Estimating the uncertainty in annual net ecosystem carbon exchange: spatial variation in turbulent fluxes and sampling errors in eddy-covariance measurements RAM OREN * CHENG-I HSIEH *w , PAUL STOY * , JOHN ALBERTSON *z, HEATHER R MCCARTHY * , PETER HARRELL *, GABRIEL G KATUL * *Division of Environmental Sciences & Policy, Nicholas School of Environmental & Earth Sciences, Duke University, Durham, NC 27708-0328, USA, wDepartment of Bioenvironmental System Engineering, National Taiwan University, Taipei, 10673, Taiwan, zDepartment of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708-0287, USA Abstract Above forest canopies, eddy covariance (EC) measurements of mass (CO 2 ,H 2 O vapor) and energy exchange, assumed to represent ecosystem fluxes, are commonly made at one point in the roughness sublayer (RSL). A spatial variability experiment, in which EC measurements were made from six towers within the RSL in a uniform pine plantation, quantified large and dynamic spatial variation in fluxes. The spatial coefficient of variation (CV) of the scalar fluxes decreased with increasing integration time, stabilizing at a minimum that was independent of further lengthening the averaging period (here- after a ‘stable minimum’). For all three fluxes, the stable minimum (CV 5 9–11%) was reached at averaging times (s p ) of 6–7 h during daytime, but higher stable minima (CV 5 46–158%) were reached at longer s p (412h) during nighttime. To the extent that decreasing CV of EC fluxes reflects reduction in micrometeorological sampling errors, half of the observed variability at s p 5 30 min is attributed to sampling errors. The remaining half (indicated by the stable minimum CV) is attributed to underlying variability in ecosystem structural properties, as determined by leaf area index, and perhaps associated ecosystem activity attributes. We further assessed the spatial varia- bility estimates in the context of uncertainty in annual net ecosystem exchange (NEE). First, we adjusted annual NEE values obtained at our long-term observation tower to account for the difference between this tower and the mean of all towers from this experiment; this increased NEE by up to 55 g C m 2 yr 1 . Second, we combined uncer- tainty from gap filling and instrument error with uncertainty because of spatial varia- bility, producing an estimate of variability in annual NEE ranging from 79 to 127 g C m 2 yr 1 . This analysis demonstrated that even in such a uniform pine plantation, in some years spatial variability can contribute  50% of the uncertainty in annual NEE estimates. Keywords: canopy sublayer, diurnal flux, latent heat, leaf area index, nocturnal flux, sap flux, sensible heat, temperate pine plantation Received 18 February 2005; revised version received 15 December 2005; accepted 20 December 2005 Introduction Terrestrial ecosystems play a major role in the global carbon cycle, which is an important agent of climate change. Thus, it is essential to track, explain, and predict changes in terrestrial carbon metabolism (Cana- dell et al., 2000). Ecosystem metabolism, and its re- sponse to the naturally varying environment are quantified using a number of complementary tools, including eddy covariance (EC) measurements from towers. EC measures mass and energy exchange between the biosphere and atmosphere, providing a vertically Correspondence: Ram Oren, tel. 1 919 613 8032, fax 1 919 684 8741, e-mail: ramoren@duke.edu Global Change Biology (2006) 12, 883–896 doi: 10.1111/j.1365-2486.2006.01131.x r 2006 The Authors Journal compilation r 2006 Blackwell Publishing Ltd 883