New publication: Using DNA metabarcoding for water quality assessment

In a just-released article in the journal Methods in Ecology and Evolution, we investigate the potential of DNA metabarcoding of freshwater macroinvertebrates for the assessment of stream health. With the “DNA metabarcoding” method hundreds of specimen in a sample can be identified, often up to species level. The assessment results of the morphology and DNA based methods were very similar with both methods, while DNA metabarcoding  detected more taxa on species level. However, metabarcoding has also shortcomings, for example, the method  failed to detect ~ 30% of the taxa identified by morphology. This work is an important step into validation and improvement of the metabarcoding method, and it highlights it’s potential for more rapid and accurate routine monitoring of freshwater streams.

Picture 1: Vasco Elbrecht, Edith Vamos and Florian Leese (from left to right),  in cooperation with Kristian Meissner and Jukka Aroviita from the Finnish Environment institute, analysed 18 monitoring samples from Finnish streams.

Additionally, our R package PrimerMiner was featured on the cover page of the journal Methods in Ecology and Evolution.

Picture 2: The cover picture in Methods in Ecology and Evolution shows a macroinverterte sample which is homogenised using liquid nitrogen and a mortar, in order to extract the DNA from the sample.

Science meets Education

… during the international conference of “Polar Educators International” in Italy, or actually they met. For the scientific input Jana Dömel was invited to lead a workshop on genetic analyses.

During the scientific year 2016*17 Seas and Oceans the aim of the project “MEERwert. Polare Biodiversität.” (The value of the sea. Polar biodiversity.; www.meer-wert.info) is to introduce schools and anyone else who is interested to genetic methods that help us to discover the biological variety of the polar regions. In addition to the already freely available “Extraction box”, that includes all material needed for a DNA extraction of e.g. fish fingers, we designed further worksheets to present at the workshop. (The Extraction box will be send to you on request. Contact: jana.doemel@uni-due.de)

Foto: Jana supports the workshop’s participants with the genetic working sheets, that involve a lot of hands on (the computer) work.

During the conference teachers, but also scientists worked on two working sheet that introduce the basics for DNA analyses and were asked to improve the exercises from a didactical perspective. To start, fish sequences are compared to a database to find out species names. Subsequently, phylogenetic trees are reconstructed to solve the origin and relationships between fish of the so called „cod“ fishes.

We got very positive feedback, which confirmed that our project is of great educational interest.

New Publication – Primer Validation

Yesterday, a new publication by Vasco und Florian entitled “Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment“has been published in Frontiers in Environmental Science (Link). In the study we demonstrate problems with several of the currently available metabarcoding primers and tested four newly developed COI primers targeting aquatic macroinvertebrates. Our analyses show that the new primers (BF/BR) are highly suitable and amplify very equally the analysed taxa. Most importantly, however, our study shows how important careful design and validation of primers for a certain region, habitat or target taxon group is. With growing data bases there is still much potential for future improvement.

Prize awarded to Bianca!

Bianca Peinert from our group has just been awarded the Prize of the 50th Essen Water Quality and Waste Management conference. She received the highly competitive price for her innovative Master Thesis on “DNA-based aquatic biomonitoring“, which was part of the GeneStream-Project (Bode Foundation). Main supervisors of the thesis were Vasco Elbrecht and Arne Beermann, PhD students at leeselab. The award of 2000 Euros was shared this year by two winners.

Congratulations, Bianca, for this great achievement!!!  

Bild: M.Sc. Bianca Peinert with the certificate of the award.

DNAqua-Net Kick-Off conference

Since November 2016, Florian leads the large EU COST Action Network DNAqua-Net. As the Grant Manager of the Action, Alexander is the responsible coordinator of the network which already now encompasses 300 researchers, end user, managers & regulators as well as industry partners from 42 nations.

The aim of the COST Action DNAqua-Net is to explore the potential of novel DNA-based methods for bioassessment of aquatic ecosystems (lakes, rivers, oceans, groundwater) and to suggest standardised application strategies. These can only be successful in large-scale monitoring programs, such as the EU Water Framework Directive, if researchers within the scientific community agree on clear standards and work together with partners from the environmental regulators and industry partners.

Just now, from March 6th until 9th, we have hosted the Kick-Off conference of DNAqua-Net in Essen. 172 participants from 37 nations met at the Campus of our University to discuss in a highly constructive atmosphere chances and limits of the novel techniques. Some impression from the conference as well as the preceding Management Committee meeting can be found  here.

DNAqua-Net conference participants

Molecular Ecology Module

On September 5th our new module “Molecular Ecology” will start. For one week we will generate molecular data to investigate patterns and factors influencing intraspecific genetic variation in benthic macroinvertebrates at the Forschungsinstituts Senckenberg in Gelnhausen. Subsequently, we will perform bioinformatic analyses in the second part of the module at University of Duisburg-Essen.

Study area will be the Rhein-Main-Observatorium.

Molecular Ecology Module