Evaluation of marine zooplankton community structure through environmental DNA metabarcoding

Abstract

Zooplankton dominate the abundance and biomass of multicellular animals in pelagic marine environments; however, traditional methods to characterize zooplankton communities are invasive and laborious. This study compares zooplankton taxonomic composition revealed through metabarcoding of the cytochrome oxidase I (COI) and 18S rRNA genes to traditional morphological identification by microscopy. Triplicates of three different sample types were collected from three coral reef sites in the Florida Keys National Marine Sanctuary: (1) 1 L surface seawater samples prefiltered through 3 μm filters and subsequently collected on 0.22 μm filters for eDNA (PF‐eDNA); (2) 1 L surface seawater samples filtered on 0.22 μm pore‐size filters (environmental DNA; eDNA), and (3) zooplankton tissue samples from 64 μm, 200 μm, and 500 μm mesh size net tows. The zooplankton tissue samples were split, with half identified morphologically and tissue DNA (T‐DNA) extracted from the other half. The COI and 18S rRNA gene metabarcoding of PF‐eDNA, eDNA, and T‐DNA samples was performed using Illumina MiSeq. Of the families detected with COI and 18S rRNA gene metabarcoding, 40% and 32%, respectively, were also identified through morphological assessments. Significant differences in taxonomic composition were observed between PF‐DNA, eDNA, and T‐DNA with both genetic markers. PF‐eDNA resulted in detection of fewer taxa than the other two sample types; thus, prefiltering is not recommended. All dominant copepod taxa (> 5% of total abundance) were detected with eDNA, T‐DNA, and morphological assessments, demonstrating that eDNA metabarcoding is a promising technique for future biodiversity assessments of pelagic zooplankton in marine systems.

Comparing eDNA metabarcoding and species collection for documenting Arctic metazoan biodiversity

“…The sum of the detections for each genus (i.e., presence/absence) has been combined for all primer sets variable seabed characteristics, which play an important role in distribution of megafauna as they impact several factors, including larval settlement, anchorages, and shelter (Kedra, Renaud, Andrade, Goszczko, & Ambrose, 2013;Preez, Curtis, & Clarke, 2016). Our observations of distinct patterns of community structure depicted using either COI and 18S primer sets are consistent with several studies that have shown an effect of markers on the detection rate of marine invertebrates (Djurhuus et al, 2018;Drummond et al, 2015;Elbrecht et al, 2017;Kelly et al, 2017;Shaw et al, 2016). Variation in eDNA community structure was intermediate between the variation observed using the two different species collection approaches.…”

Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding

“…These facts emphasize that although eDNA has the potential of providing an enormous amount of information about an ecosystem, traditional surveys have distinct value and should continue in conjunction with eDNA surveys for more robust and accurate assessments of biodiversity (Djurhuus et al, ; Kelly et al, ). In fact, visual surveys can detect species missed by eDNA, which is something to keep in mind when using eDNA as a biodiversity monitoring tool (Djurhuus et al, ; Kelly et al, ). This discrepancy can be partly due to primer bias and the limitations of the number of distinct species a primer can recover (Parada, Needham, & Fuhrman, ; Stat et al, ).…”

“…In fact, visual surveys can detect species missed by eDNA, which is something to keep in mind when using eDNA as a biodiversity monitoring tool (Djurhuus et al, 2018;Kelly et al, 2017). This discrepancy can be partly due to primer bias and the limitations of the number of distinct species a primer can recover (Parada, Needham, & Fuhrman, 2016;Stat et al, 2017).…”

“…This discrepancy can be partly due to primer bias and the limitations of the number of distinct species a primer can recover (Parada, Needham, & Fuhrman, 2016;Stat et al, 2017). However, another reason for this is likely because of an incomplete database of marine organism sequences for the target genes (Djurhuus et al, 2018;Kelly et al, 2017).…”

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

“…DNA-based methods are revolutionizing the analysis of biodiversity, as they offer advantages over traditional, visual, and morphological survey methods (Thomsen &Willerslev, 2015). Accordingly, eDNA metabarcoding approaches have been successfully employed to characterize specific marine plankton communities in natural seawater samples, such as zooplankton, mesozooplankton, and full eukaryotic plankton diversity (Chain, Brown, MacIsaac, & Cristescu, 2016;Deagle, Clarke, Kitchener, Polanowski, & Davidson, 2017;de Vargas et al, 2015;Djurhuus et al, 2018;López-escardó et al, 2018;Villarino et al, 2018), as well as benthic communities from both soft (Guardiola et al, 2015;Lejzerowicz et al, 2015;Pawlowski, Esling, Lejzerowicz, Cedhagen, & Wilding, 2014) and hard (Leray & Knowlton, 2015;Wangensteen, Cebrian, Palacín, & Turon, 2018;Wangensteen, Palacín, Guardiola, & Turon, 2018) bottom habitats.…”