photo: Photosynthesis submodel functions

Description

Set of functions used in the calculation of photosynthesis

Usage

photo_GammaTemp(Tleaf)
photo_KmTemp(Tleaf, Oi = 209)
photo_VmaxTemp(Vmax298, Tleaf)
photo_JmaxTemp(Jmax298, Tleaf)
photo_electronLimitedPhotosynthesis(Q, Ci, GT, Jmax)
photo_rubiscoLimitedPhotosynthesis(Ci, GT, Km, Vmax)
photo_photosynthesis(Q, Catm, Gc, Tleaf, Vmax298, Jmax298, verbose = FALSE)
photo_photosynthesisBaldocchi(
  Q,
  Catm,
  Tleaf,
  u,
  Vmax298,
  Jmax298,
  leafWidth,
  Gsw_AC_slope,
  Gsw_AC_intercept
)
photo_leafPhotosynthesisFunction(
  E,
  psiLeaf,
  Catm,
  Patm,
  Tair,
  vpa,
  u,
  absRad,
  Q,
  Vmax298,
  Jmax298,
  leafWidth = 1,
  refLeafArea = 1,
  verbose = FALSE
)
photo_leafPhotosynthesisFunction2(
  E,
  psiLeaf,
  Catm,
  Patm,
  Tair,
  vpa,
  u,
  SWRabs,
  LWRnet,
  Q,
  Vmax298,
  Jmax298,
  leafWidth = 1,
  refLeafArea = 1,
  verbose = FALSE
)
photo_sunshadePhotosynthesisFunction(
  E,
  psiLeaf,
  Catm,
  Patm,
  Tair,
  vpa,
  SLarea,
  SHarea,
  u,
  absRadSL,
  absRadSH,
  QSL,
  QSH,
  Vmax298SL,
  Vmax298SH,
  Jmax298SL,
  Jmax298SH,
  leafWidth = 1,
  verbose = FALSE
)
photo_multilayerPhotosynthesisFunction(
  E,
  psiLeaf,
  Catm,
  Patm,
  Tair,
  vpa,
  SLarea,
  SHarea,
  u,
  absRadSL,
  absRadSH,
  QSL,
  QSH,
  Vmax298,
  Jmax298,
  leafWidth = 1,
  verbose = FALSE
)

Value

Values returned for each function are:

photo_GammaTemp: CO2 compensation concentration (micromol * mol-1).
photo_KmTemp: Michaelis-Menten coefficients of Rubisco for Carbon (micromol * mol-1) and Oxigen (mmol * mol-1).
photo_VmaxTemp: Temperature correction of Vmax298.
photo_JmaxTemp: Temperature correction of Jmax298.
photo_electronLimitedPhotosynthesis: Electron-limited photosynthesis (micromol*s-1*m-2) following Farquhar et al. (1980).
photo_rubiscoLimitedPhotosynthesis: Rubisco-limited photosynthesis (micromol*s-1*m-2) following Farquhar et al. (1980).
photo_photosynthesis: Calculates gross photosynthesis (micromol*s-1*m-2) following (Farquhar et al. (1980) and Collatz et al (1991).
photo_leafPhotosynthesisFunction: Returns a data frame with the following columns:
- LeafTemperature: Leaf temperature (ºC).
- LeafVPD: Leaf vapor pressure deficit (kPa).
- LeafCi: Internal CO2 concentration (micromol * mol-1).
- Gsw: Leaf stomatal conductance to water vapor (mol * s-1 * m-2).
- GrossPhotosynthesis: Gross photosynthesis (micromol*s-1*m-2).
- NetPhotosynthesis: Net photosynthesis, after discounting autotrophic respiration (micromol*s-1*m-2).
photo_sunshadePhotosynthesisFunction: Returns a data frame with the following columns:
- GrossPhotosynthesis: Gross photosynthesis (micromol*s-1*m-2).
- NetPhotosynthesis: Net photosynthesis, after discounting autotrophic respiration (micromol*s-1*m-2).
- LeafCiSL: Sunlit leaf internal CO2 concentration (micromol * mol-1).
- LeafCiSH: Shade leaf internal CO2 concentration (micromol * mol-1).
- LeafTempSL: Sunlit leaf temperature (ºC).
- LeafTempSH: Shade leaf temperature (ºC).
- LeafVPDSL: Sunlit leaf vapor pressure deficit (kPa).
- LeafVPDSH: Shade leaf vapor pressure deficit (kPa).
photo_multilayerPhotosynthesisFunction: Return a data frame with the following columns:
- GrossPhotosynthesis: Gross photosynthesis (micromol*s-1*m-2).
- NetPhotosynthesis: Net photosynthesis, after discounting autotrophic respiration (micromol*s-1*m-2).

