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Harvard Forest Data Archive


Soil Gas Exchange in the Clearcut Site at Harvard Forest 2011-2013

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  • Lead: Christopher Williams
  • Investigators: Myroslava Khomik, Richard MacLean, Melanie Vanderhoof
  • Contact: Information Manager
  • Start date: 2011
  • End date: 2013
  • Status: complete
  • Location: Prospect Hill Tract (Harvard Forest)
  • Latitude: +42.546 degrees
  • Longitude: -72.174 degrees
  • Elevation: 403 meter
  • Datum: WGS84
  • Taxa:
  • Release date: 2023
  • Language: English
  • EML file: knb-lter-hfr.223.6
  • 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 patterns
  • Keywords: carbon dioxide, coarse woody debris, decomposition, gas flux, litter, soil organic matter, soil respiration
  • Abstract:

    Soil CO2 efflux was measured at the clear cut site beginning in 2011. That year a nearby spruce site was also measured for comparison. Soil respiration was measured in 2011 and 2012 with the LI-COR 6200 instrument and soil efflux was calculated later in the lab. In 2013 soil respiration was measured with the LI-COR 6400 instrument, which computed the fluxes internally. In 2012 three trenched plots were established at the clear cut site. Those were established by trenching a 2 x 2 meter perimeter to a depth of about 50 cm, severing any roots. The trenches were lined with heavy duty landscaping cloth and backfilled. Soil collars were installed in the middle of the trenched plots and measured in 2012 (1 large one used with the LI-6200 machine) and in 2013 (two smaller ones used with the LI-6400 machine). Sampling points were scattered around the site, along vegetation transects (near the EC tower, across the fire access road).

  • Methods:

    A. Study Site

    The study site occupies roughly a 200 m x 400 m area (8 ha) near the top of Prospect Hill, within the Harvard Forest Long Term Ecological Research Site. In 2011, additional measurements were taken with the LI-6200 in a remnant mature Norway spruce stand also containing a low abundance of red pine, red oak, and red maple trees (42.534N, 72.183W, elevation 360 m) located approximately 1,500 m southwest of the clearcut site.

    B. Measuring Soil Respiration with the LI-6400 Instrument

    Go to the collar you are about to measure. Insert the soil temperature probe outside of the collar – GENTLY!. Make sure not to push the probe into the soil by force – if it hits a rock or root, try another location nearby.

    Check the collar’s depth and set the “Adjustment Stop ring” on the soil chamber, by adjusting the “set screws” (#19) and moving the stop-ring up and down as needed.

    You should adjust the stop-ring in such a way that the insertion depth is zero – i.e. you want the base of the chamber sitting just level with the ground, not inserted in or hanging above.

    Set the chamber over the collar, lowering it gently. Avoid breathing into the chamber. Also remove any green vegetation growing inside (just clip it to the soil surface, as needed).

    Go to Level 7. Press “start” (F3). You will be prompted for several inputs: (a) “Append file?” -- Always select YES (always append). (b) “Collar/Location?” – enter the number of the collar you are measuring (those can be found, marked on the blue/orange flags near each collar and/or on the collar itself (i.e. 1 to 17). Trenched collars are entered as “101, 102; 201, 202; 301, 302”. This prompt only accepts digits, not text. (c) “Insertion depth?” -- this depth should be zero, if you adjusted the chamber to sit just above the soil surface while on the collar.

    The system will go through three cycles of: draw-down, measurement and computing.

    While the LI-6400 is measuring. Take out the Hydrosense probe. Turn it on and insert it near the collar you are measuring, to its full length. Be careful, just as with the temperature probe, not to force the probe into the soil – our soils have rocks and roots! Measure soil moisture (in %VWC) and record it in the associated log- book.

    DONE! Move onto the next collar.

    C. Measuring Soil Respiration with the LI-6200 Instrument

    1. Set up equipment near first soil collar.

    2. Check that all hoses and a battery are correctly and completely attached.

    3. Record temperature and moisture of the organic layer 1-2” deep.

    4. Record ambient air temperature and relative humidity at surface for surface soil collars and in soil pit.

    LiCor IRGA Measurement

    1. Shake desiccant (if becomes crusty, replace).

    2. Turn gas analyzer on.

    3. Turn fan on.

    4. Press SETUP.

    5. Set Vt (cc) – volume of the entire system (chamber + analyzer): Vt (cc) = 1441 cm3 (top 5”, pvc collar) or Vt (cc) = 7876 cm3 (5” deep soil pit).

    6. Verify Vg (cc) (154 cm3).

    7. Verify pressure is appropriate for site (Spruce stand: set Pressure (mb) to 977 mb; CC site: set Pressure (mb) to 973 mb).

    8. Press RETURN, then OPERATING PARAMETERS. SETP(s) = 5 (time between samples). If top 5” pvc soil collar, set CHANGE to 500 (ppm). If 5” soil pit, set CHANGE to 200 (ppm).

    9. Zero the flow meter (FCT 4 8). Under SETUP. Press ↑ to “48 zero FLOW” (top line) and press RTRN. Should show channel 07, press RTRN, then RTRN again to ZERO (will be returned to SETUP list).

