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      Metabarcoding of Environmental DNA Samples to Explore the Use of Uranium Mine Containment Ponds as a Water Source for Wildlife

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      MDPI AG

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          Abstract

          Understanding how anthropogenic impacts on the landscape affect wildlife requires a knowledge of community assemblages. Species surveys are the first step in assessing community structure, and recent molecular applications such as metabarcoding and environmental DNA analyses have been proposed as an additional and complementary wildlife survey method. Here, we test eDNA metabarcoding as a survey tool to examine the potential use of uranium mine containment ponds as water sources by wildlife. We tested samples from surface water near mines and from one mine containment pond using two markers, 12S and 16S rRNA gene amplicons, to survey for vertebrate species. We recovered large numbers of sequence reads from taxa expected to be in the area and from less common or hard to observe taxa such as the tiger salamander and gray fox. Detection of these two species is of note because they were not observed in a previous species assessment, and tiger salamander DNA was found in the mine containment pond sample. We also found that sample concentration by centrifugation was a more efficient and more feasible method than filtration in these highly turbid surface waters. Ultimately, the use of eDNA metabarcoding could allow for a better understanding of the area’s overall biodiversity and community composition as well as aid current ecotoxicological risk assessment work.

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          Cutadapt removes adapter sequences from high-throughput sequencing reads

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            QIIME allows analysis of high-throughput community sequencing data.

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              Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

              S Altschul (1997)
              The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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                Author and article information

                Contributors
                (View ORCID Profile)
                (View ORCID Profile)
                Journal
                DIVEC6
                Diversity
                Diversity
                MDPI AG
                1424-2818
                December 2017
                November 21 2017
                : 9
                : 4
                : 54
                Article
                10.3390/d9040054
                9b134e59-dee4-4c72-b894-31c4dd973ca2
                © 2017

                https://creativecommons.org/licenses/by/4.0/

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