based on plant physiology and dominance, soil properties and climate, J. Biogeogr, vol.19, pp.117-134, 1992.
URL : https://hal.archives-ouvertes.fr/hal-01788308

T. Quaife, P. Lewis, M. De-kauwe, M. Williams, B. E. Law et al., Assimilating Canopy Reflectance data into an Ecosystem Model with an Ensemble Kalman Filter, Remote Sens. Environ, vol.111, pp.1347-1364, 2008.

E. B. Rastetter, C. D. Canham, J. J. Cole, W. K. Lauenroth, M. R. Raupach et al., Model-data synthesis in terrestrial carbon observation: methods, data requirements and data uncertainty specifications, The collision of hypotheses: What can be learned from comparisons of ecosystem models?, in: Models in Ecosystem Science, vol.11, pp.378-397, 2003.

M. Reichstein, J. Tenhunen, O. Roupsard, J. Ourcival, S. Rambal et al., On the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm, Global Change Biol, vol.108, issue.D23, pp.1424-1439, 2003.
URL : https://hal.archives-ouvertes.fr/hal-02683280

A. D. Richardson and D. Y. Hollinger, Statistical modeling of ecosystem respiration using eddy covariance data: Maximum likelihood parameter estimation, and Monte Carlo simulation of model and parameter uncertainty, applied to three simple models, Ag. Forest Meteorol, vol.131, pp.191-208, 2005.

A. D. Richardson, D. Y. Hollinger, G. G. Burba, K. J. Davis, L. B. Flanagan et al., A multi-site analysis of random error in tower-based measurements of carbon and energy fluxes, Ag. Forest Meteorol, vol.136, pp.1-18, 2006.

A. D. Richardson, D. Y. Hollinger, J. D. Aber, S. V. Ollinger, and B. H. Braswell, Environmental variation is directly responsible for short-but not long-term variation in forest-atmosphere carbon exchange, Global Change Biol, vol.13, pp.788-803, 2007.

S. W. Running, R. R. Nemani, F. A. Heinsch, M. S. Zhao, M. Reeves et al., A continuous satellite-derived measure of global terrestrial primary production, Bioscience, vol.54, pp.547-560, 2004.

W. J. Sacks, D. S. Schimel, R. K. Monson, R. H. Braswell, D. Santaren et al., Optimizing a process-based ecosystem model with eddy-covariance flux measurements: A pine forest in southern France, Global Biogeochem. Cy, vol.12, p.2013, 2006.

K. E. Savage, E. A. Davidson, and A. D. Richardson, A conceptual and practical approach to data quality and analysis procedures for high frequency soil respiration measurements, Funct. Ecol, vol.22, pp.1000-1007, 2008.

P. J. Sellers, R. E. Dickinson, D. A. Randall, A. K. Betts, F. G. Hall et al., Modeling the exchanges of energy, water, and carbon between continents and the atmosphere, Science, vol.275, pp.502-509, 1997.

M. B. Siqueira, G. G. Katul, D. A. Sampson, P. C. Stoy, J. Juang et al., Multi-scale model intercomparisons of CO 2 and H 2 O exchange in a maturing southeastern US pine forest, Global Change Biol, vol.12, pp.1189-1207, 2006.

S. Sitch, B. Smith, I. C. Prentice, A. Arneth, A. Bondeau et al., Evaluation of ecosystem dynamics, plant geography and terrestrial carbon cycling in the LPJ dynamic global vegetation model, Global Change Biol, vol.9, pp.161-185, 2003.
URL : https://hal.archives-ouvertes.fr/hal-01757605

J. Tang and Q. Zhang, Equifinality in parameterization of processbased biogeochemistry models: A significant uncertainty source to the estimation of regional carbon dynamics, J. Geophys. Res, vol.113, p.4010, 2008.

K. E. Taylor, Summarizing multiple aspects of model performance in a single diagram, J. Geophys. Res, vol.106, pp.7183-7192, 2001.

P. E. Thornton, Description of a numerical simulation model for predicting the dynamics of energy, water, carbon, and nitrogen in a terrestrial ecosystem, p.280, 1998.

P. E. Thornton, B. E. Law, H. L. Gholz, K. L. Clark, E. Falge et al., Modeling and measuring the effects of disturbance history and climate on carbon and water budgets in evergreen needleleaf forests, Ag. Forest Meteorol, vol.113, pp.185-222, 2002.

