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SiB3: Simple Biosphere Model

SiB3The Simple Biosphere (SiB) Model was originally developed by Piers Sellers in the mid-1980’s as an internally-consistent module to surface-atmosphere exchanges of radiation, heat, moisture, and momentum over land.

It was extended in the mid-1990’s by a team of interdisciplinary scientists to include mechanistic linkages to photosynthesis, stomatal physiology, and satellite remote sensing.

Since that time it has been extended to include improved treatment of carbon cycling, soils, snow, hydrology, stable isotopes, phenology, and crops.

Below you will find a formal model description with references, links to key publications describing model formulation and results, model code and documentation, and a complete reference list.

Model Formulation

The Simple Biosphere model (SiB) is based on a land-surface parameterization scheme originally used to compute biophysical exchanges of energy, water, and momentum in climate models (Sellers et al., 1986), and later adapted to include ecosystem metabolism (Sellers et al., 1996a; Denning et al., 1996a). The parameterization of photosynthetic carbon assimilation is based on enzyme kinetics originally developed by Farquhar et al. (1980), and is linked to stomatal conductance and thence to the surface energy budget and atmospheric climate (Collatz et al., 1991, 1992; Sellers et al., 1996a; Randall et al., 1996). The model has been updated to include prognostic calculation of temperature, moisture, and trace gases in the canopy air space (Vidale and Stöckli, 2005), and the model has been evaluated against eddy covariance measurements at a number of sites (Baker et al., 2003; Hanan et al., 2004; Baker et al, 2008). Direct-beam and diffuse solar radiation are treated separately for calculations of photosynthesis and transpiration of sunlit and shaded canopy fractions, using algorithms similar to those of DePury and Farquhar (1997). Other recent improvements include biogeochemical fractionation and recycling of stable carbon isotopes (Suits et al., 2005), improved treatment of soil hydrology and thermodynamics, and the introduction of a multilayer snow model based on the Community Land Model (Dai et al., 2003; Stöckli et al, 2008a), a prognostic phenology algorithm that assimilates vegetation imagery (Stöckli et al, 2008b), the biogeochemical cycling of carbon among decomposing organic pools (Schaefer et al, 2008), and the ecophysiology of corn, soy, and wheat crops (Lokupitiya et al, 2009). The model is now referred to as SiB3.

Model Results

SiB has been used to analyze regional to global controls on ecosystem productivity (Schaefer et al., 2002, 2005; Williams et al, 2008) and atmospheric CO2 mixing ratio (Denning et al, 1996b, 1999; Law et al, 2008; Patra et al, 2008; Parazoo et al, 2008, Corbin et al, 2008a). It has been coupled to the Regional Atmospheric Modeling System (RAMS) and used to study local- and regional-scale interactions among carbon fluxes, turbulence, and CO2 mixing ratio (Denning et al., 2003, 2008; Nicholls et al., 2004; Wang et al, 2007; Corbin et al, 2008b McGrath-Spangler et al, 2009). The model has also been used as a basis for regional carbon source/sink estimation by assimilation of atmospheric COmixing ratio (Zupanski et al, 2007; Prihodko et al, 2008; Lokupitiya et al, 2008; Schuh et al, 2009). Following previous work with CASA (van der Werf et al, 2006), we also plan to add a fire module to this model.

Key Papers

Code & Documentation

This is perpetually a work in progress. Click here to browse the full model code, data descriptors, and software structure, produced with the open-source metadata generator doxygen.

References Cited

Baker, I.T., A.S. Denning, N. Hanan, L. Prihodko, P.-L. Vidale, K. Davis and P. Bakwin, 2003: Simulated and observed fluxes of sensible and latent heat and CO2 at the WLEF-TV Tower using SiB2.5. Global Change Biology, 9, 1262-1277.

Baker, I. T., L. Prihodko, A.S. Denning, M. Goulden, S. Miller, and H.R. da Rocha, 2008. Seasonal drought stress in the Amazon: Reconciling models and observations. Jour. Geophys. Res. 113, G00B01, doi:10.1029/2007JG000644.

Ciais, P., A.S. Denning, P.P. Tans, J.A. Berry, D.A. Randall, G.J. Collatz, P.J. Sellers, J.W.C. White, M. Trolier, H.J. Meijer, R.J. Francey, P. Monfray and M. Heimann, 1997: A three-dimensional synthesis study of d18O in atmospheric CO2. Part 1: Surface fluxes. Journal of Geophysical Research, 102, 5857-5872.

