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This documentation contains guidance for the content and format of leaf-level gas exchange data and metadata. The reporting format comprises defined variable names and units for data tables, a methods metadata template, and instrument details template and guidance on inclusion of other related data and metadata.
The ESS-DIVE leaf-level gas exchange data and metadata reporting format has been developed to meet the needs of the community for a unified reporting format. This initial effort covers the most common variables and provides templates for metadata reporting. Additional reporting requirements have been developed for seven common 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
For a full description of the reporting format, refer to Ely et al (2021). A reporting format for leaf-level gas exchange data and metadata. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2021.101232
Instructions for how to use this reporting format:
Other documents to get started:
Methods metadata template: Download spreadsheet template for recording experiment and methods metadata.
Instrument details template: Download spreadsheet template to record instrument details.
Added a section to the Instructions on how to use this format in combination with other reporting formats to provide guidance on missing value, temporal and spatial data types.
See Releases for complete versioning details.
This leaf-level gas exchange data reporting format is evolving and growing to meet the needs of the community. Feedback and new contributions are welcome, and can be made by submitting an issue or feedback.
The issue templates we use are modeled from that provided by Darwin Core: Darwin Core maintenance group, Biodiversity Information Standards (TDWG) (2014). Darwin Core. Zenodo. https://doi.org/10.5281/zenodo.592792
The leaf-level gas exchange data and metadata reporting format is licensed under the Creative Commons Attribution 4.0 International (CCby4).
Funding for the development of ESS-DIVE's leaf-level gas exchange data and metadata reporting format was provided by the US Department of Energy (DOE), Biological and Environmental Research Program, Earth and Environmental Systems Sciences Division, Data Management.
The format was developed with input and feedback of over 80 subject experts, including data collectors, data scientists, data users (empiricists and modelers), and instrument manufacturers. Thank you all.
For further description of the reporting format, and the development process, refer to:
Ely et al (2021). A reporting format for leaf-level gas exchange data and metadata. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2021.101232
Ely K.S., Rogers A, Crystal-Ornelas R (2020): ESS-DIVE reporting format for leaf-level gas exchange data and metadata. Environmental Systems Science Data Infrastructure for a Virtual Ecosystem. doi:10.15485/1659484
A data package containing leaf-level gas exchange data must include, at a minimum:
Assemble the data table, using the defined variableNames and variableUnits. If the data is a described data type under this format, then the data table must include the required variables for that data type. Data tables may also include additional variables, and indicators of uncertainty if appropriate.
Collate the full instrument output files, and assess the quality control level. Note that there is no requirement to edit column headers in full instrument output files to standard variable names.
Fill in the Methods metadata template, ensuring that required protocols for each data type are described. See our methods metadata guide for descriptions and instructions for each metadata field. Save as csv file type. A separate methods metadata file should be created for each data type included in the data package.
Fill in the Instrument details template and save as csv file type.
Prepare methods supplements tables to define codes used to capture sample characteristics in the data tables. See our supplement metadata guide for guidance. Save each file as csv file type.
Inclusion of additional related datasets with gas exchange data is encouraged. This can include measurements made inline, such as fluorescence or isotopic measurements, or subsequent analysis of chemical composition or physical properties. Related data should be linked by using common sample identifiers.
Defined variables should be used where available. For variables not yet covered by this reporting format documentation, data contributors should use machine readable variable names that are in common use.
We will continue to work with the ESS community to improve data and metadata reporting formats for leaf-level gas exchange data. Please contribute by submitting issues, using our issue templates, or contact ess-dive-support@lbl.gov to provide any feedback on the process of formatting data, specific metadata fields or controlled vocabulary terms.
The ESS-DIVE collection of reporting formats includes formats for different measurement types and also for file and metadata structures. The collection is designed to be modular, so use of multiple reporting formats will be required to correctly format a data package. As such, the content of this Leaf-level gas exchange data and metadata reporting format is limited to guidance specific to gas exchange data.
For ESS-DIVE data packages, file formats should follow those presented in the csv file and file level metadata reporting format documentation. The ESS-DIVE Reporting Format for Comma-separated Values (CSV) File Structure includes guidance for many general data types, including missing values, temporal and spatial data. Supplementary data should follow the relevant data format, where available, such as the ESS-DIVE Sample ID and Metadata Reporting Format (IGSN-ESS).