    10. Zero the CO2 analyzer (SCRUB ON and adjust ZERO knob). Press MONITOR. Place FLOW and CO2 key both visible. Put PUMP ON, DES ON and SCRUB ON. Close the Des valve fully clockwise but not tight, to divert the flow through the desiccant. The flow rate should be between 900 and 1000 umol s-1. The displayed CO2 value should approach zero. Wait about 30 seconds, unlock the ZERO knob, then adjust the zero knob itself until the CO2 reading is 0. Lock the know in place by turning the locking ring clockwise.


    12. Put IRGA cover over the soil collar/pit. Make sure seal is air-tight (particularly important with 5” soil pits).

    13. Flow rate should remain between 900-1000 umol/sec.

    14. Press MONITOR and put CO2 and FLOW in the screen view.

    15. Record FLOW, Tchamb and RH in notebook.

    16. Make sure 45 seconds has passed since you put the IRGA cover over the soil collar/pit.

    17. Press LOG.

    18. Record initial CO2 value in notebook.

    19. Press TIME, so that CO2 and TIME are visible in the screen.

    20. Wait for either a change of 200 ppm (5” soil pit) / 500 ppm (top 5” soil collar) or 900 seconds. **If a program pops up mid-measurement then keep pressing return until you get through the program, then press monitor and wait for the 200 or 500 ppm change or 900 seconds.

    21. Record final CO2 and TIME at 200 or 500 ppm OR 900 seconds.

    22. Record final RH and Tchamb.

    23. Turn DES OFF and PUMP OFF between measurements.

    24. Remove IRGA top from collar.

    Calculating Soil CO2 efflux from LI-6200 data

    Soil Respiration Analysis (devised summer 2011)

    System Volume:

    First calculate the system volume for each of the 32 collars. We will assume each soil collar is a perfect cylinder: V = π r2h +154 cm3, where h is the height of the collar and 154 cm3 is the volume of the tubing and path internal to the gas analyzer.

    All of the collars had the same radius (12.7 cm), so: V = 506.45h + 154. Convert volumes from cm3 to m3 (1 m3 = 1,000,000 cm3).

    Ground surface:

    The collars all have the same radius, so the ground surface is identical for all 32 soil collars: A = π r2 = 506.45 cm3 x (1 m2)/(10,000 cm2 ) = 0.050645 m2.

    Respiration Rate:

    The respiration rate is defined as grams of CO2 emitted per ground surface area per period of time. We have the ground surface area and the period of time the measurement took. Again, the primary challenge is converting a change (Δ) in CO2 concentration (ppm) within a known volume (collar) to grams of CO2. See the log respiration sheet for details regarding the conversion methodology.

    CO2 emission (g) = (change in mols of CO2) x (CO2 molar mass) x (air pressure) x (air volume) / [(gas constant) x (air temperature)].

    Keep in mind that: 1 ppm = (1 mol)/(1 x 10^6 mol).

    Also, pressure is typically presented in Pa: 1 pa = (1 N)/m2 and 1 N = (1 J)/m so 1 pa =(1 J)/m3.

    Let’s check the units now: g = (1 mol)/(1 x 10^6 mol) x (44.01 g)/mol x J/m3 x m3 x (K mol)/(8.314 J) x 1/K.

    As you can see, all of our units cancel out as they should, leaving us with g = g.

    Now if we add the “per surface area of ground and per time" portions, we get the entire equation for calculating the respiration rate (RR):

    RR (g CO2 m-2 sec-1) = (X mol CO2)/(1 x 10^6 mol) x (44.01 g)/(mol) x (P(J))/(m3) x Y m3 x (K mol)/(8.314 J) x 1/(Temp (K)) x 1/(0.050645 m2) x 1/(Time (sec))

    Variables we need to fill in values for:

    X is the change in ppm (final – starting) of CO2.

    P is the pressure (we will use the same pressures we entered in the IRGA, but converted from mb to pa to J m-3, but these will be later substituted for more accurate values using data from our eddy covariance tower. Spruce stand = 97,700 J m-3. Clearcut site = 97,300 J m-3.

    Y is the system volume which has been calculated individually for each soil collar.

    Temp will be the starting temperature made by the IRGA (converted from Celsius to Kelvin).

    Time is the total time of the measurement

    Preparation Calculations:

    X: Add a column for CO2 change (X). Subtract the end from the start CO2 ppm.

    P: Add a column for pressure and insert either 97,700 or 97,300 depending on if the measurement was taken in the spruce or clearcut stand.

    Y: We’ve already calculated Y (system volume) for each soil collar. Add a column for volume. Sort by collar number and enter the appropriate volumes for each measurement.

    Temp: Convert the starting air temperature from Celsius to Kelvin. Add a column for Start temp (K). Kelvin = Celsius + 273.15.

    Insert RR calculation into excel pulling from the appropriate columns to calculate RR.

  • Organization: Harvard Forest. 324 North Main Street, Petersham, MA 01366, USA. Phone (978) 724-3302. Fax (978) 724-3595.

  • Project: The Harvard Forest Long-Term Ecological Research (LTER) program examines ecological dynamics in the New England region resulting from natural disturbances, environmental change, and human impacts. (ROR).

