E. S. Andrew, S. B. Verma, G. G. Burba, and T. J. Arkebauer, Gross primary production and ecosystem respiration of irrigated maize and irrigated soybean during a growing season, Agric. For. Meteorol, vol.131, pp.180-190, 2005.

J. M. Antle, S. M. Capalbo, E. T. Elliott, H. W. Hunt, S. Mooney et al., Research needs for understanding and predicting the behavior of managed ecosystems: lessons from the study of agroecosystems, Ecosystems, vol.4, pp.723-735, 2001.

M. Aubinet, C. Moureaux, B. Bodson, D. Dufranne, B. Heinesch et al., Carbon sequestration by a crop over a 4-year sugar beet/winter wheat/seed potato/winter wheat rotation cycle, Agric. For. Meteorol, vol.149, pp.407-418, 2009.

D. Baldocchi, E. Falge, L. 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, Bull. Am. Meteorol. Soc, vol.82, issue.11, pp.2415-2434, 2001.

D. Baldocchi, W. C. Bausch, and H. R. Duke, Assessing the eddy covariance technique for evaluating carbon dioxide exchange rates of ecosystems: past, present and future, Global Change Biol, vol.9, pp.1869-1875, 1996.

C. Beer, M. Reichstein, E. Tomelleri, P. Ciais, M. Jung et al., Terrestrial Gross Carbon Dioxide Uptake: Global Distribution and Covariation with Climate, Science, vol.329, issue.5993, pp.834-838, 2010.
URL : https://hal.archives-ouvertes.fr/cea-00819125

P. Béziat, E. Ceschia, and G. D. , Carbon balance of a three crop succession over two cropland sites in South West France, Agric. For. Meteorol, vol.149, pp.1628-1645, 2009.

N. Brisson, C. Gary, E. Justes, R. Roche, B. May et al.,

L. Li, STICS: a generic model for the simulation of crops and their water and nitrogen balances, Importance of crop varieties and management, vol.18, pp.311-346, 1998.

N. Brisson, F. Ruget, P. Gate, J. Lorgeou, B. Nicoullaud et al., STICS: A generic model for the simulation of crops and their water and nitrogen balance: II. Model validation for wheat and maize, Agronomie, vol.22, pp.69-93, 2002.

N. Carvalhais, M. Reichstein, J. Seixas, G. J. Collatz, J. S. Pereira et al., Implications of the carbon cycle steady state assumption for biogeochemical modeling performance and inverse parameter retrieval, Global Biogeochem. Cy, vol.22, p.2007, 2008.

F. Chevallier, N. Viovy, M. Reichstien, and P. Ciais, On the assessment of prior errors in Bayesian inversions of CO 2, Geophys. Res. Lett, vol.33, p.13802, 2006.

P. Ciais, M. Reichstein, N. Viovy, A. Granier, J. Ogée et al., Europe-wide reduction in primary productivity caused by the heat and, Nature, vol.437, pp.529-533, 2003.
URL : https://hal.archives-ouvertes.fr/insu-00373792

P. Ciais, M. Wattenbach, N. Vuichard, P. Simth, S. L. Piao et al., Synthesis Team: The European carbon balance, Global Change Biol, vol.2, pp.1409-1428, 2010.

G. J. Collatz, M. Ribas-carbo, and J. A. Berry, Coupled photosynthesis-stomatal conductance model for leaves of C 4 plants, Au. J. Plant Physiol, vol.19, pp.519-538, 1992.

D. Noblet-ducoudre, N. Gervois, S. Ciais, P. Viovy, N. Brisson et al., Coupling the soil-vegetationatmosphere-transfer scheme ORCHIDEE to the agronomy model STICS to study the influence of croplands on the European carbon and water budgets, Agronomie, vol.24, pp.397-407, 2004.

A. J. Dolman, J. Tnoilhan, P. Durand, C. Sarrat, A. Brut et al., The CarboEurope Regional Experiment Strategy, Bull. Am. Meteorol. Soc, vol.87, issue.10, pp.1367-1379, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00138642

P. Falloon and R. Betts, Climate impacts on European agriculture and water management in the context of adaptation and mitigation -The importance of an integrated approach, Sci. Total Environ, vol.408, pp.5667-5687, 2010.

