Microbial diversity in soil and water samples from uranium mining waste piles

Bacterial diversity in soil and drain water samples of uranium mining waste piles was studied by two direct (culture-independent) approaches, the16S rDNA and the ribosomal intergenic spacer amplification (RISA) retrievals. A large number of samples was studied which were drawn from the following heavy metal and radionuclide polluted sites: the uranium mill-tailings Schlema /Alberoda, Gittersee/Coschütz, in Germany, and Shiprock/New Mexico in the USA, as well as two uranium mining disposal sites, Haberlandhalde near the town of Johanngeorgenstadt and Deponie B1/Weisse Elster (Germany).
Both methods demonstrate significant differences in the microbial diversity between the samples studied. The highest diversity was found in the drain water and soil samples from the mill-tailing Gittersee/Coschütz, followed by those from Schlema/Alberoda and the Haberlandhalde. The predominant 16S rDNA fragments in those samples were affiliated to Pseudomonas, Geobacter, and to different uncultured sulfate reducing and Cytophaga-like bacteria. Interestingly, in the samples of the Gittersee/Coschütz site the presence of the recently discovered anaerobic chemolithotrophic ammonium oxidizing bacteria named Anammox [1] was demonstrated by the use of the RISA approach. Using the same approach, an abundance of Nitrosomonas sp., nitrifying bacteria belonging to b-subclass of Proteobacteria was found in the water samples from Shiprock. Both groups of bacteria were "overseen" when the 16S rDNA retrieval was applied for analyzing the same samples. These results clearly demonstrate the utility of using at least two primer pairs for PCR amplifications of environmental rDNA fragments in order to overcome the masking effect of the preferential amplification, which depends on the structure of the flanking regions of the templates.
In all kinds of uranium polluted wastes the presence of a large variety of not yet cultured bacteria belonging to Holophaga/Acidobacterium and Cytophaga/ Flexibacter clusters was shown. In addition, many 16S rDNA sequences were affiliated with various unidentified so- called "candidate" bacterial divisions such as OP1, and OP6 [2].

Acknowledgements
This work was supported by grants 7531.50-03-FZR/607 from the Sächsisches Staatministerium für Wissenschaft und Kunst, Dresden, Germany and GRP/9816 from the European Science Foundation. The authors thank David Balkwill, Florida State University, Tallahassee, USA for providing some of the water samples.