Refer to the ESS-DIVE Community Space for a complete list of available reporting formats.
Here is an example data package that follows these reporting format guidelines.
Rogers, Alistair, Kim Ely, Shawn Serbin (2019). Leaf Photosynthetic Parameters: Quantum Yield, Convexity, Respiration, Gross CO₂ Assimilation Rate and Raw Gas Exchange Data, Barrow, Alaska, 2016. Next Generation Ecosystem Experiments Arctic Data Collection, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, USA. doi.org/10.5440/1482338.
This page provides guidelines and expectations for completion of the methods metadata template. Note that while defined vocabulary terms are suggested, most variables may be complete with free text entries if required.
The main purpose of this metadata collection will be to aid data search with some common discriminators. It is not meant to be a substitute for a complete experimental description. Additional information should be included as methods supplements tables, or in a methods text file.
*
indicate required content
| |
| |
| |
| |
| |
| |
Metadata Element | dataType |
Required Recommended Optional |
|
Description | Enter data type described by this methods metadata file. Refer to data types in documentation for definitions. |
Format | Controlled vocabulary or free text |
Additional Instructions |
Controlled vocabulary terms | Refer to data types table for list. |
Metadata Element | additionalDataIncluded |
Required Recommended Optional |
|
Description | Indicate if additional data collected in-line during gas exchange is included. e.g. fluorescence, isotopic discrimination |
Format | Controlled vocabulary |
Additional Instructions |
Controlled vocabulary terms | yes; no |
Metadata Element | instrumentOutputStatus |
Required Recommended Optional |
|
Description | Indicate the highest quality status of complete instrument output included in the data package. Multiple versions may be included. |
Format | Controlled vocabulary |
Additional Instructions | 0 = data not available. 1 = direct instrument download, minimal quality control. 2 = complete quality control, files are verified to only contain valid data, or, invalid data is flagged. Measurement values are reasonable and within expected range. Area corrections are made where required. Time and dates verified as correct. User input errors corrected. |
Controlled vocabulary terms | 0; 1; 2 |
Metadata Element | plantType |
Required, Recommended, or Optional |
|
Description | Photosynthetic pathway of measured plants. |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. |
Controlled vocabulary terms | C3; C4; CAM |
Metadata Element | leafType |
Required, Recommended, or Optional |
|
Description | Describe the leaf type(s) measured. |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. |
Controlled vocabulary terms | broadleaf; graminoid; needleleaf; phyllode |
Metadata Element | requiredProtocols |
Required, Recommended, or Optional |
|
Description | Details of measurement protocols. Refer to requiredProtocols for each data type for required protocol information. Can cite reference or other source if this information is recorded elsewhere. |
Format | Free text |
Additional instructions |
Controlled vocabulary terms |
Metadata Element | mesophyllConductanceType |
Required, Recommended, or Optional |
|
Description | Describe assumption or measurement of mesophyll conductance. Infinite mesophyll conductance assumes intercellular CO2 concentration (Ci) is equal to the CO2 concentration at the site of carboxylation inside the chloroplast (Cc). |
Format | Controlled vocabulary |
Additional instructions |
Controlled vocabulary terms | assumed infinite; measured |
Metadata Element | leafStatus |
Required, Recommended, or Optional |
|
Description | Describe the leaf status during gas exchange measurement. |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. |
Controlled vocabulary terms | attached leaf; attached leaf on excised branch; excised leaf |
Metadata Element | leafAreaBasis |
Required, Recommended, or Optional |
|
Description | Describe the basis for measurement of leaf area. The default is "one-sided leaf area" which is typical for regular leaf types but there are several other alternatives, including in rare circumstances the use of mass or volume. |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. |
Controlled vocabulary terms | one-sided area; hemi-surface area; projected area; total area; dry mass; volume |
Metadata Element | leafAreaMethod |
Required, Recommended, or Optional |
|
Description | Describe the methods used for measurement of leaf area. |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. |
Controlled vocabulary terms | single leaf fills chamber of known area; multiple leaves fill chamber of known area; geometrically determined; calculated using imaging software; measured using leaf area meter |
Metadata Element | kineticConstants |
Required, Recommended, or Optional |
|
Description | Citations and values for kinetic constants, and their temperature dependance. |
Format | Free text |
Additional instructions |
Controlled vocabulary terms |
Metadata Element | growthEnvironment |
Required, Recommended, or Optional |
