Greenhouse Gas Fluxes - Static Chamber Method


In use from 2008-03-01

Replaced square chamber protocol #23 in use from 1991


Agricultural soils can serve as both sources and sinks of greenhouse gases (GHGs). To measure the flux of biogenic GHGs (CO2, CH4, and N2O) from soil, we use static flux chambers and withdraw four gas samples over the course of an hour to determine changes in chamber gas concentration over that time interval. CH4 and N2O are determined by gas chromatography; CO2 by either infrared gas analysis or spectroscopy. Fluxes are expressed as grams or kilograms of elemental gas per hectare per day.

Sampling Frequency: Depends on the experiment, time of year, and research objective. As part of our sampling program of the LTER Main Cropping System Experiment (MCSE), GHG fluxes are measured weekly to monthly throughout the growing season (since 1991) and monthly throughout the winter (since 2013). Fluxes are often episodic and associated with major agronomic events like tillage and fertilization.


In situ static (closed-cover) flux chambers consist of a cylindrical metal base and an airtight plastic cover. Bases are semi-permanently installed in the field, removed only for agronomic operations or repair. Gas fluxes are measured by fitting the chamber cover to the base and then removing headspace samples at approximate 10-20-minute intervals over the course of an hour. Gas samples are taken by inserting a 10 mL syringe through a rubber septum in the chamber cover and, after gently mixing chamber gases by slowly pumping the syringe several times, withdrawing 10 mL. The first 10 mL sample is used to flush a vented, glass storage vial. The vial’s needle vent is then removed and a second 10 mL gas sample from the chamber is injected into the sealed vial, which is stored over pressurized. For analysis of N2O, CH4, and CO2, see Analysis of Greenhouse Gases protocol.


Preparation (1 day before sampling)

  • Round chamber base (metal, 28 cm dia. × 26 cm high), semi-permanently installed and levelled in each plot at least one day before sampling
  • Rubber mallet, for installing and leveling base
  • Wood block (~2″ × 4″ × 18″) or plywood square (~16 × 16″) or stable flat surface to protect the base while hammering during base installation and leveling
  • Clippers, to clip plants to base height if necessary


  • Chamber lids with septa (at least 1 per chamber per sampling round; clean before taking to field)
  • Tins, for soil samples (1 per chamber)
  • Soil probe, for taking soil sample
  • Soil thermometer (Taylor small dial thermometers with 13 cm stems)
  • Ruler, 30 cm, to measure chamber interior height from soil surface
  • Syringes, 10 mL (at least 2 per person)
  • Needles, 25 gauge (at least 10 per person)
  • Extra septa for lids
  • Labeled gas sample vials (4 per chamber plus ambient and controls, plus a couple spare)
  • Stop watch
  • Carrying caddy, for carrying supplies
  • Pencils
  • Data sheets
  • Clipboards


Preparation (1 day before sampling):

  1. Place chamber base in ground, bottom edge buried approximately 1 inch below the soil surface. Bases must be level. If not level, place a board over the top of the base and using the mallet, carefully hammer the board where the base is higher until the board is horizontal. Bases remain in place and are not removed between sampling times except for agronomic operations and repair. When selecting a spot to redeploy chamber bases, keep in mind that the area inside the base should be as representative as possible of the area outside the base.
  2. Prior to sampling, clip plants within the chamber base to base height without disturbing the soil. Discard plant clippings outside of the chamber base. Do not clip to soil surface and leave surface litter in place.
  3. Check chamber bases and lids for damage. Replace the septum on the chamber lid if needed. Damage by repeated needle insertion occurs. Inspect the O-ring on each lid for correct placement and/or damage.
  4. Chamber lids need to be kept clean; clean the inside with water only (do not drip into chamber area).
  5. Prepare gas sample vials by replacing the septum in the sample vial cap and labeling each vial with a unique number for gas sample identification. For LTER MCSE sampling, the number of vials needed = (number of chambers * 4 sampling rounds (T0 – T3)) + 4 ambient vials + 4 duplicate vials.

