In situ imaging of microorganisms in geologic material

K. J. Tobin, Tullis C. Onstott, M. F. DeFlaun, F. S. Colwell, J. Fredrickson

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


In order to fully delineate the interactions of microorganisms with geological substrates, unequivocal identification of intact microbial cells within geologic samples is required without the disruption of either the rock texture or the relationship of the microorganisms to the mineral fabric. To achieve this objective we developed a protocol that enables the visualization of intact microbial cells in petrographic thin sections, avoids detaching the cells from their host mineral surfaces and avoids microbial contamination during the lapidary process. Propidium iodide and POPO-3, nucleic acid stains that specifically target double-stranded DNA and RNA were utilized for in situ visualization of cells in surface and subsurface basalts from northeastern Idaho. Additionally, examination of samples incubated with acetic acid-UL-14C via phosphor imagining facilitated the in situ visualization of 14C labeled biomass. Biomass observed was low (<107 cells/g). These observations indicate that the microbial distribution in these rocks exhibits a high degree of spatial heterogeneity at the sub-centimeter scale. Copyright (C) 1999 Elsevier Science B.V.

Original languageEnglish (US)
Pages (from-to)201-213
Number of pages13
JournalJournal of Microbiological Methods
Issue number3
StatePublished - Sep 1999

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Molecular Biology
  • Microbiology (medical)


  • Petrographic thin section
  • Phosphor imaging
  • Propidium iodide


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