Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

By Eva Aylagas, Á. Borja, Xabier Irigoien, N. Rodríguez‐Ezpeleta. Frontiers in Marine Science, 2016

206 citations recorded by the source corpus.

Characterization 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 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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/90fa03ffd44314b18cee17034ff4f8248d39bbfe

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Citations in the corpus

Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA (2019, unknown): “However, it currently continues to require integration or comparison with traditional methods until it is fully optimized (Cowart et al., 2015; Aylagas et al., 2016; Sinniger et al., 2016).”
Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels (2017, methodology): “…to assess taxon-specific biodiversity of higher organisms such as invertebrates (Machida et al., 2009; Yu et al., 2012; Klymus et al., 2015; Aylagas et al., 2016) and vertebrates (Kelly et al., 2016; Port et al., 2016) have been developed and benchmarked against well-established techniques…”
DNA Sequencing as a Tool to Monitor Marine Ecological Status (2017, methodology): “Some studies report adequate estimates of relative abundance (Aylagas et al., 2014, 2016; Elbrecht and Leese, 2015; Tan et al., 2015; Thomsen and Willerslev, 2015) even though read abundance does not necessarily provide a direct correlation to organism abundance because of issues that include…”
Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale (2020, background): “These measures are currently used in many monitoring programs and quantification approaches, though recent studies have suggested that presence-absence data obtained from DNA metabarcoding can provide similar trends in ecological assessment compared to measures that incorporate abundance (Aylagas et”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, background): “Virome: The genetic material from all the viruses associated with a host or environment. specific taxa (Elbrecht & Leese 2015; Aylagas et al. 2016) or sample media (Drummond et al. 2015; Klymus et al. 2107).”