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Projects / Programmes source: ARIS

Towards working protocols for the use of eDNA from spider webs

Research activity

Code Science Field Subfield
1.03.03  Natural sciences and mathematics  Biology  Ecosystems 

Code Science Field
B003  Biomedical sciences  Ecology 

Code Science Field
1.06  Natural Sciences  Biological sciences 
Keywords
Environmental DNA, eDNA, metabarcoding, DNA barcoding, spider webs
Evaluation (rules)
source: COBISS
Researchers (15)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  30854  PhD Danilo Bevk  Biology  Researcher  2019 - 2023  508 
2.  36398  PhD Klemen Čandek  Biology  Researcher  2019 - 2023  48 
3.  15157  PhD Tatjana Čelik  Biology  Researcher  2022 - 2023  243 
4.  32208  PhD Matjaž Gregorič  Biology  Head  2019 - 2023  354 
5.  28436  PhD Simona Kralj Fišer  Biology  Researcher  2019 - 2023  176 
6.  37409  PhD Maja Križnik  Biotechnology  Researcher  2021 - 2023  42 
7.  19326  PhD Matjaž Kuntner  Biology  Researcher  2019 - 2023  500 
8.  35384  PhD Denis Kutnjak  Biotechnology  Researcher  2021 - 2023  290 
9.  38268  PhD Filip Küzmič  Biology  Junior researcher  2019 - 2020  94 
10.  32700  Tjaša Lokovšek    Technical associate  2019 - 2023  25 
11.  38081  PhD Anja Pecman  Biotechnology  Junior researcher  2019 - 2022  98 
12.  05229  PhD Maja Ravnikar  Biotechnology  Researcher  2019 - 2023  1,370 
13.  17094  PhD Urban Šilc  Biology  Researcher  2019 - 2023  426 
14.  05231  PhD Meta Virant Doberlet  Biology  Researcher  2019 - 2023  281 
15.  32061  PhD Janja Zajc  Plant production  Researcher  2019 - 2020  166 
Organisations (2)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0618  Research Centre of the Slovenian Academy of Sciences and Arts  Ljubljana  5105498000  63,177 
2.  0105  National Institute of Biology  Ljubljana  5055784  13,285 
Abstract
The application of biological data to relevant societal problems is largely limited to correct specimen identification. Traditional species monitoring and specimen identification relies on morphological and behavioral character identification, but these methods have several well-known shortcomings. For example, the vast majority of biodiversity is scientifically undescribed, some higher taxa are not monophyletic, and traditional, phenotypic data sources insufficiently diagnose species and higher taxa. Consequently, traditional approaches are often inadequate in performing efficient and standardized biodiversity surveys. For example, many species can only be identified in certain life stages and their identification is highly dependent on taxonomic expertise, which is often lacking or in decline. Additionally, traditional sampling techniques are sometimes invasive, especially in invertebrates and aquatic ecosystems. The traditional taxonomic process is mostly manual and time-consuming, and thus cannot provide the effort needed for environmental monitoring related to modern challenges, such as the rapid decline of biodiversity, climate change, and invasive species. The severe limitations to traditional methods urgently call for alternative approaches.   Novel molecular approaches such as sampling of environmental DNA (eDNA), i.e. obtaining genetic material directly from environmental samples in the absence of biological source material, can potentially overcome many limitations of traditional biodiversity monitoring. Environmental DNA can be obtained and amplified either using specific primers within a single-species approach, or using generic primers in a multiple-species approach, referred to as DNA metabarcoding (massive DNA sequencing in order to simultaneously identify multiple taxa). Accordingly, eDNA is increasingly used to address fundamental questions in basic and applied research fields, such as ecology, molecular biology, nature conservation, and paleontology. New approaches in both sampling of diverse environments and organisms, as well as bioinformatical data manipulation will likely lead to new valuable methodological insights. Our preliminary results from an ongoing pilot project (see below) show that spider webs are a good source of eDNA from diverse organisms, thus providing a new powerful tool, with a variety of potential applications. In this context, we here propose to develop working protocols for the use of eDNA from spider webs in three diverse and important research fields: classical biodiversity monitoring, monitoring of airborne microbiota, and detection of agricultural pests and invasive species.   We will address these fields in three work packages (WP). The goal of WP1 is to develop protocols for the use of eDNA from spider webs to complement classical sampling of spiders as the producers of these webs, bees of the superfamily Apoidea as potential spider prey and the most important pollinators, and vascular plants as organisms not in direct contact with webs. The goal of WP2 is to conduct pilot investigations into the utility of eDNA from spider webs as a complementary sampling tool of airborne microbiota. The goal of WP3 is to work towards developing protocols for the use of eDNA from spider webs in monitoring of fungal agricultural pests, and invasive plant and animal species. We will check whether spider webs in nature permit us to trace fungal agricultural pests known to occur in Slovenia, as well as detect some that are yet undocumented. Furthermore, we will develope protocols for using eDNA from spider webs to monitor representatives of the numerous invasive plants in the region, as well as Aedes mosquitos as a representative group of invasive animals.
