Calculate C4 assimilation rates — calculate_c4

Calculates C4 assimilation rates based on the von Caemmerer (2000) model. This function can accomodate alternative colum names for the variables taken from Licor files in case they change at some point in the future. This function also checks the units of each required column and will produce an error if any units are incorrect.

Usage

calculate_c4_assimilation(
    exdf_obj,
    alpha_psii,
    gbs,
    Jmax_at_opt,
    RL_at_25,
    Rm_frac,
    Vcmax_at_25,
    Vpmax_at_25,
    Vpr,
    absorptance = 0.85,
    f_spectral = 0.15,
    rho = 0.5,
    theta = 0.7,
    x_etr = 0.4,
    ao_column_name = 'ao',
    gamma_star_column_name = 'gamma_star',
    jmax_norm_column_name = 'Jmax_norm',
    kc_column_name = 'Kc',
    ko_column_name = 'Ko',
    kp_column_name = 'Kp',
    oxygen_column_name = 'oxygen',
    pcm_column_name = 'PCm',
    qin_column_name = 'Qin',
    rl_norm_column_name = 'RL_norm',
    total_pressure_column_name = 'total_pressure',
    vcmax_norm_column_name = 'Vcmax_norm',
    vpmax_norm_column_name = 'Vpmax_norm',
    hard_constraints = 0,
    perform_checks = TRUE,
    return_exdf = TRUE
  )

Arguments

exdf_obj: An exdf object.
alpha_psii: The fraction of photosystem II activity in the bundle sheath (dimensionless). If alpha_psii is not a number, then there must be a column in exdf_obj called alpha_psii with appropriate units. A numeric value supplied here will overwrite the values in the alpha_psii column of exdf_obj if it exists.
gbs: The bundle sheath conductance to CO2 in mol m^(-2) s^(-1) bar^(-1). If gbs is not a number, then there must be a column in exdf_obj called gbs with appropriate units. A numeric value supplied here will overwrite the values in the gbs column of exdf_obj if it exists.
Jmax_at_opt: The RuBP regeneration rate at its optimal temperature, expressed in micromol m^(-2) s^(-1). If Jmax_at_opt is not a number, then there must be a column in exdf_obj called Jmax_at_opt with appropriate units. A numeric value supplied here will override the values in the Jmax_at_opt column of exdf_obj if it exists.
RL_at_25: The total rate of mitochondrial respiration across the mesophyll and bundle sheath at 25 degrees C, expressed in micromol m^(-2) s^(-1). If RL_at_25 is not a number, then there must be a column in exdf_obj called RL_at_25 with appropriate units. A numeric value supplied here will overwrite the values in the RL_at_25 column of exdf_obj if it exists.
Rm_frac: The fraction of the total mitochondrial respiration that occurs in the mesophyll. If Rm_frac is not a number, then there must be a column in exdf_obj called Rm_frac with appropriate units. A numeric value supplied here will overwrite the values in the Rm_frac column of exdf_obj if it exists.
Vcmax_at_25: The maximum rate of rubisco carboxylation at 25 degrees C, expressed in micromol m^(-2) s^(-1). If Vcmax_at_25 is not a number, then there must be a column in exdf_obj called Vcmax_at_25 with appropriate units. A numeric value supplied here will overwrite the values in the Vcmax_at_25 column of exdf_obj if it exists.
Vpmax_at_25: The maximum rate of PEP carboxylase activity at 25 degrees C, expressed in micromol m^(-2) s^(-1). If Vpmax_at_25 is not a number, then there must be a column in exdf_obj called Vpmax_at_25 with appropriate units. A numeric value supplied here will overwrite the values in the Vpmax_at_25 column of exdf_obj if it exists.
Vpr: The rate of PEP carboxylase regeneration, expressed in micromol m^(-2) s^(-1). If Vpr is not a number, then there must be a column in exdf_obj called Vpr with appropriate units. A numeric value supplied here will overwrite the values in the Vpr column of exdf_obj if it exists.
absorptance: The leaf absorptance (dimensionless). See Equation 35 from S. von Caemmerer (2021).
f_spectral: The spectral quality adjustment factor (dimensionless). See Equation 35 from S. von Caemmerer (2021).
rho: The fraction of light absorbed by photosystem II rather than photosystem I (dimensionless). See Equation 35 from S. von Caemmerer (2021).
theta: An empirical curvature factor (dimensionless). See Equation 34 from S. von Caemmerer (2021).
x_etr: The fraction of whole-chain electron transport occurring in the mesophyll (dimensionless). See Equation 29 from S. von Caemmerer (2021).
ao_column_name: The name of the column in exdf_obj that contains the dimensionless ratio of solubility and diffusivity of O2 to CO2.
gamma_star_column_name: The name of the column in exdf_obj that contains the dimensionless gamma_star values.
jmax_norm_column_name: The name of the column in exdf_obj that contains the normalized Jmax values (with units of normalized to Jmax at its optimal temperature).
kc_column_name: The name of the column in exdf_obj that contains the Michaelis-Menten constant for rubisco carboxylation in microbar.
ko_column_name: The name of the column in exdf_obj that contains the Michaelis-Menten constant for rubisco oxygenation in mbar.
kp_column_name: The name of the column in exdf_obj that contains the Michaelis-Menten constant for PEP carboxylase carboxylation in microbar.
oxygen_column_name: The name of the column in exdf_obj that contains the concentration of O2 in the ambient air, expressed as a percentage (commonly 21% or 2%); the units must be percent.
pcm_column_name: The name of the column in exdf_obj that contains the partial pressure of CO2 in the mesophyll, expressed in microbar.
qin_column_name: The name of the column in exdf_obj that contains values of the incident photosynthetically active flux density in micromol m^(-2) s^(-1).
rl_norm_column_name: The name of the column in exdf_obj that contains the normalized RL values (with units of normalized to RL at 25 degrees C).
total_pressure_column_name: The name of the column in exdf_obj that contains the total pressure in bar.
vcmax_norm_column_name: The name of the column in exdf_obj that contains the normalized Vcmax values (with units of normalized to Vcmax at 25 degrees C).
vpmax_norm_column_name: The name of the column in exdf_obj that contains the normalized Vpmax values (with units of normalized to Vpmax at 25 degrees C).
hard_constraints: An integer numerical value indicating which types of hard constraints to place on the values of input parameters; see below for more details.
perform_checks: A logical value indicating whether to check units for the required columns. This should almost always be TRUE. The option to disable these checks is only intended to be used when fit_c4_aci calls this function, since performing these checks many times repeatedly slows down the fitting procedure.
return_exdf: A logical value indicating whether to return an exdf object. This should almost always be TRUE. The option to return a vector is mainly intended to be used when fit_c4_aci calls this function, since creating an exdf object to return will slow down the fitting procedure.

