Calculate CO2 concentration in the chloroplast or mesophyll

Calculates CO2 concentration in the chloroplast or mesophyll, the CO2 drawdown across the stomata, and the CO2 drawdown across the mesophyll. This function can accomodate alternative column names for the variables taken from the Licor file 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

apply_gm(
    exdf_obj,
    gmc_at_25 = '',
    photosynthesis_type = 'C3',
    calculate_drawdown = TRUE,
    a_column_name = 'A',
    ca_column_name = 'Ca',
    ci_column_name = 'Ci',
    gmc_norm_column_name = 'gmc_norm',
    total_pressure_column_name = 'total_pressure',
    perform_checks = TRUE,
    return_exdf = TRUE
  )

Arguments

exdf_obj: An exdf object, typically representing data from a Licor gas exchange measurement system.
gmc_at_25: The mesophyll conductance to CO2 diffusion at 25 degrees C, expressed in mol m^(-2) s^(-1) bar^(-1). In the absence of other reliable information, gmc_at_25 is often assumed to be infinitely large. If gmc_at_25 is not a number, then there must be a column in exdf_obj called gmc_at_25 with appropriate units. A numeric value supplied here will overwrite the values in the gmc_at_25 column of exdf_obj if it exists.
photosynthesis_type: A string indicating the type of photosynthesis being considered (either 'C3' or 'C4').
calculate_drawdown: A logical value indicating whether to calculate drawdown values.
a_column_name: The name of the column in exdf_obj that contains the net assimilation in micromol m^(-2) s^(-1).
ca_column_name: The name of the column in exdf_obj that contains the ambient CO2 concentration in the chamber in micromol mol^(-1).
ci_column_name: The name of the column in exdf_obj that contains the intercellular CO2 concentration in micromol mol^(-1).
gmc_norm_column_name: The name of the column in exdf_obj that contains the normalized mesophyll conductance values (with units of normalized to gmc at 25 degrees C).
total_pressure_column_name: The name of the column in exdf_obj that contains the total pressure in bar.
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_c3_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_c3_aci calls this function, since creating an exdf object to return will slow down the fitting procedure.

Details

For a C3 plant, the mesophyll conductance to CO2 (gmc) is said to be the conductance satisfying the following one-dimensional flux-conductance equation:

(1) An = gmc * (PCi - PCc)

where An is the net CO2 assimilation rate, PCi is the partial pressure of CO2 in the intercellular spaces, and PCc is the partial pressure of CO2 in the chloroplast. A key underlying assumption for this equation is that the flow of CO2 has reached a steady state; in this case, the flow across the stomata is equal to the flow across the mesophyll.

This equation can be rearranged to calculate PCc:

(2) PCc = PCi - An / gmc

This version of the equation can be found in many places, for example, as Equation 4 in Sharkey et al. "Fitting photosynthetic carbon dioxide response curves for C3 leaves" Plant, Cell & Environment 30, 1035–1040 (2007) [doi:10.1111/j.1365-3040.2007.01710.x ].

It is common to express the partial pressures in microbar and the assimilation rate in micromol m^(-2) s^(-1); in this case, the units of mesophyll conductance become mol m^(-2) s^(-1) bar^(-1).

Licor measurement systems provide CO2 levels as relative concentrations with units of parts per million (ppm), or equivalently, micromol mol^(-1). Concentrations and partial pressures are related by the total gas pressure according to:

(3) partial_pressure = total_pressure * relative_concentration

Thus, it is also possible to calculate the CO2 concentration in the choloroplast (Cc) using the following equation:

(4) Cc = Ci - An / (gmc * P)

where Ci is the intercellular CO2 concentration and P is the total pressure. In this function, Equation (4) is used to calculate Cc, where the total pressure is given by the sum of the atmospheric pressure and the chamber overpressure.

When a plant is photosynthesizing, it draws CO2 into its chloroplasts, and this flow is driven by a concentration gradient. In other words, as CO2 flows from the ambient air across the stomata to the intercellular spaces and then across the mesophyll into the chloroplast, there is a decrease in CO2 concentration at each step. Sometimes it is useful to calculate these changes, which are usually referred to as "CO2 drawdown" values. So, in addition to Ci, this function (optionally) calculates the drawdown of CO2 across the stomata (drawndown_cs = Ca - Ci) and the drawdown of CO2 across the mesophyll (drawdown_cm = Ci - Cc).

_Note_: mesophyll conductance is not specified in typical Licor files, so it usually must be added using set_variable before calling apply_gm.

For a C4 plant, mesophyll conductance instead refers to the conductance associated with the flow of CO2 from the intercellular spaces into the mesophyll (rather than into the chloroplast). In this case, the equations above just require a small modification where Pcc and Cc are replaced by PCm and Cm, the partial pressure and concentration of CO2 in the mesophyll.

Value

The return value depends on the value of return_exdf:

If return_exdf is TRUE, the return value is an exdf object based on exdf_obj with the following columns, calculated as described above: Pci and Ci (for C3 plants) or PCm and Cm (for C4 plants), drawndown_s, and drawdown_cm. The category for each of these new columns is apply_gm to indicate that they were created using this function.
If return_exdf is FALSE, the return value is a list with a single named element (internal_c), which contains values of Cc or Cm as a numeric vector.

Examples

# Read an example Licor file included in the PhotoGEA package
licor_file <- read_gasex_file(
  PhotoGEA_example_file_path('ball_berry_1.xlsx')
)

# Calculate the total pressure in the Licor chamber
licor_file <- calculate_total_pressure(licor_file)

# Calculate temperature-dependent parameter values, including gmc_norm
licor_file <- calculate_temperature_response(licor_file, c3_temperature_param_sharkey)

# Calculate Cc and drawdowns assuming a mesophyll conductance of
# 1 mol / m^2 / s / bar at 25 degrees C
licor_file <- apply_gm(licor_file, 1)

licor_file$units$Cc      # View the units of the new `Cc` column
#> [1] "micromol mol^(-1)"
licor_file$categories$Cc # View the category of the new `Cc` column
#> [1] "apply_gm"
licor_file[, 'Cc']       # View the values of the new `Cc` column
#>  [1] 227.9750 264.4588 238.0217 214.3254 266.2391 289.8527 348.1129 284.2256
#>  [9] 289.2213 285.1018 324.0571 295.4103 313.8207 344.2157 256.2342 295.6076
#> [17] 303.3559 294.7550 328.8761 247.5899 326.4344 218.9675 229.7293 245.0303
#> [25] 276.8719 310.5874 304.1105 250.1419