| Method . | Gas Analyzed . | High-Throughput . | Dynamic . | Other Experimental Advantages/Disadvantages . | Protocol or Theory References . |
|---|---|---|---|---|---|
| Clark Type O2 Electrode | O2 | No | Yes | Experimental Advantage − Liquid phase measurements are suitable for mitochondrial activity assays because of rapid dynamic responses combined with easy, mid-assay addition of chemical effectors (e.g. inhibitors, ADP, substrates) − Can be combined with a light source to also measure photosynthetic O2 release from tissues Experimental Disadvantage −Gas-phase assays are possible but are less sensitive compared to IRGA and thus infrequently used for respiration − Short duration: aqueous O2 depletion is on the order of minutes, limiting observations of dynamics in tissues − During tissue measurements, the requirement for submersion and rapid stirring may have unintended effects | (Clark et al., 1953; Jacoby et al., 2015) |
| O2 Luminescence Quenching | O2 | Yes | Yes | Experimental Advantage − Long duration: gas-phase measurements lasting several days are possible, suitable for observing dynamic responses in tissues that involve changes in gene expression, acclimation or development. − Adaptable: the fluorescent dyes can be placed in any type of sealed container and measurements conducted in gas or liquid phase − Combinable with measurements of other fluorescent metabolite probes in multi-parameter plate reader assays Experimental Disadvantage − Mostly employed in a closed system where buildup of gaseous H2O, CO2 and ethylene can occur; but Schilling et al. 2015 introduce an open/closed hybrid system. −Gas-phase measurements are sensitive to temperature and physical disturbances, increasing background noise. | (Tyystjärvi et al., 1998; Schilling et al., 2015; Sew et al., 2015; Scafaro et al., 2017; Wagner et al., 2019; O’Leary et al., 2022) |
| Mass spectrometry | O2 and CO2 | No | Yes | Experimental Advantage: − Multiple gases can be analyzed simultaneously − Allows isotope discrimination measurements needed for certain determinations of day respiration and measurement of alternative oxidase versus cytochrome pathway flux − Highly sensitive instruments can enable detection of minimal flux rates − Online versus offline versions offer adaptable sample collection regimes Experimental Disadvantage − Expensive to maintain and run − Can be technically challenging and specialized skills required | (Ribas-Carbo et al., 2005; Beckmann et al., 2009; Cheah et al., 2014) |
| Differential O2 Analyzer | O2 | No | Yes | Experimental Advantage − Precise quantification of O2 uptake by respiration in an open system − Can be paired with IRGA Experimental Disadvantage − Prone to leaks from cuvette or chamber creating error − Difficult to calibrate − Short lifespan of oxygen fuel cell sensors | (Hunt, 2003) |
| Infrared Gas Analyzer | CO2 | Partly | Yes | Experimental Advantage − Relatively fast, straightforward measurement process allows higher sample throughputs and scalable data collection − Often designed as portable, field use instruments − Adaptable technology: open and closed systems; large range of sample (chamber) sizes; − Can be combined with H2O measurements for stomatal analysis or light and dark measurement combinations Experimental Disadvantage − Prone to leaks from cuvette or chamber creating error | (Flexas et al., 2006; Fonseca et al., 2021) |
| Eddy Covariance | CO2 | No | Yes | Experimental Advantage − Large spatial and temporal scale of measurement − Non-destructive, non-intrusive Experimental Disadvantage − Specific environmental and geographical conditions must be met to satisfy assumptions within the calculations | (Goulden et al., 1996; Baldocchi, 2003) |
| Hyperspectral Imaging | n/a | Yes | No | Experimental Advantage − Largest spatial and temporal scale (can be implemented from satellites and aircraft) − Non-destructive, non-intrusive Experimental Disadvantage − An indirect measurement: dependent upon a large training data set that requires direct respiratory measurements to create a predictive model; therefore, only as reliable as the training data − Large data storage required − Images must be captured in the light, but training respiration rate data typically measured in the dark | (Coast et al., 2019) |
