A cross-site comparison of ecosystem- and plot-scale methane fluxes across multiple sites

Wetland and upland ecosystems play significant but opposing roles in the global methane (CH₄) budget, acting as natural sources and sinks, respectively. Two of the most common approaches for measuring CH₄ fluxes (FCH₄) are chambers, which measure fluxes at fine spatial scales (ca. 1 m²), and eddy covariance (EC) towers, which integrate fluxes across larger footprints (ca. 100–10 000 m²). Although chamber and EC observations have been combined in various syntheses and databases to estimate CH₄ budgets, a unified cross-site evaluation of FCH₄ estimates at plot and ecosystem scales is lacking. As a first step toward a systematic spatiotemporal scaling of EC tower and chamber footprints, we quantified differences in site-level aggregate FCH₄ between EC and chamber measurements (ΔFCH₄) across ten wetland and upland sites at half-hourly, hourly, daily, weekly, monthly, and annual timescales. We found that ecosystem-scale median FCH₄ was consistently higher than plot-scale FCH₄ at all temporal scales, with the smallest difference at the daily timescale (multi-site median ΔFCH₄: 1.36 nmol m⁻² s⁻¹; median ecosystem-scale FCH₄ = 1.56 nmol m⁻² s⁻¹, median plot-scale FCH₄ = 0.06 nmol m⁻² s⁻¹) and the largest at annual scales (2.58 nmol m⁻² s⁻¹; median ecosystem-scale FCH₄ = 25.91 nmol m⁻² s⁻¹, median plot-scale FCH₄ = 6.55 nmol m⁻² s⁻¹). In general, the agreement between ecosystem- and plot-scale FCH₄ decreased with finer temporal resolution (from Spearman ρ = 0.95 at the annual scale to ρ = 0.65 at the half-hourly scale), while ΔFCH₄ variation was greatest at daily-to-annual scales. Key environmental predictors of ΔFCH₄ across the ten sites included plot-scale spatial heterogeneity, dominant vegetation type, vapor pressure deficit, atmospheric pressure, and friction velocity at the daily and monthly scales. Wind direction was a significant predictor only at the monthly scale, suggesting EC footprint effects at these sites. These findings suggest that accounting for variability in EC footprint extent, chamber measurement placement, and measurement artifacts is key to reconciling multi-scale FCH₄ observations across diverse ecosystems and refining CH₄ budgets.