ARPHA Conference Abstracts : Conference Abstract
Conference Abstract
Environmental DNA in subterranean biology update: from “Where?” to “How many?”
expand article infoŠpela Gorički, Primož Presetnik§, Uršula Prosenc-Zmrzljak|, Matej Blatnik, Tajda Gredar#, Blaž Kogovšek, Oliver Koit¤, Sara Strah«, Helena Bilandžija», Branko Jalžić˄, Gregor Aljančič˅, Rok Košir¦, Cyril Mayaud, Dejan Štebihˀ, Andrej Hudoklinˁ, William Jeffery
‡ Scriptorium biologorum, Murska Sobota, Slovenia
§ Tolstojeva 1b, Ljubljana, Slovenia
| BIA Separations CRO, Labena d.o.o, Ljubljana, Slovenia
¶ Karst Research Institute - ZRC SAZU, Postojna, Slovenia
# Department of Biology, University of Ljubljana, Ljubljana, Slovenia
¤ Institute of Ecology, Tallinn University, Tallinn, Estonia
« University of Primorska, Koper, Slovenia
» Ruđer Bošković Institute, Zagreb, Croatia
˄ Croatian Biospeleological Society, Zagreb, Croatia
˅ Society for Cave Biology, Kranj, Slovenia
¦ BIA Separations CRO, Labena d.o.o., Ljubljana, Slovenia
ˀ National Institute of Biology, Ljubljana, Slovenia
ˁ Institute of the Republic of Slovenia for Nature Conservation, Novo Mesto, Slovenia
₵ University of Maryland, Maryland, United States of America
Open Access


Recent records of Proteus anguinus outside its historically known range (Gorički et al. 2017), discovered through detection of its DNA dissolved in groundwater (environmental DNA or eDNA), mark the beginning of a new era in the study and conservation of cryptic subterranean biodiversity. An upgraded technology, droplet digital PCR (ddPCR), initially developed for studies of gene expression, detection of genetically modified organisms and in medical diagnostics, is being tested for improved detection of the much smaller and rare stygobiont, the cave clam Congeria jalzici. In parallel to eDNA assay development for various stygobiotic species of the Dinaric Karst, a groundwater-sample library is being created. The samples will be available for future analysis of their species composition and will also serve as a source of information on any changes in species distribution over time. In another line of eDNA research, the utility of ddPCR for direct quantification of eDNA molecules in groundwater is being explored by using the large, accessible and well-characterized (Zakšek and Trontelj 2017) natural Proteus population in the Planina Cave (Slovenia) as a model. The eDNA methodology may in the future be applied in estimation and monitoring of Proteus population sizes without having to see, mark or otherwise disturb the animals themselves.

Presenting author

Špela Gorički

Presented at

24th International Conference on Subterranean Biology, 20-24 August 2018


We are grateful to Jasmina Kotnik, Eva Pavlovič, Rudi Kraševec, Damjan Vinko, Klemen Kramar, Petra Kovač-Konrad, Jenny Barnjak, Tjaša Lokovšek, Franci Gabrovšek, Matjaž Kuntner, Peter Trontelj, Larry Cohen and everyone who donated to the project Through a glass darkly: assessing population size of an endangered cave salamander from samples of spring and cave water. The 2018 ddPCR part of the analysis was performed in collaboration and under sponsorship of Labena d.o.o. and their ddPCR Grant Challenge.

Hosting institution

University of Aveiro, Aveiro, Portugal


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