  • Funding: National Science Foundation LTER grants: DEB-8811764, DEB-9411975, DEB-0080592, DEB-0620443, DEB-1237491, DEB-1832210.

  • 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.

  • License: Creative Commons Zero v1.0 Universal (CC0-1.0)

  • Citation: Williams C. 2023. Soil Gas Exchange in the Clearcut Site at Harvard Forest 2011-2013. Harvard Forest Data Archive: HF223 (v.6). Environmental Data Initiative:

Detailed Metadata

hf223-01: Licor 6400

  1. datetime: date and time sampled
  2. date: date sampled
  3. obs: observation number
  4. time: time
  5. plot: collar number
  6. efflux: soil CO2 efflux in micromol CO2 per meter squared per second (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
  7. vtot: total volume of soil chamber (unit: milliliter / missing value: NA)
  8. rh.cmbr: relative humidity in the soil chamber (unit: dimensionless / missing value: NA)
  9. tsoil: soil temperature measured by external temperature probe (at depth of 15cm) (unit: celsius / missing value: NA)
  10. rh.irga: relative humidity in the IRGA (unit: dimensionless / missing value: NA)
  11. ins.depth: chamber insertion depth (unit: centimeter / missing value: NA)
  12. tblk: temperature of cooler block (unit: celsius / missing value: NA)
  13. co2s: sample cell CO2 concentration in micromol CO2 per mol (ppm) (unit: dimensionless / missing value: NA)
  14. h2os: sample cell H2O concentration in millimol H2O per mol (ppm) (unit: dimensionless / missing value: NA)
  15. tair: temperature in sample cell (unit: celsius / missing value: NA)
  16. press: atmospheric pressure (kPa) (unit: kilopascal / missing value: NA)
  17. status: LI6400 stability diagnostics
  18. soil.mois: volumetric water content (%) measured with Hydrosense soil probes (20cm depths) (unit: dimensionless / missing value: NA)
  19. trenched: whether or not the collar was located in a trenched plot
    • 0: collar not located in a trenched plot
    • 1: collar located in a trenched plot

hf223-02: Licor 6200

  1. site: site where measurement was taken
    • CC: clear cut
    • SS: spruce stand
    • CCT: clear cut trenched plot
  2. collar: collar number
  3. trenched: whether or not the collar was in a trenched plot
    • 0: collar not located in a trenched plot
    • 1: collar located in a trenched plot
  4. datetime: date and time sampled
  5. date: date of measurement
  6. year: year measured
  7. month: month measured
  8. time: time of measurement
  9. am: whether or not the measurement was taken in the morning
    • 0: measurement was not taken in the morning
    • 1: measurement was taken in the morning
  10. pm: whether or not the measurement was taken in the afternoon
    • 0: measurement was not taken in the afternoon
    • 1: measurement was taken in the afternoon
  11. measurement of the day
  12. recorder: initials of the person who measured that day
  13. flow.rate: flow rate in micromols per second (unit: micromolePerSecond / missing value: NA)
  14. start.rh: relative humidity at start of measurement (%) (unit: dimensionless / missing value: NA)
  15. start.temp: temperature inside the chamber at start of measurement (unit: celsius / missing value: NA)
  16. start.co2: starting CO2 concentration (ppm) (unit: dimensionless / missing value: NA)
  17. end.co2: ending CO2 concentration (ppm) (unit: dimensionless / missing value: NA)
  18. meas.time: total time of measurement (total time chamber sat on the collar) (unit: second / missing: NA)
  19. end.rh: relative humidity at end of measurement (%) (unit: dimensionless / missing value: NA)
  20. end.temp: temperature inside the chamber at end of measurement (unit: celsius / missing value: NA)
  21. weather: weather conditions that day
  22. last.rain: time of last precipitation event at the site
    • 1: now
    • 2: less than 8 hours
    • 3: less than 12 hours
    • 4: less than 24 hours
    • 5: more than 24 hours
    • 6: more than 40 hours
    • 7: less than 48 hours
    • 8: more than 48 hours
    • 9: less than 96 hours
  23. air.temp: ambient air temperature (unit: celsius / missing value: NA)
  24. air.rh: ambient relative humidity (%) (unit: dimensionless / missing value: NA)
  25. soil.temp: soil temperature (unit: celsius / missing value: NA)
  26. soil.mois: soil moisture - recorded by a relative probe, before we got a Hydrosense (unit: dimensionless / missing value: NA)
  27. soil pH recorded with a manual probe (unit: dimensionless / missing value: NA)
  28. light: ambient PAR measurement
  29. comment: comments
  30. co2.flux1: soil CO2 efflux (grams CO2 m-2 s-1) (unit: gramPerMeterSquaredPerSecond / missing value: NA)
  31. co2.flux2: soil CO2 efflux (milligrams CO2 m-2 s-1) (unit: milligramPerMeterSquaredPerSecond / missing value: NA)
  32. co2.flux3: soil CO2 efflux (micromol CO2 m-2 s-1) (unit: micromolePerMeterSquaredPerSecond / missing value: NA)