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

Yıl 2016, Cilt: 1 Sayı: 3, 42 - 48, 22.11.2016

Servet Ahmet Doğdu Cemal Turan

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

Cited By: 2

Öz

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.

Anahtar Kelimeler

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

Kaynakça

• Begon M, Townsend CR, Harper JL (2005). Ecology: from individuals to ecosystems. Hoboken, NJ, USA: Wiley-Blackwell. 752 p.
• Brabon, H. A., Eisenhour, D. J., Washburn, B. A., Eisenhour, L. V., Stull, M. A., & Brammell, B. (2015). Detection of Percopsis omiscomaycus (trout-perch) using eDNA in eastern Kentucky streams.
• Costanza R. (1999). The ecological, economic, and social importance of the oceans. Ecological Economics 31: 199–213
• Davison, P. I., Créach, V., Liang, W. J., Andreou, D., Britton, J. R., & Copp, G. H. (2016). Laboratory and field validation of a simple method for detecting four species of non‐native freshwater fish using eDNA. Journal of Fish Biology,89(3), 1782-1793.
• FAO (2010) The State of World Fisheries and Aquaculture 2010. Rome: FAO.197 p.
• Ficetola, G. F., Miaud, C., Pompanon, F., & Taberlet, P. (2008). Species detection using environmental DNA from water samples. Biology letters, 4(4), 423-425
• Goldberg, C. S., Pilliod, D. S., Arkle, R. S., & Waits, L. P. (2011). Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders. PloS one, 6(7), e22746
• Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic acids symposium series (Vol. 41, pp. 95-98).
• Jerde, C. L., Mahon, A. R., Chadderton, W. L., & Lodge, D. M. (2011). “Sight‐unseen” detection of rare aquatic species using environmental DNA. Conservation Letters, 4(2), 150-157
• Keskin, E., Unal, E. M., & Atar, H. H. (2016). Detection of rare and invasive freshwater fish species using eDNA pyrosequencing: Lake Iznik ichthyofauna revised. Biochemical Systematics and Ecology, 67, 29-36.
• Mächler, E., Deiner, K., Spahn, F., & Altermatt, F. (2015). Fishing in the water: effect of sampled water volume on environmental DNA-based detection of macroinvertebrates. Environmental science & technology, 50(1), 305-312.
• Nielsen, C. (2012). Animal evolution: interrelationships of the living phyla. Oxford University Press on Demand, University Press. 464 p.
• Port, J. A., O'Donnell, J. L., Romero‐Maraccini, O. C., Leary, P. R., Litvin, S. Y., Nickols, K. J., & Kelly, R. P. (2016). Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA. Molecular ecology, 25(2), 527-541.
• Rees, H. C., Maddison, B. C., Middleditch, D. J., Patmore, J. R., & Gough, K. C. (2014). REVIEW: The detection of aquatic animal species using environmental DNA–a review of eDNA as a survey tool in ecology. Journal of Applied Ecology,51(5), 1450-1459.
• Robson, H. L., Noble, T. H., Saunders, R. J., Robson, S. K., Burrows, D. W., & Jerry, D. R. (2016). Fine‐tuning for the tropics: application of eDNA technology for invasive fish detection in tropical freshwater ecosystems. Molecular ecology resources.
• Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences,74(12), 5463-5467.
• Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research, 22(22), 4673-4680.
• Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M. (2012). Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol doi:10.1111/j.1365-294X.2011.05418.x
• Valentini A, Pompanon F, Taberlet P. (2009). DNA barcoding for ecologists. Trends Ecol Evol 24: 110–117.
• Yamamoto S, Minami K, Fukaya K, Takahashi K, Sawada H, et al. (2016) Correction: Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan. doi: info:doi/10.1371/journal.pone.0153291
• Willerslev, E., Hansen, A. J., Binladen, J., Brand, T. B., Gilbert, M. T. P., Shapiro, B., & Cooper, A. (2003). Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science, 300(5620), 791-795.