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International audience ; Soil carries out functions that are crucial for the environment and life on earth and is therefore an essential non-renewable resource for mankind. Recently, the European Soil Framework Directive proposal (COM(2006)232) indicated that soil is under increasing environmental pressure mostly due to the intensification of human activities, which are damaging the capacity of soil to continue to perform in full its broad variety of crucial functions. Most of these soil functions are dependent on microorganisms inhabiting the soil. The diversity of soil microorganisms is the highest on earth with estimates of several thousand to several million different genomes per gram of soil (Whitman et al. 1998; Torsvik et al. 2002; Zhang and Xu 2008). However, fundamental understanding of the diversity and ecology of microbial communities carrying out soil functions has been hampered by our inability to grow most microorganisms under laboratory conditions.Since the early eighties, direct DNA-based methods have been developed to circumvent the biases resulting from the low number of microorganisms that could be cultured, thus hampering our understanding of microbial diversity in soil (Torsvik 1980; Porteous et al. 1991; Tsai et al. 1991; Smalla et al. 1993; Zhou et al. 1996; He et al. 2005). These methods were based on direct extraction of the DNA from micro-organisms living in the soil, using various lysis treatments. Since then, numerous articles have been published describing either new or improved methods for soil DNA extraction and at least ten companies are commercializing “Soil DNA” extraction kits. The on-going success of these direct molecular methods for studying soil micro-organisms is reflected by the fact that more than 1,000 articles are now published yearly using some type of soil DNA extraction method. Unfortunately, the wide use of these methods has resulted in a huge number of laboratory or even user-specific protocols, which contain minor to major modifications of the existing methods or ...
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