Skip to main content
Image
Crab in the hand of researcher.
Photo: Mattias Obst
Breadcrumb

SWEDNA - Swedish eDNA lab

Research group

Short description

Welcome to the Swedish eDNA (SWEDNA) website, a research group financed by the environmental research fund (miljöforskningsanslag) from the Swedish Environmental Protection Agency’s (SEPA), in collaboration with the Swedish Agency of Marine and Water Management (SwAM).

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.

The Swedish eDNA lab will customize the use of eDNA detection methods for applications in environmental monitoring of aquatic environments.

Welcome to SWEDNA

Welcome to the Swedish eDNA (SWEDNA) website, a research group financed with 5.3 million by the environmental research fund (miljöforskningsanslag) from the Swedish Environmental Protection Agency’s (SEPA), in collaboration with the Swedish Agency of Marine and Water Management (SwAM).

You can find an overview over all financed DNA-based research projects at SEPA’s website ”Forskning om DNA-metoder inom miljöövervakning”.

Our research

Environmental 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. invasive 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 applications 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 systems 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 DNA 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 various 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

Research projects

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)
Carin Nilsson (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)
Vacant (Swedish Environmental Protection Agency)

Social Media

Join us on

Twitter

@mucofloris, #eDNA

LinkedIn

Mattias Obst Marine

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.    Biodiversit-Next Conference, 21-25. October 2019, Leiden, Netherlands, https://biodiversitynext.org/
2.    GEANS annual project meeting, 8-9 October, 2019 Gothenburg, Sweden
3.    National workshop on eDNA processing and data management, 12. September 2019, Gothenburg
4.    Miljöövervakningsdagarna, 24-25 September, Karlstad, Sweden, https://www.naturvardsverket.se/Kalendarium/Miljoovervakningsdagar/
5.    International Barcoding of Life Conference (iBOL), 17-20 Juni, Trondheim, Norway, http://dnabarcodes2019.org/
6.    Genomics Standards Consortium meeting, 22-24. May 2019, Vienna, Austria https://press3.mcs.anl.gov/gensc/meetings/gsc21/
7.    Project Kick Off, 1. April 2019 Gothenburg, Sweden

Results

Exter K, Decruw C, Portier M, Gerovasileiou V, Pavloudi C, Obst M (2020) Genomics Observatory Use-Case: The challenge to standardise image and sequence data to Darwin Core format. Biodiversity Information Science and Standards 4: e58938
doi: 10.3897/biss.4.58938

Pavloudi, C.; Chrismas, N.; Troncoso, J.S.; Norkko, J.; Viard, F.; Mortelmans, J.; Mavric, B.; Gerovasileiou, V.; Arvanitidis, C.; Kotoulas, G.; Obst, M. (2019) Artificial Reef Monitoring Structures (ARMS) providing insights on the marine biodiversity and community structure. http://www.eurobis.org/imis?module=ref&refid=311999

Exeter K, Obst M, et al 2020. Genomics Observatory Use-Case: The challenge to standardise image and sequence data to Darwin Core format. TDWG 2020 conference. In review.

Kutti T, Johnsen IA, Skaar KS, Ray JL, Husa V and Dahlgren TG (2020) Quantification of eDNA to Map the Distribution of Cold-Water Coral Reefs. Front. Mar. Sci. 7:446. doi: 10.3389/fmars.2020.00446

Hestetun JT, …Dahlgren T (2020) Significant taxon sampling gaps in DNA databases limit the operational use of marine macrofauna metabarcoding. Marine Biodiversity 50:70 https://doi.org/10.1007/s12526-020-01093-5

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

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. https://pub.epsilon.slu.se/15801/

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.  https://www.havochvatten.se/hav/uppdrag--kontakt/publikationer/publikationer/2018-08-23-utvardering-av-ny-overvakning-av-frammande-arter.html

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.

Members

Per Sundberg

Project tasks: Principal investigator, Project coordinator

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

Personal website Per Sundberg

Per Sundberg

Marina Panova

Project tasks: Planning, data analyses and synthesis.

Marina Panova works with various aspects of genomics in the sea: from de novo genome projects for target species to metabarcoding and metagenomics of marine communities.  She is an expert in applying NGS tools to non-model hard-to-sequence organisms. Her main research interests are evolution of genes and genomes, development of genomic tools and recently, eDNA applications in biodiversity and monitoring.

Competence: evolutionary biology, population genomics, transcriptomics, metabarcoding, bioinformatics, statistics.

Personal website Marina Panova

Marina Panova

Matthias Obst    

Project tasks: Communication, liaison, networking, data management

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

Personal website Mattias Obst

Matthias Obst

Thomas Dahlgren

Project tasks: Planning, field work, and synthesis

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

Personal website Thomas Dahlgren 

Thomas Dahlgren

Alizz Axberg

Project tasks: Master student

Alice Axberg will work with the European ARMS project to develop metabarcoding methods for detection of alien species in hard bottom communities.

More information here

Alizz Axberg

Nauras Daraghmeh

Project tasks: ERASMUS+ exchange student
 
Nauras is an ERASMUS+ student in the field of marine sciences working with biodiversity genetics and its application in conservation biology. He has a strong background in coral reef science, from reef monitoring in Egypt, to transdisciplinary studies of anthropogenic impacts on tropical shores, to coral nutrient stoichiometry. For his bachelor thesis, he analyzed DNA metabarcoding data derived from ARMS to investigate biodiversity and inter-specific co-occurrence patterns in Red Sea coral reefs. Nauras has experience in standardized monitoring field work, as well as bioinformatic methods such as sequence data denoising and analysis in R and co-occurrence network analysis.

Nauras Daraghmeh