Collatz, G. J., Ball, J. T., Grivet, C. and Berry, J. A., Physiological and environmental regulation of stomatal conductance, photosynthesis, and transpiration: a model that includes a laminar boundary layer, Agric. and Forest Meteorol., 54, 107-136, 1991.

Collatz, G. J., Ribas-Carbo, M. and Berry, J. A., Coupled photosynthesis-stomatal conductance model for leaves of C4 plants, Aust. J. Plant Physiol., 19, 519-538, 1992.

Corbin, K.D., A.S. Denning, J.-W. Wang, L. Lu, L. Prihodko, and I.T. Baker, 2008.  Representation error in potential atmospheric CO2 retrievals from satellites. Jour. Geophys. Res., 113, D02301, doi:10.1029/2007JD008716.

Corbin, K. D., A. S. Denning, and N. Parazoo, 2008. Assessing temporal clear-sky errors in assimilation of satellite CO2 retrievals using a global transport model. Atmos. Chem. Phys., 9, 3043-3048.

Dai, Y., X. Zeng, R.E. Dickinson, I. Baker, G. Bonan, M. Bosilovich, S. Denning, P. Dirmeyer, P. Houser, G. Niu, K. Oleson, A. Schlosser and Z.-L. Yang, 2003: The common land model (CLM). Bull. Amer. Meteorol. Soc., 84, 1013–1023.

Denning, A.S., J.G. Collatz, C. Zhang, D.A. Randall, J.A. Berry, P.J. Sellers, G.D. Colello and D.A. Dazlich, Simulations of terrestrial carbon metabolism and atmospheric CO2 in a general circulation model. Part 1: Surface carbon fluxes, Tellus, 48B, 521-542, 1996a.

Denning, A.S., D.A. Randall, G.J. Collatz and P.J. Sellers, Simulations of terrestrial carbon metabolism and atmospheric CO2 in a general circulation model. Part 2: Spatial and temporal variations of atmospheric CO2, Tellus, 48B, 543-567, 1996b.

Denning, A.S., T. Takahashi and P. Friedlingstein, 1999. Can a strong atmospheric CO2 rectifier effect be reconciled with a “reasonable” carbon budget? Tellus, 51B, 249-253.

Denning, A.S., M. Nicholls, L. Prihodko, I. Baker, P.-L. Vidale, K. Davis, and P. Bakwin, 2003. Simulated and observed variations in atmospheric CO2 over a Wisconsin forest. Global Change Biology, 9, 1241-1250.

Denning, A. S., N. Zhang, X. Yi, M. Branson, P. Bakwin, K. Davis, and J. Kleist, 2008.  Evaluation of simulated boundary layer depth at the WLEF-TV Tower Site. Agric. Forest Meteorol., 148, 206-215, doi:10.1016/j.agrformet.2007.08.012.

De Pury, D. G. G. and G. D. Farquhar, Simple scaling of photosynthesis from leaves to canopies without the errors of big-leaf models,  Plant, Cell, and Environment, 20, 537-557, 1997.

Farquhar, G. D., S. V. Caemmerer, and J. A. Berry, A biochemical model of photosynthetic CO2 assimilation in leaves of C3 Species, Planta, 149, 78-90, 1980.

Hanan, N. P., J. A. Berry, S. B. Verma, E. A. Walter-Shea, A. E. Suyker, G. G. Burba, and A. S. Denning, 2004. Model analyses of biosphere-atmosphere exchanges of CO2, water and energy in Great Plains tallgrass prairie and wheat ecosystems. Agric. Forest Meteorol, 131, 162-179.

Law, R. M., W. Peters, C. Rodenbeck, C. Aulagnier, I. Baker, D. J. Bergmann, P. Bousquet, J. Brandt, L. Bruhwiler, P. J. Cameron-Smith, J. H. Christensen, F. Delage, A. S. Denning, S. Fan, C. Geels, S. Houweling, R. Imasu, U. Karstens, S. R. Kawa, J. Kleist, M. C. Krol, S.-J. Lin, R. Lokupitiya, T. Maki, S. Maksyutov, Y. Niwa, R. Onishi, N. Parazoo, P. K. Patra, G. Pieterse, L. Rivier, M. Satoh, S. Serrar, S. Taguchi, M. Takigawa, R. Vautard, A. T. Vermuelen, and Z. Zhu, 2008. TransCom model simulations of hourly atmospheric CO2: experimental overview and diurnal cycle results for 2002. Global Biogeochem. Cycles, 22, GB3009, doi:10.1029/2007GB003050.

