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“Deciphering Archaeal Communities” Omics Tools in the Study of Archaeal Communities

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Microbial Environmental Genomics (MEG)

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1399))

Abstract

Archaea constitute one of the three recognized phylogenetic groups of organisms living on the planet, and the latest to be discovered. Most Archaea resist cultivation and are studied using molecular methods. High-throughput amplicon sequencing and metagenomic approaches have been key in uncovering hitherto unknown archaeal diversity, their metabolic potential, and have even provided an insight into genomes of a number of uncultivated members of this group. Here, we summarize protocols describing sampling, molecular, metagenomic, and metatranscriptomic analyses as well as bioinformatics approaches that have proved useful for the study of archaea in natural samples.

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Acknowledgements

L.P. is supported by Slovenian Research Agency project J1-6741 and programme P1-0198. A.B.M.C. is supported by Spanish Ministerio de Economia y Competitividad project MEDIMAX BFPU2013-48007-P. P.L.G. acknowledges the support of CNRS. The authors thank Céline Petitjean and David Moreira for providing rooted Bayesian phylogenetic tree of Archaea.

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    Authors and Affiliations

    1. Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia

      Lejla Pašić

    2. Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, 03550, Alicante, Spain

      Ana-Belen Martin-Cuadrado

    3. Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France

      Purificación López-García

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    1. Lejla Pašić
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    2. Ana-Belen Martin-Cuadrado
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    3. Purificación López-García
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    Correspondence to Lejla Pašić .

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    Editors and Affiliations

    1. "Tree-Microbe Interactions" (IAM), UMR1136 INRA/University of Lorraine, Nancy, France

      Francis Martin

    2. "Tree-Microbe Interactions" (IAM);, UMR1136 INRA/University of Lorraine, Champenoux, France

      Stephane Uroz

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    Pašić, L., Martin-Cuadrado, AB., López-García, P. (2016). “Deciphering Archaeal Communities” Omics Tools in the Study of Archaeal Communities. In: Martin, F., Uroz, S. (eds) Microbial Environmental Genomics (MEG). Methods in Molecular Biology, vol 1399. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3369-3_1

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    • DOI: https://doi.org/10.1007/978-1-4939-3369-3_1

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    • Publisher Name: Humana Press, New York, NY

    • Print ISBN: 978-1-4939-3367-9

    • Online ISBN: 978-1-4939-3369-3

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