Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment
KAUST DepartmentRed Sea Research Center (RSRC)
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AbstractCharacterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing (HTS) represents an alternative to rapidly, accurately, and cost-effectively analyze thousands of environmental samples simultaneously, and this method is increasingly used to characterize the metazoan taxonomic composition of a wide variety of environments. However, a comprehensive study benchmarking visual and metabarcoding-based taxonomic inferences that validates this technique for environmental monitoring is still lacking. Here, we compare taxonomic inferences of benthic macroinvertebrate samples of known taxonomic composition obtained using alternative metabarcoding protocols based on a combination of different DNA sources, barcodes of the mitochondrial cytochrome oxidase I gene and amplification conditions. Our results highlight the influence of the metabarcoding protocol in the obtained taxonomic composition and suggest the better performance of an alternative 313 bp length barcode to the traditionally 658 bp length one used for metazoan metabarcoding. Additionally, we show that a biotic index inferred from the list of macroinvertebrate taxa obtained using DNA-based taxonomic assignments is comparable to that inferred using morphological identification. Thus, our analyses prove metabarcoding valid for environmental status assessment and will contribute to accelerating the implementation of this technique to regular monitoring programs.
CitationBenchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment 2016, 3 Frontiers in Marine Science
SponsorsThis manuscript is a result of the DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status—http://www.devotes-project.eu) project funded by the European Union (7th Framework Program “The Ocean of Tomorrow” Theme, grant agreement no. 308392) and the Basque Water Agency (URA) through a Convention with AZTI. EA is supported by the “Fundación Centros Tecnológicos” through an “Iñaki Goenaga” doctoral grant.
PublisherFrontiers Media SA
JournalFrontiers in Marine Science
ReferencesAylagas, E., Borja, A., Irigoien, X., & Rodriguez-Ezpeleta, N. (2016). Data from: Benchmarking DNA metabarcoding for biodiversity-based monitoring and assessment (Version 1) [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.0sc0s