Significance for science
The use of eDNA is a rapidly developing tool for tackling several societal challenges. Among the wide range of applications are environmental (biodiversity) monitoring, animal diet assessment, reconstruction of paleo communities, invasive species, climate change, etc. In this context, spider webs represent a novel and potentially very powerful source of contemporary genetic material of a variety of organisms, from animals, plants and fungi, to even bacteria and viruses. The here proposed research will assess in detail the utility of eDNA from spider webs and develop working protocols for its use across diverse possible applications, from classical biodiversity monitoring of arthropod and plant communities, to monitoring of airborne microbiota, and the detection of invasive species and agricultural pests. Thus, our results will be highly relevant in diverse scientific settings, with potential implications for both basic research as well as application to relevant societal problems. In three work packages, we aim at developing working protocols for the use of eDNA from spider webs in diverse scientific settings. In WP1, we expect to successfully establish working protocols to estimate the use of spider web eDNA in estimating local arthropod (represented by spiders and bees) and vascular plant communities. These findings will establish first working platforms for eDNA from spider webs as a cheap and fast complementary tool for biodiversity monitoring. In WP2, we expect to establish eDNA from spider webs as a useful tool for the monitoring of the under-researched airborne microbiota, an important field of microbiology. Developing protocols in WP2 could be used in microbial ecology, atmospheric science, as well as for pathogen-spread and possibly even fields like bioterrorism detection. In WP3, we expect to successfully demonstrate the utility of eDNA from spider webs in the monitoring of agricultural pests and invasive species. We expect our results to highlight a reduction in the labour intensiveness and costs associated with conventional monitoring of at least some agricultural pests and invasive species. In sum, we will provide first working and field tested platforms for future research in a variety of research fields connected to web derived eDNA, many of which are probably beyond our current imagination.
Significance for the country
The use of eDNA is a rapidly developing tool for tackling several societal challenges. Among the wide range of applications are environmental (biodiversity) monitoring, animal diet assessment, reconstruction of paleo communities, invasive species, climate change, etc. In this context, spider webs represent a novel and potentially very powerful source of contemporary genetic material of a variety of organisms, from animals, plants and fungi, to even bacteria and viruses. The here proposed research will assess in detail the utility of eDNA from spider webs and develop working protocols for its use across diverse possible applications, from classical biodiversity monitoring of arthropod and plant communities, to monitoring of airborne microbiota, and the detection of invasive species and agricultural pests. Thus, our results will be highly relevant in diverse scientific settings, with potential implications for both basic research as well as application to relevant societal problems. In three work packages, we aim at developing working protocols for the use of eDNA from spider webs in diverse scientific settings. In WP1, we expect to successfully establish working protocols to estimate the use of spider web eDNA in estimating local arthropod (represented by spiders and bees) and vascular plant communities. These findings will establish first working platforms for eDNA from spider webs as a cheap and fast complementary tool for biodiversity monitoring. In WP2, we expect to establish eDNA from spider webs as a useful tool for the monitoring of the under-researched airborne microbiota, an important field of microbiology. Developing protocols in WP2 could be used in microbial ecology, atmospheric science, as well as for pathogen-spread and possibly even fields like bioterrorism detection. In WP3, we expect to successfully demonstrate the utility of eDNA from spider webs in the monitoring of agricultural pests and invasive species. We expect our results to highlight a reduction in the labour intensiveness and costs associated with conventional monitoring of at least some agricultural pests and invasive species. In sum, we will provide first working and field tested platforms for future research in a variety of research fields connected to web derived eDNA, many of which are probably beyond our current imagination.
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