Exchange opportunity MIND06:

In-house DNA extraction protocol for bentonite, clay samples

The Institute of Resource Ecology (HZDR/IRE) provides a wide range of spectroscopic, microscopic, and biological methods, which are all implemented in controlled areas.

Our in-house DNA extraction protocol based on the references Selenska-Pobell, 1995, and Selenska-Pobell et al., 2001, could be successfully adapted for Opalinus clay samples as well as bentonite samples. This method uses SDS to lyse the cells and release bacterial DNA instead of a mechanical lysis step often used in commercial DNA extraction kits. The very effective direct lysis of microorganisms in environmental samples is combined with the precipitation of the extracted DNA with polyethyleneglycol, and the final purification steps based on the use of AXG-100 cartridges (Macherey-Nagel, Düren, Germany).

Selenska-Pobell S (1995) Direct and simultaneous extraction of DNA and RNA from soil. In: Molecular Microbial Ecology Mannual 1.5.1, Akkermanns, ADL; Van Elsas JD; De Bruijn FD (eds), Kluwer Academic Publishers, Dordrecht, Boston, London, p. 1-17.
Selenska-Pobell S, Kampf G, Flemming K, Radeva G, Satchanska G (2001) Bacterial diversity in soil samples from two uranium waste piles as determined by rep-APD, RISA and 16S rDNA retrieval. Antonie Van Leeuwenhoek 79:149–161.


• Preparing of all the solution necessary for DNA extraction protocol
• Performance of the DNA extraction protocol with an selected Clay or Bentonite sample
• Measurement of DNA content and Test-PCR


1-2 weeks

The Candidate

Exchange opportunity for PhD or Professional.

The candidate needs to have a background in molecular biology or microbiology.

Application modalities

About 8 weeks in advance of the planned research stay; CV and publication list

Practical modalities

Accomodation is possible at HZDR Guesthouse.

Additional information


Country: Germany

Language: English

Mentor: Andrea Cherkouk, Nicole Matschiavelli

Contact email:a.cherkouk[at]


MIND reference: MIND06

Host reference: MIND-HZDR-1


Applications should be submitted by email to mind.project[at] and should contain

– a motivation letter with MIND-reference to the opportunity as mentioned on this website;

– a CV of the candidate.

Approval of your request will be subject to the evaluation of your application file by a Jury composed by members of the MIND project WP3, as well as the host institution. You will be informed about the status of your application via email.

In case of questions, please contact us via mind.project[at] and always mention the MIND reference number of the opportunity.