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The objective of this paper was to determine whether CO2 exchange rates could be used as an indicator for determining the state of development and species or functional composition of biological soil crusts in different successional stages. We quantified the CO2 exchange rates, i.e., CO2 assimilation and respiration, in samples from different microhabitats at two different sites in the Negev desert. In the successional pathway of the crust communities, the pioneers in colonising the soil surface are the cyanobacteria; green algae, mosses and lichens then follow. Physical influences such as soil structure and types, radiation intensity, and topographic traits such as slope directions that affect water availability and soil moisture, influence the successional pathways and the soil crust community. When physical conditions are the same, disturbances are key factors for a specific successional stage. We found a substantial gradient of CO2 exchange at the Nizzana site for both respiration and photosynthesis. Samples from the sand dunes at the Nizzana site showed a pronounced activity gradient with high rates for assimilation (around 70 mu mol CO2 m(-2) min(-1)) as well as respiration (60-70 pmol CO2 m(-2) min(-1)) at the base of dunes, decreasing towards the top. The soil crust samples of the Negev desert show comparable values. Hence, as ecotypes containing such biological soil crusts with dominant photosynthetically active organisms are a widespread phenomenon in desert, boreal and arctic systems, their contribution to the global cycling of trace gases and elements can be significant for global budgets. (C) 2000 Elsevier Science Ltd. All rights reserved.