Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples

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From: PLoS ONE(Vol. 7, Issue 8)
Publisher: Public Library of Science
Document Type: Report
Length: 6,119 words
Lexile Measure: 1590L

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Author(s): Philip Francis Thomsen 1 , * , Jos Kielgast 1 , Lars Lønsmann Iversen 2 , Peter Rask Møller 3 , Morten Rasmussen 1 , Eske Willerslev 1 , *


The marine environment represents considerable value in terms of biodiversity [1] and economics through fisheries and other products derived from the sea [2], [3]. Fish are the most species-rich group of vertebrates and constitute a keystone in present-day monitoring of environmental health of marine ecosystems. Nevertheless, fish species and populations worldwide are under threat and suffer from over-exploitation [4]-[7] with considerable impact on human health [8]. Contemporary monitoring of marine fish biodiversity and resources is largely dependent on invasive and selective methods, such as bottom trawls and rotenone poisoning [9], which can only be carried out in particular areas where conditions are favourable. Furthermore, correct identification of many species across both non-commercial (e.g. Syngnathidae) and commercial (e.g. Ammodytidae) groups is problematic using traditional methods; leaving databases flawed with errors [10] and checklists incomplete [11], [12].

An alternative approach for monitoring marine fish is that of environmental DNA (eDNA), i.e. the extraction and analysis of genetic material obtained directly from environmental samples [13]. For macro-organisms, the approach was first applied to terrestrial sediment samples revealing ecosystems of extinct and extant mammals, birds, and plants [14]. Later the same approach was successfully used on ancient cave sediments [15] and ice cores [16] as well as ancient and contemporary sediments across a variety of taxa, habitats and climates [17]-[28]. Recently, eDNA from Bull frogs was successfully retrieved from contemporary pond water samples [29]. This approach has since been used to detect other amphibians [30] and invasive fish species [31] in freshwater. Furthermore, it has been demonstrated that rare and endangered freshwater insects, crustaceans, amphibians, fish and mammals can be monitored and quantified using eDNA, and that such an approach can account for entire lake faunas [32]. Despite these successful applications, the detection of macro-organisms by eDNA has to our knowledge never been reported from marine water samples.

In this study we present the first recording of marine fish biodiversity using eDNA from seawater samples.


Three seawater samples were collected in a temperate marine ecosystem in Denmark (Fig. 1). Samples were filtered, DNA amplified and sequenced (see Materials and Methods section). A comparison with the GenBank sequence database revealed DNA from 15 different fish species, representing a diversity of 9 orders and 11 families (Fig. 1, Table 1). These include both important consumption species, such as Atlantic cod (Gadus morhua ), European eel (Anguilla anguilla ), European plaice (Pleuronectes platessa ) and Atlantic herring (Clupea harengus ), as well as non-commercial species like Goldsinny-wrasse ( Ctenolabrus rupestris ), Shorthorn sculpin (Myoxocephalus scorpius ) and Greater pipefish (Syngnathus acus ). We also detected DNA from European pilchard (Sardina pilchardus ) - a vagrant fish species in the region - and 4 species of birds, including the Red-throated loon (Gavia stellata ), which only passes the area occasionally during migration. There was a small difference...

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Gale Document Number: GALE|A498244383