Stable isotopes are a powerful research tool in environmental sciences and their use in ecosystem research is increasing. In this review we introduce and discuss the relevant details underlying the use of carbon and oxygen isotopic compositions in ecosystem gas exchange research. The current use and potential developments of stable isotope measurements together with concentration and flux measurements of CO2 and water vapor are emphasized. For these applications it is critical to know the isotopic identity of specific ecosystem components such as the isotopic composition of CO2, organic matter, liquid water, and water vapor, as well as the associated isotopic fractionations, in the soil-plant- atmosphere system. Combining stable isotopes and concentration measurements is very effective through the use of ”Keeling plots.” This approach allows the identification of the isotopic composition and the contribution of ecosystem, or ecosystem components, to the exchange fluxes with the atmosphere. It also allows the estimation of net ecosystem discrimination and soil disequilibrium effects. Recent modifications of the Keeling plot approach permit examination of CO2 recycling in ecosystems. Combining stable isotopes with dynamic flux measurements requires precision in isotopic sampling and analysis, which is currently at the limit of detection. Combined with the micrometeorological gradient approach (applicable mostly in grasslands and crop fields), stable isotope measurements allow separation of net CO2 exchange into photosynthetic and soil respiration components, and the evapotranspiration flux into soil evaporation and leaf transpiration. Similar applications in conjunction with eddy correlation techniques (applicable to forests, in addition to grasslands and crop fields) are more demanding, but can potentially be applied in combination with the Keeling plot relationship. The advance and potential in using stable isotope measurements should make their use a standard component in the limited arsenal of ecosystem-scale research tools.
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