Guide to data types and required protocol details

Data Type Content - Click on the Data Type you are using for more details
data type
​Protocols for all data types​
​Survey​
​Response of photosynthesis to intercellular CO₂ concentration (ACi curves)​
​Photosynthetic parameters derived from ACi curves​
​Vcmax from one-point​
​Response of photosynthesis to irradiance (AQ curves)​
​Photosynthetic parameters derived from AQ curves​
​Dark adapted respiration​
Protocols for all data types
data type
Protocols for all data types
summary
measurementProtocols required for all data types
description
The measurementProtocol elements listed in this row are required for all data types.
requiredProtocols
The following should be included in the protocols for all data types. Stability criteria and minimum/maximum wait times. Leak testing and leak correction procedures. Handling of instrument bias and calibration. Details of instrument time used and UTC offset of location. Methods for calculating leaf temperature. Approach used if multiple leaves/leaflets/needles were in the chamber at the same time.
references
NA
Survey
data type
Survey
summary
Single point measurement of leaf gas exchange.
description
Survey measurements are typically a single measurement of the exchange of gases at a given point in time. Survey measurements can take many forms and be part of a sequence, e.g. measurement of gas exchange over a diurnal time course. Survey measurements might involve establishing chamber conditions that closely resemble ambient conditions and then taking a measurement as rapidly as possible after placing the leaf in the chamber. These type of measurements typically take less than 90 seconds and data are recorded as soon as the chamber has flushed. The goal is to measure prevailing gas fluxes. Alternatively, survey measurements can also be made under non-ambient conditions including under saturating irradiance and both saturating irradiance and saturating carbon dioxide concentration. Under some circumstances a survey measurement may include a period of stabilization to allow the leaf to acclimate to the chamber conditions set by the user.
requiredProtocols
Where relevant, methods used to determine environmental condition set points (air temperature, relative humidity, VPD, irradiance, CO₂ concentration). Measurement methods, including use of ambient or altered conditions, and how long leaf was in chamber prior to data collection. Indicate if reported values are single measurements or averaged values.
references
Jarvis & Davies (1998), Rogers et al (2004), Halbritter et al (2020).
Response of photosynthesis to intercellular CO₂ concentration (ACi curves)
data type
Response of photosynthesis to intercellular CO₂ concentration (ACi curves)
summary
Sequential measurements on a the same leaf material of leaf gas exchange with varying CO₂ concentration.
description
The response of photosynthesis to intercellular carbon dioxide concentration determined by measuring the response of photosynthesis to changes in chamber carbon dioxide concentrations at saturating irradiance and stable leaf temperature. Measurements are typically made after a stabilization period to achieve steady state gas exchange. An alternative approach where CO₂ concentration is adjusted rapidly after no period of stabilization can also be used for some species (RACiR).
requiredProtocols
Time period of leaf acclimation to chamber conditions, and if steady state gas exchange was achieved. Irradiance used, if it is considered saturating and how saturating light levels were determined. Sequence and timing of CO₂ concentration changes.
references
Long & Bernacchi (2003), Stinziano et al (2017)
Photosynthetic parameters derived from ACi curves
data type
Photosynthetic parameters derived from ACi curves
summary
Results of fitting photosynthetic CO₂ response curves to derive parameters, e.g. apparent Vcmax, Jmax, TPU
description