|
Description | Describe the plant growth environment. Provide details in Methods. |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. |
Controlled vocabulary terms | natural in ground; cultivated in ground; potted; glasshouse; controlled environment chamber; other chamber type; hydroponic |
Metadata Element | experimentalManipulation |
Required, Recommended, or Optional |
|
Description | Indicate if any samples were subject to a manipulation. For naturally grown plants, or cultivated plants with standard fertilizer and pesticide application across all samples, select "none". Provide further treatment details in methodsSupplements tables. |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. |
Controlled vocabulary terms | none; atmosphere; genetic; growth media; pesticide; light; nutrients; salinity; soil modification; source-sink; temperature; water availability |
Metadata Element | plantAge |
Required, Recommended, or Optional |
|
Description | Age in appropriate units (days, months, years) or relative age category (e.g. seedling, germling, sapling, mature) or other classification relevant to experiment. |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. Include a methods supplements table if required. |
Controlled vocabulary terms | unknown; seedling; germling; sapling; mature |
Metadata Element | leafAge |
Required, Recommended, or Optional |
|
Description | Age in appropriate units (days, months, years) or relative age category (e.g. young, mature, old) or other classification (e.g. most recent fully expanded, physiologically mature leaf; LPI classification). |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. Include a methods supplements table if required. |
Controlled vocabulary terms | young; mature; old; unknown; multiple ages |
Metadata Element | canopyPosition |
Required, Recommended, or Optional |
|
Description | Position of leaf samples within canopy. |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. |
Controlled vocabulary terms | top of canopy; within canopy |
Metadata Element | canopyHeight |
Required, Recommended, or Optional |
|
Description | Sample canopy position and canopy height or LAI recorded. |
Format | Controlled vocabulary |
Additional instructions | If yes, provide details in metadata supplements and/or data tables. |
Controlled vocabulary terms | yes; no |
Metadata Element | lightExposure |
Required, Recommended, or Optional |
|
Description | Light environment of leaf samples. |
Format | Controlled vocabulary or free text |
Additional instructions | List all that apply, use a semi-colon to delimit multiple terms. |
Controlled vocabulary terms | sunlit; shade |
Data tables for a described data type must contain variables as indicated in this table. Note that this is a minumum requirement, any data table may also contain any additional variables. Refer to the variable definitions table for variable names and units that should be used in data tables.
Supplementary metadata tables should be provided to explain codes used in data tables used to describe samples and experimental variables. Supplementary metadata tables or text should also record additional experimental detail not recorded in the methods metadata template.
Here are some typical examples of how to present these metadata. Tables should be included in data packages as .csv files.
Guidance on variable names and descriptions should be taken from other ESS-DIVE data formats where available, for example, the Sample ID and Metadata Reporting Format.
The requirement for methods supplement tables or text documents will depend on the experimental setup. Where available and appropriate consider including the following information in a gas exchange data package: biome, ecosystem type, climate, local seasonality, timing of measurements relative to the growing season, data time zone and relationship with solar noon, environmental conditions at time of measurement, soil type, canopy exposure, canopy height and depth, terrain, aspect, seed provenance, genetic or cultivar details, pot size, leaf age classes, instrument configuration and measurement scripts.
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.
data type |
---|
data type | Protocols for all data types |
---|---|
data type | Survey |
---|---|
data type | Response of photosynthesis to intercellular CO₂ concentration (ACi curves) |
---|---|
data type | Photosynthetic parameters derived from ACi curves |
---|---|
data type | Vcmax from one-point |
---|---|
data type | Dark adapted respiration |
---|---|
variableName
survey
ACi curves
Photosynthetic parameters derived from ACi curves
Vcmax from one-point
AQ curves
Photosynthetic parameters derived from AQ curves
Dark adapted respiration
A
x
x
x
x
x
Ci
x
x
x
x
x
CO2s
x
x
x
gsw
x
Patm
x
x
x
x
x
x
x
Qin
x
x
x
x
x
x
RHs
x
x
x
x
x
x
x
Tleaf
x
x
x
x
x
x
x
Fitted parameters
x
x
x
Metadata variable
Format
Description
Example
speciesCode
Free text
Code used to identify species in data tables
JUOC
species
Free text
Full species name and subspecies if applicable
Juniperus occidentalis
genotype
Free text
Identified genotype or mutant
citation
Free text
Reference for species authority
Hook.
