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Microbiology of diverse acidic and non-acidic microhabitats within a sulfidic ore mine

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Abstract

A wide variety of microhabitats within the extremely acidic abandoned underground copper mine Zlaté Hory (Czech Republic) was investigated. SSU rDNA libraries were analyzed from 15 samples representing gossan, sulfide-leaching environments in the oxidation zone, and acidic water springs in the mine galleries. Microbial analyses were extended by analyses of chemical composition of water and solid phases and identification of arising secondary minerals. The microbial communities of the three main classes of microenvironments differed in almost every aspect. Among others, ecological partitioning of Acidithiobacillus ferrooxidans and the recently described A. ferrivorans was observed. Distinct types of communities inhabiting the water springs were detected. The more extreme springs (pH <3, conductivity >2 mS/cm) were inhabited by “Ferrovum” spp. and A. ferrivorans, whereas Gallionella sp. dominated the less extreme ones. A new role for gossan in the extremely acidic ecosystem is proposed. This zone was inhabited by a large diversity of neutrophilic heterotrophs that appeared to be continuously washed out to the acidic environments localized downstream. Five species originating in gossan were found in several acidic habitats. Here they can survive and probably serve as scavengers of dead biomass, particularly from chemoautotrophic growths. No such process has been described from acidic mine environments so far.

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Acknowledgments

This work was supported by Institutional Research Concept MSM0021620858 and the Czech Science Foundation project (P506/11/1317) and SVV (project SVV-2012-265 206). We thank Jan Černý for providing laboratory facilities; Jan Kotris (Diamo, RD Jeseník) for enabling prospection of the site; Václav Krištůfek for providing access to the Cryo-FESEM facility; Petr Drahota and Radek Procházka for XRD analyses; Linda Nedbalová for statistical analyses; Marie Mikšaníková and Tomáš Machač for graphic design of some illustrations and Naděžda Brdičková for language corrections. The authors also wish to thank anonymous reviewers for providing a thorough and thoughtful critique of the manuscript.

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  1. Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44, Prague, Czech Republic

    Lukáš Falteisek & Ivan Čepička

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  1. Lukáš Falteisek
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  2. Ivan Čepička
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Correspondence to Lukáš Falteisek.

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Communicated by M. da Costa.

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792_2012_488_MOESM1_ESM.jpg

Fig. S1 Axonometric map of the Zlaté Hory-south deposit. Only mine galleries lying between 538 and 735 m a.s.l. are shown. Most mining chambers, sublevel galleries and chimneys were omitted. (JPEG 339 kb)

792_2012_488_MOESM2_ESM.jpg

Fig. S2. Typical in situ appearance of bacterial growths and associated secondary mineral accumulations. Bar = 10 cm in all images a. Partially encrusted gelatinous bacterial growth typical for water springs with pH about 2,7; sample ZH7/7a. b. Hard ferrous stalactites growing in water spring with pH slightly higher than 3; the longest stalactite was sampled as ZH10. c, d. Another field evidence of differences between growths in water springs with pH lower (c) or greater (d) than 3. Growths were found in outfalls of two ore passes filled by ore for the last 20 years. e. Hard and pendulous soda straw stalactites at a weak seepage in the roof of the mine gallery. f. A field evidence of the sorption of iron oxides on the Al- and Si-rich secondary minerals in gossan. The color of the wall crust changes from red-brown to blue due to the decreased concentration of iron in water flowing over the crust. g. Bacterial streamers in an extremely acidic and moderately mineralized water stream; sample ZH14. h. Various types of secondary mineral sediments in the mine chimney, probably corresponding to different geochemical processes occurring in the proximity of the gossan-oxidation zone boundary. Positions of sampling sites ZH16/16a, 16b and 19 are marked. Real width ca. 2.5 m. (JPEG 1166 kb)

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Fig. S3. Results of phylogenetic analyses of the SSU rDNA sequences of Bacteria (excluding Proteobacteria) (JPEG 867 kb)

Fig. S4. Results of phylogenetic analyses of the SSU rDNA sequences of Proteobacteria (JPEG 561 kb)

Fig. S5. Results of phylogenetic analyses of the SSU rDNA sequences of Archaea (JPEG 399 kb)

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Fig. S6. Results of phylogenetic analyses of the SSU rDNA sequences of mitochondria. The trees were constructed by the maximum likelihood method under GTRGAMMAI model. Sequences from the present study are shown in bold. Samples were numbered sequentially as taken, multiple samples from the same place were indexed a, b, etc. The acronym UB stands for “uncultured bacterium”, UA “uncultured archeon”. Bootstrap values are shown for branches with bootstrap higher than 50 %. (JPEG 250 kb)

792_2012_488_MOESM7_ESM.doc

Table S1. A basic taxonomic and ecological characterization of microbial species from Zlaté Hory deposit. pH – pH requirements: A – acidophiles, N – neutrophiles tr – trophy: A – chemolithoautotroph, H – heterotroph, F – facultative autotroph Fe, S, N: R – reduce, O – oxidize, F - fixate. O – oxygen requirements: A – aerobic, F – facultatively anaerobic, M – microaerophilic, N – anaerobic. NA – no characterized isolate or clone was found 1 One or two representatives were selected for each species from each sampling site (DOC 436 kb)

792_2012_488_MOESM8_ESM.doc

Table S2. The elementary composition of sampled materials determined by SEM-EDS. All proportions of elements are in atomic % and converted to the sum of 100%. organic – bulk of presumably organic material; schw. – schwertmannite; area – average composition of an area of tens of micrometres in diameter; O calc. – calculated ideal content of oxygen in oxides of all elements (DOC 63 kb)

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Falteisek, L., Čepička, I. Microbiology of diverse acidic and non-acidic microhabitats within a sulfidic ore mine. Extremophiles 16, 911–922 (2012). https://doi.org/10.1007/s00792-012-0488-2

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