Details

General Description of the Model

This function generally follows Sections 4.2.1 and 4.2.2 from S. von Caemmerer (2000), which provides equations for calculating the enzyme-limited net assimilation rate Ac, the light- and electron-transport limited rate Aj, and the overall net assimilation rate An in a C4 leaf. (These equations are also reproduced in S. von Caemmerer (2021), although we use the equation numbers from the 2000 textbook here. Also note there is a typo in Equation 22 from the 2021 paper.) The enzyme-limited assimilation rate in this model is calculated according to Equation 4.21:

Ac = (-b - sqrt(b^2 - 4 * a * c)) / (2 * a)

where the parameters a, b, and c are determined by Equations 4.22, 4.23, and 4.24, respectively. These equations are fairly long, so we do not reproduce them here. Similarly, the light-limited rate Aj is also calculated according to a quadratic equation. Finally, the overall rate is calculated as the smaller of Ac and Aj:

An = min(Ac, Aj)

An Approximation to the Full Equations

The complicated equations above can be approximiated by simpler ones. For Ac, we can use Equation 4.25:

Ac = min(Vp + gbs * PCm - RLm, Vcmax - RL)

where Vp is the rate of PEP carboxylation, gbs is the bundle sheath conductance to CO2, PCm is the partial pressure of CO2 in the mesophyll, RLm is the rate of mitochondrial respiration occuring in the mesophyll, Vcmax is the maximum rate of Rubisco carboxylation, and RL is the rate of mitochondrial respiration occurring in the bundle sheath and mesophyll. Essentially, the first term in the equation above (Vp + gbs * PCm - RLm) can be thought of as a PEP-carboxylase-limited assimilation rate Ap, while the second term (Vcmax - RL) is a Rubisco-limited rate Ar.

The PEP carboxylation rate Vp is calculated according to Equation 4.19:

Vp = min(Pcm * Vpmax / (PCm + Kp), Vpr)

where Vpmax is the maximum rate of PEP carboxylation, Kp is a Michaelis-Menten constant for PEP carboxylation, and Vpr is the carboxylation rate when PEP carboxylase activity is limited by regeneration rather than carbon availability. Thus, we can see that the approximation above actually calculates the enzyme-limited rate as the smaller of three separate assimilation rates:

Ac = min(Apc, Apr, Ar)

where Apc = Pcm * Vpmax / (PCm + Kp) + gbs * PCm - RLm is the rate due to carbon-limited PEP carboxylation, Apr = Vpr + gbs * PCm - RLm is the rate due to regeneration-limited PEP carboxylation, and Ar = Vcmax - RL is the rate due to Rubisco-limited assimilation.

