Modelling the carbon balance in bryophytes and lichens: Presentation of PoiCarb 1.0, a new model for explaining distribution patterns and predicting climate-change effects
Data files
Jan 09, 2024 version files 59.56 KB
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Nikolic_et_al_2023_CO2_curve_data_Lange_2002.csv
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Nikolic_et_al_2023_Light_curve_data_Lange_2004.csv
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Nikolic_et_al_2023_Microclimatic_input_data_17-24-Sep-93.csv
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Nikolic_et_al_2023_Microclimatic_input_data_17-Sept-01-Oct-1993_Lange_2004.csv
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Nikolic_et_al_2023_Microclimatic_input_data_24-Sep-1-Oct-93.csv
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Nikolic_et_al_2023_Parameters_for_the_model_P_aurata_and_L_muralis.csv
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Nikolic_et_al_2023_Tempetarure_curve_data_Lange_2004.csv
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Nikolic_et_al_2023_Tempetarure_dark_respiration_curve_data_Lange_2004.csv
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Nikolic_et_al_2023_Water_curve_data_Lange_2004.csv
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Nikolic_et_al_2023_Water_dark_respiration_curve_data_Lange_2002.csv
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README.md
Abstract
Premise
Bryophytes and lichens have important functional roles in many ecosystems. Insight into how their CO2 exchange responds to climatic conditions is essential for understanding current and predicting future productivity and biomass patterns, but responses are hard to quantify at time-scales beyond instantaneous measurements. We present PoiCarb 1.0, a model to study how CO2 exchange rates of these poikilohydric organisms change through time as a function of weather conditions.
Methods
PoiCarb simulates diel fluctuations of CO2 exchange and estimates long-term carbon balances, identifying optimal and limiting climatic patterns. Modelled processes are net photosynthesis, dark respiration, evaporation and water uptake. Measured CO2-exchange responses to light, temperature, atmospheric CO2 concentration, and thallus water content (calculated in a separate module) are used to parameterise the model's carbon module. We validated the model by comparing modelled diel courses of net CO2 exchange to such courses from field measurements on the tropical lichen Crocodia aurata. To demonstrate the model's usefulness, we simulated potential climate-change effects.
Results
Diel patterns were reproduced well and modelled and observed diel carbon balances were strongly positively correlated. Simulated warming effects via changes in metabolic rates were consistently negative, while effects via faster drying were variable, depending on the timing of hydration.
Conclusions
Being able to reproduce the weather-dependent variation in diel carbon balances is a clear improvement compared to simple extrapolations of short-term measurements or potential photosynthetic rates. Apart from predicting climate-change effects, future uses of PoiCarb include testing hypotheses about distribution patterns of poikilohydric organisms and guiding species' conservation.
README: Data and code for: Modelling the carbon balance in bryophytes and lichens: presentation of PoiCarb 1.0, a new model for explaining distribution patterns and predicting climate-change effects
https://doi.org/10.5061/dryad.v15dv422v
Description of the data and file structure
File list
· Nikolic_et_al_2023_CO2_curve_data_Lange_2002.csv
· Nikolic_et_al_2023_Light_curve_data_Lange_2004.csv
· Nikolic_et_al_2023_Tempetarure_curve_data_Lange_2004.csv
· Nikolic_et_al_2023_Tempetarure_dark_respiration_curve_data_Lange_2004.csv
· Nikolic_et_al_2023_Water_curve_data_Lange_2004.csv
· Nikolic_et_al_2023_Water_dark_respiration_curves_data_Lange_2002.csv
· Nikolic_et_al_2023_Microclimatic_input_data_17-Sept-01-Oct-1993_Lange_2004.csv
· Nikolic_et_al_2023_Parameters_for_the_model_P_aurata_and_L_muralis.csv
· Nikolic_et_al_2023_Microclimatic_input_data_17-24-Sep-93.csv
· Nikolic_et_al_2023_ Microclimatic_input_data_24-Sep-1-Oct-93.csv
· Nikolic_et_al_2023_Getting_parameters_from_response_curves.R
· Nikolic_et_al_2023_PoiCarb_model.R
File descriptions
Nikolic_et_al_2023_CO2_curve_data_Lange_2002.csv
Data of measured responses of CO2-exchange rates to different CO2 levels. Gas-exchange measurements were made on the lichen Protoparmeliopsis muralis (Lange, 2002). We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations.
