Despite the increasing recognition of the quantitative importance of Archaea in all marine systems, the protocols for a rapid estimate of Archaeal diversity patterns in deep-sea sediments have been only poorly tested yet. We collected sediment samples from 11 deep-sea sites covering a wide latitudinal range (from 79°N to 36°N, at depths comprised from 469 to 5500 m) and compared the performance of two different primer sets (ARCH21f/ARCH958r and ARCH109f/ARCH 915r) and three restriction enzymes (AluI, Rsa I and HaeIII) for the fingerprinting analysis (T-RFLP) of Archaeal diversity. In silico and experimental analyses consistently indicated that different combinations of primer sets and restriction enzymes can result in different values of benthic Archaeal ribotype richness and different Archaeal assemblage compositions. The use of the ARCH109f/ARCH 915r primer set in combination with AluI provided the best results (a number ribotypes up to 4-folds higher than other combinations), suggesting that this primer set should be used in future studies dealing with the analysis of the patterns of Archaeal diversity in deep-sea sediments. Multivariate, multiple regression analysis revealed that, whatever the T-RFLP protocol utilized, latitude and temperature explained most of the variance in benthic Archaeal ribotype richness, while water depth had a negligible role
