Environmental DNA for Detection of Endangered Grouper Species (Epinephelus spp.)

Year 2016, Volume: 1 Issue: 3, 42 - 48, 22.11.2016

Servet Ahmet Doğdu , Cemal Turan

https://doi.org/10.28978/nesciences.286311

Cited By: 2

Abstract

Marine ecosystems nestle species or populations known to be threatened due to human
overexploitation. Reliable detection and monitoring of threatened organisms is crucial for
data-driven conservation actions. Furthermore, misidentification of species represents a major
problem. Here, we investigate the potential of using metabarcoding of environmental DNA
(eDNA) obtained directly from seawater samples to detect endangered grouper species
(Epinephelus spp.). Cytochrome c oxidase subunit I (COI) fragment of mtDNA was used to
detect groupers species in the Mediterranean Coasts. We conducted eDNA sampling at sites
by underwater diving across the range of the Grouper species habitats in Northeastern
Mediterranean (Antalya-Kas Region and Iskenderun Bay). eDNA was isolated from 2 liter
seawater samples which were vacuum-filtered onto 0.45-mm membrane filters. Filters were
then folded inwards, placed in 2 ml tubes and stored at -20 oC until DNA extraction, which
took place within 24 hours. DNA was extracted from the water sample filters using the
DNeasy Blood and Tissue Kit (Qiagen, USA). Manufacturer’s protocols were used during all
steps. PCR amplification of eDNA samples were done using selective primers of COI region
of mitochondrial DNA, and next-generation DNA sequencing of PCR application was
conducted. For the successfully obtained COI sequences, maximum matching rates were
revealed as 80% for Epinephelus marginatus, 78,95% for Epinephelus aeneus, 73,48% for
Epinephelus costae, 63,45% for Epinephelus caninus, 60,12% for Mycteroperca rubra and
57,12% for Hyporthodus haifensis. Despite the methodological challenges inherent in eDNA
analysis, the results demonstrated that eDNA method may be proved to step towards a new
beginning to detect and monitor endangered grouper species.

Keywords

Environmental DNA, COI, Endangered Grouper Species, Epinephelus spp.

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