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Metabarcoding Approaches for Soil Eukaryotes, Protists, and Microfauna

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Microbial Environmental Genomics (MEG)

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2605))

Abstract

There have been major developments in the molecular characterization of soil protist and micrometazoan diversity, leading to a better understanding of these minute soil eukaryotes. Like in all newly developing research fields, several approaches are currently used in parallel to study these organisms. Here, we synthesize these various approaches and propose a best practice manual that should help researchers to efficiently target soil eukaryotic diversity as a whole. We cover the whole working pipeline, ranging from sampling to nucleic acids extraction to bioinformatic processing and sequence identification. Synchronous approaches to molecularly survey microbial-sized eukaryotes and other soil biodiversity groups are needed in order to provide a cumulative knowledge of soil biodiversity, as here shown for the soil eukaryome. This will be crucial in understanding the important ecosystem functions provided by soil biodiversity.

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Author information

Authors and Affiliations

  1. Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland

    Guillaume Lentendu

  2. Department of Mycology, Real Jardín Botánico/CSIC, Madrid, Spain

    Enrique Lara

  3. Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands

    Stefan Geisen

Authors
  1. Guillaume Lentendu
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  2. Enrique Lara
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  3. Stefan Geisen
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Corresponding author

Correspondence to Stefan Geisen .

Editor information

Editors and Affiliations

  1. Tree-Microbe Interact (IAM); Biogeochem, UMR1136 INRA/University of Lorraine, Labex ARB, Champenoux, France

    Francis Martin

  2. Université de Lorraine, INRAE, UMR1136 “Interactions Arbres-Microorganismes”, F-54280 Champenoux, France

    Stephane Uroz

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Lentendu, G., Lara, E., Geisen, S. (2023). Metabarcoding Approaches for Soil Eukaryotes, Protists, and Microfauna. In: Martin, F., Uroz, S. (eds) Microbial Environmental Genomics (MEG). Methods in Molecular Biology, vol 2605. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2871-3_1

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  • DOI: https://doi.org/10.1007/978-1-0716-2871-3_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2870-6

  • Online ISBN: 978-1-0716-2871-3

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