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DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

Proceedings of the National Academy of Sciences - PNAS, 2015-02, Vol.112 (7), p.2076-2081 [Peer Reviewed Journal]

Volumes 1–89 and 106–112, copyright as a collective work only; author(s) retains copyright to individual articles ;Copyright National Academy of Sciences Feb 17, 2015 ;ISSN: 0027-8424 ;EISSN: 1091-6490 ;DOI: 10.1073/pnas.1424997112 ;PMID: 25646458

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  • Title:
    DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity
  • Author: Leray, Matthieu ; Knowlton, Nancy
  • Subjects: Biodiversity ; Biological Sciences ; DNA Barcoding, Taxonomic ; Environmental monitoring ; Eukaryotes ; Marine Biology ; Molecular Sequence Data ; Oysters ; Taxonomy
  • Is Part Of: Proceedings of the National Academy of Sciences - PNAS, 2015-02, Vol.112 (7), p.2076-2081
  • Description: Documenting the diversity of marine life is challenging because many species are cryptic, small, and rare, and belong to poorly known groups. New sequencing technologies, especially when combined with standardized sampling, promise to make comprehensive biodiversity assessments and monitoring feasible on a large scale. We used this approach to characterize patterns of diversity on oyster reefs across a range of geographic scales comprising a temperate location [Virginia (VA)] and a subtropical location [Florida (FL)]. Eukaryotic organisms that colonized multilayered settlement surfaces (autonomous reef monitoring structures) over a 6-mo period were identified by cytochrome c oxidase subunit I barcoding (>2-mm mobile organisms) and metabarcoding (sessile and smaller mobile organisms). In a total area of ∼15.64 m ² and volume of ∼0.09 m ³, 2,179 operational taxonomic units (OTUs) were recorded from 983,056 sequences. However, only 10.9% could be matched to reference barcodes in public databases, with only 8.2% matching barcodes with both genus and species names. Taxonomic coverage was broad, particularly for animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding could not be confidently assigned to a taxonomic group. The smallest size fraction (500 to 106 μm) was the most diverse (more than two-thirds of OTUs). There was little taxonomic overlap between VA and FL, and samples separated by ∼2 m were significantly more similar than samples separated by ∼100 m. Ground-truthing with independent assessments of taxonomic composition indicated that both presence–absence information and relative abundance information are captured by metabarcoding data, suggesting considerable potential for ecological studies and environmental monitoring. Significance High-throughput DNA sequencing methods are revolutionizing our ability to census communities, but most analyses have focused on microbes. Using an environmental DNA sequencing approach based on cytochrome c oxidase subunit 1 primers, we document the enormous diversity and fine-scale geographic structuring of the cryptic animals living on oyster reefs, many of which are rare and very small. Sequence data reflected both the presence and relative abundance of organisms, but only 10.9% of the sequences could be matched to reference barcodes in public databases. These results highlight the enormous numbers of marine animal species that remain genetically unanchored to conventional taxonomy and the importance of standardized, genetically based biodiversity surveys to monitor global change.
  • Publisher: United States: National Academy of Sciences
  • Language: English
  • Identifier: ISSN: 0027-8424
    EISSN: 1091-6490
    DOI: 10.1073/pnas.1424997112
    PMID: 25646458
  • Source: GFMER Free Medical Journals
    MEDLINE
    PubMed Central
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