Applied Microbiology and Biotechnology

, Volume 98, Issue 14, pp 6453–6466 | Cite as

International Space Station environmental microbiome — microbial inventories of ISS filter debris

  • Kasthuri VenkateswaranEmail author
  • Parag Vaishampayan
  • Jessica Cisneros
  • Duane L. Pierson
  • Scott O. Rogers
  • Jay Perry
Environmental biotechnology


Despite an expanding array of molecular approaches for detecting microorganisms in a given sample, rapid and robust means of assessing the differential viability of the microbial cells, as a function of phylogenetic lineage, remain elusive. A propidium monoazide (PMA) treatment coupled with downstream quantitative polymerase chain reaction (qPCR) and pyrosequencing analyses was carried out to better understand the frequency, diversity, and distribution of viable microorganisms associated with debris collected from the crew quarters of the International Space Station (ISS). The cultured bacterial counts were more in the ISS samples than cultured fungal population. The rapid molecular analyses targeted to estimate viable population exhibited 5-fold increase in bacterial (qPCR-PMA assay) and 25-fold increase in microbial (adenosine triphosphate assay) burden than the cultured bacterial population. The ribosomal nucleic acid-based identification of cultivated strains revealed the presence of only four to eight bacterial species in the ISS samples, however, the viable bacterial diversity detected by the PMA-pyrosequencing method was far more diverse (12 to 23 bacterial taxa) with the majority consisting of members of actinobacterial genera (Propionibacterium, Corynebacterium) and Staphylococcus. Sample fractions not treated with PMA (inclusive of both live and dead cells) yielded a great abundance of highly diverse bacterial (94 to 118 taxa) and fungal lineages (41 taxa). Even though deep sequencing capability of the molecular analysis widened the understanding about the microbial diversity, the cultivation assay also proved to be essential since some of the spore-forming microorganisms were detected only by the culture-based method. Presented here are the findings of the first comprehensive effort to assess the viability of microbial cells associated with ISS surfaces, and correlate differential viability with phylogenetic affiliation.


International Space Station Vacuum cleaner debris Pyrosequencing Microbial diversity Closed habitat PMA ATP qPCR 



Part of the research described in this publication was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with NASA. This research was funded by a 2012 Space Biology NNH12ZTT001N grant # 19-12829-26 under Task Order NNN13D111T award to K. Venkateswaran. J. Cisneros, a Louis Stokes Alliance for Minority Participation – Bridge to the Doctorate (LSAMP-BD) fellow, was supported by the LSAMP-BD (Cohort X) program (National Science Foundation grant # HRD-1246662). The authors gratefully acknowledge ISS Expedition 31 crew for sample collection and D. Eisenman, JPL for effective coordination of sample procurement. We would also like to thank JSC Microbiology Laboratory members in performing culture-based analysis and Y. Sun (Research and Testing Laboratory) for trouble shooting discussion on the pyrosequencing method. The authors are indebted to M. Jones and C. Guethe from JPL for critical review of this manuscript. © 2014 California Institute of Technology. Government sponsorship acknowledged.

Supplementary material

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Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2014

Authors and Affiliations

  • Kasthuri Venkateswaran
    • 1
    Email author
  • Parag Vaishampayan
    • 1
  • Jessica Cisneros
    • 1
  • Duane L. Pierson
    • 2
  • Scott O. Rogers
    • 3
  • Jay Perry
    • 4
  1. 1.Biotechnology and Planetary Protection Group, Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaUSA
  2. 2.Johnson Space CenterHoustonUSA
  3. 3.Department of Biological SciencesBowling Green State UniversityBowling GreenUSA
  4. 4.Marshall Space Flight CenterHuntsvilleUSA

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