You are here

Home » Data & Archives

Harvard Forest Data Archive

HF224

Leaf Gas Exchange in the Clearcut Site at Harvard Forest 2010-2012

Related Publications

Data

Overview

  • Lead: Christopher Williams
  • Investigators: Sophie Dillen, Myroslava Khomik, Richard MacLean, Melanie Vanderhoof
  • Contact: Information Manager
  • Start date: 2010
  • End date: 2012
  • Status: completed
  • Location: Prospect Hill Tract (Harvard Forest)
  • Latitude: +42.546
  • Longitude: -72.174
  • Elevation: 403 meter
  • Taxa: Acer rubrum (red maple), Aralia nudicaulis (wild sarsaparilla), Betula papyrifera (paper birch), Carex spp. (sedge), Dennstaedtia punctilobula (hayscented fern), Dryopteris spp. (woodfern), Maianthemum canadense (Canadian may-lily), Oryzopsis asperifolia (rough-leaved rice grass), Polygonum sp. (knotweed), Prunus pensylvanica (pin cherry), Prunus serotina (black cherry), Quercus rubra (red oak), Rubus allegheniensis (Allegheny blackberry), Sambucus pubens (elderberry)
  • Release date: 2015
  • Revisions:
  • EML file: knb-lter-hfr.224.6
  • DOI: digital object identifier
  • EDI: data package
  • DataONE: data package
  • Related links:
  • Study type: short-term measurement, modeling
  • Research topic: ecological informatics and modelling; forest-atmosphere exchange; physiological ecology, population dynamics and species interactions
  • LTER core area: primary production, disturbance
  • Keywords: aboveground production, carbon dioxide, gas flux, leaves, photosynthesis, photosynthetically active radiation, plant physiology, transpiration
  • Abstract:

    Clearcutting a forest ecosystem can result in a drastic reduction of the stand’s productivity. Despite the severity of this disturbance type, past studies have found that the productivity of young regenerating stands can quickly rebound, approaching that of mature undisturbed stands within a few years. One of the obvious reasons is increased leaf area with each year of recovery. However, a less obvious reason may be the variability in species composition and distribution during the natural regeneration process. The purpose of this study was to investigate to what extent the increase in GEP, observed during the first four years of recovery, in a naturally regenerating clearcut stand was due to 1) an overall expansion of leaf area, and 2) an increase in the canopy’s photosynthetic capacity stemming from either species compositional shifts or drift in physiological traits within species. We found that the multi-year rise in GEP following harvest was clearly attributed to the expansion of leaf area rather than a change in vegetation composition. Sizeable changes in relative abundance of species were masked by remarkably similar leaf physiological attributes for a range of vegetation types present in this early successional environment. Comparison of upscaled leaf-chamber to eddy-covariance-based light-response curves revealed broad consistency in both maximum photosynthetic capacity and quantum yield efficiency. The approaches presented here illustrate how chamber- and ecosystem-scale measurements of gas exchange can be blended with species-level leaf area data to draw conclusive inferences about changes in ecosystem processes over time in a highly dynamic environment.

  • Methods:

    LIGHT RESPONSE CURVES

    1. Select mid-canopy, well lit (normally in sun) leaf. Make sure it’s healthy looking. Make note of it in your notebook and also write a remark in the file on LI-6400.

    2. Adjust tri-pod, to leaf level and angle.

    3. Set Reference CO2 to 380 ppm (note your CO2 should be on full scrub and desiccant on BYPASS) – this will be temporary, shortly we will switch to sample control.

    4. Set leaf temperature to ambient Tair (measure ambient Tair with open chamber first).

    5. Set light to 1800 umol/s.

    6. Clamp onto the selected leaf and monitor H2OS_mml value, make note of it in your note book. Then set flow control for constant water mole fraction targeting the value you noted.

    7. Set Sample CO2 to 380 ppm.

    8. When CO2 and H2O are stabilized, match IRGAs.

    9. wait about 10-15 minutes for Ci to stabilize (that is when stomata will be fully adjusted).

    10. Log (you’ll be prompted for stomatal ratio, leaf area, species, replicate). Note the date of measurement, file name, your name (person collecting the data, species name, leaf replicate #, and the measured values: light level, stable Ci, and logged photosynthesis and conductivity values in your field notebook – a table is good.

    11. Next, change the light to 1200 and repeat steps 9 and 10.

    12. Repeat step 11, going through the following light levels: 1000, 800, 600, 400, 200, 50, 0 (light off and branch shaded).

    13. Remove the leaf from the chamber.

    14. Carefully detach it and place in envelope. Mark the envelope with: CLARKU/Williams, the date of measurement (mmm.dd.yyyy), file name, species, replicate, and “LIGHT CURVE”. If area below 6cm2, will need to scan.