In the example at the end of this documentation page, we compare Apc, Apr, and Ar to Ac as calculated by Equation 4.21. From this example, it is clear that the approximation Ac = min(Apc, Apr, Ar) is quite accurate for low values of PCm, but introduces significant errors as PCm increases. Thus, while the approximation can be helpful for gaining an intuitive understanding of C4 photosynthesis, it should not be used for realistic calculations.

To be more precise, the approximation is only reliable when Vcmax is much larger than gbs * Kc * (1 + POm / Ko), which is rarely the case; otherwise, the limiting value of An at high PCm will be smaller than Ar = Vcmax - RL. Conversely, if gbs and alpha_psii are both set to zero, then the approximation is exact.

For Aj, the simplified version is Equation 4.45:

Aj = min(x_etr * J / 2 - RLm + gbs * PCm, (1 - x_etr) * J / 3 - RL)

where x_etr is the fraction of whole-chain electron transport occurring in the mesophyll and J is the electron transport rate. We can therefore think of this equation as

Aj = min(Ajm, Ajbs)

where Ajm is the mesophyll light-limited rate and Ajbs is the bundle sheath light-limited rate. These are given by Ajm = x_etr * J / 2 - RLm + gbs * PCm and (1 - x_etr) * J / 3 - RL As in the case with Ac, this approximation is not exact.

Combining these two simplifications, we can see that the overall net assimilation rate can be approximated as the smallest of five potential rates:

An = min(Apc, Apr, Ar, Ajm, Ajbs).

Here it is very important to note that some of these potential rates have identical or similar dependence on PCm. More specifically, Apr and Ajm have identical dependence, as do Ar and Ajbs. If gbs is zero, all four of these rates have no dependence on PCm. Thus, from a fitting point of view, it is not usually possible to distinguish between these potential limiting states. For this reason, it is not advisable to fit more than one of Vcmax, Vpr, and Jmax when estimating parameters from an experimentally measured curve.

Limiting Cases of the Approximate Equation

The bundle sheath conductance gbs is generally very small and can be ignored in a simple analysis of the above equations. In that case, when Pcm is very high, the approximate equation for Ac simplifies further to:

Ac = min(Vpmax - RLm, Vpr - RLm, Vcmax - RL)

Since respiration costs are also generally much smaller than the maximum enzyme activity and regeneration rates, the enzyme-limited assimilation rate at high levels of CO2 is therefore determined by the smaller of Vpmax, Vpr, and Vcmax. As shown in Table 4.1 of the textbook, Vpmax is typically much larger than the other two rates, so light- and CO2-saturated assimilation in C4 leaves is usually limited by either Vpr or Vcmax. The exact limiting factor can depend on many possible variables, such as the temperature. For example, see Wang (2008).

At lower values of PCm, enzyme-limited net assimilation is determined by CO2-limited PEP carboxylation according to:

An = PCm * Vpmax / Kp - RLm

where we have approximated gbs * PCm = 0 and PCm + Kp = Kp, as appropriate for small values of Pcm. Thus, we can see that for low CO2 levels, assimilation is linearly related to PCm with a slope of Vpmax / Kp and intercept of -RLm.

Respiration

Table 4.1 from von Caemmerer (2000) suggests that RL = 0.01 * Vcmax and RLm = 0.5 * RL. To allow more flexibility, we allow RL to be specified independently of Vcmax, and we also consider the ratio of RLm / RL = Rm_frac to be a variable (so that RLm is calculated from RL according to RLm = Rm_frac * RL). If Rm_frac is set to 1, then there is no distinction between RL and RLm.

Hard constraints:

Most input parameters to the C4 assimilation model have hard constraints on their values which are set by their biochemical or physical interpretation; for example, Vcmax cannot be negative and alpha_psii must lie between 0 and 1. Yet, because of measurement noise, sometimes it is necessary to use values outside these ranges when fitting an A-Ci curve with fit_c4_aci. To accomodate different potential use cases, it is possible to selectively apply these hard constraints by specifying different values of the hard_constraints input argument:

hard_constraints = 0: Constraints are only placed on inputs that are user-supplied and cannot be fit, such as Kc.
hard_constraints = 1: Includes the same constraints as when hard_constraints is 0, with the additional constraint that all PCm values must be non-negative.
hard_constraints = 2: Includes the same constraints as when hard_constraints is 1, which additional constraints on the parameters that can be fitted. For example, Vcmax_at_25 must be non-negative and alpha_psii must lie between 0 and 1.