Metadata variable
Format
Description
Example
siteIdentifier
Free text
Plot or plant within this experiment for which position is being reported
Plot07
longitude
Decimal degrees
Longitude
-122.18877
latitude
Decimal degrees
Latitude
46.197905
elevation
Meters above sea level
Elevation of location
2155
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
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).
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)
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)
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
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
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)
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)
This table shows variable names and units that should be used in data tables. Expected range values cover most plants for standard experimental conditions and may be used as a guide for quality checking.
variableName
variableUnit
variableDescription
expectedValueRangeMin
expectedValueRangeMax
Instrument outputs
date
YYYY-MM-DD
Date of observation
time
HH:MM:SS
Time of observation
record
-
Observation record number
area
cm²
Leaf area
A
µmol m⁻² s⁻¹
Net CO₂ exchange per leaf area
-20
120
Amax
µmol m⁻² s⁻¹
Highest rate of light and CO₂ saturated A
-20
120
Asat
µmol m⁻² s⁻¹
Highest rate of light saturated A at ambient CO₂ concentration
-20
120
Ci
µmol mol⁻¹
Intercellular CO₂ concentration in air
0
5000
CO2r
µmol mol⁻¹
CO₂ concentration in wet air entering chamber
0
5000
CO2s
µmol mol⁻¹
CO₂ concentration in wet air inside chamber
0
5000
dCO2
µmol mol⁻¹
Sample minus reference CO₂ concentration in air
dH2O
mmol mol⁻¹
Sample minus reference H₂O concentration in air
E
mmol m⁻² s⁻¹
Transpiration rate of H₂O per leaf area. Note that output units from some instruments are in mol and will require conversion.
flow
µmol s⁻¹
Flow rate of air into chamber
gbw
mmol m⁻² s⁻¹
Boundary layer conductance to water vapor per leaf area
gsw
mmol m⁻² s⁻¹
Stomatal conductance to water vapor per leaf area
0
1000
H2Or
mmol mol⁻¹
H₂O concentration in air entering chamber
H2Os
mmol mol⁻¹
H₂O concentration in air inside chamber
Patm
kPa
Atmospheric pressure
50
120
Qin
µmol m⁻² s⁻¹
In-chamber photosynthetic flux density (PPFD) incident on the leaf, quanta per area
0
5000
Qout
µmol m⁻² s⁻¹
External photosynthetic flux density (PPFD), quanta per area
0
5000
RHr
%
Relative humidity of air entering the chamber
0
100
RHs
%
Relative humidity of air inside the chamber
0
100
Tair
°C
Air temperature inside the chamber
-20
70
Tleaf
°C
Leaf surface temperature
-20
70
VPDleaf
kPa
Leaf to air vapor pressure deficit
0
5
Calculated parameters
AsatG
µmol m⁻² s⁻¹
Maximum rate of gross CO₂ assimilation derived from the light response curve. Equivalent to total of CO₂ assimilation and CO₂ release.
CE
mol m⁻² s⁻¹
Maximum carboxylation efficiency, based on an empirical determination of the initial slope of an ACi curve
CiCa
-
Ratio of intercellular CO₂ to sample chamber CO₂
CO2comp
µmol mol⁻¹
CO₂ compensation point
gm
mol m⁻² s⁻¹
Mesophyll conductance to CO₂ per leaf area
J
µmol m⁻² s⁻¹
Rate of electron transport per leaf area at measurement temperature calculated assuming infinite mesophyll conductance for a given irradiance e.g. J1800. Or at reference temperature e.g., J1800,25
0
600
Jmax
µmol m⁻² s⁻¹
Maximum rate of electron transport per leaf area at measurement temperature calculated assuming infinite mesophyll conductance and saturating light
0
600
Jmax25
µmol m⁻² s⁻¹
Maximum rate of electron transport per leaf area, at the reference temperature 25°C calculated assuming infinite mesophyll conductance and saturating light
0
600
LCP
µmol m⁻² s⁻¹
Light compensation point. The lowest photosynthetic photon flux density at which positive net CO₂ assimilation is observed
LSP
µmol m⁻² s⁻¹
Light saturation point. The irradiance at which further increases in irradiance level do not increase net CO₂ assimilation rate.
