Real-time quantitative PCR (RTQ-PCR) is a highly sensitive and specic technique for detecting and quantifying prokaryotic and eukaryotic genetic sequences, down to the genus and species levels, from a large number of environmental samples (Takai and Horikoshi 2000; Skovhus et al. 2004). Therefore, RTQ-PCR can also provide an indirect estimate of the absolute and relative prokaryote abundance of Bacteria and Archaea to the total prokaryotic community.