Development of eDNA methods for monitoring two stygobiotic species of the Dinaric Karst, Proteus anguinus and Congeria jalzici, using digital PCR

Authors

  • Špela Gorički Scriptorium biologorum - Biološka pisarna d.o.o., Ulica Nikole Tesla 6, SI-9000 Murska Sobota
  • Primož Presetnik Tolstojeva ulica 9b, SI-1000 Ljubljana
  • Uršula Prosenc-Zmrzljak BIA Separations CRO, Labena d.o.o, Teslova ulica 30, SI-1000 Ljubljana
  • Tajda Gredar University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, SI-1000 Ljubljana
  • Matej Blatnik ZRC SAZU Karst Research Institute, Titov trg 2, SI-6230 Postojna
  • Blaž Kogovšek ZRC SAZU Karst Research Institute, Titov trg 2, SI-6230 Postojna
  • Oliver Koit Institute of Ecology, Tallinn University, Narva Rd 25, EE-10120 Tallinn
  • Cyril Mayaud ZRC SAZU Karst Research Institute, Titov trg 2, SI-6230 Postojna
  • Sara Strah University of Primorska, Titov trg 4, SI-6000 Koper
  • Branko Jalžić Croatian Biospeleological Society, Demetrova 1, HR-10000 Zagreb
  • Gregor Aljančič Society for Cave Biology, Oldhamska cesta 8A, SI-4000 Kranj
  • Dejan Štebih National Institute of Biology, Večna pot 111, SI-1000 Ljubljana
  • Andrej Hudoklin Institute of the Republic of Slovenia for Nature Conservation, Novo mesto Regional Unit, Adamičeva ulica 2, SI-8000 Novo mesto
  • Rok Košir BIA Separations CRO, Labena d.o.o, Teslova ulica 30, SI-1000 Ljubljana

DOI:

https://doi.org/10.14720/ns.20.2.47-50

Keywords:

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Abstract

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References

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Bilandžija H, Morton B, Podnar M, Ćetković H. 2013. Evolutionary history of relict Congeria (Bivalvia: Dreissenidae): unearthing the subterranean biodiversity of the Dinaric Karst. Frontiers in Zoology. 10: 5. https://doi.org/10.1186/1742-9994-10-5 DOI: https://doi.org/10.1186/1742-9994-10-5

Buxton AS, Groombridge JJ, Zakaria NB, Griffiths RA. 2017. Seasonal variation in environmental DNA in relation to population size and environmental factors. Scientific Reports. 7: 46294. https://doi.org/10.1038/srep46294 DOI: https://doi.org/10.1038/srep46294

Chambert T, Pilliod, DS, Goldberg CS, Doi H, Takahara T. 2018. An analytical framework for estimating aquatic species density from environmental DNA. Ecology and Evolution. 8: 3468-3477. https://doi.org/10.1002/ece3.3764 DOI: https://doi.org/10.1002/ece3.3764

Cristescu ME, Hebert PDN. 2018. Uses and misuses of environmental DNA in biodiversity science and conservation. Annual Review of Ecology Evolution and Systematics. 49: 209-230. https://doi.org/10.1146/annurev-ecolsys-110617-062306 DOI: https://doi.org/10.1146/annurev-ecolsys-110617-062306

Doi H, Uchii K, Takahara T, Matsuhashi S, Yamanaka H, Minamoto T. 2015a. Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys. PLoS ONE. 10(3): e0122763. https://doi.org/10.1371/journal.pone.0122763 DOI: https://doi.org/10.1371/journal.pone.0122763

Doi H, Takahara T, Minamoto T, Matsuhashi S, Uchii K, Yamanaka H. 2015b. Droplet digital polymerase chain reaction (PCR) outperforms real-time PCR in the detection of environmental DNA from an invasive fish species. Environmental Science & Technology. 49(9): 5601-5608. https://doi.org/10.1021/acs.est.5b00253 DOI: https://doi.org/10.1021/acs.est.5b00253

Doi H, Inui R, Akamatsu Y, Kanno K, Yamanaka H, Takahara T, Minamoto T. 2017. Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshwater Biology. 62: 30-39. https://doi.org/10.1111/fwb.12846 DOI: https://doi.org/10.1111/fwb.12846

Gorički Š, Stanković D, Snoj A, Kuntner M, Jeffery WR, Trontelj P, Pavićević M, Grizelj Z, Năpăruş-Aljančič M, Aljančič G. 2017. Environmental DNA in subterranean biology: range extension and taxonomic implications for Proteus. Scientific Reports. 7: 45054. https://doi.org/10.1038/srep45054 DOI: https://doi.org/10.1038/srep45054

Hudoklin A, Ilenič T. 2012. Izvir jamske školjke. Dolenjski kras. 6: 139-142.

Pezdirc M, Heath E, Bizjak Mali L, Bulog B. 2011. PCB accumulation and tissue distribution in cave salamander (Proteus anguinus anguinus, Amphibia, Urodela) in the polluted karstic hinterland of the Krupa River, Slovenia. Chemosphere. 84(7): 987-993. https://doi.org/10.1016/j.chemosphere.2011.05.026 DOI: https://doi.org/10.1016/j.chemosphere.2011.05.026

Taylor SC, Laperriere G, Germain H. 2017. Droplet digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data. Scientific Reports. 7: 2409. https://doi.org/10.1038/s41598-017-02217-x DOI: https://doi.org/10.1038/s41598-017-02217-x

Zaiko A, Pochon X, Garcia-Vasquez E, Olenin S, Wood SA. 2018. Advantages and limitations of environmental DNA/RNA tools for marine biosecurity: management and surveillance of non-indigenous species. Frontiers in Marine Science. 5: 322. https://doi.org/10.3389/fmars.2018.00322 DOI: https://doi.org/10.3389/fmars.2018.00322

Zakšek V, Trontelj P. 2017. Conservation genetics of proteus in the Postojna-Planina Cave System. Natura Slovrniae. 19(1): 33-34.

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Published

30.12.2018

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How to Cite

Gorički, Špela, Presetnik, P., Prosenc-Zmrzljak, U., Gredar, T., Blatnik, M., Kogovšek, B., Koit, O., Mayaud, C., Strah, S., Jalžić, B., Aljančič, G., Štebih, D., Hudoklin, A., & Košir, R. (2018). Development of eDNA methods for monitoring two stygobiotic species of the Dinaric Karst, Proteus anguinus and Congeria jalzici, using digital PCR. Natura Sloveniae, 20(2), 47-50. https://doi.org/10.14720/ns.20.2.47-50

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