PhiCO2a
mol mol⁻¹
Maximum quantum yield of CO₂ assimilation based on absorbed irradiance
PhiCO2i
mol mol⁻¹
Maximum quantum yield of CO₂ assimilation based on incident irradiance
PhiJa
mol mol⁻¹
Maximum quantum yield of electron transport based on arbsorbed irradiance
PhiJi
mol mol⁻¹
Maximum quantum yield of electron transport based on incident irradiance
Rdark
µmol m⁻² s⁻¹
CO₂ release from the leaf in the dark, at measurement temperature, reported as a positive value
Rdark25
µmol m⁻² s⁻¹
CO₂ release from the leaf in the dark, at the reference temperature of 25°C, reported as a positive value
Rday
µmol m⁻² s⁻¹
CO₂ release from the leaf in the light, reported as a positive value
Rday25
µmol m⁻² s⁻¹
CO₂ release from the leaf in the light, at the reference temperature of 25°C, reported as a positive value.
Theta
-
Empirical convexity parameter derived from the non-rectangular hyperbolic model of the light response curve
TPU
µmol m⁻² s⁻¹
Triose phosphate utilization rate per leaf area at measurement temperature
TPU25
µmol m⁻² s⁻¹
Triose phosphate utilization rate per leaf area at the reference temperature 25°C
Vcmax
µmol m⁻² s⁻¹
Maximum rate of carboxylation at measurement temperature, calculated assuming infinite mesophyll conductance, i.e. apparent Vcmax
0
500
Vcmax25
µmol m⁻² s⁻¹
Maximum rate of carboxylation, at the reference temperature 25°C, calculated assuming infinite mesophyl conductance, i.e. apparent Vcmax
0
500
Vpmax
µmol m⁻² s⁻¹
Phosphoenolpyruvate (PEP) saturated PEP carboxylation at measurement temperature
WUEi
µmol mol⁻¹
Intrinsic water use efficiency. Net CO₂ exchange per leaf area divided by stomatal conductance to water vapor per leaf area
Constants
Alpha
-
Leaf absorptance of visible radiation (400-730 nm)
0
1
EaGammaStar
kJ mol⁻¹
Activation energy associated with the temperature response of gammaStar
EaKc
kJ mol⁻¹
Activation energy associated with the temperature response of Kc
EaKo
kJ mol⁻¹
Activation energy associated with the temperature response of Ko
EaVcmax
kJ mol⁻¹
Activation energy associated with the temperature response of Vcmax
EaVomax
kJ mol⁻¹
Activation energy associated with the temperature response of Vomax, the maximum rate of oxygenation
f
-
Fraction of light absorbed by photosystem II that is not used for photochemistry
gammaStar25
µmol mol⁻¹
CO₂ compensation point in the absence of non-photorespiratory CO₂ release at the reference temperature of 25°C
Kc25
µmol mol⁻¹
Michaelis constant for CO₂ concentration in air at the reference temperature of 25°C
Ko25
mmol mol⁻¹
Michaelis constant for O₂ concentration in air at the reference temperature of 25°C
Oi
mmol mol⁻¹
Intercellular O₂ concentration in air (default 210 unless experimentally manipulated)
Tau25
-
CO₂:O₂ specificity ratio at a reference temperature of 25°C
TauQ10
-
Q10 temperature response parameter used to scale Tau25
This table shows the mapping of variable names from the default instrument output files to the corresponding variables defined in this reporting format. Note that copying and pasting the content of this table from GitHub into a spreadsheet may improve readability for some viewers (this functionality does not work from GitBook).
