Projects / Programmes source: ARRS

fDNAaqua – Environmental DNA trapped by filter feeders (fDNA): Tool for aquatic biodiversity monitoring

Research activity

Code Science Field Subfield
1.03.00  Natural sciences and mathematics  Biology   

Code Science Field
1.06  Natural Sciences  Biological sciences 
environmental DNA (eDNA), invertebrate derived DNA (iDNA), natural sampler DNA (nsDNA), suspension feeding animals, filter-feeding animals, biodiversity monitoring, DNA metabarcoding, molecular taxonomy
Evaluation (rules)
source: COBISS
Data for the last 5 years (citations for the last 10 years) on May 29, 2023; A3 for period 2017-2021
Data for ARRS tenders ( 04.04.2019 – Programme tender, archive )
Database Linked records Citations Pure citations Average pure citations
WoS  284  6,124  4,899  17.25 
Scopus  301  6,585  5,300  17.61 
Researchers (9)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  36398  PhD Klemen Čandek  Natural sciences and mathematics  Researcher  2021 - 2023  45 
2.  35367  PhD Teo Delić  Natural sciences and mathematics  Researcher  2021 - 2023  111 
3.  50562  PhD Ana Fortič  Natural sciences and mathematics  Junior researcher  2021 - 2023  38 
4.  32208  PhD Matjaž Gregorič  Natural sciences and mathematics  Researcher  2021 - 2023  335 
5.  19326  PhD Matjaž Kuntner  Natural sciences and mathematics  Researcher  2021 - 2023  489 
6.  27504  PhD Borut Mavrič  Natural sciences and mathematics  Researcher  2021 - 2023  329 
7.  15367  PhD Andreja Ramšak  Natural sciences and mathematics  Researcher  2021 - 2023  321 
8.  33151  PhD David Stanković  Biotechnical sciences  Principal Researcher  2021 - 2023  111 
9.  33669  PhD Anamarija Žagar  Natural sciences and mathematics  Researcher  2021 - 2023  200 
Organisations (3)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0105  National Institute of Biology  Ljubljana  5055784  12,929 
2.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  64,869 
3.  0618  Research Centre of the Slovenian Academy of Sciences and Arts  Ljubljana  5105498000  59,796 
The analysis of genomic inventories derived from environmental DNA (eDNA) sources are revolutionizing the way we assess biodiversity and have the potential to change practices and policies in management and conservation. eDNA has become an established tool for ecologists, particularly for monitoring of rare and cryptic species or for those species where conventional methods may be ineffective, labour-intensive, or detrimental. Although eDNA methods for conducting faunal inventories present great promises, there are still technical limitations, which hamper the correct interpretation of ecological data. In aquatic environments eDNA samples are usually concentrated from the environment by filtering variable volumes of water. This initial step often presents the major drawback, as the efficiency of filtration determines the quality and quantity of eDNA in the downstream analysis. Namely, studies have found eDNA in particles of strikingly varying diameters from 0.2 to 180 µm. While using filters with smallest pores (0.2-0.45 µm) might seem the best choice for eDNA surveys, this often leads to early clogging of filters and subsequently reduces the volume that can be inspected. How do we best overcome this technical limitations, which alternatives might lead to a more effective collection of multi-sized eDNA particles in larger quantities. Here, we propose to replace the usage of artificial filtering devices in eDNA studies by commonly occurring filter feeders, organisms that are naturally predisposed to filter water. In the fDNAaqua project, we aim to explore the recovery of what we call fDNA (environmental DNA trapped by filter feeders). Our overall goal is to evaluate the efficiency of fDNA method for various types of biodiversity monitoring in different aquatic environments, including freshwater, marine, and subterranean. We envisage a series of carefully planned experimental studies, that will be run in silico, in vitro and in vivo to address the following objectives a) to identify the most suitable filter feeders for fDNA harvesting in different aquatic environments; b) to estimate the spatio-temporal dynamics of fDNA and to evaluate the method’s sensitivity; c) to evaluate the fDNA approach for target-specific monitoring with qPCR assays; and d) to evaluate the fDNA approach for universal multiple-species monitoring with DNA metabarcoding. Our Work Package 1 will test the fDNA harvesting performance of several freshwater and marine candidates and define best fDNA extraction protocols. Work Package 2 will test how well fDNA reflects the recent community assemblages, by evaluating its spatio-temporal dynamics and its sensitivity (LOD, LOQ false negative rate). This will build up our understanding of the fDNA phenomena, which will be further exploited in the pilot surveys done in Work Packages 3 and 4, whose main idea is to test the performance of laboratory fDNA methods for target-specific and universal multiple-species biodiversity monitoring in various natural environments (surface freshwater, subterranean freshwater, marine). The fDNA approach we are developing in the fDNAaqua has immense potential for aquatic biodiversity monitoring and surveillance. If fDNA can outperform or match eDNA filtration approaches, it will significantly speed up and ease the eDNA/fDNA monitoring process and we will be able to use naturally occurring filter-feeders of as a kind of sentinels of the local biodiversity.
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