P. D. Falloon, C. D. Jones, M. Ades, P. , and K. , Direct soil moisture controls of future global soil carbon changes; an important source of uncertainty, FAOSTAT: FAO Statistical Databases, 2003.

A. Freibauer, M. D. Rounsevell, P. Smith, and J. Verhagen, Carbon sequestration in the agricultural soils of Europe, Geoderma, vol.122, pp.1-23, 2004.

S. Gervois, P. Ciais, N. De-noblet-ducoudre, N. Brisson, N. Vuichard et al., Carbon and water balance of European croplands throughout the 20th century, Global Biogeochem. Cy, vol.22, p.2022, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00716545

S. Gervois, N. De-noblet-ducoudre, N. Viovy, P. Ciais, N. Brisson et al., Including croplands in a global biosphere model: Methodology and evaluation at specific sites, Earth Interaction, vol.8, pp.1-25, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02674408

J. Goudriaan, J. J. Groot, P. W. Uithol, J. Roy, B. Sangier et al., IPCC (Intergovernmental Panel on Climate Change), Climate change 2007: impacts, adaptation and vulnerability, Contribution of Working Group II to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, p.976, 2001.

R. D. Jackson, S. B. Idso, R. J. Reginato, and P. J. Pinter, Canopy temperature as a crop water stress indicator, Water Resour. Res, vol.17, pp.1133-1138, 1981.

I. A. Janssens, A. Freibauer, P. Ciais, P. Smith, G. J. Nabuurs et al., Europe's terrestrial biosphere absorbs 7 to 12 % of European anthropogenic CO 2 emissions, Science, vol.300, pp.1538-1542, 2003.

M. Jung, M. Reichstein, and A. Bondeau, Towards global empirical upscaling of FLUXNET eddy covariance observations: validation of a model tree ensemble approach using a biosphere model, Biogeosciences, vol.6, 2001.
URL : https://hal.archives-ouvertes.fr/hal-01788228

S. H. Kim, D. C. Gitz, R. C. Sicher, J. T. Baker, D. J. Timlin et al., Temperature dependence of growth, development, and photosynthesis in maize under elevated CO 2, Environ. Exp. Bot, vol.62, pp.224-236, 2007.

Z. Kothavala, M. A. Arain, T. A. Black, and D. Verseghy, The simulation of energy, water vapor and carbon dioxide fluxes over common crops by the Canadian Land Surface Scheme (CLASS), Agric. For. Meteorol, vol.133, pp.89-108, 2005.

G. Krinner, N. Viovy, N. De-noblet-ducoudre, J. Ogée, 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

C. J. Kucharik and T. E. Twine, Residue, respiration, and residuals: evaluation of a dynamic agroecosystem model using eddy flux measurements and biometric data, Agric. For. Meteorol, vol.146, issue.3-4, pp.134-158, 2007.

G. Lemaire, X. Charrier, and Y. Htébert, TNitrogen uptake capacities of maize and sorghum crops in different nitrogen and water supply conditions, Agronomie, vol.16, issue.4, pp.231-246, 1996.

L. H. Li and Q. Yu, Quantifying the effects of advection on canopy energy budgets and water use efficiency in an irrigated wheat field in the North China Plain, Agric. Water Manage, vol.89, pp.116-122, 2007.

Y. Q. Luo, E. S. Weng, X. W. Wu, C. Gao, X. H. Zhou et al., Parameter identifiability, constraint, and equifinality in data assimilation with ecosystem models, Ecol. Appl, vol.19, pp.571-574, 2009.

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, Agric. For. Meteorol, vol.147, pp.209-232, 2007.

M. S. Moran, T. R. Clarke, Y. Inoue, and A. Vidal, Estimating crop water deficit using the relation between surface-air temperature and spectral vegetation index, Remote Sens. Environ, vol.49, pp.246-263, 1994.
URL : https://hal.archives-ouvertes.fr/hal-02574103

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

D. Papale, M. Reichstein, E. Canfora, M. Aubinet, C. Bernhofer et al., Towards a more harmonized processing of eddy covariance CO 2 fluxes: algorithms and uncertainty estimation, Biogeosciences Discuss, vol.3, pp.961-992, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00330225

P. Peylin, P. J. Rayner, P. Bousquet, C. Carouge, F. Hourdin et al., Daily CO 2 flux estimates over Europe from continuous atmospheric measurements: 1, inverse methodology, Atmos. Chem. Phys, vol.5, pp.3137-3186, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00328413

S. Piao, P. Ciais, P. Friedlingstein, P. Peylin, M. Reichstein et al., TNet carbon dioxide losses of northern ecosystems in response to autumn warming, Nature, vol.451, pp.49-52, 2008.