If any input values violate any of the specified constraints, an error message will be thrown.

References

von Caemmerer, S. "Biochemical Models of Leaf Photosynthesis" (CSIRO Publishing, 2000) [doi:10.1071/9780643103405 ].
von Caemmerer, S. "Updating the steady-state model of C4 photosynthesis." Journal of Experimental Botany 72, 6003–6017 (2021) [doi:10.1093/jxb/erab266 ].
Wang, D., Portis, A. R., Jr., Moose, S. P. & Long, S. P. "Cool C4 Photosynthesis: Pyruvate Pi Dikinase Expression and Activity Corresponds to the Exceptional Cold Tolerance of Carbon Assimilation in Miscanthus × giganteus." Plant Physiology 148, 557–567 (2008) [doi:10.1104/pp.108.120709 ].

Value

The return value depends on the value of return_exdf:

If return_exdf is TRUE, the return value is an exdf object with the following columns: alpha_psii, gbs, Jmax_at_opt, Jmax_tl, J_tl, Rm_frac, Vcmax_tl, Vpmax_tl, RL_tl, RLm_tl, Vpc, Vpr, Vp, Apc, Apr, Ap, Ar, Ajm, Ajbs, Ac, Aj, An, and c4_assimilation_msg. Most of these are calculated as described above, while several are copies of the input arguments with the same name. The c4_assimilation_msg is usually blank but may contain information about any issues with the inputs. The category for each of these new columns is calculate_c4_assimilation to indicate that they were created using this function.
If return_exdf is FALSE, the return value is a numeric vector containing the calculated values of An.

Examples

# Simulate a C4 A-Cm curve with specified leaf temperature and photosynthetic
# parameters and plot the net assimilation rate.
npts <- 101

inputs <- exdf(data.frame(
  PCm = seq(0, 500, length.out = npts),
  Tleaf = 25,
  Qin = 1800,
  total_pressure = 1,
  oxygen = 21
))

inputs <- document_variables(
  inputs,
  c('', 'PCm',            'microbar'),
  c('', 'Tleaf',          'degrees C'),
  c('', 'Qin',            'micromol m^(-2) s^(-1)'),
  c('', 'total_pressure', 'bar'),
  c('', 'oxygen',         'percent')
)

inputs <- calculate_arrhenius(inputs, c4_arrhenius_von_caemmerer, 'Tleaf')

inputs <- calculate_peaked_gaussian(inputs, c4_peaked_gaussian_von_caemmerer, 'Tleaf')

assim <- calculate_c4_assimilation(inputs, 0, 0.003, 400, 1, 0.5, 40, 200, 80)

# Now we can plot Ac, Apr, Apc, and Ar. From this plot, we can see that
# replacing the complicated quadratic equation with a simple minimum yields
# very different results. Although this approximation is helpful for
# understanding C4 photosythesis, it should not be used for calculations.
lattice::xyplot(
  Apr + Apc + Ar + Ac ~ PCm,
  data = cbind(inputs, assim)$main_data,
  type = 'l',
  grid = TRUE,
  auto = TRUE,
  ylim = c(-5, 100),
  xlab = paste0('Partial pressure of CO2 in the mesophyll (', inputs$units$PCm, ')'),
  ylab = paste0('Net CO2 assimilation rate (', assim$units$An, ')')
)


# Likewise, we can look at Ajm, Ajbs, and Aj
lattice::xyplot(
  Ajm + Ajbs + Aj ~ PCm,
  data = cbind(inputs, assim)$main_data,
  type = 'l',
  grid = TRUE,
  auto = TRUE,
  ylim = c(-5, 45),
  xlab = paste0('Partial pressure of CO2 in the mesophyll (', inputs$units$PCm, ')'),
  ylab = paste0('Net CO2 assimilation rate (', assim$units$An, ')')
)


# Finally, we can see whether enzyme activity or light limits overall
# assimilation. In this case, assimilation is always enzyme-limited.
lattice::xyplot(
  Ac + Aj + An ~ PCm,
  data = cbind(inputs, assim)$main_data,
  type = 'l',
  grid = TRUE,
  auto = TRUE,
  ylim = c(-5, 40),
  xlab = paste0('Partial pressure of CO2 in the mesophyll (', inputs$units$PCm, ')'),
  ylab = paste0('Net CO2 assimilation rate (', assim$units$An, ')')
)