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

Abstract

Environmental DNA (eDNA) is the DNA suspended in the environment (e.g., water column), which includes cells, gametes, and other material derived from but not limited to shedding of tissue, scales, mucus, and fecal matter. Amplifying and sequencing marker genes (i.e., metabarcoding) from eDNA can reveal the wide range of taxa present in an ecosystem through analysis of a single water sample. Metabarcoding of eDNA provides higher resolution data than visual surveys, aiding in assessments of ecosystem health. This study conducted eDNA metabarcoding of two molecular markers (cytochrome c oxidase I (COI) and 18S ribosomal RNA (rRNA) genes) to survey eukaryotic diversity across multiple trophic levels in surface water samples collected at three sites along the coral reef tract within the Florida Keys National Marine Sanctuary (FKNMS) during four research cruises in 2015. The 18S rRNA gene sequences recovered 785 genera while the COI gene sequences recovered 115 genera, with only 33 genera shared between the two datasets, emphasizing the complementarity of these marker genes. Community composition for both genetic markers clustered by month of sample collection, suggesting that temporal variation has a larger effect on biodiversity than spatial variability in the FKNMS surface waters. Sequences from both marker genes were dominated by copepods, but each marker recovered distinct phytoplankton groups, with 18S rRNA gene sequences dominated by dinoflagellates and COI sequences dominated by coccolithophores. Although eDNA samples were collected from surface waters, many benthic species such as sponges, crustaceans, and corals were identified. These results show the utility of eDNA metabarcoding for cataloging biodiversity to establish an ecosystem baseline against which future samples can be compared in order to monitor community changes.

Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

“…One of the most game-changing promises of eDNA metabarcoding is the ability to detect biodiversity across the tree of life from simple environmental samples (Stat et al, 2017;Sawaya et al, 2019). We focused exclusively on water samples and the target group of bony fish here because there was a relatively large number of comparative observations across aquatic systems.…”

Marine Vertebrate Biodiversity and Distribution Within the Central California Current Using Environmental DNA (eDNA) Metabarcoding and Ecosystem Surveys

“…While this study provides one example of eDNA assessment for pelagic ecosystem biomonitoring targeting fish and mammal biodiversity, the method can be expanded to also detect other groups such as seabirds (Ushio et al, 2018) and sea turtles (Kelly et al, 2014). In addition, eDNA surveys beyond vertebrates is possible (Kelly et al, 2017;Berry et al, 2019;Sawaya et al, 2019), making the biomonitoring of entire ecosystems by eDNA plausible. Future studies should consider connecting microorganism assemblages with invertebrate and vertebrate assemblages to have a more robust understanding of the biodiversity interactions within an ecosystem.…”

“…eDNA can be isolated from water samples and analyzed to detect unique sequences from microorganisms to large vertebrates, thus allowing biodiversity assessments to be completed without visually observing organisms (Foote et al, 2012;Thomsen et al, 2012;Kelly et al, 2014;Djurhuus et al, 2017). eDNA has been used to indicate presence of invasive species (Pochon et al, 2013), assess changes in taxa assemblages over time (Sawaya et al, 2019), and track ecologically important marine species (Sassoubre et al, 2016). In the CCE, eDNA has been used to detect vertebrates in Monterey Bay Andruszkiewicz et al, 2017b) and off the coast of Santa Barbara (Lafferty et al, 2018).…”

Strengthening marine amphipod DNA barcode libraries for environmental monitoring

“…The breakthrough in eDNA barcoding technology is in its ability to monitor the ecosystem without causing unnecessary harm to ecosystem or their organisms by non-invasive sampling strategy (Antognazza et al 2019;Mora et al 2019;Leempoel et al 2020) and to detect elusive, rare, and cryptic species effectively even in low density occurrences (Franklin et al 2019;Shelton et al 2019;Takahara et al 2020). Single eDNA sampling could simultaneously monitor biodiversity in the given environment over a broad taxonomic spectrum (Sawaya et al 2019;Thomsen and Sigsgaard 2019;Zhang et al 2020).…”

“…Large DNA barcode reference library that contains barcodes for a wide range os species is essential for monitoring any environments using eDNA barcoding successfully. For example; while monitoring marine ecosystems, a previous study could not assign more than 92 percent of the PCR amplified eDNA sequences to any known phyla and the sequences were classified as unassigned phyla (Jeunen et al, 2019;Sawaya et al, 2019). A comprehensive, parameterized reference library with barcodes of most of the locally occurring species, its image data is critical for the reliable application of eDNA technology, and the success of such efforts has been witnessed in probing marine fish diversity (Stoeckle et al, 2020).…”