Microbial Ecology

, Volume 60, Issue 3, pp 539–550 | Cite as

Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota

  • Gurdeep Rastogi
  • Shariff Osman
  • Ravi Kukkadapu
  • Mark Engelhard
  • Parag A. Vaishampayan
  • Gary L. Andersen
  • Rajesh K. Sani
Soil Microbiology


A microbial census on deep biosphere (1.34 km depth) microbial communities was performed in two soil samples collected from the Ross and number 6 Winze sites of the former Homestake gold mine, Lead, South Dakota using high-density 16S microarrays (PhyloChip). Soil mineralogical characterization was carried out using X-ray diffraction, X-ray photoelectron, and Mössbauer spectroscopic techniques which demonstrated silicates and iron minerals (phyllosilicates and clays) in both samples. Microarray data revealed extensive bacterial diversity in soils and detected the largest number of taxa in Proteobacteria phylum followed by Firmicutes and Actinobacteria. The archael communities in the deep gold mine environments were less diverse and belonged to phyla Euryarchaeota and Crenarchaeota. Both the samples showed remarkable similarities in microbial communities (1,360 common OTUs) despite distinct geochemical characteristics. Fifty-seven phylotypes could not be classified even at phylum level representing a hitherto unidentified diversity in deep biosphere. PhyloChip data also suggested considerable metabolic diversity by capturing several physiological groups such as sulfur-oxidizer, ammonia-oxidizers, iron-oxidizers, methane-oxidizers, and sulfate-reducers in both samples. High-density microarrays revealed the greatest prokaryotic diversity ever reported from deep subsurface habitat of gold mines.



This research was funded by the South Dakota Board of Regents Competitive Research Grant (Award No. SDBOR/SDSMT 2010-09-05). Powder XRD, XPS, and Mössbauer spectroscopy measurements were conducted using EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory. We would like to acknowledge Colleen Russell (PNNL) for her help in XRD measurements and Mössbauer sample preparations. Authors appreciate the assistance provided by Dr. L. D. Stetler of Department of Geology and Geological Engineering, SDSM&T in sample collection. We also would like to thank the anonymous reviewers whose critiques were instrumental in improving the quality of manuscript.

Supplementary material

248_2010_9657_MOESM1_ESM.pdf (72 kb)
Supplementary Class Table 1Bacterial and archael classes detected in the Ross and Winze sites using PhyloChip analyses. A total of 1,511 and 1,678 OTUs found at the Ross and Winze sites, respectively, were distributed in 49 and 51 classes. (PDF 72 kb)
248_2010_9657_MOESM2_ESM.pdf (87 kb)
Supplementary Order Table 2Bacterial and archael orders detected in the Ross and Winze sites using PhyloChip analyses. A total of 1,511 and 1,678 OTUs found at the Ross and Winze sites, respectively, were distributed in 91 and 97 orders. (PDF 86 kb)
248_2010_9657_MOESM3_ESM.pdf (104 kb)
Supplementary Family Table 3Bacterial and archael families detected in the Ross and Winze sites using PhyloChip analyses. A total of 1,511 and 1,678 OTUs found at the Ross and Winze sites, respectively, were distributed in 149 and 154 families. (PDF 104 kb)
248_2010_9657_MOESM4_ESM.pdf (189 kb)
Supplementary Genera Table 4Bacterial and archael genera retrieved on PhyloChips from Ross and Winze sites. (PDF 189 kb)


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Gurdeep Rastogi
    • 1
    • 5
  • Shariff Osman
    • 2
  • Ravi Kukkadapu
    • 3
  • Mark Engelhard
    • 3
  • Parag A. Vaishampayan
    • 4
  • Gary L. Andersen
    • 2
  • Rajesh K. Sani
    • 1
  1. 1.Department of Chemical and Biological EngineeringSouth Dakota School of Mines and TechnologyRapid CityUSA
  2. 2.Ecology Department, Earth Sciences DivisionLawrence Berkeley National LaboratoryBerkeleyUSA
  3. 3.WR Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandUSA
  4. 4.California Institute of TechnologyJet Propulsion LaboratoryPasadenaUSA
  5. 5.Department of Plant PathologyUniversity of CaliforniaDavisUSA

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