Extraction of microbial DNA from Muschelkalk formations in the Thuringian Basin

Wenke Stoll1, Cassandre S. Lazar2, Robert Lehmann3, Kirsten Küsel2, Kai Uwe Totsche3
1 Lehrstuhl Aquatische Geomikrobiologie & Lehrstuhl für Hydrogeologie, Friedrich-Schiller-Universität Jena, Germany
2 Lehrstuhl Aquatische Geomikrobiologie, Friedrich-Schiller-Universität Jena, Germany
3 Lehrstuhl für Hydrogeologie, Friedrich-Schiller-Universität Jena, Germany

P 6.3 in Grundwasserbiologie


Microbial communities can be used as bioindicators for groundwater and reservoir quality, if the community structure and their functions are determinable. In the course of the establishment of monitoring nets and groundwater monitoring well construction, we recovered non-fractured to karstified rock core samples, from different drillings and depths in the Thuringian Basin, representing different habitat and reservoir properties. The DNA of rock-attached and unattached microorganisms was extracted after grinding the aquifer rock samples to powder. The primarily investigated formations of the Upper Muschelkalk, mainly composed of limestones and marlstones, provided challenging samples, as their components (such as calcium) interfered with the DNA extractions and subsequent molecular biology analyses. Optimization of the DNA extraction protocol resulted in DNA recovered from 18 of 25 rock samples, although DNA concentrations were extremely low. Preliminary analysis of the bacterial and archaeal 16S rRNA genes by fingerprinting methods showed significant differences in the community structure patterns of the different rock samples, as well as a seemingly high microbial diversity in most samples.  16S rRNA genes will be amplified and sequenced via Illumina technique in order to further taxonomically identify the microorganisms found in the aquifer rocks.