Arguments

Tleaf: Leaf temperature (in ºC).
Oi: Oxigen concentration (mmol*mol-1).
Vmax298, Vmax298SL, Vmax298SH: Maximum Rubisco carboxylation rate per leaf area at 298ºK (i.e. 25 ºC) (micromol*s-1*m-2) (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction). 'SH' stands for shade leaves, whereas 'SL' stands for sunlit leaves.
Jmax298, Jmax298SL, Jmax298SH: Maximum electron transport rate per leaf area at 298ºK (i.e. 25 ºC) (micromol*s-1*m-2) (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction). 'SH' stands for shade leaves, whereas 'SL' stands for sunlit leaves.
Q: Active photon flux density (micromol * s-1 * m-2).
Ci: CO2 internal concentration (micromol * mol-1).
GT: CO2 saturation point corrected by temperature (micromol * mol-1).
Jmax: Maximum electron transport rate per leaf area (micromol*s-1*m-2).
Km: Km = Kc*(1.0+(Oi/Ko)) - Michaelis-Menten term corrected by temperature (in micromol * mol-1).
Vmax: Maximum Rubisco carboxylation rate per leaf area (micromol*s-1*m-2).
Catm: CO2 air concentration (micromol * mol-1).
Gc: CO2 leaf (stomatal) conductance (mol * s-1 * m-2).
verbose: Boolean flag to indicate console output.
u: Wind speed above the leaf boundary (in m/s) (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).
leafWidth: Leaf width (in cm).
Gsw_AC_slope: Slope of the An/C vs Gsw relationship
Gsw_AC_intercept: Intercept of the An/C vs Gsw relationship
E: Transpiration flow rate per leaf area (mmol*s-1*m-2).
psiLeaf: Leaf water potential (MPa).
Patm: Atmospheric air pressure (in kPa).
Tair: Air temperature (in ºC).
vpa: Vapour pressure deficit (in kPa).
absRad: Absorbed long- and short-wave radiation (in W*m^-2).
refLeafArea: Leaf reference area.
SWRabs: Absorbed short-wave radiation (in W·m-2).
LWRnet: Net long-wave radiation balance (in W·m-2).
SLarea, SHarea: Leaf area index of sunlit/shade leaves (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).
absRadSL, absRadSH: Instantaneous absorbed radiation (W·m-2) per unit of sunlit/shade leaf area (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).
QSL, QSH: Active photon flux density (micromol * s-1 * m-2) per unit of sunlit/shade leaf area (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).

Author

Miquel De Cáceres Ainsa, CREAF

Details

Details of the photosynthesis submodel are given in the medfate book

References

Bernacchi, C. J., E. L. Singsaas, C. Pimentel, A. R. Portis, and S. P. Long. 2001. Improved temperature response functions for models of Rubisco-limited photosynthesis. Plant, Cell and Environment 24:253–259.

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

Farquhar, G. D., S. von Caemmerer, and J. A. Berry. 1980. A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149:78–90.

Leuning, R. 2002. Temperature dependence of two parameters in a photosynthesis model. Plant, Cell and Environment 25:1205–1210.

Sperry, J. S., M. D. Venturas, W. R. L. Anderegg, M. Mencuccini, D. S. Mackay, Y. Wang, and D. M. Love. 2016. Predicting stomatal responses to the environment from the optimization of photosynthetic gain and hydraulic cost. Plant Cell and Environment.