Environmental DNA center at Aarhus University, Danish Center for Energy and Environment

Aarhus University, Danish Center for Energy and Environment

With participation of Department of Environmental Science and Department of Bioscience


Environmental DNA (eDNA) is defined as genetic material obtained directly from environmental samples such as soil, sediment, water, snow, etc. or leftovers from an organisms such as hair, feces or carcasses. eDNA is an efficient, non-invasive and easy-to-standardize sampling approach with great potential as a monitoring tool for wildlife. It constitutes a great opportunity to study the role and ecology of organisms and get insight into their metabolism, function and evolutionary relationship.

The fast development within the area of DNA and RNA sequencing techniques combined with the reduction in prices of sequencing analysis have strengthened the interest in wide-spread use of techniques based on eDNA for monitoring and research applications. The Danish monitoring program of water and nature (NOVANA) is currently under revision and the development of up-to-date techniques that are less expensive and/or provide more detailed information on plants, animals and microorganisms in the environment are needed. 

In the eDNA center at AU-DCE investigations of potentials and feasability of employing eDNA in environmental monitoring of both state of environment and tracking of specific organisms will performed. The objective is to perform preparatory investigations facilitating incorporation of eDNA techniques in environmental monitoring.


How does it work?

Methodology for eDNA metarbacoding approach

Analysis of eDNA involves the collection of a small volume of water, soil, sediment, feces, etc which is sent to the laboratory where it is treated to extract the eDNA present. This method uses either universal primers that amplify DNA from a group of target species (e.g. bacteria, amphibians, fishes, crustaceans, plants, etc.) or total environmental DNA as input. After amplification in the PCR process or shotgun library preparation the DNA fragments are subsequently sequenced using in-house state of the arts sequencing platforms. The resulting sequences are then assembled to genes/genomes or compared with a reference database to establish a list of species from which DNA is present in the sample. Accordingly, eDNA is used to address applied and fundamental research questions within areas ranging from molecular biology, ecology, palaeontology and environmental sciences.    


Objectives

General objectives: to develop a strong national focal point for eDNA in environmental monitoring of the state of the environment and individual species of interest.

The specific objectives of the DCE financed eDNA center is to Develop eDNA tools and applications for detecting specific species, invertebrates, phytoplankton and microorganisms of high ecological and public interest.

The technical issues of eDNA extraction, PCR-primer design and DNA amplification within the different groups of organisms varies. In the eDNA center these will be verified and bioinformatic analysis developed. This includes mirroring the results in various available databases. However, these databases are often insufficient and some updating of the databases with known sequences can also be foreseen. This will include contributing to established collaboration with research groups (wolves in Germany; soil invertebrates in COST action).

Services/Protocols

The eDNA center houses state-of-the-art sequencing facilities to support participation in all types of projects involving analysis of eDNA. This includes identification of microorganisms, plants and animals within the boundaries of the databases and primers identified. Gene expression relevant for provision of important ecosystem services and health are included in the competences harboured by the eDNA center. Protocols and equipment for collecting different eDNA samples.

Ongoing projects

There are still many questions to be answered concerning eDNA approach for biomonitorization projects and species detection. For example, can the technique be used for detecting all species? Can it be used in all environments? Can we develop primers for other species? Will it be possible to assess feasible quantitative data for different species? What are the effects of abiotic factors like temperature, pH, conductivity etc on the amount of eDNA in the water. When, where and what is the most effective way of sampling?

Collaborative research is being carried out combining the analytical expertise in genetics and bioinformatics of senior scientists at Environmental Microbiology and Biotechnology section with the thorough knowledge of the ecology and distribution of species of senior scientists at the Bioscience Department, Aarhus University.

Read about the 2015/2016 projects below.

- Freshwater pearl mussle

- Marine reefs

- Freshwater lakes

- Soil

- Microorganisms

If you have ideas for research please feel free to contact Anne Winding (aw@envs.au.dk)  to talk about the possibilities.