leakiness_hl: Leakiness calculations in C4 photosynthesis under high light...

In bvsonawane/photosynthesis: Leaf phosynthesis: Data cleaning, computations and C3 and C4 modelling

Description

Calculates leakiness under high light assuming that the, 1. bundle-sheath CO2 concentration much higher than the CO2 concentration in mesophyll cells, 2. High rate CO2 hydration i.e. Vp/Vh = 0 and Vc = A+Rd, 3. No photorespiration Vo= 0, and 4. Fractionation during day respiration = 0.

Eqn referes to Ubierna et al., 2018 (See references).

Usage

leakiness_hl(data, varnames = c(unique_id = "unique_id", Anet = "Photo",
  Rd = "Rd", CibyCa = "Ci.Ca", gm = "gm", D13 = "D13", Ci_Pa = "Ci_Pa",
  Ca_Pa = "Ca_Pa", CL_Pa = "CL_Pa", E = "E", Cond_CO2 = "CndCO2", Tleaf =
  "Tleaf", d13_growth_air = "dgrowth_air", d13_measure_air = "d13.31"),
  e = 0, a = 4.4, b3 = 29, s = 1.8, ab = 2.9, am = 1.8, ...)

Arguments

data	dataframe with variables
varnames	List of names of variables in the dataset (see Details).
e	CO2 fractionation during day respiration, assumed = 0‰
a	Weighter 12C/13 fractionation for diffusion across the boundary layer and stomata in series (4.4‰).
b3	12C/13C fractionation during Rubisco carboxylation (29‰).
s	12C/13C fractionation during CO2 diffusion in the boundary layer (2.9‰)
ab	12C/13C fractionation during CO2 leackage out bundle-sheath cell assuming there is no HCO3 leackage (1.8‰).
am	Summed 12C/13C fractionation during liquid-phase diffusion and dissolution of CO2 (1.8‰)
...	Further arguments (ingore at the moment).

Details

List of variables and their units need to suply in varnames. unique_id: This is a unique id for each row. Makes easy to combine output with other dataframes. Anet: Net rate of CO2 assimilation; umol m^-2s^-1, Rd: Rate of respiration in light; umol m^-2s^-1, CibyC: Ratio of intercelluar CO2 concentration to the ambient, gm: Measoplyll cell CO2 conductance' umol m^-2s^-1 Pa^-1, D13: Observed 13C photsynthetic discrimination (Eqn5); ‰, Ci_Pa: CO2 partial pressure inside the leaf; Pa, Ca_Pa: CO2 partial pressure in the ambient air; Pa, CL_Pa: CO2 partial pressure at the leaf surface; Pa, E: Transpiration rate; mol m^-2s^-1, Cond_CO2: Total conductance to diffusion of CO2 in air; mol m^-2 s^-1, Tleaf: Leaf temperature; degree C, d13_growth_air: delta13C of the CO2 at the plant growth environment, d13_measureair: delta13C of the CO2 in the air used during gas-exchange measurement (Licor reference line).

Value

A dataframe with components:

t	ternary correction factor (‰); Eqn 9
b3_bar	(‰); Eqn 62
b4_bar	(‰); Eqn 63
e_prime	12C/13C fractionation during decarboxylation including the effect of a respiratoy substrate isotipically distinct from recent photosynthate (‰); Eqn 28
leakiness	unitless; Eqn 52 and 64

References

Ubierna N, Holloway-Phillips M-M, Farquhar GD (2018) Using Stable Carbon Isotopes to Study C3 and C4 Photosynthesis: Models and Calculations. In S Covshoff, ed, Photosynthesis: Methods and Protocols. Springer New York, New York, NY, pp 155–196

von Caemmerer S, Ghannoum O, Pengelly JJL, Cousins AB (2014) Carbon isotope discrimination as a tool to explore C4 photosynthesis. J Exp Bot 65: 3459–3470.

Farquhar G (1983) On the nature of carbon isotope discrimination in C4 species. Functional Plant Biol 10: 205–226

bvsonawane/photosynthesis documentation built on Sept. 10, 2019, 3:12 a.m.