Two methods are commonly used to measure the community metabolism (primary production, respiration, and calcification) of shallow-water marine communities and infer air-sea CO2 fluxes: the pH-total alkalinity and pH-O2 techniques. The underlying assumptions of each technique are examined to assess the recent claim that the most widely used technique in coral reefs (pH-total alkalinity), may have provided spurious results in the past because of high rates of nitrification and release of phosphoric acid in the water column [Chisholm, J. R. M. & Barnes, D. J. (1998) Proc. Natl. Acad. Sci. USA 95, 6566 -6569]. At least three lines of evidence suggest that this claim is not founded. First, the rate of nitrification required to explain the discrepancy between the two methods recently reported is not realistic as it is much higher than the rates measured in another reef system and greater than the highest rate measured in a marine environment. Second, fluxes of ammonium, nitrate, and phosphorus are not consistent with high rates of nitrification and release of phosphoric acid. Third, the consistency of the metabolic parameters obtained by using the two techniques is in good agreement in two sites recently investigated. The pH-total alkalinity technique therefore appears to be applicable in most coral reef systems. Consequently, the conclusion that most coral reef flats are sources of CO2 to the atmosphere does not need revision. Furthermore, we provide geochemical evidence that calcification in coral reefs, as well as in other calcifying ecosystems, is a long-term source of CO2 for the atmosphere.T he contribution of an ecosystem to the global carbon cycle primarily results from (i) the balance between organic carbon production (photosynthetic CO 2 fixation) and consumption (respiratory CO 2 release) and (ii) the balance between calcium carbonate precipitation (a source of CO 2 ) and dissolution (a sink for CO 2 ) (1). Two methods are used to measure community metabolism of calcifying communities in flowing seawater: the alkalinity anomaly technique [pH-TA (2, 3)] and the pH-O 2 technique (4). In a recent paper, Chisholm and Barnes (5) cast doubt on the validity of the former method and suggest that it may explain the recent controversy on the role of coral reefs in the global carbon cycle. The validity of techniques used to estimate the metabolism of coastal marine communities is a critical issue at a time where unprecedented international programs (Land-Ocean Interaction in the Coastal Zone, LOICZ, and European Land-Ocean Interaction Studies, ELOISE) seek to estimate the contribution of the coastal zone to the global carbon cycle.The aim of the present paper is to examine the assumptions involved in the pH-TA and pH-O 2 techniques, to assess the claims of Chisholm and Barnes (5) by using both published and unpublished data, and to address the problem of the effect of reef metabolism on the global carbon cycle, in both the short and the long term.The pH-TA Technique. This technique is based on measurements of pH and t...