Indeed, soil houses very large quantities of microorganisms with enormous biodiversity, resulting in numerous biological interactions and ecological processes. To date, most studies have focused on soil bacteria and analyzed their diversity, ecology, or role in biogeochemical cycles. Despite the important role of fungi in ecosystem functioning and their huge biodiversity, studies of soil fungal communities represent only about 30% of the total investigations of soil microbial communities reported in the literature. In the context of molecular ecology, this trend may be observed because fewer molecular tools are available for the in situ characterization of soil fungi, the genetic sequence databases for soil fungi are smaller than those for soil bacteria, and also because fewer groups are working on soil fungi. However, the need to develop new tools to improve our ability to characterize the diversity and abundance of soil fungal communities has been highlighted by the rapid Vorinostat evolution from descriptive to quantitative approaches in microbial ecology. An absolute quantification of soil fungal communities could i) provide a simple bio-indicator for evaluating the impact of human activities on soil; ii) reveal the relative importance of soil fungi, as compared to bacteria, in the total microbial biomass. This result could also be combined to the quantification of specific fungal phyla to estimate their relative abundance. Finally, this would lead to a better understanding of the role of fungi in soil biological functioning. Real-time quantitative PCR has recently become a valuable molecular tool for quantifying indigenousorganisms in environmental samples directly from environmental DNA extracts. This method is powerful, accurate and cultureindependent. Different taxonomic levels can be attained by targeting different regions in the genome ). The real-time Q-PCR method has been used successfully to BKM120 side effects measure total bacterial abundance and the abundance of bacteria involved in the nitrogen cycle in soils. In addition, the suitability of the method for quantifying soil fungal communities has been demonstrated in vitro. Raidl et al. demonstrated a linear relationship between the number of copies of the ITS region detected by real-time Q-PCR and the hyphal length of Piloderma croceum, an ectomycorrhizal fungus. Nevertheless, real-time QPCR still needs to be improved for the study of soil fungal communities. Indeed, when this approach was used in different studies to target the ITS region in fungi in environmental samples, the reproducibility and accuracy of the real-time Q-PCR measurements of absolute fungal abundance in soil samples were hampered by the length of the ITS region, together with its high length polymorphism and potential resulting taxonomic bias. The reproducibility and accuracy of the method constitute strong limitations in ecological studies of soil fungal communities.