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In arid ecosystems, higher rates of biogeochemical cycles occur in soils under shrub canopies than in inter-shrubs spaces. Therefore, changes in shrub cover may have great impact on ecosystem functioning. Recently, a drought-induced massive shrub death was observed in the semi-arid northern Negev Desert in Israel. The aim of this study was to examine the consequences of the shrub death on the levels of soil inorganic nitrogen and the structure of ammonia-oxidizers communities. Compared to soil samples from the winter that preceded the shrubs death, soil samples that were collected at the end of the first winter following the shrub death contained significantly higher nitrate concentrations, exhibited lower ammonia oxidation potential and similar community structure of ammonia oxidizers. In addition, the numbers of ammonia-oxidizers were higher in the soil under dead Thymelaea hirsute shrubs than under live shrub canopies. The results suggested that the activities of the nitrogen transforming microbes were moderately affected by the drought and resulted in nitrate accumulation due to the absence of major nitrogen consumers (shrubs). During rainfall events, this nitrate can be washed away by run-off and contaminate downstream water bodies or alternatively denitrified to gaseous nitrogen (including nitrogen oxides). (C) 2012 Elsevier Masson SAS. All rights reserved.