Metabarcoding is powerful yet still blind: a comparative analysis of morphological and molecular surveys of seagrass communities

Type Article
Date 2015-02-10
Language English
Author(s) Cowart Dominique A.1, Pinheiro Miguel2, Mouchel Olivier1, Maguer Marion3, Grall Jacques3, Mine Jacques4, Arnaud-Haond SophieORCID1
Affiliation(s) 1 : IFREMER, Unite Environm Profond, Dept Ressources Phys & Ecosyst Fond Mer REM, F-29280 Plouzane, France.
2 : Univ St Andrews, St Andrews KY16 9TF, Fife, Scotland.
3 : Inst Univ Europeen Mer, F-29280 Plouzane, France.
4 : Direct HSE, F-92078 Paris, France.
Source Plos One (1932-6203) (Public Library Science), 2015-02-10 , Vol. 10 , N. 2 , P. 1-26
DOI 10.1371/journal.pone.0117562
WOS© Times Cited 95
Abstract In the context of the sixth wave of extinction, reliable surveys of biodiversity are increasingly needed to infer the cause and consequences of species and community declines, identify early warning indicators of tipping points, and provide reliable impact assessments before engaging in activities with potential environmental hazards. DNA metabarcoding has emerged as having potential to provide speedy assessment of community structure from environmental samples. Here we tested the reliability of metabarcoding by comparing morphological and molecular inventories of invertebrate communities associated with sea-grasses through estimates of alpha and beta diversity, as well as the identification of the most abundant taxa. Sediment samples were collected from six Zostera marina seagrass meadows across Brittany, France. Metabarcoding surveys were performed using both mitochondrial (Cytochrome Oxidase I) and nuclear (small subunit 18S ribosomal RNA) markers, and compared to morphological inventories compiled by a long-term benthic monitoring network. A sampling strategy was defined to enhance performance and accuracy of results by preventing the dominance of larger animals, boosting statistical support through replicates, and using two genes to compensate for taxonomic biases. Molecular barcodes proved powerful by revealing a remarkable level of diversity that vastly exceeded the morphological survey, while both surveys identified congruent differentiation of the meadows. However, despite the addition of individual barcodes of common species into taxonomic reference databases, the retrieval of only 36% of these species suggest that the remaining were either not present in the molecular samples or not detected by the molecular screening. This finding exemplifies the necessity of comprehensive and well-curated taxonomic reference libraries and multi-gene surveys. Overall, results offer methodological guidelines and support for metabarcoding as a powerful and repeatable method of characterizing communities, while also presenting suggestions for improvement, including implementation of pilotstudies prior to performing full "blind" metabarcoding assessments to optimize sampling and amplification protocols.
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Cowart Dominique A., Pinheiro Miguel, Mouchel Olivier, Maguer Marion, Grall Jacques, Mine Jacques, Arnaud-Haond Sophie (2015). Metabarcoding is powerful yet still blind: a comparative analysis of morphological and molecular surveys of seagrass communities. Plos One, 10(2), 1-26. Publisher's official version : https://doi.org/10.1371/journal.pone.0117562 , Open Access version : https://archimer.ifremer.fr/doc/00255/36596/