Methodology & Tools

Link to Tools Section

The eddy covariance method is used to assess trace gas fluxes between the biosphere and atmosphere at each site within the FLUXNET community. Vertical flux densities of CO2 (Fc), latent (LE) and sensible heat (H) between vegetation and the atmosphere are proportional to the mean covariance between vertical velocity (w') and the respective scalar (c') fluctuations (e.g., CO2, water vapor, and temperature). By convention, positive flux densities represent mass and energy transfer into the atmosphere and away from the surface and negative values denote the reverse; ecologist use an opposite sign convention where the uptake of carbon by the biosphere is positive. Turbulent fluctuations are computed as the difference between instantaneous and mean scalar quantities.

Figure 1. Mass balance for CO2 in a forest. The time-average eddy flux is assumed equal to the time- and-space-average across the upper surface of the control volume. The time-average change in storage term measured on a single tower is assumed to equal that of the whole control volume. In this figure, cc molar density of carbon, cd molar density of dry air, Chic is the molar mixing ratio of (cc/cd), L length of control volume, and hr reference height. Neglecting advection during day time is less of a problem than at night, when turbulent mixing is reduced.

The presentation by Ray Leuning provides an excellent introduction to the eddy covariance technique.

Our community is interested in assessing the net uptake of carbon dioxide by the biosphere, not the flux across some arbitrary horizontal plane. When the thermal stratification of the atmosphere is stable and turbulent mixing is weak, material diffusing from leaves and the soil may not reach the reference height zr in a time that is small compared to the averaging time T, thereby violating the assumption of steady state conditions and a constant flux layer. Under such conditions the storage term becomes non-zero, so it must be added to the eddy covariance measurement to represent the balance of material flowing into and out of the soil and vegetation. With respect to CO2, the storage term is small over short crops and is an important quantity over taller forests. The storage term value is greatest around sunrise and sunset when there is a transition between respiration and photosynthesis and between the stable nocturnal boundary layer and daytime convective turbulence. Summed over 24 hours, the storage term is assumed to be zero.

Instrumentation, Data Acquisition, and Processing

Typical instrumentation at FLUXNET field sites includes a three-dimensional sonic anemometer, to measure wind velocities and virtual temperature, and a fast responding sensor to measure CO2 and water vapor. Scalar concentration fluctuations are measured with open and closed path infrared gas analyzers. Standardized data processing routines are used to compute flux covariances.

Application of the eddy covariance methods involves issues relating to site selection, instrument placement, sampling duration and frequency, calibration and post-processing. Ideally the field site should be flat, with an extensive fetch of uniform vegetation. In practice many of the FLUXNET sites are on undulating or gently sloping terrain, as this is where native vegetation exists. Sites on complex terrain, which may force flow separation and advection, are generally excluded.

The degree of uniformity of the underlying vegetation varies across the network, too. The sites range from monospecific vegetation, to a mixture of species, to different plant functional types in different wind quadrants. All sites have sufficient fetch to generate an internal boundary layer where fluxes are constant with height.

The height of the sensors depends on the height of the vegetation, the extent of fetch, the range of wind velocity and the frequency response of the instruments. Agricultural scientists mount their sensors on small poles, while forest scientists use either walk-up scaffolding or low-profile radio towers. To minimize tower interference on scaffold towers, investigators place their instruments booms that point several meters up wind or at the top of the tower.

Spatial separation between anemometry and gas analyzers depends on whether one uses a closed or open path gas sensor. With the closed path systems, the intake is often near or within the volume of the sonic anemometers. A delay occurs as air flows through the tubing to the sensor, which is compensated with software during post-processing. Some investigators place their gas transducer on the tower in a constant environment box to minimize the lag time from the sample port and the sensor. Others draw air down long tubes to instruments housed in an air-conditioned hut below the tower. In either circumstance, flow rates are high (6 liter per minute) to insure turbulent flow and minimize the diffusive smearing of eddies. Open path gas sensors are typically placed within a 0.5 m of a sonic anemometer, a distance that minimizes flow distortion and lag effects.

Sampling rates between 10 and 20 Hz ensure complete sampling of the high frequency portion of the flux co-spectrum. The sampling duration must be long enough to capture low frequency contributions to flux covariances, but not too long to be affected by diurnal changes in temperature, humidity and CO2. Adequate sampling duration and averaging period vary between 30 and 60 minutes for most teams. Coordinate rotation calculations of the orthogonal wind vectors (w,u,v) are performed to correct for instrument misalignment and non-level terrain. The vertical velocity, w, is rotated to zero, allowing flux covariances to be computed orthogonal to the mean streamlines.

Calibration frequencies of gas instruments vary from team to team. With
closed path sensors, investigators are able to calibration frequently and
automatically, such as hourly or once a day. Teams with open path sensors
calibrate less frequency, e.g. every few weeks. However, a body of accumulating data indicates that calibration coefficients of contemporary instruments remain steady within that duration (+/- 5%). Scientists using open path sensors also compare their instrument responses to an independent measure of CO2 concentration and humidity. Members of this network do not use a uniform standard for calibrating CO2, yet. But many of us use CO2 gas standards that are traceable to the standards at the Earth System Research Laboratory of the National Oceanic and Atmospheric Administration, the standards of the global flask network.

Tools and Procedures for gap-filling:

Comprehensive comparison of gap-filling techniques for
eddy covariance net carbon fluxes (Moffat et al. (2007))

Online Gap-filling/Fluxpartitioning tool (Lasslop et al. (2010))

CarboEurope gap-filling process (beta version)