S. Piao, P. Friedlingstein, P. Ciais, N. Viovy, and J. Demarty, Growing season extension and its impact on terrestrial carbon cycle in the Northern Hemisphere over the past 2 decades, Global Bimgeochem. Cy, vol.21, p.3018, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01863532

J. Pongratz, C. H. Reich, T. Raddatz, and M. Claussen, Effects of anthropogenic land cover change on the carbon cycle of the last millennium, Global Biogeochemical Cy, vol.23, p.4001, 2009.

M. C. Reeves, M. Zhao, and S. W. Running, Usefulness and limits of MODIS GPP for estimating wheat yield, Int. J. Remote Sens, vol.26, issue.7, pp.1403-1421, 2005.

M. Reichstein, E. Falge, D. Baldocchi, D. Papale, M. Aubinet et al., On the separation of net ecosystem exchange into assimilation and ecosystem respiration: Review and improved algorithm, Global Change Biol, vol.11, pp.1424-1439, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02683280

A. Ruimy, G. Dedieu, B. Saugier, P. Smith, N. De-noblet-ducoudré et al., European-wide simulations of present croplands using an improved terrestrial biosphere model, Part 1: phenology and productivity, Glob. Biogeochem. Cy, vol.10, p.1014, 1996.

P. Smith, D. S. Powlson, P. Falloon, C. , and K. , Meeting Europe's climate change commitments: quantitative estimates of the potential for carbon mitigation by agriculture, Glob. Change Biol, vol.6, issue.6, pp.525-539, 2002.

A. E. Suyker, S. B. Verma, G. G. Burba, T. J. Arkebauer, D. T. Walters et al., Growing season carbon dioxide exchange in irrigated rainfed maize, Agric. Forest. Meteorol, vol.124, pp.1-13, 2004.

K. E. Taylor, Summarizing multiple aspects of model performance in a single diagram, J. Geophys. Res, vol.106, issue.D7, pp.7183-7192, 2001.

S. E. Trumbore and R. Valentini, Carbon respired by terrestrial ecosystems -recent progress and challenges, Glob. Change Biol, vol.12, p.274, 2003.

S. B. Verma, A. Dobermann, K. G. Gassman, D. T. Walters, J. M. Knops et al., Annual carbon dioxide exchange in irrigated and rainfed maize-based agroecosystems, Agric. For. Meteorol, vol.131, pp.77-96, 2005.

A. Viña, A. A. Gitelson, D. C. Rundquist, G. Keydan, B. Leavitt et al., Monitoring maize (Zea mays L.) phenology with remote sensing, Agron. J, vol.96, pp.1139-1147, 2004.

N. Viovy, C. François, A. Bondeau, G. Krinner, J. Polcher et al., Assimilation of remote sensing measurements into the ORCHIDEE/STOMATE DGVM biosphere model, Recueil des actes du 8ème Symposium International "Mesures Physiques et Signatures en Télédétection, pp.713-718, 2001.

N. Viovy, Interannuality and CO 2 sensitivity of the SECHIBA-BGC coupled SVAT-BGC model, Phys. Chem. Earth, vol.21, pp.489-497, 1997.

L. M. Vleeshouwers and A. Verhagen, Carbon emission and sequestration by agricultural land use: a model study for Europe, Glob. Change Biol, vol.8, pp.519-530, 2002.

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

L. Xu and D. D. Baldocchi, Seasonal variation in carbon dioxide exchange over Mediterranean annual grassland in California, Agric. Forest Meteorol, vol.123, pp.79-96, 2004.

H. Yan, M. Cao, J. Liu, and B. Tao, Potential and sustainability for carbon sequestration with improved soil management in agricultural soils of China, Agric. Syst. Environ, vol.121, pp.325-335, 2007.