MSc Thesis: Romahn-1

Ciliates in the Baltic Sea: Comparison of eDNA data with biomarkers

Background:

Environmental DNA (eDNA) metabarcoding is a novel and but well-accepted method for assessing biodiversity via environmental samples like water or soil. In these samples, DNA can be stored over periods of time depending on the environmental condition. The longest time period is in ice, frozen soil or sediments of seas and lakes for several thousand years. In the latter case, it is so called sedimentary ancient DNA (sedaDNA) which gives the opportunity to study biodiversity of the past. The DNA it contains can be extracted and sequenced for further community analyses.
At the same time, biomarkers are the molecular fossils of natural products like lipids and remain in sedimentary environments also for a long time period. They can be used as a proxy/indicator for past climate conditions like temperature and salinity produced by indicator species. Both combined and compared with recent monitoring data, the ecosystem and the biodiversity of the past can be investigated, evaluated and new techniques can be developed to assess paleoclimate.

Aim of thesis:

The main aim of this proposed thesis topic is to test if the ciliate biomarker reflects changes in redoxcline, the layer of water between the upper oxygenated and lower anoxic water.

Methods:

To test the functionality of biomarkers, the master student would compare the environmental DNA with biomarkers produced by ciliates and recent biomonitoring data.

Therefore, the chosen student will process DNA metabarcoding data with a bioinformatic pipeline and check them for the presence and richness of various ciliate genera. These ciliate eDNA data will then be compared with provided biomarker information of two MUCs(short cores) from the Baltic Sea. We will test if a high abundance of the biomarker goes along with the richness of ciliates.
Additionally, we will compare the results with monitoring data from the Baltic Sea for which the environmental conditions are well-known and biodiversity studied since decades.

The chosen student will gain expertise in bioinformatics, paleoclimatology and metabarcoding.
The topic is a cooperation with Jérôme Kaiser from the Leibniz Institute for Baltic Sea Research in Warnemünde.

If interested, an introduction into the work within a clean room for seda DNA is possible.

Student requirements:

Knowledge about general genetics and barcoding, experience working with R, basic statistical knowledge, Linux experience preferable

Possible beginning:

Possible start date would be no earlier than February 2023

Contact:

Ph.D. candidate Juliane Romahn: juliane.romahn@senckenberg.de