Defined variables
ADC iFL
ADC LCi T
ADC proT
CID CI-340
Licor 6400XT
Licor 6800
PP Systems CIRAS-2
PP Systems CIRAS-3
PP Systems TARGAS-1
Walz GFS-3000
variableName
variableUnit
variableDescription
variableName
variableUnit
variableDescription
variableName
variableUnit
variableDescription
variableName
variableUnit
variableDescription
variableName
variableUnit
variableDescription
variableName
variableUnit
variableDescription
variableName
variableUnit
variableDescription
variableName
variableUnit
variableDescription
variableName
variableUnit
variableDescription
variableName
variableUnit
variableDescription
variableName
variableUnit
variableDescription
date
YYYY-MM-DD
Date of observation
Dt
-
Date (text)
Dt
-
Date (text)
Dt
-
Date (text)
Year, M, D
-
Current year; Current month; Current day (3 separate columns)
YYYYMMDD
-
Date code (integer)
date
-
Date of last observation
Date
ExcelTime
Date
dd/mm/yy
Date
yyyy-mm-dd
Date
time
HH:MM:SS
Time of observation
Tm
-
Time of day
tm
-
Time of day
tm
-
Time of day
H, m, and s
-
Time experiments conducted
HHMMSS
-
real time clock
hhmmss
-
Time of last observation
Time
ExcelTime
Time
hh:mm:ss
Time
hh:mm:dd
Time
record
-
Observation record number
Record
-
Current record number
Record
-
Current record number
Record
-
Measurement number
Count
-
Number of measurements that have been saved
Obs
-
# Obs stored in log file
obs
-
Number of observations logged
Rec Num
Number
Object
Object number
area
cm²
Leaf area
Area
cm2
projected leaf surface area
Area
cm2
projected leaf surface area
Area
cm2
projected leaf surface area
Area
cm²
In-chamber leaf area
S
cm²
Leaf area
Leaf Area
cm²
Leaf Area
Leaf Area
cm²
Leaf Area
Area
Area
cm²
Value of the sample used for calculations
A
µmol m⁻² s⁻¹
Net CO2 exchange per leaf area
A
μmol m-2 s-1
Photosynthetic rate
A
μmol m-2 s-1
Photosynthetic rate
A
μmol m-2 s-1
Photosynthetic assimilation rate
Pn
μmol m-2 s-1
net photosynthesis rate
Photo
µmol m⁻² s⁻¹
Photosynthetic rate
A
µmol m⁻² s⁻¹
Assimilation rate
Pn
µmol m⁻² s⁻¹
Net Photosynthetic Rate
A
µmol CO2 m⁻² s⁻¹
Assimilation
A
µmol CO2 m⁻² s⁻¹
Assimilation
A
µmol m⁻² s⁻¹
Assimilation rate
Ci
µmol mol⁻¹
Intercellular CO2 concentration in air
cI
vpm
Sub-stomatal CO2
Ci
vpm
Sub-stomatal CO2
cI
vpm
Sub-stomatal CO2
IntCO2
µmol mol⁻¹
Internal CO2 concentration
Ci
µmol mol⁻¹
Intercellular CO2 concentration
Ci
µmol mol⁻¹
Intercellular CO2
Ci
ppm
Substomatal CO2 Concentration
Ci
µmol mol⁻¹
Sub-Stomatal CO2 Concentration
Ci
µmol mol⁻¹
Leaf internal CO2 Concentration
ci
ppm
Intercellular CO2 mole fraction
CO2r
µmol mol⁻¹
CO2 concentration in wet air entering chamber
cref
vpm
CO2 reference
Cref
vpm
CO2 reference
Cref
ppm
CO2 reference
CO2in
ppm
Inlet CO2
CO2R
µmol mol⁻¹
Reference cell CO2
CO2_r
µmol mol⁻¹
Reference cell CO2 concentration
Cr
ppm
Reference CO2
CO2r
µmol mol⁻¹
CO2 Reference
CO2r
ppm
CO2 Reference
CO2abs
ppm
CO2 mole fraction in the reference cell of analyzer
CO2s
µmol mol⁻¹
CO2 concentration in wet air inside chamber
c'an
vpm
CO2 analysis (correction for dilution)
C'an
vpm
CO2 analysis (correction for dilution)
Can
vpm
CO2 analysis (correction for dilution)
CO2out
ppm
Outlet CO2
CO2S
µmol mol⁻¹
Sample cell CO2
CO2_s
µmol mol⁻¹
Sample cell CO2 concentration
Ca
ppm
Analysis CO2
CO2a
µmol mol⁻¹
CO2 Analysis
CO2a
ppm
CO2 Analysis
ca
ppm
CO2 mole fraction in the cuvette
dCO2
µmol mol⁻¹
Sample minus reference CO2 concentration in air
Δc
vpm
Delta CO2 (Cref - C'an)
^C
vpm
Delta CO2 (Cref - C'an)
ΔCO2
vpm
Delta CO2 (Cref - C'an)
DCO2
µmol mol⁻¹
ΔCO2
ΔCO2
µmol mol⁻¹
Sample - reference CO2
Cd
ppm
Differential CO2
CO2d
µmol mol⁻¹
CO2 Differential
CO2d
ppm
CO2 Differential
dCO2MP
ppm
Difference between CO2 mole fraction in the sample cell and reference cell of the analyzer in measuring point mode.
