Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding
The diversity of soil bacteria was analyzed via metabarcoding and metagenomic approaches using DNA samples isolated from the biocrusts of 12 different Arctic and Antarctic sites. For the metabarcoding approach, the V3-4 region of the 16S rRNA was targeted. Our results showed that nearly all operatio...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/4/812 |
| _version_ | 1797605310181933056 |
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| author | Burkhard Becker Ekaterina Pushkareva |
| author_facet | Burkhard Becker Ekaterina Pushkareva |
| author_sort | Burkhard Becker |
| collection | DOAJ |
| description | The diversity of soil bacteria was analyzed via metabarcoding and metagenomic approaches using DNA samples isolated from the biocrusts of 12 different Arctic and Antarctic sites. For the metabarcoding approach, the V3-4 region of the 16S rRNA was targeted. Our results showed that nearly all operational taxonomic units (OTUs = taxa) found in metabarcoding analyses were recovered in metagenomic analyses. In contrast, metagenomics identified a large number of additional OTUs absent in metabarcoding analyses. In addition, we found huge differences in the abundance of OTUs between the two methods. The reasons for these differences seem to be (1) the higher sequencing depth in metagenomics studies, which allows the detection of low-abundance community members in metagenomics, and (2) bias of primer pairs used to amplify the targeted sequence in metabarcoding, which can change the community composition dramatically even at the lower taxonomic levels. We strongly recommend using only metagenomic approaches when establishing the taxonomic profiles of whole biological communities. |
| first_indexed | 2024-03-11T05:00:18Z |
| format | Article |
| id | doaj.art-9d413c8ec9df4735a9e90649f6d2479f |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T05:00:18Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-9d413c8ec9df4735a9e90649f6d2479f2023-11-17T19:22:48ZengMDPI AGGenes2073-44252023-03-0114481210.3390/genes14040812Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than MetabarcodingBurkhard Becker0Ekaterina Pushkareva1Institute for Plant Sciences, University of Cologne, 50923 Cologne, GermanyInstitute for Plant Sciences, University of Cologne, 50923 Cologne, GermanyThe diversity of soil bacteria was analyzed via metabarcoding and metagenomic approaches using DNA samples isolated from the biocrusts of 12 different Arctic and Antarctic sites. For the metabarcoding approach, the V3-4 region of the 16S rRNA was targeted. Our results showed that nearly all operational taxonomic units (OTUs = taxa) found in metabarcoding analyses were recovered in metagenomic analyses. In contrast, metagenomics identified a large number of additional OTUs absent in metabarcoding analyses. In addition, we found huge differences in the abundance of OTUs between the two methods. The reasons for these differences seem to be (1) the higher sequencing depth in metagenomics studies, which allows the detection of low-abundance community members in metagenomics, and (2) bias of primer pairs used to amplify the targeted sequence in metabarcoding, which can change the community composition dramatically even at the lower taxonomic levels. We strongly recommend using only metagenomic approaches when establishing the taxonomic profiles of whole biological communities.https://www.mdpi.com/2073-4425/14/4/812metagenomicsmetabarcodingpolar regionsterrestrial communitiesmicrobiomes |
| spellingShingle | Burkhard Becker Ekaterina Pushkareva Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding Genes metagenomics metabarcoding polar regions terrestrial communities microbiomes |
| title | Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding |
| title_full | Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding |
| title_fullStr | Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding |
| title_full_unstemmed | Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding |
| title_short | Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding |
| title_sort | metagenomics provides a deeper assessment of the diversity of bacterial communities in polar soils than metabarcoding |
| topic | metagenomics metabarcoding polar regions terrestrial communities microbiomes |
| url | https://www.mdpi.com/2073-4425/14/4/812 |
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