Greenhouse gas emissions from soils are often measured using trace-gas flux chamber techniques without a standardized protocol, raising concerns about measurement accuracy and consistency. To address this, we compared measurements from non-steady-state non-through-flow (NTF) chambers with a non-steady-state through-flow (TF) chamber system in three bioenergy cropping systems located in Wisconsin. Additionally, we investigated the effects of the NTF flux calculation method and deployment time on flux measurements. In all cropping systems, when NTF chambers were deployed for 60 min and a linear regression (LR) flux calculation was used, soil CO2 and N2O fluxes were, on average, 18 and 12% lower, respectively, than fluxes measured with a 15-min deployment. Fluxes calculated with the HMR method, a hybrid of nonlinear and linear approaches, showed no deployment time effects for CO2 and N2O and produced 27 to 32% higher CO2 fluxes and 28 to 33% higher N2O fluxes in all crops than the LR approach with 60-min deployment. Across all crops, CO2 fluxes measured with the TF chamber system were higher by 24.4 to 84.9 mg CO2-C m(-2) h(-1) than fluxes measured with NTF chambers using either flux calculation method. These results suggest that NTF chamber deployment time should be shortened if the LR approach is used, although detection limits should be considered, and the HMR approach may be more appropriate when long deployment times are necessary. Significant differences in absolute flux values with different chamber types highlight the need for significant effort in determining the accuracy of methods or alternative flux measurement technologies.