Explanation for each column in the file:
CO2abs – CO2 concentration in ppm
A – The instantaneous gas-exchange rate in nmolg-1s-1
Nikolic_et_al_2023_Light_curve_data_Lange_2004.csv
Data of measured responses of CO2-exchange rates (net photosynthesis and dark respiration) to different light (PAR) levels. Gas-exchange measurements were made on the broad-lobed lichen *Crocodia aurata *from a montane rainforest (at ca 1200 m a.s.l) in Panama (Lange et al., 2004). We did not have access to original data, so we used WebPlotDigitizer to extract data points from the published data visualizations.
Explanation for each column in the file:
PAR - Photosynthetic Active Radiation expressed in µmol m-2 s-1
A – The instantaneous gas-exchange rate in nmolg-1s-1
Nikolic_et_al_2023_Tempetarure_curve_data_Lange_2004.csv
Data of measured responses of CO2-exchange rates (net photosynthesis and dark respiration) to different temperature levels. Gas-exchange measurements were made on the broad-lobed lichen *Crocodia aurata *from a montane rainforest (at ca 1200 m a.s.l) in Panama (Lange et al., 2004). We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations.
Explanation for each column in the file:
Tcuv - Temperature in Celsius degrees measured
A – The instantaneous gas-exchange rate in nmolg-1s-1
Nikolic_et_al_2023_Tempetarure_dark_respiration_curve_data_Lange_2004.csv
Data of measured responses of CO2-exchange rates (dark respiration) to different temperature levels. Gas-exchange measurements were made on the broad-lobed lichen *Crocodia aurata *from a montane rainforest (at ca 1200 m a.s.l) in Panama (Lange et al., 2004). We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations.
Explanation for each column in the file:
Tcuv - Temperature in Celsius degrees measured
A – The instantaneous gas-exchange rate in nmolg-1s-1
Nikolic_et_al_2023_Water_curve_data_Lange_2004.csv
Data of measured responses of CO2-exchange rates to changes in lichen water content. Gas-exchange measurements were made on the broad-lobed lichen *Crocodia aurata *from a montane rainforest (at ca 1200 m a.s.l) in Panama (Lange et al., 2004). We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations.
Explanation for each column in the file:
WC - Relative Water content expressed in % of the dry mass
A – The instantaneous gas-exchange rate in nmolg-1s-1
Nikolic_et_al_2023_Water_dark_respiration_curves_data_Lange_2002.csv
Data of measured responses of CO2-exchange rates (dark respiration) to changes in lichen water content. Gas-exchange measurements were made on the lichen Protoparmeliopsis muralis (Lange, 2002). We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations.
Explanation for each column in the file:
WC - Relative Water content expressed in % of the dry mass
A – The instantaneous gas-exchange rate in µmol m-2 s-1
Nikolic_et_al_2023_Microclimatic_input_data_17-Sept-01-Oct-1993_Lange_2004.csv
Microclimatic data together with gas-exchange measurements data which we used for model validation and also to run the climate change experiments examples. There are data for 15 days of in situ gas-exchange measurements on the broad-lobed lichen *Crocodia aurata *from a montane rainforest (at ca 1200 m a.s.l) in Panama (Lange et al., 2004) together with the following climatic factors: air temperature, PAR, and lichen water content, determined at the same time as the CO2-exchange measurements. We did not have access to the original data, so we used WebPlotDigitizer to extract data points from the published data visualizations.
