We investigated the relationship between taxonomy and functioning of soil bacterial communities in soils from a Mediterranean Holm-oak forest using a high throughput DNA pyrosequencing technique. We used non-parametric tests (U Mann-Whitney) to evaluate the sensitivity of each single bacterial genus within the community to the fluctuations of plant physiological and environmental abiotic variables, as well as to fluctuations in soil microbial respiration. Within-lineage (phylum/class) functional similarities were evaluated by the distribution of the Mann-Whitney standardized coefficients (z) obtained for all genera within a given lineage. We further defined different ecological niches and within-lineage degree of functional diversification based on multivariate analyses (Principal Component Analyses, PCA). Our results indicate that strong within-lineage functional diversification causes extensive functional overlapping between lineages, which hinders the translation of taxonomic diversity into a meaningful functional classification of bacteria. Our results further suggest a widespread colonization of possible ecological niches as taxonomic diversity increases. While no strong functional differentiation could be drawn from the analyses at the phylum/class level, our results suggest a strong ecological niche differentiation of bacteria based mainly on the distinct response of Gram-positive and Gram-negative bacteria to fluctuations in soil moisture. This article is protected by copyright. All rights reserved.