Lokupitiya, R. S., D. Zupanski, A. S. Denning, S. R. Kawa, K. R. Gurney, and M. Zupanski, 2008. Estimation of global CO2 fluxes at regional scale using the Maximum Likelihood Ensemble Filter. Jour. Geophys. Res. 113, D20110, doi:10.1029/2007JD009679.

Lokupitiya, E., A. S. Denning, K. Paustian, I. T. Baker, K. Schaefer, S. Verma, T. Meyers, C. Bernacchi, A. Suyker, and M. Fischer, 2009. Incorporation of crop phenology in Simple Biosphere Model (SiBcrop) to improve land-atmosphere carbon exchanges from croplands. Biogeosciences, 6, 969-986.

McGrath-Spangler, E., A. S. Denning, K. Corbin, and I. Baker, 2008. Implementation of a boundary layer heat flux parameterization into the Regional Atmospheric Modeling System (RAMS). Atmos. Chem. Phys. Discussions acpd-2008-0252.

Moorthi S., and M. J. Suarez, 1992: Relaxed Arakawa–Schubert: A parameterization of moist convection for general circulation models. Mon. Weather Rev, 120, 978–1002.

Nicholls, M.E., A.S. Denning, L. Prihodko, P.-L. Vidale, K. Davis, P. Bakwin, 2004:  A multiple-scale simulation of variations in atmospheric carbon dioxide using a coupled biosphere-atmospheric model. Jour. Geophys. Res, 109, D18117, doi:10.1029/2003JD004482.

Patra, P. K., R. M. Law, W. Peters, C. Rӧdenbeck, M. Takigawa, C. Aulagnier, I. Baker, D. J. Bergmann, P. Bousquet, J. Brandt, L. Bruhwiler, P. J. Cameron-Smith, J. H. Christensen, F. Delage, A. S. Denning, S. Fan, C. Geels, S. Houweling, R. Imasu, U. Karstens,, S. R. Kawa, J. Kleist, M. C. Krol,, S.-J. Lin, R. Lokupitiya, T. Maki, S. Maksyutov,, Y. Niwa, R. Onishi, N. Parazoo, G. Pieterse,, L. Rivier, M. Satoh,, S. Serrar, S. Taguchi, R. Vautard, A. T. Vermeulen, Z. Zhu, 2008. TransCom model simulations of hourly atmospheric CO2: analysis of synoptic scale variations for the period 2002-2003. Glob. Biogeochem. Cycles, 22, GB4013, doi:10.1029/2007GB003081.

Pieterse, G., Vermeulen, A. T., Baker, I. T., and Denning, A. S., 2008. Lagrangian transport modelling for CO2 using two different biosphere models, Atmos. Chem. Phys. Discuss., 8, 4117-4154.

Prihodko, L., A.S. Denning, N.P. Hanan,  I. Baker, K. Davis, 2008. Sensitivity, uncertainty  and time dependence of parameters in a complex land surface model. Agric. Forest Meteorol., 148, 268-287, doi:10.1016/j.agrformet.2007.08.006.

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Schaefer, K., A. S. Denning, and O. Leonard, 2005.  The winter Arctic Oscillation, the timing of spring, and carbon fluxes in the northern hemisphere. Global Biogeochemical Cycles, 19, GB3017, doi:10.1029/2004GB002336.

Schaefer, K., P. Tans, S. Denning, I. Baker, J. Berry, L. Prihodko,  N. Suits, and A. Philpott, 2008. The combined Simple Biosphere/Carnegie-Ames-Stanford Approach (SiBCASA) Model, Jour. Geophys. Res., 113, G03034, doi:10.1029/2007JG000603.

Schuh, A. E., A. S. Denning, M. Uliasz, K. D. Corbin, 2009. Seeing the forest through the trees:  Recovering large scale carbon flux biases in the midst of small scale variability. Jour. Geophys. Res., doi:10.1029/2008JG000842.

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Zupanski, D., A. S. Denning, M. Uliasz, M. Zupanski, A. E. Schuh, P. J. Rayner, W. Peters, and K. D. Corbin, 2007. Carbon flux bias estimation employing the Maximum Likelihood Esemble Filter (MLEF). Jour. Geophys. Res. 112, D17107, doi:10