title: DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity.
abstract: 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.
authors: National Museum of Natural History, Smithsonian Institution, Washington, DC 20013.
authors: Matthieu
authors: M
authors: Leray
authors: National Museum of Natural History, Smithsonian Institution, Washington, DC 20013 knowlton@si.edu.
authors: Nancy
authors: N
authors: Knowlton
mesh_terms: D044822:Biodiversity; D058893:DNA Barcoding, Taxonomic; D008386:Marine Biology; D008969:Molecular Sequence Data
keywords: ARMS; cryptic species; meiofauna; operational taxonomic units; oyster reefs
references: Am Nat. 2004 Feb;163(2):192-211
references: 14970922
references: Curr Biol. 2012 Dec 4;22(23):2189-202
references: 23159596
references: Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6241-6
references: 22454494
references: PLoS Biol. 2011 Aug;9(8):e1001127
references: 21886479
references: Bioinformatics. 2011 Aug 15;27(16):2194-200
references: 21700674
references: Nature. 2004 Dec 9;432(7018):747-50
references: 15592411
references: Ecol Lett. 2006 Jun;9(6):683-93
references: 16706913
references: Mar Pollut Bull. 2013 Sep 15;74(1):19-31
references: 23806673
references: Nature. 2010 Aug 26;466(7310):1098-101
references: 20668450
references: Nat Methods. 2010 May;7(5):335-6
references: 20383131
references: Front Zool. 2013 Jun 14;10:34
references: 23767809
references: Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8007-12
references: 24808136
references: PLoS One. 2011;6(10):e25026
references: 22022371
references: Bioinformatics. 2011 Mar 1;27(5):611-8
references: 21233169
references: PLoS Biol. 2012;10(11):e1001419
references: 23139639
references: Mol Ecol Resour. 2013 Sep;13(5):851-61
references: 23848937
references: Gigascience. 2013 Mar 27;2(1):4
references: 23587339
references: Proc Biol Sci. 2002 Aug 22;269(1501):1715-20
references: 12204133
references: PLoS One. 2012;7(3):e33801
references: 22457790
references: PLoS One. 2011;6(9):e22594
references: 21949676
references: Syst Biol. 2008 Oct;57(5):750-7
references: 18853361