Greenhouse Gas Fluxes - Recirculating Chamber Method


In use from 2019-05-01


Agricultural soils can serve as both sources and sinks of greenhouse gases (GHG). To instantaneously measure the flux of GHG (CO2, CH4, and N2O) from soil, we use an Integrated Cavity Output Spectroscopy (ICOS) instrument (Los Gatos Research, Inc.) with an inline Infrared Gas Analyzer (IRGA), both mounted on an electric-powered John Deere Gator making the ICOS unit conveniently mobile (MICOS). The instrumentation is connected to a round stainless steel chamber with ¼” OD Teflon tubing that recirculates chamber headspace between the instrument and chamber. A web application calculates the slope of changes in GHG concentrations over time (ppm/min) and provides a final flux value for each trace gas. For sampling of LTER plots, a five-minute closure period (1-2 min equilibration included) is sufficient for each flux measurement, though timing can vary. Fluxes are expressed as grams of gas (N2O-N for example) per hectare per day (g/ha/d) or ug/m2/hr. The data are stored on a server and can be downloaded after sampling.

Sampling Frequency: Depends on the experiment, time of year, and research objective. Fluxes are often episodic and associated with major agronomic events like tillage and fertilization. Winter fluxes may be measured by manual static chamber methods if conditions are not conducive to MICOS sampling. Extensive testing has established no measurement bias between the two methods.


In-situ (closed-cover) flux chambers consist of a stainless-steel base and a plastic HDPE lid with a rubber chamber seal (see Kahmark et al. 2020). Bases are semi-permanently installed in the field, temporarily removed only when needed due to agronomic operations. The bases are leveled and any plant material taller than the base height is clipped at base height and removed from the plot at least 1 day prior to measurement. Chamber height is measured in at least three places along the inside wall of the chamber before securing the chamber lid to the base. The lid is fitted with two ¼” Swagelok bulkhead unions that are connected via teflon tubing to input and output ports on the ICOS and IRGA units, respectively, which allows for the continuous recirculation and flow-through measurement of chamber gases. After clamping the lid on the chamber, the web application is used for selecting a plot name, inputting height values, and selecting start. A two minute countdown ensures fresh chamber air is entering the instrument. After the countdown, the user can save the concentration and slope data at anytime, or use the default five minute flux.


Preparation (at least 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
  • Nylon square or plywood square (~16” × 16″), to protect the base from hammering during base installation
  • Clippers, to clip plants to base height if necessary
  • Gator and ICOS unit: ensure Gator and ICOS batteries, and iPad are fully charged. ICOS batteries take approximately 6-8 hours for a full charge. The gator charge typically takes a few hours. The ICOS and IRGA instruments should run at least six hours on a fully charged battery bank.
  • Trimble unit and Verizon hotspot unit for determining chamber locations, if not previously completed. Follow GPS downloading instructions available in the Robertson lab and save the location data.


  • MICOS unit: Gator, ICOS, Licor-820 IRGA, power inverter, 500 aH battery bank, iPad, monitor or laptop, Raspberry Pi, and working wifi network
  • Check that URL connects after startup
  • Check inflow and outflow Teflon tubes for integrity issues such as cracks and kinks
  • Chamber lid (lid with two ¼” sampling ports for flow-through measurement)
  • Teflon sampling lines (3m, ¼” OD) connected to each port on the chamber lid: one connected to the ICOS input port and one to the IRGA output port.
  • Rain cover for ICOS in case of rain
  • Tins, for soil samples (1 per chamber)
  • iPad, for data collection
  • 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
  • Stopwatch
  • Pencils
  • Data sheets
  • Clipboards

Preparation (at least 1 day before sampling)

  1. Select and collect chamber location data via GPS.
  2. The general position of the chamber on the LTER plots should be 15 feet in from the plot edge, in a non-wheel row.
  3. Place chamber base in the ground, bottom edge buried approximately 5 cm below the soil surface. Bases must be level and in direct contact with soil with no obvious gaps. If not level, place a wooden board over the top of the base and using a 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. 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. Make certain the chamber does not have gaps between the wall and soil. If gaps are present, gently tamp the soil to the wall to create a good seal.
  4. 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.
  5. Check chamber bases, lids, and Teflon sampling lines for damage. Inspect the o-ring on the chamber lid for correct placement and/or damage.
  6. The chamber lid needs to be kept clean; clean the inside surface with water only.
  7. Prepare a randomized sampling sequence for each sampling campaign. Although sampling only takes one technician, it will take most of the day.
  8. Check that the Gator and ICOS units are charging properly. The Gator charging indicator should be solid green (drivers side), and the ICOS power inverter should read 75% charged or more. The Gator should be in neutral with the parking brake engaged and the key in the off position.

