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Review

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

1
Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany
2
Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
*
Author to whom correspondence should be addressed.
Academic Editor: Anna Reale
Microorganisms 2021, 9(2), 361; https://doi.org/10.3390/microorganisms9020361
Received: 23 November 2020 / Revised: 4 February 2021 / Accepted: 9 February 2021 / Published: 12 February 2021
(This article belongs to the Special Issue Microbial Isolation and Characterization)
Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies. View Full-Text
Keywords: DNA metabarcoding workflow; high-throughput sequencing; terrestrial ecosystem; bacteria; archaea; fungi; protists; soil and plant-associated microorganisms DNA metabarcoding workflow; high-throughput sequencing; terrestrial ecosystem; bacteria; archaea; fungi; protists; soil and plant-associated microorganisms
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MDPI and ACS Style

Francioli, D.; Lentendu, G.; Lewin, S.; Kolb, S. DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions. Microorganisms 2021, 9, 361. https://doi.org/10.3390/microorganisms9020361

AMA Style

Francioli D, Lentendu G, Lewin S, Kolb S. DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions. Microorganisms. 2021; 9(2):361. https://doi.org/10.3390/microorganisms9020361

Chicago/Turabian Style

Francioli, Davide, Guillaume Lentendu, Simon Lewin, and Steffen Kolb. 2021. "DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions" Microorganisms 9, no. 2: 361. https://doi.org/10.3390/microorganisms9020361

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