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Archaeal Diversity in Deep-Sea Sediments Estimated by Means of Different Terminal-Restriction Fragment Length Polymorphisms (T-RFLP) Protocols

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Abstract

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. Sediment samples from 11 deep-sea sites (from 79°N to 36°N, at depths comprised from 469 to 5,571 m) were used to compare 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 of Archaeal diversity using terminal-restriction fragment length polymorphisms (T-RFLP). In silico and experimental analyses indicated that different combinations of primer sets and restriction enzymes provided 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 of ribotypes up to four 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.

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Acknowledgments

This work has been carried out within the frame of the HERMES (Hotspot Ecosystem Research on the Margins of European Seas), EC contract number GOCE-CT-2005-511234, funded by the European Commission’s Framework Six Programme and HERMIONE (Hotspot Ecosystem Research and Man’s Impact on European Seas) funded by the European Commission’s Framework Seven Programme.

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Authors and Affiliations

  1. Department of Marine Science, Faculty of Science, Polytechnic University of Marche, Ancona, 60131, Italy

    Gian Marco Luna, Karen Stumm, Antonio Pusceddu & Roberto Danovaro

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  1. Gian Marco Luna
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  2. Karen Stumm
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  3. Antonio Pusceddu
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  4. Roberto Danovaro
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Correspondence to Gian Marco Luna.

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Luna, G.M., Stumm, K., Pusceddu, A. et al. Archaeal Diversity in Deep-Sea Sediments Estimated by Means of Different Terminal-Restriction Fragment Length Polymorphisms (T-RFLP) Protocols. Curr Microbiol 59, 356–361 (2009). https://doi.org/10.1007/s00284-009-9445-4

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  • DOI: https://doi.org/10.1007/s00284-009-9445-4

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