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The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 10 9 cells g ؊1 dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Mining residues from mining activities are dumped as waste rock or as tailings, which are metal-degraded materials from ore processing. Both kinds of dumps often contain sulfide minerals such as pyrite (FeS 2 ) or pyrrhotite (Fe 1Ϫx S, x ϭ 0 to 0.125) and release acidic metal-rich waters known as acid mine drainage (AMD)/acid rock drainage (ARD) because of chemical and microbial sulfide oxidation processes, e.g.,Over a period of several years, an oxidized zone with depleted sulfide content, low pH, and enrichment of secondary minerals develops above an unoxidized zone with unaltered material in the waste dump (e.g., references 4, 14, 21, 40, and 49).Several geomicrobiological investigations of sulfidic mine waste dumps located in different climate zones have been undertaken to gather information about microbial processes and diversity in these extreme environments. At such sites, aerobic, acidophilic, chemolithotrophic Bacteria or Archaea dissolve metal sulfides by oxidizing Fe(II) and sulfur compounds and generate AMD/ARD. Products resulting from these oxidation processes can be used by Fe(III)-and sulfate-reducing prokaryotes. When Fe(III) (hydr)oxides are dissolved, adsorbed or precipitated metals are released. Sulfate-reducing Bacteria or Archaea may also precipitate metals as metal sulfides (22,49,50).Primarily cultivation techniques have been used to enumerate prokaryotes involved in oxidation and reduction processes in sulfidic mine waste dumps (3,17,52,57,64). Cultivation techniques yield cell numbers merely according to physiological properties; therefore, only a subset of the whole microbial community is detected. Up to this point, only qualitative molecular biological tests were applied to sulfidic mine dumps such as cloning and subsequent sequencing (7), denaturing gradient gel electrophoresis (12, 38), and terminal restriction fragment length polymorphism (7, 13). In addition, protein and lipid analysis (37, 58) were performed with tailing samples. These investigations provided valuable information about the microbial diversity in mine dumps but little information about the quantities of the different microbial groups or species. The molecular biological quantification technique fluorescence in situ hybridization (FISH) and metagenomic an...

Organic-rich subsurface marine sediments were taken by gravity coring up to a depth of 10 m below seafloor at six stations from the anoxic Black Sea and the Benguela upwelling system off Namibia during the research cruises Meteor 72-5 and 76-1, respectively. The quantitative microbial community composition at various sediment depths was analyzed using total cell counting, catalyzed reporter deposition – fluorescence in situ hybridization (CARD–FISH) and quantitative real-time PCR (Q-PCR). Total cell counts decreased with depths from 109 to 1010 cells/mL at the sediment surface to 107–109 cells/mL below one meter depth. Based on CARD–FISH and Q-PCR analyses overall similar proportions of Bacteria and Archaea were found. The down-core distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes (16S and 18S rRNA) as well as functional genes involved in different biogeochemical processes was quantified using Q-PCR. Crenarchaeota and the bacterial candidate division JS-1 as well as the classes Anaerolineae and Caldilineae of the phylum Chloroflexi were highly abundant. Less abundant but detectable in most of the samples were Eukarya as well as the metal and sulfate-reducing Geobacteraceae (only in the Benguela upwelling influenced sediments). The functional genes cbbL, encoding for the large subunit of RuBisCO, the genes dsrA and aprA, indicative of sulfate-reducers as well as the mcrA gene of methanogens were detected in the Benguela upwelling and Black Sea sediments. Overall, the high organic carbon content of the sediments goes along with high cell counts and high gene copy numbers, as well as an equal abundance of Bacteria and Archaea.

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