    15. Put envelopes in ziplock bags into COOLER, till end of day. Take out of cooler and ziplock bags and dry in Oven for 24 hours at 70oC (158 oF). Make sure to dry as soon as possible, don’t want leaf to rot.

    16. Prep dried leaves for CN analysis.

    CO2 RESPONSE CURVES (A-Ci)

    1. Select mid-canopy, well lit (normally in sun) leaf. Make sure it’s healthy looking. Make note of it in your notebook and also write a remark in the file on LI-6400.

    2. Adjust tri-pod, to leaf level and angle.

    3. Set Reference CO2 to 380 ppm (note your CO2 should be on full scrub and desiccant at mid range).

    4. Set leaf temperature to ambient Tair (measure ambient Tair with open chamber first).

    5. Set light to 1800 µmol/s.

    6. Clamp onto the selected leaf and monitor H2OS_mml value, make note of it in your note book. Then set flow control for constant water mole fraction targeting the value you noted (but flow should be at about 400 µmol/s).

    7. When CO2 and H2O are stabilized, match IRGAs. You will need to match IRGAs after every time you change CO2 concentration.

    8. Wait for Ci to stabilize (that is when stomata will be fully adjusted). Make sure not to wait too long at low CO2 concentrations, so not to deactivate RUBISCO.

    9. Log (you’ll be prompted for stomatal ratio, leaf area, species, replicate). Note the date of measurement, file name, your name (person collecting the data, species name, leaf replicate #, and logged PAR, photosynthesis and conductivity values in your field notebook – a table is good.

    10. Move onto the next leaf.

    11. Repeat step 10, going through the following CO2 levels (in this order): 100, 50, 380, 380 (yes that’s a duplicate), 500, 800, 1000.

    12. Remove the leaf from the chamber.

    13. Carefully detach it and place in envelope. Mark the envelope with: CLARKU/Williams, the date of measurement (mmm.dd.yyyy), file name, species, replicate, and “LIGHT CURVE”. If area below 6cm2, will need to scan.

    14. Put envelopes in ziplock bags into COOLER, till end of day. Take out of cooler and ziplock bags and dry in Oven for 24 hours at 70oC (158 oF). Make sure to dry as soon as possible, don’t want leaf to rot.

    15. Prep dried leaves for CN analysis.

    ECOLOGICAL SURVEY / Instantaneous Measurements

    1. Select mid-canopy, well lit (normally in sun) leaf. Make sure it’s healthy looking. Make note of it in your notebook and also write a remark in the file on LI-6400.

    2. Mark the branch with flagging tape, and note the leaf location (you will be measuring the same leaf throughout the summer, so you do this step only once).

    3. Adjust tri-pod, to leaf level and angle.

    4. Set Sample CO2 to 380 ppm (note your CO2 should be on full scrub and desiccant on full BYPASS).

    5. Set leaf temperature to ambient Tair (measure ambient Tair with open chamber first).

    6. Set light to follow the outside PAR sensor.

    7. Set flow to high (~ 500 umol/s).

    8. When CO2 and H2O are stabilized, match IRGAs. (match once on 1st leaf and then every 30 minutes, or so, esp. if temperature changes).

    9. wait for photosynthesis and conductivity to stabilize.

    10. Log (you’ll be prompted for stomatal ratio, leaf area, species, replicate). Note the date of measurement, file name, your name (person collecting the data, species name, leaf replicate #, and the measured values CO2 concentration, stable Ci, and logged photosynthesis and conductivity values in your field notebook – a table is good.).

    11. Gently release the leaf from the chamber and move onto the next species.

    12. Repeat steps 1 to 3 and 9 to 11 (going through all 5-10 species, with 3 replicates per species). Make sure to match every 30 minutes to an hour and to check ambient Tair (over the course of a day it will likely change).

    Note: if area is smaller than 6cm2, you will need to detach that leaf and measure it’s area with the scanner at the end of the season.

  • Use:

    This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.

  • Citation:

    Williams C. 2015. Leaf Gas Exchange in the Clearcut Site at Harvard Forest 2010-2012. Harvard Forest Data Archive: HF224 (v.6). Environmental Data Initiative: https://doi.org/10.6073/pasta/18acf7c9de8f7bcf5ff4ff274ec67e93.

