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      Toward a national eDNA strategy for the United States

      1 , 2 , 3 , 4 , 5 , 6 , 7 , 1 , 8 , 8 , 9 , 10 , 6 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 16 , 4 , 21 , 22 , 23 , 4 , 24 , 25 , 26 , 27 , 4 , 28 , 4
      Environmental DNA
      Wiley

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          Abstract

          Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use‐cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and state agencies are individually using eDNA data in various applications and developing relevant scientific expertise. A national strategy for eDNA implementation would capitalize on recent scientific developments, providing a common set of next‐generation tools for natural resource management and public health protection. Such a strategy would avoid patchwork and possibly inconsistent guidelines in different agencies, smoothing the way for efficient uptake of eDNA data in management. Because eDNA analysis is already in widespread use in both ocean and freshwater settings, we focus here on applications in these environments. However, we foresee the broad adoption of eDNA analysis to meet many resource management issues across the nation because the same tools have immediate terrestrial and aerial applications.

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          The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

          SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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            STATISTICAL METHODS FOR ASSESSING AGREEMENT BETWEEN TWO METHODS OF CLINICAL MEASUREMENT

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              The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.

              Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader's ability to evaluate critically the quality of the results presented or to repeat the experiments. The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement. Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.
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                Author and article information

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                Journal
                Environmental DNA
                Environmental DNA
                Wiley
                2637-4943
                2637-4943
                January 2024
                May 24 2023
                January 2024
                : 6
                : 1
                Affiliations
                [1 ] University of Washington, School of Marine and Environmental Affairs Seattle Washington USA
                [2 ] Cornell Atkinson Center for Sustainability Cornell University Ithaca New York USA
                [3 ] Owl of Minerva LLC Indianapolis Indiana USA
                [4 ] Southern California Coastal Water Research Project Authority Costa Mesa California USA
                [5 ] U.S. Geological Survey Northern Rocky Mountain Science Center Bozeman Montana USA
                [6 ] Monterey Bay Aquarium Research Institute Moss Landing California USA
                [7 ] Jonah Ventures Boulder Colorado USA
                [8 ] Northwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle Washington USA
                [9 ] Atlantic Oceanographic & Meterological Laboratory (stationed at Southwest Fisheries Science Center) National Oceanic and Atmospheric Administration La Jolla California USA
                [10 ] NOAA Pacific Marine Environmental Laboratory Seattle Washington USA
                [11 ] Department of Earth, Marine, and Environmental Sciences, Institute of Marine Sciences UNC Chapel Hill Morehead North Carolina USA
                [12 ] Pacific Biological Station Fisheries and Oceans Canada Nanaimo British Columbia Canada
                [13 ] Division of Integrated Science and Engineering California Department of Water Resources Sacramento California USA
                [14 ] NatureMetrics North America Ltd Guelph Ontario Canada
                [15 ] Johns Hopkins University Applied Physics Laboratory Laurel Maryland USA
                [16 ] Department of Ecology and Evolutionary Biology University of California, Santa Cruz Santa Cruz California USA
                [17 ] University of California Santa Barbara California USA
                [18 ] U.S. Geological Survey, Western Fisheries Research Center Seattle Washington USA
                [19 ] U.S. Geological Survey, Wetland and Aquatic Research Center Gainesville Florida USA
                [20 ] Northwest Indian Fisheries Commission Olympia Washington USA
                [21 ] Program for the Human Environment The Rockefeller University New York New York USA
                [22 ] Department of Marine Sciences and Institute of Bioinformatics University of Georgia Athens Georgia USA
                [23 ] National Museum of Natural History, Smithsonian Institution Washington District of Columbia USA
                [24 ] Maine Center for Genetics in the Environment University of Maine Orono Maine USA
                [25 ] Molecular Division Smith‐Root, Inc Vancouver Washington USA
                [26 ] Oceankind Palo Alto California USA
                [27 ] National Geographic Society Washington District of Columbia USA
                [28 ] Office of Naval Research, Marine Mammals & Biology Program Arlington Virginia USA
                Article
                10.1002/edn3.432
                da5c7955-dbfa-4da9-815d-eeb2f63a3974
                © 2024

                http://creativecommons.org/licenses/by-nc-nd/4.0/

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