Sequence analysis of PCR-amplied and subsequently cloned 16S ribosomal RNA genes (also dened as 16S rDNA) is a widely utilized approach to assess microbial diversity and community composition in marine sediments (Bowman and McCuaig 2003; Polymenakou et al. 2005; Hunter et al. 2006; Stevens et al. 2007). Despite not being immune, analogously to all other PCR-based methods, of known potentially occurring biases (von Wintzingerode et al. 1997), this method allows an accurate description of prokaryotic biodiversity in marine sediments, and identication of the taxonomic identity of Bacteria (or Archaea) present in the investigated sample. Compared to ngerprinting techniques described here (such as automated ribosomal intergenic spacer analysis [ARISA] or terminal-restriction fragment length polymorphism [T-RFLP]), this method has the advantage of providing more detailed information in terms of species composition and allowing a phylogeneticbased identication of bacteria in the sediment sample.