Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics
DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodive...
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PeerJ Inc.
2025-04-01
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| author | Karlijn Doorenspleet Amalia Aikaterini Mailli Berry B. van der Hoorn Kevin K. Beentjes Annelies De Backer Sofie Derycke Albertinka J. Murk Henning Reiss Reindert Nijland |
| author_facet | Karlijn Doorenspleet Amalia Aikaterini Mailli Berry B. van der Hoorn Kevin K. Beentjes Annelies De Backer Sofie Derycke Albertinka J. Murk Henning Reiss Reindert Nijland |
| author_sort | Karlijn Doorenspleet |
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| description | DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring. |
| format | Article |
| id | doaj-art-aab4e3c56d174ad8aa0a492e06352f5b |
| institution | DOAJ |
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| language | English |
| publishDate | 2025-04-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj-art-aab4e3c56d174ad8aa0a492e06352f5b2025-08-20T03:18:49ZengPeerJ Inc.PeerJ2167-83592025-04-0113e1915810.7717/peerj.19158Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomicsKarlijn Doorenspleet0Amalia Aikaterini Mailli1Berry B. van der Hoorn2Kevin K. Beentjes3Annelies De Backer4Sofie Derycke5Albertinka J. Murk6Henning Reiss7Reindert Nijland8Marine Animal Ecology, Wageningen University and Research, Wageningen, NetherlandsFaculty of Biosciences and Aquaculture, Nord University, Bodø, NorwayNaturalis Biodiversity Center, Leiden, NetherlandsNaturalis Biodiversity Center, Leiden, NetherlandsILVO Marine Research, Flanders Research Institute for Agriculture, Fisheries and Food, Oostende, BelgiumILVO Marine Research, Flanders Research Institute for Agriculture, Fisheries and Food, Oostende, BelgiumMarine Animal Ecology, Wageningen University and Research, Wageningen, NetherlandsFaculty of Biosciences and Aquaculture, Nord University, Bodø, NorwayMarine Animal Ecology, Wageningen University and Research, Wageningen, NetherlandsDNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring.https://peerj.com/articles/19158.pdfNorth SeaBenthic communitiesDNAMetabarcodingMetagenomicsNanopore |
| spellingShingle | Karlijn Doorenspleet Amalia Aikaterini Mailli Berry B. van der Hoorn Kevin K. Beentjes Annelies De Backer Sofie Derycke Albertinka J. Murk Henning Reiss Reindert Nijland Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics PeerJ North Sea Benthic communities DNA Metabarcoding Metagenomics Nanopore |
| title | Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics |
| title_full | Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics |
| title_fullStr | Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics |
| title_full_unstemmed | Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics |
| title_short | Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics |
| title_sort | advancing molecular macrobenthos biodiversity monitoring a comparison between oxford nanopore and illumina based metabarcoding and metagenomics |
| topic | North Sea Benthic communities DNA Metabarcoding Metagenomics Nanopore |
| url | https://peerj.com/articles/19158.pdf |
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