Results of fitting ACi curves to a photosynthesis model to derive parameters, e.g. apparent Vcmax, Jmax, TPU. Apparent Vcmax is calculated based on Ci (rather than Cc) and assumes an infinite mesophyll conductance to CO₂.
requiredProtocols
Method for fitting data (provide reference or code repository). Include kineticConstants and their temperature dependency in methodsMetadata.
references
Bernacchi et al. (2013), Collatz (1992), von Caemmerer (2000), Dubois et al (2007), Duursma et al (2015), Farquhar et al (1980), Gu et al. (2010), Sharkey et al (2007), Zhou et al (2019)
Vcmax from one-point
data type
Vcmax from one-point
summary
Apparent Vcmax calculated from Asat measurements using the one-point method
description
Results of calculating apparent Vcmax from Asat measurements using the one-point method.
requiredProtocols
See details for Survey. Include kineticConstants in methodsMetadata.
references
De Kauwe (2017), Corrigendum (2017), also see Burnett (2019).
Response of photosynthesis to irradiance
data type
Response of photosynthesis to irradiance (AQ curves)
summary
Sequential measurements on the same leaf material of photosynthetic rate with varying irradiance
description
The response of photosynthesis to irradiance determined by measuring the response of photosynthesis to changes in irradiance at constant leaf temperature and atmospheric CO₂ concentration. Response curves can be measured slowly to allow full stomatal acclimation to each new level of irradiance (> 15 minutes at each step) or rapidly when the response of stomata is not of interest. To estimate Rlight a high number of points at low irradiance are required.
requiredProtocols
Time period of leaf acclimation to chamber conditions, and if steady state gas exchange was achieved. Sequence and timing of irradiance changes. Use of incident or absorbed light. State value used for leaf absorptance, if assumed or measured, and method if measured. Indicate if reported values are single measurements or averaged values.
references
Posada et al (2009), Verryckt et al (2020)
Photosynthetic parameters derived from AQ curves
data type
Photosynthetic parameters derived from AQ curves
summary
Results of fitting light response curves to derive parameters
description
Results of fitting light response curves to a photosynthesis model to derive parameters, e.g. quantum yield of CO₂ fixation, light compensation point
requiredProtocols
Method for fitting data (provide reference or code repository).
references
Posada et al (2009)
Dark adapted respiration
data type
Dark adapted respiration
summary
Respiration rate of dark adapted leaf
description
Respiration rate of dark adapted leaf
requiredProtocols
Dark adaptation period. Time of measurement (day, night, pre-dawn). Measurement time period and number of data points used. Details of dark adaption, including which plant parts (leaf section, entire leaf, entire plant) and method (in cuvette, covered, at night). Flow rate used.
references
Aspinwall et al (2016), Crous et al (2011)
References
Aspinwall MJ, Drake JE, Campany C, Varhammar A, Ghannoum O, Tissue DT, Reich PB, Tjoelker MG. (2016). Convergent acclimation of leaf photosynthesis and respiration to prevailing ambient temperatures under current and warmer climates in Eucalyptus tereticornis. New Phytologist, 212, 354-367.
Bernacchi, C. J., Bagley, J. E., Serbin, S. P., Ruiz-Vera, U. M., Rosenthal, D. M., & Vanloocke, A. (2013). Modelling C3photosynthesis from the chloroplast to the ecosystem. In Plant, Cell & Environment (Vol. 36, Issue 9, pp. 1641–1657). https://doi.org/10.1111/pce.12118​
Burnett, A. C., Davidson, K. J., Serbin, S. P., & Rogers, A. (2019). The “one‐point method” for estimating maximum carboxylation capacity of photosynthesis: A cautionary tale. In Plant, Cell & Environment (Vol. 42, Issue 8, pp. 2472–2481). https://doi.org/10.1111/pce.13574​
Collatz GJ, Ribas-Carbo M, Berry JA (1992) Coupled photosynthesis - stomatal conductance model for leaves of C4 plants. Australian Journal of Plant Physiology, 19, 519-538.
Corrigendum. (2017). The New Phytologist, 213(3), 1555.
