DNA methods in environmental monitoring

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.

Per Sundberg, Gothenburg University

5 330 000 SEK

Analysis of phytoplankton is an important part of the marine environmental monitoring. The analyses are normally based on microscopy, which is time-consuming and requires personnel with high taxonomic skills. DNA-analysis has been discussed as a compliment to microscopy, but there is a need for optimization and validation of this method to be able to use it in the monitoring programmes. The goal of this project is to do a full comparison between microscopy- and DNA analysis of phytoplankton.

Agneta Andersson, Umeå University

5 900 000 SEK

Christer Erséus, Gothenburg University

4 630 000 SEK

A four-year (2019–2022) international research project on development of methodology and quality control for monitoring of aquatic animals in various habitats such as lakes, running waters and marine environments using environmental DNA (eDNA) and metabarcoding.

Traditional aquatic species surveys typically require vast investments in equipment, time and skilled taxonomists to identify species. Besides often being invasive and harmful to the study species, they are often characterized by inefficiencies and limitations in detection rate. During the last decade a powerful census tool – environmental DNA or eDNA – has emerged. In principle this non-invasive method can provide a comprehensive species inventory including rare, dangerous, invasive and difficult-to-sample taxa by analysing environmental samples. Proof-of-concept studies have demonstrated that eDNA approaches has a high detection rate for most aquatic taxa compared to traditional methods and especially for fish and amphibians. Method development in eDNA-studies is rapid and has led to great improvements during the last few years, but there is an urgent need for optimisation in both sampling strategies and sample processing. The project Life-DNAquatic will build on knowledge that is available within the project team and research network to develop methods and techniques applicable for field sampling, sample processing and storage of eDNA samples in four aquatic environments: streams, lakes, wetlands and the marine environment. Specifically, the project aims to:

• Compare spatial and temporal differences in sampling design to find the optimal season and sampling effort for different aquatic habitats.
• Compare cost performance and handling time of different sampling and filter methods.
• Provide a robust field collecting protocol to avoid contamination of samples.
• Fully assess the integrity of eDNA under variable conservation methods.
• Compare the outcome of different eDNA extraction methods.
• Assess costs, benefits and disadvantages of eDNA approaches in comparison with conventional monitoring methods.

Martin Andersson-Li, AquaBiota Water Research ABWR AB

5 000 000 SEK

DNA can be used to identify freshwater organisms in a lakes or stream using only a water sample. DNA-based assessment methods can provide better insight into the taxonomy of aquatic organisms and increase cost-efficiency of biological monitoring.

The ultimate aim of FRESHBAR is to establish DNA-barcoding techniques in operative national monitoring and improve assessment of biodiversity human-induced stress on freshwater ecosystems. However, several challenges remain before DNA-based methods can be operational in environmental monitoring. One of them is to improve barcode libraries. The barcode is a portion of a specific gene used to identify species, and the library contains information on which barcodes belongs to which species. FRESHBAR aims at improving reference databases by generating many new species’ barcodes.

In FRESHBAR, different molecular methods will also be compared, to resolve taxonomic uncertainties of closely related species.

Specific tasks

• providing new reference sequences for diatoms and invertebrates that are important for monitoring
• guaranteeing the taxonomical correctness of new sequence identifications by molecular and morphological taxonomical curation
• contribute to the development of metabarcoding using long marker sequences (diatoms) and testing shorter barcodes (invertebrates)
• comparing morphological and DNA-based identifications across environmental gradients
• depositing results and samples in quality-assured public databases and collections.

Maria Kahlert, Sveriges lantbruksuniversitet SLU.

4 440 000 SEK

The aim of this project is to set the foundation for a comprehensive inventory of biodiversity in Swedish forest soils. This foundation could then be implemented at the start of the forthcoming period of the Swedish Forest Soil Inventory, i.e. in 2023 (the current period runs during 2013–2022).

Forest ecosystems represent a valuable natural resource in Sweden, providing not only timber but also supporting a rich diversity of organisms. The Swedish Forest Agency states that the current biological functions of forest soil have to be maintained, but also stresses an urgent need for new biological indicators. In spite of their key role in the boreal forest biome, systematic monitoring of soil biota is currently lacking.

Björn Lindahl, Swedish University of Agricultural Sciences.

3 370 000 SEK

Francisco Nascimento, Stockholm University.

4 480 000 SEK

Anti Vasemägi, Swedish University of Agricultural Sciences

4 950 000 SEK