Detailed Metadata

hf224-01: leaf gas exchange

  1. datetime: date and time of measurement
  2. year: year sampled
  3. month: month sampled
  4. day: day of month
  5. doy: corresponding day of the year (unit: nominalDay / missing value: NA)
  6. date: date sampled
  7. am: whether or not sampling was done in the morning
    • 0: not sampled in the morning
    • 1: sampled in the morning
  8. pm: whether or not sampling was done in the afternoon
    • 0: sampling was not done in the afternoon
    • 1: sampling was done in the afternoon
  9. obs: observation number
  10. time: time of measurement
  11. leaf: leaf number - measured on the same plant
  12. plant: plant number
  13. species: species name
    • rual: Rubus allegheniensis
    • depu: Dennstaedtia punctilobula
    • prpe: Prunus pensylvanica
    • acru: Acer rubrum
    • quru: Quercus rubra
    • sapu: Sambucus pubens
    • posp1: Polygonum sp.
    • prse: Prunus serotina
    • drsp: Dryopteris spp.
    • casp: Carex spp.
    • oras: Oryzopsis asperifolia
    • bepa: Betula papyrifera
    • maca: Maianthemum canadense
    • grass: grass
    • arnu: Aralia nudicaulis
  14. photo: net assimilation in micromols CO2 per meter squared per second (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
  15. cond: conductance to H2O in millimols of H2O per meter squared per second (unit: millimolePerMeterSquaredPerSecond / missing value: NA)
  16. ci: intercellular CO2 concentration (calculated) in micromols CO2 per mol (unit: dimensionless / missing value: NA)
  17. trans: transpiration rate in millimol H2O per meter squared per second (unit: millimolePerMeterSquaredPerSecond / missing value: NA)
  18. area: total area of leaf enclosed within the chamber (unit: squareCentimeters / missing value: NA)
  19. stm.ratio: stomatal ratio used in calculations (unit: dimensionless / missing value: NA)
  20. tair: temperature in sample cell (unit: celsius / missing value: NA)
  21. tleaf: temperature of leaf thermocouple (unit: celsius / missing value: NA)
  22. co2.r: reference cell CO2 concentration in micromol CO2 per mol (ppm) (unit: dimensionless / missing value: NA)
  23. co2.s: sample cell CO2 concentration in micromol CO2 per mol (ppm) (unit: dimensionless / missing value: NA)
  24. h2o.r: reference cell H2O concentration in millimol H2O per mol (ppm) (unit: dimensionless / missing value: NA)
  25. h2o.s: sample cell H2O concentration in millimol H2O per mol (ppm) (unit: dimensionless / missing value: NA)
  26. rh.r: relative humidity in the reference cell (%) (unit: dimensionless / missing value: NA)
  27. rh.s: relative humidity in the sample cell (%) (unit: dimensionless / missing value: NA)
  28. par.in: quantum sensor inside the chamber (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
  29. par.out: external quantum sensor (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
  30. press: atmospheric pressure (unit: kilopascal / missing value: NA)
  31. sp.code: code for species sampled
    • bb: Rubus allegheniensis
    • hf: Dennstaedtia punctilobula
    • pc: Prunus pensylvanica
    • rm: Acer rubrum
    • ro: Quercus rubra
    • eb: Sambucus pubens
    • kw: Polygonum sp.
    • bc: Prunus serotina
    • rr: Oryzopsis asperifolia
    • wf: Dryopteris spp.
    • grass: Carex spp.
    • pb: Betula papyrifera
    • canadian: Maianthemum canadense
    • ws: Aralia nudicaulis
  32. notes: notes

hf224-02: light response curves

  1. data.id: data id
  2. datetime: date and time of measurement
  3. date: date sampled
  4. year: year sampled
  5. month: month sampled
  6. day: day of month
  7. doy: corresponding day of the year (unit: nominalDay / missing value: NA)
  8. common.name: common species name
  9. scientific.name: scientific species name
  10. short.code: two letter code for species name
  11. species.code: two letter code for species name
  12. curve.no: curve number
  13. time: time
  14. leaf: leaf replicate
  15. anet: net assimilation in micromols CO2 per meter squared per second (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
  16. cond: conductance to H2O in millimols of H2O per meter squared per second (unit: millimolePerMeterSquaredPerSecond / missing value: NA)
  17. ci: intercellular CO2 concentration (calculated) in micromols CO2 per mol (unit: dimensionless / missing value: NA)
  18. trans: transpiration rate in millimol H2O per meter squared per second (unit: millimolePerMeterSquaredPerSecond / missing value: NA)
  19. vpdl: vapour pressure deficit based on leaf temperature (kPa) (unit: kilopascal / missing value: NA)
  20. ctleaf: computed leaf temperature. Same as Tleaf unless doing energy balance (unit: celsius / missing value: NA)
  21. area: total area of leaf enclosed within the chamber in centimeters squared (unit: squareCentimeters / missing value: NA)
  22. stm.ratio: stomatal Ratio used in calculations (unit: dimensionless / missing value: NA)
  23. tair: temperature in sample cell (unit: celsius / missing value: NA)
  24. tleaf: temperature of leaf thermocouple (unit: celsius / missing value: NA)
  25. tblk: temperature of cooler block (unit: celsius / missing value: NA)
  26. co2.r: reference cell CO2 concentration in micromol CO2 per mol (ppm) (unit: dimensionless / missing value: NA)
  27. co2.s: sample cell CO2 concentration in micromol CO2 per mol (ppm) (unit: dimensionless / missing value: NA)
  28. h2o.r: reference cell H2O concentration in millimol H2O per mol (ppm) (unit: dimensionless / missing value: NA)
  29. h2o.s: sample cell H2O concentration in millimol H2O per mol (ppm) (unit: dimensionless / missing value: NA)
  30. rh.r: relative humidity in the reference cell (%) (unit: dimensionless / missing value: NA)
  31. rh.s: relative humidity in the sample cell (%) (unit: dimensionless / missing value: NA)
  32. flow: flow rate to the sample cell in micromols per second (unit: micromolePerSecond / missing value: NA)
  33. par.in: quantum sensor inside the chamber (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
  34. par.out: external quantum sensor (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
  35. press: atmospheric pressure (unit: kilopascal / missing value: NA)
  36. stability: stability status (unit: dimensionless / missing value: NA)
  37. status: LI6400 stability diagnostics
  38. period.sd: period when measured, according to Sophie Dyllan
  39. species.sd: species code used by Sophie Dyllan
  40. tree.sd: tree number used by Sophie Dyllan
  41. n.id: code used to match up leaf nitrogen analysis with gas flux measurements
  42. leaf.n: leaf nitrogen in milligrams of N per gram of dry leaf (unit: milligramsPerGram / missing value: NA)

