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This study investigated if atmospheric ammonia (NH3) pollution around a sheep farm influences the photosynthetic performance of the lichens Evernia prunastri and Pseudevernia furfuracea. Thalli of both species were transplanted for up to 30 days in a semi-arid region (Crete, Greece), at sites with concentrations of atmospheric ammonia of ca. 60 mu g/m(3) (at a sheep farm), ca. 15 mu g/m(3) (60 m from the sheep farm) and ca. 2 mu g/m(3) (a remote area 5 km away). Lichen photosynthesis was analysed by the chlorophyll a fluorescence emission to identify targets of ammonia pollution. The results indicated that the photosystem II of the two lichens exposed to NH3 is susceptible to this pollutant in the gas-phase. The parameter PIABs, a global index of photosynthetic performance that combines in a single expression the three functional steps of the photosynthetic activity (light absorption, excitation energy trapping, and conversion of excitation energy to electron transport) was much more sensitive to NH3 than the F-V/F-M ratio, one of the most commonly used stress indicators. (C) 2010 Elsevier Ltd. All rights reserved.