A B S T R A C T The long-term effects of deforestation on the soil microbial community and its functionality are largely unknown. In order to assess simultaneously the phylogeny and functionality, we applied phospholipid fatty acid analysis (PLFAs), metaproteomics and enzyme activities in soil samples from a natural area located in Southeast Spain (Caravaca de la Cruz), dominated by Pinus halepensis (F), and an adjacent area deforested 15-years ago (DF). Deforestation induced a long-term loss of bacterial biomass and enzyme activity, but an increase in the bacterial diversity as estimated by metaproteomics. Protein abundances analysis revealed that Proteobacteria was higher in F than DF. In addition, the abundance of cyanobacterial proteins was significantly higher in DF (7.3%) when compared to F (0.9%). Interestingly, cyanobacterial proteins involved in carbon fixation (Ribulose 1,5-bisphosphate carboxylase, phycocyanins and photosystem proteins) were only identified in DF. The data suggest that Cyanobacteria play a critical role in the ecosystem functioning and biotic carbon fixation when soil is deforested in semiarid areas. ã 2015 Published by Elsevier B.V.