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...
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ftmdpi:oai:mdpi.com:/2073-4425/14/4/812/ 2023-08-20T04:02:14+02:00 Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding Burkhard Becker Ekaterina Pushkareva agris 2023-03-28 application/pdf https://doi.org/10.3390/genes14040812 EN eng Multidisciplinary Digital Publishing Institute Population and Evolutionary Genetics and Genomics https://dx.doi.org/10.3390/genes14040812 https://creativecommons.org/licenses/by/4.0/ Genes; Volume 14; Issue 4; Pages: 812 metagenomics metabarcoding polar regions terrestrial communities microbiomes Text 2023 ftmdpi https://doi.org/10.3390/genes14040812 2023-08-01T09:27:47Z 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. Text Antarc* Antarctic Arctic MDPI Open Access Publishing Antarctic Arctic Genes 14 4 812 |
institution |
Open Polar |
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MDPI Open Access Publishing |
op_collection_id |
ftmdpi |
language |
English |
topic |
metagenomics metabarcoding polar regions terrestrial communities microbiomes |
spellingShingle |
metagenomics metabarcoding polar regions terrestrial communities microbiomes Burkhard Becker Ekaterina Pushkareva Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding |
topic_facet |
metagenomics metabarcoding polar regions terrestrial communities microbiomes |
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. |
format |
Text |
author |
Burkhard Becker Ekaterina Pushkareva |
author_facet |
Burkhard Becker Ekaterina Pushkareva |
author_sort |
Burkhard Becker |
title |
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_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_sort |
metagenomics provides a deeper assessment of the diversity of bacterial communities in polar soils than metabarcoding |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2023 |
url |
https://doi.org/10.3390/genes14040812 |
op_coverage |
agris |
geographic |
Antarctic Arctic |
geographic_facet |
Antarctic Arctic |
genre |
Antarc* Antarctic Arctic |
genre_facet |
Antarc* Antarctic Arctic |
op_source |
Genes; Volume 14; Issue 4; Pages: 812 |
op_relation |
Population and Evolutionary Genetics and Genomics https://dx.doi.org/10.3390/genes14040812 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/genes14040812 |
container_title |
Genes |
container_volume |
14 |
container_issue |
4 |
container_start_page |
812 |
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1774712616442134528 |