## 3 Methods--Field Experiment
### Soil CO\({}_{2}\) Efflux  
Automated chambers were used to continuously measure soil CO\({}_{2}\) efflux in the control and treatment plots. Air was circulated from the chamber to an infrared gas analyzer (IRGA, LI-6252, Li-Cor, Lincoln, NE, USA) and then returned to the chamber. At the treatment and control sites, eight closed system automated chambers were randomly distributed on the forest floor near the base of each flux tower. Each chamber consisted of an aluminum frame with a pneumatic actuator to control the opening and closing of the lid and a clear plexiglass cylinder (radius 14.75 cm) with a small fan near the top of the chamber to homogenize the chamber air as samples were taken (Figure 1). Within each chamber a manifold returned sampled air to the bottom of the chamber. Air from the chamber headspace was sampled through a polyethylene coated aluminum tube and pumped to the IRGA for analysis. The system was controlled by a data logger (CR23X, Campbell Scientific Inc., Logan, UT, USA) and each chamber was sampled at 10 Hz for seven minutes each hour, so that each of the eight chambers in each array was sampled once every hour. Measurements started at both sites in 18 April 2008. The program fit a non-linear curve (Equation (1)) to those data points which yielded coefficients from which \(R_{s}\) was calculated:  
\[C_{C}(t)=C_{s}-(C_{s}-C_{0})\times e^{-(k*t)} \tag{1}\]  
When _C\({}_{c}\)(t)_ is the concentration of CO\({}_{2}\) in ppm at time \(t\) (s), _C\({}_{s}\)_ is the soil CO\({}_{2}\) concentration (ppm), _C\({}_{o}\)_ is the CO\({}_{2}\) concentration of the air sample (ppm) at time \(t=0\), and \(k\) is the concentration saturation rate (1/s). The initial rate of change of carbon concentration in the chamber immediately after closing the lid can be solved as:  
Figure 1: (**A**) Automated chambers closed when pressure was applied to the pneumatic actuator which created a seal between the lid and the chamber. (**B**) Samples were collected from the black tube near the top center of the chamber, and analyzed air was returned via the perforated manifold at the base of the chamber. (**C**) Respiration was determined by analyzing the timeseries of concentration accumulation in the chambers—raw CO\({}_{2}\) concentration data (blue line) were graphed for 330 s while CO\({}_{2}\) accumulated in the closed automated chambers. Each accumulation curve was fit individually with a non-linear curve (black line) in MATLAB [29] (see methods). Coefficients were computed from the curve and exported to yield \(R_{s}\). \[\lim_{t\to 0}\left(\frac{\partial C_{c}}{\partial t}\right)=(C_{s}-C_{0})k \tag{2}\]  
As this rate of CO\({}_{2}\) accumulation is true at the instant of closing the lid it is also characteristic to the rate of emission from the soil immediately before closing the lid, an thus used to calculate the diffusional flux of CO\({}_{2}\) from the soil (\(D_{c}\)), which is equivalent to soil respiration, \(R_{s}\) (\(\upmu\)mol/m\({}^{2}\)/s):  
\[D_{C}=(C_{s}-C_{0})*k\left(\frac{\rho V}{S}\right)=R_{s} \tag{3}\]  
where \(S\) is the chamber surface area (0.068 m\({}^{2}\)), \(V\) is the chamber volume (0.0144 m\({}^{3}\)) and \(\rho\) is the molar density of air (41.6 mol/m\({}^{3}\)). To solve for \(C_{s}\)and \(k\) an estimate of \(C_{0}\)is needed. To obtain \(C_{0}\) a minimizing function was employed to find the lowest 20 s moving average within the first 70 data points. Using \(C_{0}\), \(t\), and \(C_{c}\) data, a non-linear least squares fit with least absolute residuals returned estimates of \(C_{s}\)and \(k\). Figure 1C shows examples of raw CO\({}_{2}\) data and the fitted curve for one hourly 7 min period of data from which coefficients were calculated. \(C_{0}\), \(C_{s}\), and \(k\) values for each seven minute period for each site, day, hour, and year and chamber combination were calculated. Periods for which the estimated \(C_{0}\) value was less than 380 ppm, the current ambient air CO\({}_{2}\) concentration, were removed.