Identifications rely on an accurate, comprehensive library. Assessing relative fish abundance based on frequency of detection or number of reads looks promising, although more work is needed ( Lodge et al., 2012 Buxton et al., 2017 Yamamoto et al., 2017 Lamb et al., 2019). Primers targeting the vertebrate mitochondrial 12S rRNA gene, for example, detect marine fish diversity with similar recovery as traditional surveys ( Kelly et al., 2014 Port et al., 2016 Thomsen et al., 2016 Andruszkiewicz et al., 2017).
Metabarcoding profiles ecological communities by high-throughput sequencing of eDNA amplified with broad-range primers ( Pompanon et al., 2011 Riaz et al., 2011 Thomsen et al., 2012 Miya et al., 2015 Kelly et al., 2017). Degradation and dispersal typically limit detection to a few days after animals leave, although the sources and fates of eDNA from different organisms and in different environments need more study ( Collins et al., 2018 Andruszkiewicz et al., 2019). Most aquatic eDNA is in particulate form that can be captured with a small-pore size (0.2–10 μM) filter ( Turner et al., 2014). Potential sources of aquatic eDNA include cells lost from body surfaces, body wastes, and tissue fragments following predation, death, or injury ( Taberlet et al., 2018).
Taberlet and colleagues were the first to show that a small volume of water suffices to detect resident fauna, demonstrating that pond water eDNA reliably reports an invasive frog’s presence ( Ficetola et al., 2008). Aquatic environmental DNA (eDNA) offers a relatively low-cost, low-impact tool that may help in sustainable ocean management ( Hansen et al., 2018). Censusing marine fish and other nekton – animals that move – is challenging, as surveys typically involve costly specialized equipment, personnel, and time. Addressing human impacts asks for up-to-date, spatially detailed reporting on the diversity, distribution, and abundance of near-shore marine life. Human activities increasingly crowd the neritic zone ocean, from shoreline recreation to wind farms at the edge of the continental shelf. Our results highlight the value of strengthening reference libraries and demonstrate that eDNA can help detect range shifts including those of species overlooked by traditional surveys. A beach wrack specimen corroborated the local presence of Brazilian cownose ray. species as relatively common warm season migrants: Gulf kingfish ( Menticirrhus littoralis) and Brazilian cownose ray ( Rhinoptera brasiliensis). Newly obtained reference sequences revealed two southern U.S. Bioinformatic analysis of Illumina MiSeq fastq files with the augmented library yielded exact matches for 90% of the 104 fish amplicon sequence variants generated from field samples. Metabarcoding was performed using separate 12S primer sets targeting bony and cartilaginous fishes. For eDNA time series, we collected water samples approximately twice monthly for 24 months at an ocean and a bay site in New Jersey. Combined with existing GenBank accessions, the enhanced 12S dataset covered most (74%) of 341 fishes on New Jersey State checklist including 95% of those categorized abundant or common. We obtained 60 specimens representing 31 species from NOAA trawl surveys and institutional collections, and analyzed 12S and COI barcode regions, the latter to confirm specimen identification.
coastal fishes lacking reference sequences.
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Here, we used a regional checklist and early results from an ongoing eDNA time series to target mid-Atlantic U.S. Program for the Human Environment, The Rockefeller University, New York, NY, United StatesĪn accurate, comprehensive reference sequence library maximizes information gained from environmental DNA (eDNA) metabarcoding of marine fishes.Stoeckle *, Mithun Das Mishu and Zachary Charlop-Powers
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