PhotoGEA (version 1.4.0)

calculate_isotope_discrimination: Calculate photosynthetic isotope discrimination

Description

Calculates photosynthetic carbon isotope discrimination from combined gas exchange and tunable diode laser absorption spectroscopy measurements.

Usage

calculate_isotope_discrimination(
    exdf_obj,
    co2_r_column_name = 'CO2_r',
    co2_s_column_name = 'CO2_s',
    delta_C13_r_column_name = 'delta_C13_r',
    delta_C13_s_column_name = 'delta_C13_s',
    h2o_r_column_name = 'H2O_r',
    h2o_s_column_name = 'H2O_s',
    tdl_12C_r_column_name = 'calibrated_12c_r',
    tdl_12C_s_column_name = 'calibrated_12c_s'
  )

Value

An exdf object based on exdf_obj that includes several new columns: CO2_r_corrected, CO2_s_corrected,

Delta_obs_gasex, Delta_obs_tdl, xsi_gasex, and

xsi_tdl.

Arguments

exdf_obj

An exdf object representing combined data from a gas exchange + isotope discrimination measurement system. Typically exdf_obj is produced by calling pair_gasex_and_tdl.

co2_r_column_name

The name of the column in exdf_obj that contains the CO2 concentration in the gas exchange reference line (incoming air) as measured by the gas exchange system in micromol mol^(-1).

co2_s_column_name

The name of the column in exdf_obj that contains the CO2 concentration in the gas exchange sample line (outgoing air) in micromol mol^(-1).

delta_C13_r_column_name

The name of the column in exdf_obj that contains the CO2 isotope ratio in the gas exchange reference line (incoming air) in ppt.

delta_C13_s_column_name

The name of the column in exdf_obj that contains the CO2 isotope ratio in the gas exchange sample line (outgoing air) in ppt.

h2o_r_column_name

The name of the column in exdf_obj that contains the H2O concentration in the gas exchange reference line (incoming air) as measured by the gas exchange system in mmol mol^(-1).

h2o_s_column_name

The name of the column in exdf_obj that contains the H2O concentration in the gas exchange sample line (outgoing air) as measured by the gas exchange system in mmol mol^(-1).

tdl_12C_r_column_name

The name of the column in exdf_obj that contains the 12CO2 concentration in the gas exchange reference line (incoming air) as measured by the TDL in ppm.

tdl_12C_s_column_name

The name of the column in exdf_obj that contains the 12CO2 concentration in the gas exchange sample line (outgoing air) as measured by the TDL in ppm.

Details

As described in Ubierna et al. (2018), photosynthetic 13C discrimination can be determined from combined gas exchange and tunable diode laser (TDL) absorption spectroscopy measurements according to:

Delta_obs = xsi * (delta_out - delta_in) / (1 + delta_out - xsi * (delta_out - delta_in)),

where Delta_obs is the observed discrimination, delta_in and delta_out are the carbon isotope ratios in dry air flowing in and out of the leaf chamber. xsi is given by

xsi = C_in / (C_in - C_out),

where C_in and C_out are the mole fractions of 12CO2 in dry air flowing in and out of the leaf chamber. (See equations 5 and 6 in Ubierna et al. (2018)).

In practice, there are multiple options for calculating Delta_obs and xsi because CO2 concentrations are measured by both the gas exchange system and the TDL. For example, we can alternately calculate xsi as xsi_tdl = C_in_tdl / (C_in_tdl - C_out_tdl) or xsi_gasex = C_in_gasex / (C_in_gasex - C_out_gasex). Likewise, we can also calculate Delta_obs_tdl using xsi_tdl or Delta_obs_gasex using xsi_gasex. The TDL values are typically preferred in subsequent calculations, but it can be useful to compare the two different versions as a consistency check; the TDL and gas exchange values should be similar to each other.

