Category Archives: News

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

Conference video: Metabarcoding primer development

We have presented our latest research in DNA metabarcoding and primer development at the annual meeting for freshwater science in Sacramento. A YouTube video is available below, with a PrePrint also being available here.

We are currently focusing on development and optimisation of DNA metabarcoding primers. As part of this process we have developed the R package “PrimerMiner” (GitHub) which can be used to obtain and process sequence data from BOLD and NCBI databases.

Screen Shot 2016-06-01 at 14.40.04

Video Tutorial: How we dry and grind samples for DNA metabarcoding!

The first step for DNA metabarcoding of invertebrate kick samples from stream ecosystems is sample homogenisation. The samples often contain hundreds of organisms which have to be dried and then homogenised, to assure that the DNA of all specimens in mixed. Only then every individual in the sample can be detected, extracting just a small subset of the ground tissue. We are using the IKA ULTRA-TURRAX Tube Drive control system for tissue grinding, as discussed in a previous video. In this new video we are detailing the complete process from sample handling, drying over night and grinding using invertebrate kick samples from Finland.

New article in the Barcode Bulletin

We just published a short article in the Barcode Bulletin.

In the march issue (pages 10-12), Florian and Jan write about how different cryptic Deleatidium mayfly species from New Zealand show strongly different responses to anthropogenic stressors in the stream and the cosequences this has for ecosystem assessments.

http://ibol.org/wp-content/uploads/2016/03/iBOL-Barcode-Bulletin-Mar-2016-Reduced.pdf

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 PrePrint: Testing the potential of 16S for DNA metabarcoding

Together with our colleges from France we just have published our first PrePrint, where we test the potential of the 16S marker for DNA metabarcoding. We were able to show that freshwater insects are more consistently amplified with the developed 16S primer than with standard Folmer COI barcoding primer. While the taxonomic resolution of the 16S marker remains unknown for insects, the ribosomal marker might be a viable alternative metabarcoding marker when local reference databases can be easily established. For now we will however continue using the COI marker, due to availability of good reference databases and optimised freshwater COI markers which show similar performance.

Untitled-1