Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem

Abstract

Given the rapid rise of environmental DNA (eDNA) surveys in ecology and environmental science, it is important to be able to compare the results of these surveys to traditional methods of measuring biodiversity. Here we compare samples from a traditional method (a manual tow-net) to companion eDNA samples sequenced at three different genetic loci. We find only partial taxonomic overlap among the resulting datasets, with each reflecting a portion of the larger suite of taxa present in the sampled nearshore marine environment. In the larger context of eDNA sequencing surveys, our results suggest that primer amplification bias drives much of the taxonomic bias in eDNA detection, and that the baseline probability of detecting any given taxon with a broad-spectrum primer set is likely to be low. Whether catching fish with different nets or using different PCR primer sets, multiple data types can provide complementary views of a common ecosystem. However, it remains difficult to cross-validate eDNA sequencing techniques in the field, either for presence/absence or for abundance, particularly for primer sets that target very wide taxonomic ranges. Finally, our results highlight the breadth of diversity in a single habitat, and although eDNA does capture a richer sample of the community than traditional methods of sampling, a large number of eDNA primer sets focusing on different subsets of the biota would be necessary to survey any ecological community in a reasonably comprehensive way.

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

“…Indeed, the use of several markers in metabarcoding is rapidly gaining momentum (e.g., Clarke et al, 2017;Harvey et al, 2017;Kelly et al, 2017). It is reassuring that the same general conclusions were reached with both markers used here.…”

Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels

“…Biodiversity studies using eDNA involve sampling environmental media (e.g., water, soil, air), extracting genomic DNA, and using metabarcoding to determine the diversity of organisms present. The application of metabarcoding (i.e., PCR amplification and sequencing of specific gene targets) to eDNA present in both marine and terrestrial environments has opened new windows into monitoring species diversity (Thomsen and Willerslev, 2015;Kelly et al, 2017). For over three decades, researchers have used metabarcoding to amplify marker genes from complex mixtures of single-celled organisms, often captured on filters from liquid matrices, to describe the diversity and composition of marine microbial and phytoplankton communities (Pace et al, 1985;Pace, 1997;Hugenholtz et al, 1998).…”

DNA Sequencing as a Tool to Monitor Marine Ecological Status

“…The eDNA approach promises information about bioindicators and commercially important or protected species without the need to collect tissue or trawl through sensitive habitats (Foote et al, 2012;Bohmann et al, 2014;Thomsen and Willerslev, 2015;Evans et al, 2016;Lacoursière-Roussel et al, 2016;Shelton et al, 2016). Some studies show promising results with regard to abundance estimates (Hänfling et al, 2016;Port et al, 2016), but others show significant differences between eDNA results and traditional tows for epibenthic macroinvertebrates (Kelly et al, 2017) and zooplankton (Hirai et al, 2015b), suggesting that these methods require further research.…”

“…Lack of intercalibration between morphological and molecular methods presents an additional issue, and transferability across taxa is a concern, particularly if the initial assessment used to establish the database is limited to one or two taxonomic groups (Kelly, 2016). Although comparable molecular and traditional approaches are reported (Lejzerowicz et al, 2015;Aylagas et al, 2016Aylagas et al, , 2017Hänfling et al, 2016;Valentini et al, 2016), other studies show discrepancies (Cowart et al, 2015;Hirai et al, 2015b;Mohrbeck et al, 2015;Giner et al, 2016;Kelly et al, 2017); therefore, it has been advised to use both approaches in a complementary fashion rather than outright substitution of morphotaxonomic approaches (Borja et al, 2008;Pedersen et al, 2015;Thomsen and Willerslev, 2015). Although such an approach may deliver a holistic perspective of marine ecological status, it would not produce the desired effect of streamlining monitoring efforts, which is needed to transition research into practice (de Jonge et al, 2006).…”