dH2O
mmol mol⁻¹
Sample minus reference H2O concentration in air
Δe
mBar
Delta H2O (e'an - eref), partial pressure
^e
mBar
Delta H2O (e'an - eref), partial pressure
Δe
mBar
Delta H2O (e'an - eref), partial pressure
DH2O
mmol mol⁻¹
ΔH2O
ΔH2O
mmol mol⁻¹
Sample - reference H2O
Hd
mb
Differential CO2
H2Od
mb
H2O Differential
H2Od
mb
H2O Differential
dH2OMP
ppm
Difference between H2O mole fraction in the sample cell and reference cell of the analyzer in measuring point mode.
E
mmol m⁻² s⁻¹
Transpiration rate of H2O per leaf area. Note that output units from some instruments are in mol and will require conversion.
E
mmol m-2 s-1
Transpiration rate
E
mmol m-2 s-1
Transpiration rate
E
mmol m-2 s-1
Transpiration rate
E
mmol m⁻² s⁻¹
Transpiration rate
Trmmol
mmol m⁻² s⁻¹
Transpiration rate
E
mol m⁻² s⁻¹
Transpiration rate
E
mmol m⁻² s⁻¹
Transpiration rate
E
mmol H2O m⁻² s⁻¹
Transpiration
E
mmol H2O m⁻² s⁻¹
Transpiration
E
mmol m⁻² s⁻¹
Transpiration rate
flow
µmol s⁻¹
Flow rate of air into chamber
u
μmol s-1
ASU mass flow (measured)
U
μmol s-1
ASU mass flow (measured)
U
μmol s-1
ASU mass flow (measured)
Flow
lpm
Flow rate
Flow
µmol s⁻¹
Flow rate
Flow
µmol s⁻¹
Flow rate to chamber
V
ml min-1
Chamber flow rate
Flow
cc min-1
Cuvette Flow Rate
Flow
cc min-1
Cuvette Flow Rate
Flow
µmol s⁻¹
Gas flow through the cuvette
gsw
mmol m⁻² s⁻¹
Stomatal conductance to water vapor per leaf area
gs
mmol m-2 s-1
Stomatal conductance of H2O
Gs
mol m-2 s-1
Stomatal conductance of H2O
Gs
mmol m-2 s-1
Stomatal conductance of H2O
C
mmol m⁻² s⁻¹
Stomatal conductance rate
Cond
mol m⁻² s⁻¹
Conductance to water
gsw
mol m⁻² s⁻¹
Stomatal conductance to water vapor
gs
mmol m⁻² s⁻¹
Stomatal Conductance
gs
mmol H2O m⁻² s⁻¹
Stomatal Conductance
gs
mmol H2O m⁻² s⁻¹
Stomatal Conductance
GH2O
mmol m⁻² s⁻¹
Water vapor conductance
H2Or
mmol mol⁻¹
H2O concentration in air entering chamber
eref
mBar
H2O reference, as partial pressure
eref
mBar
H2O reference, as partial pressure
eref
mBar
H2O reference, as partial pressure
H2Oin
kPa
Inlet water pressure
H2OR
mmol mol⁻¹
Reference H2O
H2O_r
mmol mol⁻¹
Reference cell H2O concentration
Hr
mb
Reference H2O
H2Or
mb
H2O Reference
H2Or
mb
H2O Reference
H2Oabs
ppm
H2O mole fraction in the reference cell of analyzer
H2Os
mmol mol⁻¹
H2O concentration in air inside chamber
e'ad
mBar
H2O analysis, dilution corrected
e'ad
mBar
H2O analysis, dilution corrected
e'an
mBar
H2O analysis, dilution corrected
H2Oout
kPa
Outlet water pressure
H2OS
mmol mol⁻¹
Sample H2O
H2O_s
mmol mol⁻¹
Sample cell H2O concentration
Ha
mb
Analysis H20
H2Oa
mb
H2O Analysis
H2Oa
mb
H2O Analysis
wa
ppm
H2O mole fraction in the cuvette
Patm
kPa
Atmospheric pressure
P
mBar
atmospheric pressure
P
mBar
atmospheric pressure
P
mBar
atmospheric pressure
Pressure
kPa
Atmospheric pressure (also ATM)
Press
kPa
Atmospheric pressure
Pa
kPa
Atmospheric pressure
Ap
mb
Atmospheric pressure
Patm
mb
Atmospheric pressure
atm
mb
Atmospheric pressure
Pamb
kPa
Ambient barometric pressure
Qin
µmol m⁻² s⁻¹
In-chamber photosynthetic flux density (PPFD) incident on the leaf, quanta per area
Qleaf
μmol m-2 s-1
P.A.R. incident on leaf surface
Qleaf
μmol m-2 s-1
P.A.R. incident on leaf surface
Qleaf
μmol m-2 s-1
P.A.R. incident on leaf surface corrected for Trw
PAR
μmol m-2 s-1
Photosynthetically Active Radiation
PARi
µmol m⁻² s⁻¹
In-chamber PAR
Qin
µmol m⁻² s⁻¹
PPFD incident on the leaf
Q
µmol m⁻² s⁻¹
PAR
PARi
µmol m⁻² s⁻¹
PAR Internal
PARi
µmol m⁻² s⁻¹
PAR Internal
PARtop
µmol m⁻² s⁻¹
Photosynthetically active radiation measured with sensor in upper cuvette half. Also see PARbot.
