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The aim of the current study was to gain a better understanding of the changes that occur in soil microbial community and in its functional diversity as a result of the use of nematocide and biocide inhibitors in natural ecosystems. Both inhibitors are known to have a great effect on the nematode community and total biota, playing an important role in soil food web and biota interactions. The experiment was set up in the Negev Desert using sixteen 1 x 1 m soil plots, to which two chemical inhibitors were applied: (a) a biocide, to eliminate the whole biotic community; and (b) a nematocide, to eliminate the nematode community in soil. In addition, water treatment was applied to the same soil plots, while untreated soil plots were used as control. Microbial functional diversity, together with abiotic parameters such as soil moisture and total organic carbon, was tested monthly in soil samples collected from the 0-10 and 10-20 cm soil layers. The results of the abiotic parameters showed similar patterns in the two soil layers regardless of the inhibitor treatments. An increase in soil water content followed rainfall patterns. Total organic carbon was low during the wet season and increased during the dry seasons. The Shannon-Weaver index value for microbial functional diversity was found to increase in spring after the wet season in both soil layers. In the upper soil layer, an increase was observed both in the inhibitor and water treatments. However, the increase in the water treatment lasted longer compared to the increase observed in the inhibitor-treated soil plots. In the 10-20 cm soil layer, a different pattern was observed: an increase in microbial functional diversity was observed in the inhibitor-treated soil plots, while an increase in the water-treated soil plots was seen at a later stage. Principal Component Analysis was also conducted, revealing different patterns between inhibitors and water treatments on both a temporal scale, when changes from a homogeneous to heterogeneous consumption pattern were observed, and in the nature of communities that proliferate in the soil. Differences were also observed in the microbial community between the upper 0-10 and the lower 10-20 cm soil layers, where an opposite pattern of substrate consumption was observed. This study emphasizes the important role the biotic component plays in the soil of an and climate, studying the long-term effects of key species elimination on the microbial community in desert soil. (c) 2006 Elsevier Ltd. All rights reserved.