Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes

Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope depths in Southwest Greenland. We collected seawater samples at depths of 188-918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites showed good correspondence with catch sizes. Environmental DNA sequence reads from the fish assemblages correlated with biomass and abundance data obtained from trawling. Interestingly, the Greenland shark (Somniosus microcephalus) showed high abundance of eDNA reads despite only a single specimen being caught, demonstrating the relevance of the eDNA approach for large species that can probably avoid bottom trawls in most cases. Quantitative detection of marine fish using eDNA remains to be tested further to ascertain whether this technique is able to yield credible results for routine application in fisheries. Nevertheless, our study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic habitats. This relates directly to applied fisheries as well as to monitoring effects of ongoing climate change on marine biodiversity-especially in polar ecosystems

Data from: Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes

Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope depths in Southwest Greenland. We collected seawater samples at depths of 188–918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites showed good correspondence with catch sizes. Environmental DNA sequence reads from the fish assemblages correlated with biomass and abundance data obtained from trawling. Interestingly, the Greenland shark (Somniosus microcephalus) showed high abundance of eDNA reads despite only a single specimen being caught, demonstrating the relevance of the eDNA approach for large species that can probably avoid bottom trawls in most cases. Quantitative detection of marine fish using eDNA remains to be tested further to ascertain whether this technique is able to yield credible results for routine application in fisheries. Nevertheless, our study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic habitats. This relates directly to applied fisheries as well as to monitoring effects of ongoing climate change on marine biodiversity—especially in polar ecosystems

Greenland eDNA raw sequencing data

This contains the raw fastq files from eDNA sequencing from the study. Data is Illumina MiSeq paird-end in four libraries

Detections of fish families using eDNA and trawl.

<p>Relationship between number of samples positive for eDNA and for trawling, respectively. Maximum number of detections is 21. The red line (y = x) separates the families into those better detected using trawling (below) and those better detected using eDNA (above).</p

Overview of quantitative results.

<p>Barplot of mean + SE of relative fish abundance (red), biomass (green) and eDNA read abundance (blue) across all samples. Data shown for families (A) and lower taxonomic resolution (B). Taxa for which the means of all three variables are <1% are shown together (remaining*) as summed means. Only taxa that are found using both methods are included. Full list of taxa is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165252#pone.0165252.t001" target="_blank">Table 1</a>.</p

Interpolated eDNA abundances.

<p>Heat maps for the two important commercial species, showing interpolated eDNA read abundance (colour) and catch biomass (circles). The size of the circles indicates the relative catch size in % for the species in the given sample, and colour (blue to red) indicates interpolated relative eDNA read abundance. A) Greenland halibut (<i>Reinhardtius hippoglossoides</i>), B) redfishes (<i>Sebastes</i> spp.). Fish drawings by SWK. Maps: [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165252#pone.0165252.ref041" target="_blank">41</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165252#pone.0165252.ref042" target="_blank">42</a>]</p

Overview of results from trawling and eDNA.

<p>Venn diagrams showing overlap between the qualitative results obtained from eDNA metabarcoding of seawater and trawling, respectively. 26 families were detected using both methods, while three families were only detected using eDNA and two families were only detected using trawling. All drawings by SWK.</p

Map of sampling sites.

<p>Overview of study site in Greenland (left), and detailed map of sampling sites in the Davis Strait, SW Greenland (right). Numbers corresponds to the sampling sites as in Table A in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165252#pone.0165252.s001" target="_blank">S1 File</a>. Map: NASA, Visible Earth, Blue Marble.</p

Overview of results.

<p>Table shows the fish families detected by trawling and eDNA, respectively, as well as lower taxonomic assignments within each family. For each taxon, the total catch number of individuals and biomass for trawling, and total number of eDNA reads for water samples is given. Some taxa were only found with eDNA (¹) and some were only found with trawling (²). For some eDNA assignments, the initial taxonomic identification was either downgraded to family level (*) or upgraded to genus/species level (§), based on the taxonomic coverage of the reference database and occurrences of Greenlandic fish species (Table C in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165252#pone.0165252.s001" target="_blank">S1 File</a>). The table also shows the number of samples (out of 21) that a family was detected in using trawling and eDNA, respectively.</p

Environmental DNA and fish density.

<p>Relationship between relative eDNA read frequencies and relative biomass (A) as well as relative abundance (number of individuals) (B). Results are shown for all fish families detected using both methods across all samples. Regression lines are shown, and a linear model (on log transformed data) showed that eDNA reads correlated with biomass (p<0.0001, R² = 0.26) and number of individuals (p<0.0001, R² = 0.24).</p