| Method . | Gas Analyzed . | High-Throughput . | Dynamic . | Other Experimental Advantages/Disadvantages . | Protocol or Theory References . |
|---|---|---|---|---|---|
| Clark Type O2 Electrode | O2 | No | Yes | Experimental Advantage − Liquid phase measurements are suitable for mitochondrial activity assays because of rapid dynamic responses combined with easy, mid-assay addition of chemical effectors (e.g. inhibitors, ADP, substrates) − Can be combined with a light source to also measure photosynthetic O2 release from tissues Experimental Disadvantage −Gas-phase assays are possible but are less sensitive compared to IRGA and thus infrequently used for respiration − Short duration: aqueous O2 depletion is on the order of minutes, limiting observations of dynamics in tissues − During tissue measurements, the requirement for submersion and rapid stirring may have unintended effects | (Clark et al., 1953; Jacoby et al., 2015) |
| O2 Luminescence Quenching | O2 | Yes | Yes | Experimental Advantage − Long duration: gas-phase measurements lasting several days are possible, suitable for observing dynamic responses in tissues that involve changes in gene expression, acclimation or development. − Adaptable: the fluorescent dyes can be placed in any type of sealed container and measurements conducted in gas or liquid phase − Combinable with measurements of other fluorescent metabolite probes in multi-parameter plate reader assays Experimental Disadvantage − Mostly employed in a closed system where buildup of gaseous H2O, CO2 and ethylene can occur; but Schilling et al. 2015 introduce an open/closed hybrid system. −Gas-phase measurements are sensitive to temperature and physical disturbances, increasing background noise. | (Tyystjärvi et al., 1998; Schilling et al., 2015; Sew et al., 2015; Scafaro et al., 2017; Wagner et al., 2019; O’Leary et al., 2022) |
| Mass spectrometry | O2 and CO2 | No | Yes | Experimental Advantage: − Multiple gases can be analyzed simultaneously − Allows isotope discrimination measurements needed for certain determinations of day respiration and measurement of alternative oxidase versus cytochrome pathway flux − Highly sensitive instruments can enable detection of minimal flux rates − Online versus offline versions offer adaptable sample collection regimes Experimental Disadvantage − Expensive to maintain and run − Can be technically challenging and specialized skills required | (Ribas-Carbo et al., 2005; Beckmann et al., 2009; Cheah et al., 2014) |
| Differential O2 Analyzer | O2 | No | Yes | Experimental Advantage − Precise quantification of O2 uptake by respiration in an open system − Can be paired with IRGA Experimental Disadvantage − Prone to leaks from cuvette or chamber creating error − Difficult to calibrate − Short lifespan of oxygen fuel cell sensors | (Hunt, 2003) |
| Infrared Gas Analyzer | CO2 | Partly | Yes | Experimental Advantage − Relatively fast, straightforward measurement process allows higher sample throughputs and scalable data collection − Often designed as portable, field use instruments − Adaptable technology: open and closed systems; large range of sample (chamber) sizes; − Can be combined with H2O measurements for stomatal analysis or light and dark measurement combinations Experimental Disadvantage − Prone to leaks from cuvette or chamber creating error | (Flexas et al., 2006; Fonseca et al., 2021) |
| Eddy Covariance | CO2 | No | Yes | Experimental Advantage − Large spatial and temporal scale of measurement − Non-destructive, non-intrusive Experimental Disadvantage − Specific environmental and geographical conditions must be met to satisfy assumptions within the calculations | (Goulden et al., 1996; Baldocchi, 2003) |
| Hyperspectral Imaging | n/a | Yes | No | Experimental Advantage − Largest spatial and temporal scale (can be implemented from satellites and aircraft) − Non-destructive, non-intrusive Experimental Disadvantage − An indirect measurement: dependent upon a large training data set that requires direct respiratory measurements to create a predictive model; therefore, only as reliable as the training data − Large data storage required − Images must be captured in the light, but training respiration rate data typically measured in the dark | (Coast et al., 2019) |
Dynamic refers to whether a technique is amenable to continuous measurement, over an appropriate timescale, to observe how rates change.