Day of Sampling

Turning on the MICOS unit:

  1. In the LTER shop, turn off the power inverter charging system by pushing the red square button on the top of the inverter until a loud beep is heard. This may take a few seconds.
  2. Unplug the charging cord from the inverter and plug it into the black and clear female receptacle pigtail on the inverter.
  3. Turn on the inverter by pushing the red button until you hear the beep again. This will put the inverter into power supply mode and convert DC to AC power.
  4. Turn on the ICOS unit by pressing the power switch located on the front of the unit just behind the driver’s seat.
  5. Turn on the monitor by pressing the button just below the screen. After a few seconds, the unit will start a 180 second countdown.
  6. The monitor will show actual values once the 180 seconds pass. It is important that the sampling line ports on the lid are not obstructed; they should be open to the atmosphere.
  7. Unplug the Gator charger from the driver’s side charging port. When the charger is plugged in, the charging indicator light will be solid green if fully charged, blinking green if actively charging, or red if discharged.
  8. Always travel with a tarp or cover for the ICOS unit in case of rain.
  9. NOTE: Complete steps to here in the LTER shop. The unit must warm up for 30-45 minutes or until the temperature of the unit is stable.

Transporting the MICOS:

  1. Please drive the Gator with care. The operator should travel at a speed low enough to prevent excessive vibration or movement of the instruments. It is best to minimize dust by driving on the grass alleyways when possible.
  2. Make sure the Gator has been fully charged prior to a full day of sampling. The gauge on the dashboard will read full scale.
  3. Drive to the first plot.
  4. Do not drive in the plot but pull up as close as possible.

Sampling with the MICOS:

  1. Please note that the following instructions may need adjustment depending on chamber sampling regime and desired accuracy. For example, if traveling a considerable distance between chambers, the instrument may have enough time to flush the previous sample air to ambient levels. Sampling chambers in close proximity may require more time to ensure the chamber air is flushed to ambient levels. Care must be taken to restrict any condensed water from entering the sampling tubes. Please discuss sampling plan with Kevin Kahmark and/or Sven Bohm prior to the start of a campaign.
  2. At the first plot, turn on the iPad and hotspot and make sure there is a connection to the ICOS. Open Safari. The app URL will be the default home page or in the Safari history.
  3. Once the app is open, select the correct treatment and replication for the plot to be measured from the dropdown list on the web application.
  4. Measure the base height at least three points along the inside wall of the chamber. Input the base heights for that treatment chamber on the web application.
  5. Insert a soil temperature probe in a shady area outside the chamber and record temperature in the soil temperature box on the app.
  6. At some point in the sampling regime, use the soil probe to collect a sample for analysis of soil nitrogen content and/or moisture. Record the soil tin number on the datasheet.
  7. It is important to make sure the previous chamber air is flushed from the system before installing the lid on the next chamber. Three minutes of ambient air flow-through is typically enough time to ensure the optical cell of the ICOS is clear of the previous chamber air and is measuring ambient air.
  8. Uncoil the lid tubing carefully and double check there are no kinks or leaks in the sampling or return lines.
  9. Place the flow-through lid on the chamber and start the two-minute countdown on the web application. The chamber air will circulate through the now closed system. A response in the CO2 trace should occur during this time.
  10. After the countdown, watch the CO2 trace for a positive flux response. Once the R2 approaches the acceptable value (for the LTER plots, we use >80%), select stop on the app, remove the lid and repeat steps 3-9, as needed, for the next chamber. If N2O is the desired focus (in addition to CO2 and CH4) the sampling run time will likely be longer than run time for an acceptable CO2 flux response because of lower slopes. It is the researcher’s responsibility to determine the R2 that sufficiently measures CO2, N2O, and CH4 fluxes and the sampling time frame that should be used.
  11. Note: The pump for circulating flow is internal on the ICOS and is not adjustable. The cell plus sampling line is roughly 300ml (+/- 50ml) and the flow of the system is 100ml/min.
  12. Repeat steps above for all remaining chambers.
  13. If you plan a prolonged break, return to the LTER shop, shut down the MICOS, and re-charge both sets of batteries. When finished for the day, return to the LTER shop and turn off the monitor, ICOS unit, and inverter. Recharge the inverter and Gator.

Data Download and Calculations

  1. No calculations are needed. Data collected include slope (ppm or ppb/min), time, plot/treatment name or chamber name, chamber height, soil temperature, and a calculated flux.
  2. All data are also saved to the ICOS as a txt file. See Kevin Kahmark if you require the txt files from the instrument.
  3. See Sven Bohm for a download of Flux data from the web application files.


Kahmark, K., N. Millar, and G. P. Robertson. 2020. Static chamber method for measuring greenhouse gas fluxes. KBS LTER Special Publication, Zenodo.

Date modified: Tuesday, Oct 24 2023



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