Qout
µmol m⁻² s⁻¹
External photosynthetic flux density (PPFD), quanta per area
Q
μmol m-2 s-1
P.A.R. at window
Q
μmol m-2 s-1
P.A.R. at window
Q
μmol m-2 s-1
P.A.R. at window corrected for Trw
PARo
µmol m⁻² s⁻¹
External PAR
Qamb_out
µmol m⁻² s⁻¹
External quantum sensor
PARe
µmol m⁻² s⁻¹
PAR External
PARe
µmol m⁻² s⁻¹
PAR External
PARamb
µmol m⁻² s⁻¹
Ambient photosynthetically active radiation measured with extenrnal sensor
RHr
%
Relative humidity of air entering the chamber
Wref
%RH
H2O reference, as %RH
Wref
%RH
H2O reference, as %RH
Wref
%RH
H2O reference, as %RH
RHin
%
Inlet relative humidity
RH_R
%
Relative humidity in the reference cell
RHs
%
Relative humidity of air inside the chamber
w'an
%RH
H2O analysis, corrected
w'ad
%RH
H2O analysis, dilution corrected
W'an
%RH
H2O analysis, corrected as %RH
RHout
%
Outlet relative humidity
RH_S
%
Relative humidity in the sample cell
RHcham
%
Relative humidity in the chamber
RH
%
Relative Humidity (calculated)
RH
%
Relative Humidity inside Leaf Chamber
rH
%
Relative humidity in the cuvette
Tair
°C
Air temperature inside the chamber
Tch
°C
Leaf chamber temperature
Tch
°C
Leaf chamber temperature
Tch
°C
Leaf chamber temperature
Tair
°C
Air temperature
Tair
°C
Chamber Air Temp
Tair
°C
Chamber air temperature
Tc
°C
Cuvette Air Temperature
Tcuv
°C
Temperature in Cuvette
Tcuv
°C
Cuvette air temperature
Tcuv
°C
Cuvette temperature measured in lower half
Tleaf
°C
Leaf surface temperature
Tleaf
°C
Leaf surface temperature (also Tl)
Tleaf
°C
Leaf surface temperature
Tleaf
°C
Leaf surface temperature
Tleaf
°C
Leaf temperature
Tleaf
°C
Leaf Temp, measured with the thermocouple. Also see CTleaf. Same as Tleaf unless doing energy balance.
Tleaf
°C
Leaf thermocouple #1
Tl
°C
Leaf Temperature
Tleaf
°C
Leaf Temperature
Tleaf
°C
Leaf surface temperature
Tleaf
°C
Leaf temperature
VPDleaf
kPa
Leaf to air vapor pressure deficit
VPD
-
Vapor pressure deficit
VpdL
kPa
Vapor pressure deficit based on leaf temp
VPDleaf
kPa
Vapor pressure deficit at leaf temperature
VPD
mb
Vapr Pressure Deficit
VPD
kPa
Leaf to air Vapor Pressure Deficit
VPD
mb
Vapor Pressure Deficit
VPD
Pa/kPa
Vapor pressure deficit between object (leaf) and air