Crous, K. Y., Zaragoza-Castells, J., Löw, M., Ellsworth, D. S., Tissue, D. T., Tjoelker, M. G., Barton, C. V. M., Gimeno, T. E., & Atkin, O. K. (2011). Seasonal acclimation of leaf respiration in Eucalyptus saligna trees: impacts of elevated atmospheric CO₂> and summer drought. In Global Change Biology (Vol. 17, Issue 4, pp. 1560–1576). https://doi.org/10.1111/j.1365-2486.2010.02325.x​
De Kauwe, M. G., Lin, Y.-S., Wright, I. J., Medlyn, B. E., Crous, K. Y., Ellsworth, D. S., Maire, V., Prentice, I. C., Atkin, O. K., Rogers, A., Niinemets, Ü., Serbin, S. P., Meir, P., Uddling, J., Togashi, H. F., Tarvainen, L., Weerasinghe, L. K., Evans, B. J., Ishida, F. Y., & Domingues, T. F. (2016). A test of the “one-point method” for estimating maximum carboxylation capacity from field-measured, light-saturated photosynthesis. The New Phytologist, 210(3), 1130–1144.
Dubois, J.-J. B., Fiscus, E. L., Booker, F. L., Flowers, M. D., & Reid, C. D. (2007). Optimizing the statistical estimation of the parameters of the Farquhar-von Caemmerer-Berry model of photosynthesis. The New Phytologist, 176(2), 402–414.
Farquhar, G. D., von Caemmerer, S., & Berry, J. A. (1980). A biochemical model of photosynthetic CO₂ assimilation in leaves of C3 species. In Planta (Vol. 149, Issue 1, pp. 78–90). https://doi.org/10.1007/bf00386231​
Gu, L., Pallardy, S. G., Tu, K., Law, B. E., & Wullschleger, S. D. (2010). Reliable estimation of biochemical parameters from C3 leaf photosynthesis-intercellular carbon dioxide response curves. In Plant, Cell & Environment (Vol. 33, Issue 11, pp. 1852–1874). https://doi.org/10.1111/j.1365-3040.2010.02192.x​
Halbritter, A., De Boeck, H., Vandvik, V., & Amy E. Eycott Sabine Reinsch David A. Robinson Sara Vicca Bernd Berauer Casper T. Christiansen Marc Estiarte José M. Grünzweig Ragnhild Gya Karin Hansen Anke Jentsch Hanna Lee Sune Linder John Marshall Josep Peñuelas Inger Kappel Schmidt E. (2020). The handbook for standardized field and laboratory measurements in terrestrial climate change experiments and observational studies (ClimEx). https://doi.org/10.5194/egusphere-egu2020-16136​
Jarvis, A. J., & Davies, W. J. (1998). The coupled response of stomatal conductance to photosynthesis and transpiration. In Journal of Experimental Botany (Vol. 49, Issue Special, pp. 399–406). https://doi.org/10.1093/jxb/49.special_issue.399​
Long, S. P., & Bernacchi, C. J. (2003). Gas exchange measurements, what can they tell us about the underlying limitations to photosynthesis? Procedures and sources of error. Journal of Experimental Botany, 54(392), 2393–2401.
Posada, J. M., Lechowicz, M. J., & Kitajima, K. (2009). Optimal photosynthetic use of light by tropical tree crowns achieved by adjustment of individual leaf angles and nitrogen content. Annals of Botany, 103(5), 795–805.
Rogers, A., Allen, D. J., Davey, P. A., Morgan, P. B., Ainsworth, E. A., Bernacchi, C. J., Cornic, G., Dermody, O., Dohleman, F. G., Heaton, E. A., Mahoney, J., Zhu, X.-G., Delucia, E. H., Ort, D. R., & Long, S. P. (2004). Leaf photosynthesis and carbohydrate dynamics of soybeans grown throughout their life-cycle under Free-Air Carbon dioxide Enrichment. Plant, Cell and Environment (Vol. 27, Issue 4, pp. 449–458). https://doi.org/10.1111/j.1365-3040.2004.01163.x​
Sharkey, T. D., Bernacchi, C. J., Farquhar, G. D., & Singsaas, E. L. (2007). Fitting photosynthetic carbon dioxide response curves for C3leaves. In Plant, Cell & Environment (Vol. 30, Issue 9, pp. 1035–1040). https://doi.org/10.1111/j.1365-3040.2007.01710.x​
Stinziano, J. R., Morgan, P. B., Lynch, D. J., Saathoff, A. J., McDermitt, D. K., and Hanson, D. T. (2017) The rapid A–Ci response: photosynthesis in the phenomic era. Plant Cell & Environment, 40: 1256– 1262. doi: 10.1111/pce.12911.
Verryckt, LT, Ellsworth, DS, Vicca, S, et al. Can light‐saturated photosynthesis in lowland tropical forests be estimated by one light level?. Biotropica. 2020; 00: 1– 11. https://doi.org/10.1111/btp.12817​
Von Caemmerer, S. (2000). Biochemical models of leaf photosynthesis. Clayton: CSIRO Publishing.