| Method . | Gas Analyzed . | High-Throughput . | Dynamic . | Other Experimental Advantages/Disadvantages . | Protocol or Theory References . |
|---|---|---|---|---|---|
| Clark Type O2 Electrode | O2 | No | Yes | Experimental Advantage − Liquid phase measurements are suitable for mitochondrial activity assays because of rapid dynamic responses combined with easy, mid-assay addition of chemical effectors (e.g. inhibitors, ADP, substrates) − Can be combined with a light source to also measure photosynthetic O2 release from tissues Experimental Disadvantage −Gas-phase assays are possible but are less sensitive compared to IRGA and thus infrequently used for respiration − Short duration: aqueous O2 depletion is on the order of minutes, limiting observations of dynamics in tissues − During tissue measurements, the requirement for submersion and rapid stirring may have unintended effects | (Clark et al., 1953; Jacoby et al., 2015) |
| O2 Luminescence Quenching | O2 | Yes | Yes | Experimental Advantage − Long duration: gas-phase measurements lasting several days are possible, suitable for observing dynamic responses in tissues that involve changes in gene expression, acclimation or development. − Adaptable: the fluorescent dyes can be placed in any type of sealed container and measurements conducted in gas or liquid phase − Combinable with measurements of other fluorescent metabolite probes in multi-parameter plate reader assays Experimental Disadvantage − Mostly employed in a closed system where buildup of gaseous H2O, CO2 and ethylene can occur; but Schilling et al. 2015 introduce an open/closed hybrid system. −Gas-phase measurements are sensitive to temperature and physical disturbances, increasing background noise. | (Tyystjärvi et al., 1998; Schilling et al., 2015; Sew et al., 2015; Scafaro et al., 2017; Wagner et al., 2019; O’Leary et al., 2022) |
| Mass spectrometry | O2 and CO2 | No | Yes | Experimental Advantage: − Multiple gases can be analyzed simultaneously − Allows isotope discrimination measurements needed for certain determinations of day respiration and measurement of alternative oxidase versus cytochrome pathway flux − Highly sensitive instruments can enable detection of minimal flux rates − Online versus offline versions offer adaptable sample collection regimes Experimental Disadvantage − Expensive to maintain and run − Can be technically challenging and specialized skills required | (Ribas-Carbo et al., 2005; Beckmann et al., 2009; Cheah et al., 2014) |
| Differential O2 Analyzer | O2 | No | Yes | Experimental Advantage − Precise quantification of O2 uptake by respiration in an open system − Can be paired with IRGA Experimental Disadvantage − Prone to leaks from cuvette or chamber creating error − Difficult to calibrate − Short lifespan of oxygen fuel cell sensors | (Hunt, 2003) |
| Infrared Gas Analyzer | CO2 | Partly | Yes | Experimental Advantage − Relatively fast, straightforward measurement process allows higher sample throughputs and scalable data collection − Often designed as portable, field use instruments − Adaptable technology: open and closed systems; large range of sample (chamber) sizes; − Can be combined with H2O measurements for stomatal analysis or light and dark measurement combinations Experimental Disadvantage − Prone to leaks from cuvette or chamber creating error | (Flexas et al., 2006; Fonseca et al., 2021) |
| Eddy Covariance | CO2 | No | Yes | Experimental Advantage − Large spatial and temporal scale of measurement − Non-destructive, non-intrusive Experimental Disadvantage − Specific environmental and geographical conditions must be met to satisfy assumptions within the calculations | (Goulden et al., 1996; Baldocchi, 2003) |
| Hyperspectral Imaging | n/a | Yes | No | Experimental Advantage − Largest spatial and temporal scale (can be implemented from satellites and aircraft) − Non-destructive, non-intrusive Experimental Disadvantage − An indirect measurement: dependent upon a large training data set that requires direct respiratory measurements to create a predictive model; therefore, only as reliable as the training data − Large data storage required − Images must be captured in the light, but training respiration rate data typically measured in the dark | (Coast et al., 2019) |
| Method . | Gas Analyzed . | High-Throughput . | Dynamic . | Other Experimental Advantages/Disadvantages . | Protocol or Theory References . |
