above and within a temperate broad-leaved forest canopy on hourly to seasonal time scales

Fluxes and concentrations of carbon dioxide and 13 CO 2 provide information about ecosystem physiological processes and their response to environmental variation. The biophysical model, CANOAK, was adapted to compute concentration profiles and fluxes of 13 CO 2 within and above a temperate deciduous forest (Walker Branch Watershed, Tennessee, USA). Modifications to the model are described and the ability of the new model ( CANISOTOPE ) to simulate concentration profiles of 13 CO 2 , its flux density across the canopy–atmosphere interface and leaf-level photosynthetic discrimination against 13 CO 2 is demonstrated by comparison with field measurements. The model was used to investigate several aspects of carbon isotope exchange between a forest ecosystem and the atmosphere. During the 1998 growing season, the mean photosynthetic discrimination against 13 CO 2 , by the deciduous forest canopy (∆ canopy ), was computed to be 22·4‰, but it varied between 18 and 27‰. On a diurnal basis, the greatest discrimination occurred during the early morning and late afternoon. On a seasonal time scale, the greatest diurnal range in ∆ canopy occurred early and late in the growing season. Diurnal and seasonal variations in ∆ canopy resulted from a strong dependence of ∆ canopy on photosynthetically active radiation and vapour pressure deficit of air. Model calculations also revealed that the relationship between canopy-scale water use efficiency (CO 2 assimilation/transpiration) and ∆ canopy was positive due to complex feedbacks among fluxes, leaf temperature and vapour pressure deficit, a finding that is counter to what is predicted for leaves exposed to wellmixed environments. Key-words : biogeochemistry; biosphere–atmosphere interactions; canopy photosynthesis; carbon isotopes; water use efficiency. INTRODUCTION Stable isotopes act as tracers for studying flows of material through ecosystems and the atmosphere (Farquhar, Ehleringer & Hubick 1989; Ehleringer, Hall & Farquhar 1993; Flanagan & Ehleringer 1998; Yakir & Sternberg 2000). In practice, ecologists and biogeochemists use information on the stable carbon isotope content of air, plants and soil to provide information on: (1) plant water use efficiency (Farquhar & Richards 1984; Farquhar et al . 1988; Condon, Richards & Farquhar 1993; Hall, Ismail & Menendez 1993); (2) recycling of respired carbon dioxide within forests (Schleser & Jayasekera 1985; Sternberg 1989; Lloyd et al . 1996; Sternberg et al . 1997; Yakir & Sternberg 2000); (3) the partitioning of net ecosystem carbon exchange into its components, photosynthesis and respiration (Yakir & Wang 1996; Bowling, Monson & Tans 2001); (4) identifying and quantifying the distribution and contributions of C 3 and C 4 species to global primary productivity (Lloyd & Farquhar 1994; Ehleringer, Cerling & Helliker 1997; Sage, Wedin & Li 1999); and (5) the partitioning of CO 2 exchange between terrestrial biosphere and oceanic reservoirs in global carbon cycle models (Ciais et al . 1995; Fung et al . 1997). Plant material and the CO 2 respired by plants or the decomposition of plant material are depleted in 13 C relative to that in the atmosphere. This depletion is due to discrimination against CO 2 molecules containing the heavier isotope, 13 C, when molecules diffuse across the laminar boundary layer of leaves and are carboxylated by the enzyme Rubisco during photosynthesis (Farquhar et al . 1989; O’Leary, Madhaven & Paneth 1992; O’Leary 1993; Lloyd & Farquhar 1994; Yakir & Sternberg 2000). Other discriminating processes include the hydration of CO 2 , and the diffusion of CO 2 in aqueous solution (O’Leary 1993). The isotopic signature of respiring roots, soil microbes and leaves, on the other hand, differ from one another due to their unique turnover times (Flanagan & Ehleringer 1998). Each respiring carbon pool possesses a different isotopic content because the isotopic content of the atmospheric CO 2 fixed by the plants is decreasing with time; fossil fuel combustion is diluting the isotopic content of the atmo232 D. D. Baldocchi and D. R. Bowling © 2003 Blackwell Publishing Ltd , Plant, Cell and Environment , 26 , 231–244 sphere because it is oxidizing organic compounds that are depleted in 13 C, due to their photosynthetic origin (Francey et al . 1995). Consequently, carbon in older pools generally contains more 13 C than carbon that was assimilated more recently. Other factors leading to variation in the 13 C content of respiration include selective degradation of various organic compounds by microbes, leaching of soluble organic components, and refixation of diffusively enriched CO 2 within the soil gas (Gleixner et al . 1998; Ehleringer, Buchmann & Flanagan 2000). Isotopic mixing lines, called ‘Keeling plots’ (Keeling 1958), are used to quantify the carbon isotope composition of respiring sources, such as an ecosystem and soil (Flanagan et al . 1996; Buchmann & Ehleringer 1998; Yakir & Sternberg 2000; Bowling et al . 2002; Pataki et al . 2002). In principle, a respiring source changes the ambient CO 2 mixing ratio and its isotopic composition. The isotopic composition of the respiring source can be deduced from the two end-member mixing relationship, on the assumption that a canopy is a well-mixed vessel (Keeling 1958). However, plant canopies are not well-mixed vessels. Drag and shear imposed on the atmosphere by plants causes the turbulent transfer of trace gases between plants and the atmosphere to be intermittent and to occur against the mean scalar concentration gradient (Raupach, Finnigan & Bruwet 1996; Finnigan 2000). Furthermore, vertical variations in leaf photosynthetic capacity and canopy structure cause respiratory carbon fluxes to vary vertically throughout the canopy. Another source of variation associated with the measurement of Keeling plot intercepts arises from logistical and technological issues that compromise sampling frequency and density. Air samples must be collected in flasks and returned to a laboratory for analysis on a mass spectrometer. This time-consuming and expensive procedure limits the number of samples that can be collected and analysed during a given period, thereby producing a sample mean with a less than ideal sampling error. Quantitatively, the relative sampling error of an atmospheric trace gas concentration profile is a function of the time scale of turbulence, τ , and the time duration over which the entire profile is measured, T c (Meyers et al . 1996):