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Swedish eDNA

Introduction

Welcome to the Swedish eDNA (SWEDNA) website, a project financed with 5.3 million sek by the Swedish Agency of Marine and Water Management and the Swedish Environmental Agency.

What is eDNA? Most organisms leave trace of DNA in the surrounding environment – so-called environmental DNA (or eDNA). Today, molecular biology has developed sensitive methods, which allow us to discover even the smallest pieces of such DNA traces. Such diagnostic tools can be used to study the population and community structure of habitats as well as presence and absence of particular species of interest. In this project, we will customize the use of eDNA detection methods for applications in environmental monitoring of aquatic environments.

This project is linked to ongoing and planned programs national environmental monitoring programs. The project started in April 2019 and will run until March 2022.

About us

Per Sundberg

Portrait Per Sundberg

 

 

 

 

 

 

Project tasks: Principal investigator, Project coordinator

Short summary: Per Sundberg is an expert in eDNA technology, marine biodiversity, and the IMO Ballast water convention. He is CEO for an environmental consultancy company offering eDNA services. He has a long-standing experienence as project coordinator, principal investigator, and authors of reports and scientific papers.

Competence: marine biodiversity and conservation, monitoring of red-listed, alien, and invasive species ecological modelling, IMO Ballast Water Convention, Biological risk assessments, marine field work

Please visit the personal web page of Per Sundberg for more information.

Matthias Obst

Portrait of Matthias Obst

Project tasks: Communication, liaison, networking, data management

Short summary: Matthias Obst works with biodiversity modelling, especially for alien, invasive, and endangered species. He is also expert in testing genetic observation systems for biological diversity in the ocean, so-called genomic observatories. Obst leads several programs to establish early warning systems and monitoring networks for marine invasive species based on DNA methods, including to the European ARMS-program and ARMS pilot in the INTERREG program GEANS.

Competence: marine biodiversity and conservation, monitoring of red-listed, alien, and invasive species ecological modelling, IMO Ballast Water Convention, Biological risk assessments, marine field work, biodiversity informatics

Please visit the personal web page of Matthias Obst for more information.

Thomas Dahlgren

Porträtt av Thomas Dahlgren

Project tasks: Planning, data analyses and synthesis



Short summary: Thomas Dahlgren is a molecular taxonomist expert on marine invertebrate taxa. He has a long working experience in the field of monitoring impact from activities such as oil and gas exploration, aquaculture and deep-sea mining. Thomas Dahlgren is part time employed at GU. His main employer is NORCE in Bergen, Norway.

Competence: molecular taxonomy, marine ecology, deep-sea biodiversity, connectivity and population genetics, marine biodiversity and conservation, marine field work

Please visit the Thomas Dahlgren’s webpage at NORCE for more information.

Research

Projects

solaborreEnvironmental DNA (eDNA) analysis is a rapid and non-invasive biodiversity tool that is increasingly used in environmental monitoring and biodiversity assessment. It is claimed to be more cost-efficient and more accurate, especially when it comes to detecting rare species, as for e.g. methodinvasive or endangered species. Its main advantage lies in the fact that we do not actually need to see, or collect, the organisms we are monitoring. It is based on the fact that all organisms leave traces of DNA in the environment, to a larger or less degree.

There are many successful ballast waterapplications of eDNA approaches in environmental monitoring today, but some important methodological questions remain until these methods can be implemented in national monitoring program. These questions are addressed by this project, and include, among others:

  • How far from the source can we detect DNA in various aquatics smorbultsystems and for various groups of organisms?
  • How long can we successfully detect eDNA in the marine environment and for various groups of organisms?
  • What is the risk of false positives, i.e. detecting DNAblåskrabba from an organism not present in the system?
  • How can we optimize sampling and filtering techniques to yield maximum possible amounts of DNA?
  • Can we estimate population sizes from eDNA results in benthos sivvarious groups of organisms?
  • How does eDNA detection perform in comparison to alternative methods such as metabarcoding and microscope-based identification
  • What is the statistical power in eDNA identification and how should eDNA studies be statistical designed

 

During the course of this project we will perform a series of field and laboratory experiments to investigate important methodological questions in detail. These include.

1. How far from the source can we detect DNA?

Different organisms leave different amounts of DNA traces in the water, depending on size, movement patterns, their general biology, as well as the environmental conditions. There are many studies of eDNA for monitoring fish communities, but the picture is not equally clear when it comes to other taxonomic or ecological groups. For example, how well can we trace hard-shelled organisms like crustaceans, or very small molluscs? In addition, most eDNA trace studies have been carried out in freshwater systems, which are more enclosed than open marine environments. Hence, we will perform experiments also in coastal habitats.