Explanation for each column in the file:
Datum – date of each record in the form: 17-Sep-93
time – date and time of each record
PAR - Photosynthetic Active Radiation expressed in µmol m-2 s-1
T - Temperature in Celsius degrees measured
WC - Relative Water content expressed in % of the dry mass
CO2 - CO2 levels expressed in ppm
Ameasured – Measured gas-exchange rate in nmolg-1s-1
dWC – Difference in water content between two measurements (this we used to determine coefficient k, would not be needed if you have the water loss curve measured on different VPDs)
coef_k – drying speed coefficient
start – contains the date and time for the beginning of the daylight for each day, the rest of the column is filled with NAs (NA stands for not available, this is how the missing values are represented in R). This column is added to the original data to be able to plot the periods of daylight and night in different colors
end – contains the date and time for the end of the daylight for each day, the rest of the column is filled with NAs (NA stands for not available, this is how the missing values are represented in R). This column is added to the original data to be able to plot the periods of daylight and night in different colors
day_night - contains the string value either day, night or NA (NA stands for not available, this is how the missing values are represented in R), this column is added to the original data to be able to plot the periods of daylight and night in different colors
Nikolic_et_al_2023_Parameters_for_the_model_P_aurata_and_L_muralis.csv
Table with parameters we used for validation. To use the PoiCarb 1.0 model, you will need a table like this with parameters for your species. You can obtain the same table by running the Nikolic_et_al_2023_Getting_parameters_from_response_curves.R
Explanation for each column in the file:
LC_par_a, LC_par_b, LC_par_c are the columns containing parameters from the light-response curve; WC_par_a, WC_par_b, WC_par_c are the columns containing parameters from the water-response curve; WC_Rd_par_a, WC_Rd_par_b, WC_Rd_par_c are the columns containing parameters from the dark respiration water-response curve; CO2_par_a, CO2_par_b, CO2_par_c are the columns containing parameters from the CO2-response curve; T_par_a, T_par_b, T_par_c are the columns containing parameters from the temperature-response curve; T_Rd_par_a, T_Rd_par_b are the columns containing parameters from the dark respiration temperature-response curve.
Nikolic_et_al_2023_Microclimatic_input_data_17-24-Sep-93.csv
Nikolic_et_al_2023_ Microclimatic_input_data_24-Sep-1-Oct-93.csv
These two files contain microclimatic data, the same columns and data as in Nikolic_et_al_2023_Microclimatic_input_data_17-Sept-01-Oct-1993_Lange_2004.csv, just separated into two different files, it was better for plotting.
Nikolic_et_al_2023_Getting_parameters_from_response_curves.R
R script to be used to get the parameters from the environmental gas exchange response curves and drying speed curves.
Nikolic_et_al_2023_PoiCarb_model.R
PoiCarb model R script. The script is commented, in case something is not clear enough or you have questions write to the author (nada.m.nikolic@gmail.com).
Sharing/Access information
Data was derived from the following sources:
- Lange, O. L. 2002. Photosynthetic productivity of the epilithic lichen Lecanora muralis: Long-term field monitoring of CO2 exchange and its physiological interpretation. I. Dependence of photosynthesis on water content, light, temperature, and CO2 concentration from laboratory measurements. *Flora *197: 233–249.
- Lange, O. L., B. Büdel, H. Zellner, G. Zotz, and A. Meyer. 1994. Field measurements of water relations and CO2 exchange of the tropical, cyanobacterial basidiolichen Dictyonema glabratum in a Panamanian rainforest*. Botanica Acta 107: 279–290.
Code/Software
There are two R scripts that can be downloaded together with the data. Nikolic_et_al_2023_Getting_parameters_from_response_curves.R and Nikolic_et_al_2023_PoiCarb_model.R. Both scripts are commented (have explanations and notes how to use them).
Methods
Usage Notes
We here present the data and code used in this paper. The list of data files together with their detailed explanations can be found in the README.PDF