Category Archives: Uncategorized

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 project: eDNA of the “Emscher sculpin”

We are starting a new project:

Gunnar Jacobs (who is also working for Emschergenossenschaft, the local water board) starts his PhD thesis.  He will investigate the occurrence, distribution and dispersal ability of the “Emscher sculpin” (Cottus cf. rhenanus) in the river Emscher and its tributaries.

The Emscher sculpin is a fish which survived the major industrial pollution of rivers in the Emscher catchment during the last 100 years in the upper reaches of a few streams. Specimens from these relic populations are now used to repopulate ecologically restored streams and rivers in the region.

Gunnar will use eDNA (environmental DNA) to study the occurrence and distribution of the Emscher sculpin and how fast it can disperse and repopulate streams after the reintroduction. Using eDNA means that that Gunnar will filter water from the stream and analyze the sculpin DNA in it, which also means that he does not need to catch the fishes. Gunnar’s work will greatly help to understand the Emscher sculpin and the Emscher ecosystem and to subsequently make protection of the ecosystem easier.

Welcome, Gunnar! We are looking forward to the exciting project!

 

Cottus IMG_3417

New paper: Drastic underestimation of amphipod biodiversity in the endangered Irano-Anatolian and Caucasus biodiversity hotspots

Together with colleagues from the University of Tehran, we just published a paper on the diversity of amphipods in the highly endangered Irano-Anatolian and Caucasus biodiversity hotspots. So far, only five morphospecies had been known from the streams and rivers of these regions. By using molecular techniques, we could identify 42 mostly unknown species, showing that also the scarcely studied freshwater ecosystems of the region harbour a great biodiversity and deserve protection.

Scientific Reports: Drastic underestimation of amphipod biodiversity in the endangered Irano-Anatolian and Caucasus biodiversity hotspots

Florian on the radio

Florian was recently interviewed by Radio Leonardo. He talked about how new molecular tools can help to revolutionize and improve ecological water quality assessment of streams and rivers.

Link to the interview (podcast 25.02.2015, Florian’s part starts at minute 25):
http://www1.wdr.de/mediathek/audio/wdr5/wdr5-leonardo/leonardo302.html