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Reliability of CARD-FISH Procedure for Enumeration of Archaea in Deep-Sea Surficial Sediments

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Abstract

The enumeration of Archaea in deep-sea sediment samples is still limited, although different methodological procedures have been applied. Among these, catalysed reporter deposition-fluorescence in situ hybridisation (CARD-FISH) technique is a promising tool for estimation of archaeal abundance in deep-sea sediment samples. Comparing different permeabilisation treatments, the best results obtained both on archaeal pure cultures and on natural assemblages were with hydrochloric acid (0.1 M) and proteinase K (0.004 U/ml) treatments. The application of CARD-FISH on deep-sea sediments revealed that Archaea reach up to 41% of total prokaryotic cells. Specific probes for planktonic Archaea showed that marine Crenarchaea dominated archaeal seafloor communities. No clear bathymetric trends were observed for archaeal abundances and the morphology of continental margin (slope vs. canyon) seems not to have a direct influence on archaeal relative abundances. The site-specific sediment habitat—both abiotic environmental setting and sedimentary organic matter quality—explain up to 65% of variance of archaeal, crenarchaeal and euryarchaeal relative abundance, suggesting a wide ecophysiological adaptation to deep-sea benthic ecosystems. The findings demonstrate that Archaea are an important component of benthic microbial assemblages so far neglected, and hence they lay the groundwork for more focused research on their ecological importance in the functioning of deep-sea benthic ecosystems.

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Acknowledgments

This study has been conducted in the framework of integrated Project HERMES (Hotspot Ecosystem Research on the Margins of European Seas) founded by the European Commission under the Framework Research Program VI (Contract No. GOCE-CT-2005-511234-1). The authors are indebted to the Captain and the crew of the ships Pelagia (The Netherlands) for their expert handling and support during sea going activities. The authors are also grateful to Dr. A. Dell’Anno and Prof. A. Pusceddu for precious comments on an early draft of the manuscript, and Prof. R. Danovaro for promoting and stimulating this study.

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  1. Institute of Marine Science, National Research Council (CNR), Largo Fiera della Pesca, 60121, Ancona, Italy

    Massimiliano Molari & Elena Manini

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  1. Massimiliano Molari
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  2. Elena Manini
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Correspondence to Massimiliano Molari.

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Molari, M., Manini, E. Reliability of CARD-FISH Procedure for Enumeration of Archaea in Deep-Sea Surficial Sediments. Curr Microbiol 64, 242–250 (2012). https://doi.org/10.1007/s00284-011-0056-5

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