2. Rate of DNA degradation in aquatic environments, and the risk of "false positives"

Decay rates for eDNA often depend on the environmental conditions, which are principally different in freshwater and marine systems. To better understand the variation in decay rates among different organisms and environments, we will perform ddPCR analyses with fish, molluscs and arthropods in a controlled coastal field study across seasons and a range of environmental gradients.

3. The effect of filtering, fixatives, and extraction procedures

Few studies have systematically investigated the effect of different filtration and fixation methods for eDNA and we will carry out some tests to optimize pre-filtering and fixation protocols. These protocols should not only be adjusted to improve the eDNA yield, but also allow easy integration into existing monitoring practice.

4. Sampling strategies in general, and the detecting of rare species in particular

Few theoretical studies have been performed to date to investigate the effect of abundance, spatial distribution, patchiness, and sampling effort on the successful detection of eDNA traces. We will address this issue with a series of modelling and experiments in order to simulate and optimize our sampling strategies for various groups and environments.

5. Quantification and population size estimates

Some pioneering studies have shown that it is possible to deduct population size and structure from eDNA. We will explore this application further and conduct experiments to investigate the applicability of eDNA in monitoring population sizes of endangered species in Sweden.

Reference group

Sara Peilot (Vänerns vattenvårdsförbund)
Martin Ljungman (Medins Havs och Vattenkonsulter AB)
Johanna Bergkvist (Marine Monitoring AB)
Patrik Bohman (SLU, Uppsala)
Malin Strand (SLU, Artdatabanken)
Cecilia Andersson (Stena Line Maritime Sector)
Erland Lettevall (Swedish Agency for Marine and Water Management)

N.N. (Swedish Environmental Protection Agency)

Collaborations

Our project actively collaborates with the following networks, programs, and SME’s

logotypes

Title: Genetic tools for Ecosystem health Assessment in the North Sea region (GEANS)
Type: Interreg project

Title: European ARMS program
Type: H2020 financed project

Title: DNAqua-Net
Type: EU COST action

Title: SweBol / EDNA
Type: Scientific network

Title: High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of marine sediments" (METAMON)
Type: Research project funded by the Research Council of Norway

Title: SeAnalytics AB
Type: Environmental Consultancy

Title: Medins Havs och Vattenkonsulter AB
Type: Environmental Consultancy

Title: Marine Monitoring AB
Type: Environmental Consultancy

Title: Swedish Biodiversity Data Infrastructure
Type: Infrastructure

Title: Genomic Observatories
Type: Scientific network

Results

Research articles

Bohman P, Sundberg P, Klint M, Obst M (2018). Jakten på solabborren (Lepomis gibbosus) - en eDNA-studie i Kungsbackaån. Drottningholm Lysekil Öregrund: (NL, NJ). Department of Aquatic Resources, Sveriges lantbruksuniversitet. Aqua Reports 2018:21.

Sundberg P, Liungman M (2019) Övervakning av flodpärlmussla med eDNA – en pilotstudie. Rapport till Länsstyrelsen i Jönköpings län. version 1.2. Projektnr. 3343.

Sundberg, P., Obst, M., Bourlat, S., Bergkvist, J. & M. Magnusson, (2018). Utvärdering av ny övervakning av främmande arter. (Evaluation of new ways to monitor alien species). Swedish Agency for Marine and Water Management Report 2018:24 55 pp.

Sundberg, P., M. Berggren & T. Dahlgren (2017). Test av eDNA och ddPCR som metod för att upptäcka/övervaka invasiva främmande arter (IAS): svartmunnad smörbult och blåskrabba. Rapport till Havs- och vattenmyndigheten.

Sundberg, P., Q. Haenel & S. Bourlat (2016). Utvärdering av DNA-streckkodning och referensbibliotek för övervakning av invasiva främmande arter. Rapport till Havs- och vattenmyndigheten.

News

Social media

Join us on

  1. Twitter: @mucofloris, #eDNA
  2. LinkedIn: https://www.linkedin.com/in/matthiasobstmarine/

Events

Below is a list of past and upcoming meetings, where we present progress, discuss results, and plan upcoming scientific activities with collaborating networks.

  1. Project Kick Off, 1. April 2019 Gothenburg, Sweden
  2. Genomics Standards Consortium meeting, 22-24. May 2019, Vienna, Austria
  3. International Barcoding of Life Conference (iBOL), 17-20 Juni, Trondheim, Norway,
  4. Miljöövervakningsdagarna, 24-25 September, Karlstad, Sweden
  5. National workshop on eDNA processing and data management, 12. September 2019, Gothenburg
  6. GEANS annual project meeting, 8-9 October, Gothenburg, Sweden
  7. Biodiversit-Next Conference, 21-25. October 2019, Leiden, Netherlands

 

Page Manager: Matthias Obst|Last update: 9/26/2019
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