There are two subtelties associated with xsi_gasex. One is that the gas exchange system generally measures the total CO2 concentration, not just the 12CO2 concentration. Typically there is much less 13CO2 than 12CO2 so this is usually not a large source of error.

The other issue is that the gas exchange system generally measures CO2 concentrations in wet air. Thus, it is important to use "corrected" values of CO2 concentrations that account for the "dilution effect" due to water vapor in the air. This effect is described in the Licor LI-6400 manual: "This is a correction we don’t do, at least when computing CO2 concentration in the LI-6400. The dilution effect is simply this: as you add molecules of a gas (water vapor, for example) to a mixture, the fraction of that mixture that is made up of something else (mole fraction of CO2, for instance) has to decrease, since the total number of molecules in the mixture has increased. Now for an airsteam flowing though a chamber containing a transpiring leaf (or in a chamber sitting on moist soil), there very definitely is dilution. However, we ignore that effect when computing CO2 concentration, but account for it when computing photosynthetic rate (or soil CO2 efflux). Thus, the LI-6400 IRGA is always indicating the actual CO2 concentration, not what the CO2 concentration would be if there were no water vapor in it."

To account for the dilution effect, we define a "corrected" CO2 concentration as CO2_corrected = CO2 / (1 - H2O), where H2O is the water vapor concentration in the air. Note: the TDL always measures concentrations in dry air, so no correction is required.

References:

Ubierna, N., Holloway-Phillips, M.-M. and Farquhar, G. D. "Using Stable Carbon Isotopes to Study C3 and C4 Photosynthesis: Models and Calculations." in Photosynthesis: Methods and Protocols (ed. Covshoff, S.) 155–196 (Springer, 2018) [tools:::Rd_expr_doi("10.1007/978-1-4939-7786-4_10")].

Examples

## In this example we load gas exchange and TDL data files, calibrate the TDL
## data, pair the data tables together, and then calculate isotope
## discrimination

# Read the TDL data file, making sure to interpret the time zone as US Central
# time
tdl_data <- read_gasex_file(
  PhotoGEA_example_file_path('tdl_for_gm.dat'),
  'TIMESTAMP',
  list(tz = 'America/Chicago')
)

# Identify cycles within the TDL data
tdl_data <- identify_tdl_cycles(
  tdl_data,
  valve_column_name = 'valve_number',
  cycle_start_valve = 20,
  expected_cycle_length_minutes = 2.7,
  expected_cycle_num_valves = 9,
  timestamp_colname = 'TIMESTAMP'
)

# Use reference tanks to calibrate the TDL data
processed_tdl <- consolidate(by(
  tdl_data,
  tdl_data[, 'cycle_num'],
  process_tdl_cycle_erml,
  noaa_valve = 2,
  calibration_0_valve = 20,
  calibration_1_valve = 21,
  calibration_2_valve = 23,
  calibration_3_valve = 26,
  noaa_cylinder_co2_concentration = 294.996,
  noaa_cylinder_isotope_ratio = -8.40,
  calibration_isotope_ratio = -11.505
))

# Read the gas exchange data, making sure to interpret the time stamp in the US
# Central time zone
licor_data <- read_gasex_file(
  PhotoGEA_example_file_path('licor_for_gm_site11.xlsx'),
  'time',
  list(tz = 'America/Chicago')
)

# Get TDL valve information from Licor file name; for this TDL system, the
# reference valve is 12 when the sample valve is 11
licor_data <- get_sample_valve_from_filename(licor_data, list('11' = 12))

# Pair the Licor and TDL data by locating the TDL cycle corresponding to each
# Licor measurement
licor_data <- pair_gasex_and_tdl(licor_data, processed_tdl$tdl_data)

# Calculate isotope discrimination
licor_data <- calculate_isotope_discrimination(licor_data)

# View some of the results
licor_data[, c('A', 'xsi_gasex', 'xsi_tdl', 'Delta_obs_gasex', 'Delta_obs_tdl')]