|---|---|---|---|---|---|
| Clark Type O2 Electrode | O2 | No | Yes | Experimental Advantage − Liquid phase measurements are suitable for mitochondrial activity assays because of rapid dynamic responses combined with easy, mid-assay addition of chemical effectors (e.g. inhibitors, ADP, substrates) − Can be combined with a light source to also measure photosynthetic O2 release from tissues Experimental Disadvantage −Gas-phase assays are possible but are less sensitive compared to IRGA and thus infrequently used for respiration − Short duration: aqueous O2 depletion is on the order of minutes, limiting observations of dynamics in tissues − During tissue measurements, the requirement for submersion and rapid stirring may have unintended effects | (Clark et al., 1953; Jacoby et al., 2015) |
| O2 Luminescence Quenching | O2 | Yes | Yes | Experimental Advantage − Long duration: gas-phase measurements lasting several days are possible, suitable for observing dynamic responses in tissues that involve changes in gene expression, acclimation or development. − Adaptable: the fluorescent dyes can be placed in any type of sealed container and measurements conducted in gas or liquid phase − Combinable with measurements of other fluorescent metabolite probes in multi-parameter plate reader assays Experimental Disadvantage − Mostly employed in a closed system where buildup of gaseous H2O, CO2 and ethylene can occur; but Schilling et al. 2015 introduce an open/closed hybrid system. −Gas-phase measurements are sensitive to temperature and physical disturbances, increasing background noise. | (Tyystjärvi et al., 1998; Schilling et al., 2015; Sew et al., 2015; Scafaro et al., 2017; Wagner et al., 2019; O’Leary et al., 2022) |
| Mass spectrometry | O2 and CO2 | No | Yes | Experimental Advantage: − Multiple gases can be analyzed simultaneously − Allows isotope discrimination measurements needed for certain determinations of day respiration and measurement of alternative oxidase versus cytochrome pathway flux − Highly sensitive instruments can enable detection of minimal flux rates − Online versus offline versions offer adaptable sample collection regimes Experimental Disadvantage − Expensive to maintain and run − Can be technically challenging and specialized skills required | (Ribas-Carbo et al., 2005; Beckmann et al., 2009; Cheah et al., 2014) |
| Differential O2 Analyzer | O2 | No | Yes | Experimental Advantage − Precise quantification of O2 uptake by respiration in an open system − Can be paired with IRGA Experimental Disadvantage − Prone to leaks from cuvette or chamber creating error − Difficult to calibrate − Short lifespan of oxygen fuel cell sensors | (Hunt, 2003) |
| Infrared Gas Analyzer | CO2 | Partly | Yes | Experimental Advantage − Relatively fast, straightforward measurement process allows higher sample throughputs and scalable data collection − Often designed as portable, field use instruments − Adaptable technology: open and closed systems; large range of sample (chamber) sizes; − Can be combined with H2O measurements for stomatal analysis or light and dark measurement combinations Experimental Disadvantage − Prone to leaks from cuvette or chamber creating error | (Flexas et al., 2006; Fonseca et al., 2021) |
| Eddy Covariance | CO2 | No | Yes | Experimental Advantage − Large spatial and temporal scale of measurement − Non-destructive, non-intrusive Experimental Disadvantage − Specific environmental and geographical conditions must be met to satisfy assumptions within the calculations | (Goulden et al., 1996; Baldocchi, 2003) |
| Hyperspectral Imaging | n/a | Yes | No | Experimental Advantage − Largest spatial and temporal scale (can be implemented from satellites and aircraft) − Non-destructive, non-intrusive Experimental Disadvantage − An indirect measurement: dependent upon a large training data set that requires direct respiratory measurements to create a predictive model; therefore, only as reliable as the training data − Large data storage required − Images must be captured in the light, but training respiration rate data typically measured in the dark | (Coast et al., 2019) |
Dynamic refers to whether a technique is amenable to continuous measurement, over an appropriate timescale, to observe how rates change.
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