Metabarcoding Approaches for Soil Eukaryotes, Protists, and Microfauna

Guillaume Lentendu, Enrique Lara, Stefan Geisen*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

2 Citations (Scopus)


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.

Original languageEnglish
Title of host publicationMicrobial Environmental Genomics (MEG)
EditorsF. Martin, S. Uroz
Place of PublicationNew York
Number of pages16
ISBN (Electronic)9781071628713
ISBN (Print)9781071628706
Publication statusPublished - Jan 2023

Publication series

NameMethods in molecular biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Arthropodes
  • ASV
  • Bioinformatics
  • eDNA
  • Metabarcoding
  • Microfauna
  • Nematodes
  • Protists
  • Soil


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