Methods metadata guide

Documents

Last modified 2yr ago

data type	Photosynthetic parameters derived from ACi curves
summary	Results of fitting photosynthetic CO₂ response curves to derive parameters, e.g. apparent Vcmax, Jmax, TPU
description	Results of fitting ACi curves to a photosynthesis model to derive parameters, e.g. apparent Vcmax, Jmax, TPU. Apparent Vcmax is calculated based on Ci (rather than Cc) and assumes an infinite mesophyll conductance to CO₂.
requiredProtocols	Method for fitting data (provide reference or code repository). Include kineticConstants and their temperature dependency in methodsMetadata.
references	Bernacchi et al. (2013), Collatz (1992), von Caemmerer (2000), Dubois et al (2007), Duursma et al (2015), Farquhar et al (1980), Gu et al. (2010), Sharkey et al (2007), Zhou et al (2019)

data type	Vcmax from one-point
summary	Apparent Vcmax calculated from Asat measurements using the one-point method
description	Results of calculating apparent Vcmax from Asat measurements using the one-point method.
requiredProtocols	See details for Survey. Include kineticConstants in methodsMetadata.
references	De Kauwe (2017), Corrigendum (2017), also see Burnett (2019).

data type	Protocols for all data types
summary	measurementProtocols required for all data types
description	The measurementProtocol elements listed in this row are required for all data types.
requiredProtocols	The following should be included in the protocols for all data types. Stability criteria and minimum/maximum wait times. Leak testing and leak correction procedures. Handling of instrument bias and calibration. Details of instrument time used and UTC offset of location. Methods for calculating leaf temperature. Approach used if multiple leaves/leaflets/needles were in the chamber at the same time.
references	NA

data type	Survey
summary	Single point measurement of leaf gas exchange.
description	Survey measurements are typically a single measurement of the exchange of gases at a given point in time. Survey measurements can take many forms and be part of a sequence, e.g. measurement of gas exchange over a diurnal time course. Survey measurements might involve establishing chamber conditions that closely resemble ambient conditions and then taking a measurement as rapidly as possible after placing the leaf in the chamber. These type of measurements typically take less than 90 seconds and data are recorded as soon as the chamber has flushed. The goal is to measure prevailing gas fluxes. Alternatively, survey measurements can also be made under non-ambient conditions including under saturating irradiance and both saturating irradiance and saturating carbon dioxide concentration. Under some circumstances a survey measurement may include a period of stabilization to allow the leaf to acclimate to the chamber conditions set by the user.
requiredProtocols	Where relevant, methods used to determine environmental condition set points (air temperature, relative humidity, VPD, irradiance, CO₂ concentration). Measurement methods, including use of ambient or altered conditions, and how long leaf was in chamber prior to data collection. Indicate if reported values are single measurements or averaged values.
references	Jarvis & Davies (1998), Rogers et al (2004), Halbritter et al (2020).

data type	Response of photosynthesis to intercellular CO₂ concentration (ACi curves)
summary	Sequential measurements on a the same leaf material of leaf gas exchange with varying CO₂ concentration.
description	The response of photosynthesis to intercellular carbon dioxide concentration determined by measuring the response of photosynthesis to changes in chamber carbon dioxide concentrations at saturating irradiance and stable leaf temperature. Measurements are typically made after a stabilization period to achieve steady state gas exchange. An alternative approach where CO₂ concentration is adjusted rapidly after no period of stabilization can also be used for some species (RACiR).
requiredProtocols	Time period of leaf acclimation to chamber conditions, and if steady state gas exchange was achieved. Irradiance used, if it is considered saturating and how saturating light levels were determined. Sequence and timing of CO₂ concentration changes.
references	Long & Bernacchi (2003), Stinziano et al (2017)

data type	Response of photosynthesis to irradiance (AQ curves)
summary	Sequential measurements on the same leaf material of photosynthetic rate with varying irradiance
description	The response of photosynthesis to irradiance determined by measuring the response of photosynthesis to changes in irradiance at constant leaf temperature and atmospheric CO₂ concentration. Response curves can be measured slowly to allow full stomatal acclimation to each new level of irradiance (> 15 minutes at each step) or rapidly when the response of stomata is not of interest. To estimate Rlight a high number of points at low irradiance are required.
requiredProtocols	Time period of leaf acclimation to chamber conditions, and if steady state gas exchange was achieved. Sequence and timing of irradiance changes. Use of incident or absorbed light. State value used for leaf absorptance, if assumed or measured, and method if measured. Indicate if reported values are single measurements or averaged values.
references	Posada et al (2009), Verryckt et al (2020)

data type	Dark adapted respiration
summary	Respiration rate of dark adapted leaf
description	Respiration rate of dark adapted leaf
requiredProtocols	Dark adaptation period. Time of measurement (day, night, pre-dawn). Measurement time period and number of data points used. Details of dark adaption, including which plant parts (leaf section, entire leaf, entire plant) and method (in cuvette, covered, at night). Flow rate used.
references	Aspinwall et al (2016), Crous et al (2011)