DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions
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 o...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-02-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/2/361 |
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| author | Davide Francioli Guillaume Lentendu Simon Lewin Steffen Kolb |
| author_facet | Davide Francioli Guillaume Lentendu Simon Lewin Steffen Kolb |
| author_sort | Davide Francioli |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T00:57:02Z |
| format | Article |
| id | doaj.art-da33a4caf8664397bda9f567730e52c1 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T00:57:02Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-da33a4caf8664397bda9f567730e52c12023-12-11T16:50:28ZengMDPI AGMicroorganisms2076-26072021-02-019236110.3390/microorganisms9020361DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and SolutionsDavide Francioli0Guillaume Lentendu1Simon Lewin2Steffen Kolb3Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, GermanyLaboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, SwitzerlandMicrobial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, GermanyMicrobial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, GermanySoil-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.https://www.mdpi.com/2076-2607/9/2/361DNA metabarcoding workflowhigh-throughput sequencingterrestrial ecosystembacteriaarchaeafungi |
| spellingShingle | Davide Francioli Guillaume Lentendu Simon Lewin Steffen Kolb DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions Microorganisms DNA metabarcoding workflow high-throughput sequencing terrestrial ecosystem bacteria archaea fungi |
| title | DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions |
| title_full | DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions |
| title_fullStr | DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions |
| title_full_unstemmed | DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions |
| title_short | DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions |
| title_sort | dna metabarcoding for the characterization of terrestrial microbiota pitfalls and solutions |
| topic | DNA metabarcoding workflow high-throughput sequencing terrestrial ecosystem bacteria archaea fungi |
| url | https://www.mdpi.com/2076-2607/9/2/361 |
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