Sampling Procedure:

  1. Chambers are sampled sequentially, several at a time. We generally take four samples (T0, T1, T2, T3) from each chamber over an approximate 1 hour sampling period (i.e., returning to the same chamber roughly every 20 minutes). So you will be sampling multiple chambers over each 20 minute period rather than spending 1 hour next to each chamber.
  2. Measure the base height: measure the inside base height from the soil surface at four points around the base and record to the nearest cm on data sheet.
  3. Place a chamber lid and 4 sample vials next to each chamber in the sampling sequence.
  4. Insert a 25G needle into the first chamber lid septum to equilibrate chamber pressure during lid placement. Snap the lid onto the installed chamber base; make sure lid is firmly attached; then remove the needle from the chamber lid septum. Record the time of the first chamber lid deployment on the datasheet.
  5. Insert a single needle not attached to a syringe into the first sample vial to act as a vent. Then insert a needle attached to a 10 mL syringe into the chamber lid septum and, while keeping the needle inserted, carefully pull the syringe plunger out and push it back in, withdrawing/re-injecting about 10 mL of chamber air. Repeat three times. Then withdraw a 10 ml sample and inject into the sample vial with the vent needle in place. You should hear air escaping from the vent needle while the vial is being flushed. Remove the vent needle from the vial. Reinsert the needle of the syringe into the lid septa and mix the chamber air three additional times before drawing the second 10 ml sample. Remove the syringe from the lid septa and inject the entire 10 mL sample into the flushed sample vial. Over pressurization of gases in the sample vial will occur; it guards against sample contamination and is corrected during analysis. IMMEDIATELY START THE STOPWATCH AFTER INJECTING SAMPLE INTO VIAL AND KEEP THE STOPWATCH RUNNING CONTINUOUSLY THROUGHOUT THE SAMPLING CAMPAIGN.
  6. On the data sheet, record the chamber number, vial ID, plot number, clock time of lid deployment, and time on the stopwatch. The first sampling time is sample T0.
  7. Measure soil temperature and sample soil for soil moisture at some point during the sampling campaign. Measure the soil temperature by inserting the soil thermometer one inch into soil adjacent to chamber in the shade if possible. Allow at least 1 minute before reading and recording temperature in degrees C. Use the soil probe to sample the surface soils (0-25 cm) at a spot at least 1 meter from chamber (1 soil sample per chamber). Store soil cores in labelled tins and record tin number on data sheet. This step may not be possible if the ground is frozen.
  8. Repeat the above sampling procedure for all chambers in your sampling campaign. Be sure to record the clock time (time of day) of lid deployment and the stopwatch time for all initial T0 samples. If assigned with ambient vials, sample ambient air at the same stage in each sampling round. If assigned with duplicate vials, use the same gas sampling procedure to sample the chamber air twice for a selected chamber in your sampling campaign.
  9. Return to the first sampled chamber and repeat the sampling procedure for the next round of samples (T1) and progress through all chambers in the same sequence as sample round T0. Repeat process for the number of rounds in your sampling campaign.

Helpful hints:

  • It is easiest to keep track of where you are in the vial sequence by placing the vent needle in the next vial to be used and turning the “used” vials upside down in the tray.
  • If the septa/vials leak – recognized by a hissing sound—either tighten its cap or repeat the sampling with a spare vial.
  • As a guideline, allow about 1 minute for each sampling procedure after T0.
  • If rain is expected, data sheets should be printed onto rainproof paper.

Flux Calculation:

  1. Determine the linear relationship (αv) between the concentration of each GHG in sampling vials and the sampling time (slope of T0-T3 concentrations over time), in parts per million by volume per minute (ppmv/min) which is equivalent to microliter per liter per minute (μL/L/min).

  2. Convert αv with units based on volume to αm with units based on mass, in microgram per liter per minute, and correct for field temperature using the following application of the Ideal Gas Law:

    αm = (αv x M x P) / (R x T)

    αm is expressed in μg N or C/L/min
    M = molecular weight of GHG (28 μg N/μmol N2O or 12 μg C/μmol CO2 or CH4)
    P = assumed atmospheric pressure = 1 atm
    R = Universal gas constant = 0.0821 L-atm/mol-K = 0.0821 μL-atm/μmol-K
    T = field temperature, in °K = °C + 273

  3. Calculate the flux (fm) of GHG, as microgram element (N for N2O; C for CO2 and CH4) per square meter per hour), using the equation:

    fm = (αm x V x 60 min/h) / A

    fm is expressed in μg N or C/m2/h
    αm = as above, in μg/L/min
    V = volume of gas in chamber, in L
    A = soil surface area covered by chamber, in m2

  4. Convert hourly flux in square meters to daily flux in square meters by multiplying fm by 24 h/day.

  5. Convert daily flux (fm ) in square meters to grams element per hectare (ha) per day (fha) by multiplying the flux by 1 gram/1,000,000 micrograms and 10,000 m2/ha, or:

    fha = fm x 0.01

    fha = is expressed in g N or C/ha/day

  6. Fluxes of CO2-C are typically much higher than fluxes of N2O-N and CH4-C and can be converted to kilograms CO2-C by multiplying the converted flux by 1 kilogram/1000 grams.

Date modified: Monday, Apr 01 2019