C. M. Trudinger, M. R. Raupach, P. J. Rayner, J. Kattge, Q. Liu et al., OptIC project: An intercomparison of optimization techniques for parameter estimation in terrestrial biogeochemical models, J. Geophys. Res.-Biogeosciences, vol.112, p.2027, 2007.

A. I. Dijk, A. J. Dolman, and E. Schulze, Radiation, temperature, and leaf area explain ecosystem carbon fluxes in boreal and temperate European forests, Global Biogeochem. Cy, vol.19, p.2029, 2005.

H. Verbeeck, R. Samson, F. Verdonck, and R. Lemeur, Parameter sensitivity and uncertainty of the forest carbon flux model FORUG: a Monte Carlo analysis, Tree Phys, vol.26, pp.807-817, 2006.

S. B. Verma, Micrometeorological methods for measuring surface fluxes of mass and energy, Remote sensing reviews, vol.5, pp.99-115, 1990.

M. Vetter, G. Churkina, M. Jung, M. Reichstein, S. Zaehle et al., Analyzing the causes and spatial pattern of the European 2003 carbon flux anomaly using seven models, Biogeosciences, vol.5, pp.561-583, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00330703

J. A. Vrugt, C. G. Diks, H. V. Gupta, W. Bouten, and J. M. Verstraten, Improved treatment of uncertainty in hydrologic modeling: Combining the strengths of global optimization and data assimilation, Water. Resour. Res, vol.41, p.1017, 2005.

Y. P. Wang, R. Leuning, H. A. Cleugh, and P. A. Coppin, Parameter estimation in surface exchange models using nonlinear inversion: how many parameters can we estimate and which measurements are most useful?, Global Change Biol, vol.7, pp.495-510, 2001.

M. A. White, P. E. Thornton, S. W. Running, and R. R. Nemani, Parameterization and sensitivity analysis of the BIOME-BGC terrestrial ecosystem model: net primary production controls, Earth Interactions, vol.4, pp.1-85, 2000.

M. Williams, E. B. Rastetter, D. N. Fernandes, M. L. Goulden, S. C. Wofsy et al., Modelling the soil-plantatmosphere continuum in a Quercus-Acer stand at Harvard Forest: the regulation of stomatal conductance by light, nitrogen and soil/plant hydraulic properties, Plant Cell Environ, vol.19, pp.911-927, 1996.

M. Williams, P. Schwarz, B. E. Law, J. Irvine, and M. R. Kurpius, An improved analysis of forest carbon dynamics using data assimilation, Global Change Biol, vol.11, pp.89-105, 2005.

M. Williams, L. Street, M. T. Wijk, and G. R. Shaver, Identifying differences in carbon exchange among arctic ecosystem types, Ecosystems, vol.9, pp.288-304, 2006.

K. Wilson, A. Goldstein, E. Falge, M. Aubinet, D. Baldocchi et al., Energy balance closure at FLUXNET sites, Ag. Forest Meteorol, vol.113, pp.223-243, 2002.
URL : https://hal.archives-ouvertes.fr/hal-02681830

I. J. Wright, P. B. Reich, M. Westoby, D. D. Ackerly, Z. Baruch et al., The worldwide leaf economics spectrum, Nature, vol.428, pp.821-827, 2004.

T. Wutzler and M. Reichstein, Soils apart from equilibrium -consequences for soil carbon balance modelling, Biogeosciences, vol.4, pp.125-136, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00297602

T. Xu, L. White, D. Hui, and Y. Luo, Probabilistic inversion of a terrestrial ecosystem model: Analysis of uncertainty in parameter estimation and model prediction, Global Biogeochem. Cy, vol.20, p.2007, 2006.

F. Yang, K. Ichii, M. A. White, H. Hashimoto, A. R. Michaelis et al.,

R. R. , Developing a continental-scale measure of gross primary production by combining MODIS and AmeriFlux data through Support Vector Machine approach, Remote Sens. Environ, vol.110, pp.109-122, 2007.

S. Zaehle, S. Sitch, B. Smith, and F. Hatterman, Effects of parameter uncertainties on the modeling of terrestrial biosphere dynamics, Global Biogeochem. Cy, vol.19, p.3020, 2005.