hf224-03: CO2 response curves

  1. data.id: data id
  2. datetime: date and time of measurement
  3. date: date sampled
  4. year: year sampled
  5. month: month sampled
  6. day: day of month
  7. doy: corresponding day of the year (unit: nominalDay / missing value: NA)
  8. common.name: common species name
  9. scientific.name: scientific species name
  10. short.code: shortened code for scientific name
  11. species.code: two letter code for species name
  12. curve.no: curve number
  13. time: time
  14. leaf: leaf replicate
  15. photo: net assimilation in micromols CO2 per meter squared per second (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
  16. cond: conductance to H2O in millimols of H2O per meter squared per second (unit: millimolePerMeterSquaredPerSecond / missing value: NA)
  17. ci: intercellular CO2 concentraion (calculated) in micromols CO2 per mol (unit: dimensionless / missing value: NA)
  18. trans: transpiration rate in millimol H2O per meter squared per second (unit: millimolePerMeterSquaredPerSecond / missing value: NA)
  19. vpdl: vapour pressure deficit based on leaf temperature (unit: kilopascal / missing value: NA)
  20. ctleaf: computed leaf temperature. Same as Tleaf unless doing energy balance (unit: celsius / missing value: NA)
  21. area: total area of leaf enclosed within the chamber in centimeters squared (unit: squareCentimeters / missing value: NA)
  22. stm.ratio: stomatal ratio used in calculations (unit: dimensionless / missing value: NA)
  23. tair: temperature in sample cell (unit: celsius / missing value: NA)
  24. tleaf: temperature of leaf thermocouple (unit: celsius / missing value: NA)
  25. tblk: temperature of leaf thermocouple (unit: celsius / missing value: NA)
  26. co2.r: reference cell CO2 concentration in micromol CO2 per mol (ppm) (unit: dimensionless / missing value: NA)
  27. co2.s: sample cell CO2 concentration in micromol CO2 per mol (ppm) (unit: dimensionless / missing value: NA)
  28. h2o.r: reference cell H2O concentration in millimol H2O per mol (ppm) (unit: dimensionless / missing value: NA)
  29. h2o.s: sample cell H2O concentration in millimol H2O per mol (ppm) (unit: dimensionless / missing value: NA)
  30. rh.r: relative humidity in the reference cell (%) (unit: dimensionless / missing value: NA)
  31. rh.s: relative humidity in the sample cell (%) (unit: dimensionless / missing value: NA)
  32. flow: flow rate to the sample cell in micromols per second (unit: micromolePerSecond / missing value: NA)
  33. par.in: quantum sensor inside the chamber (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
  34. par.out: external quantum sensor (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
  35. press: atmospheric pressure (unit: kilopascal / missing value: NA)
  36. stability: stability status (unit: dimensionless / missing value: NA)
  37. status: LI6400 stability diagnostics
  38. period.sd: period when measured, according to Sophie Dyllan
  39. species.sd: species code used by Sophie Dyllan
  40. tree.sd: tree number used by Sophie Dyllan
  41. n.id: code used to match up leaf nitrogen analysis with gas flux measurements
  42. leaf.n: leaf nitrogen in milligrams of N per gram of dry leaf (unit: milligramsPerGram / missing value: NA)