Archaea in artificial environments: their presence in global spacecraft clean rooms and impact on planetary protection

Abstract

The presence and role of Archaea in artificial, human-controlled environments is still unclear. The search for Archaea has been focused on natural biotopes where they have been found in overwhelming numbers, and with amazing properties. However, they are considered as one of the major group of microorganisms that might be able to survive a space flight, or even to thrive on other planets. Although still concentrating on aerobic, bacterial spores as a proxy for spacecraft cleanliness, space agencies are beginning to consider Archaea as a possible contamination source that could affect future searches for life on other planets. This study reports on the discovery of archaeal 16S rRNA gene signatures not only in US American spacecraft assembly clean rooms but also in facilities in Europe and South America. Molecular methods revealed the presence of Crenarchaeota in all clean rooms sampled, while signatures derived from methanogens and a halophile appeared only sporadically. Although no Archaeon was successfully enriched in our multiassay cultivation approach thus far, samples from a European clean room revealed positive archaeal fluorescence in situ hybridization (FISH) signals of rod-shaped microorganisms, representing the first visualization of Archaea in clean room environments. The molecular and visual detection of Archaea was supported by the first quantitative PCR studies of clean rooms, estimating the overall quantity of Archaea therein. The significant presence of Archaea in these extreme environments in distinct geographical locations suggests a larger role for these microorganisms not only in natural biotopes, but also in human controlled and rigorously cleaned environments.

Figure 1

Phylogenetic tree, showing selected archaeal 16S rRNA genes from US American, European and South American spacecraft-associated clean rooms. The tree was calculated on the basis of the maximum likelihood methodology, implemented in the ARB software package (Ludwig et al., 2004). Sequences obtained from this study are shown in bold and highlighted (gray background). Sequences from previous studies are shown with gray background. Abbreviations: FR, Friedrichshafen; ES, ESTEC; KO, Kourou; SAF, spacecraft assembly facility at the Jet Propulsion Laboratory (Pasadena, CA, USA); JSC, Johnson Space Center (Houston, TX, USA).

Figure 2

Fluorescence in situ hybridization (FISH) of an ESTEC clean room sample, showing a rod shaped microorganism stained with archaeal probes. (a) Dapi stain. (b) Same section. Rod shows a positive archaeal signal, staining with an archaeal probe mixture (rhodamine green labeled). Bar: 10 μm. No signal was obtained with bacteria-specific probe mix staining in parallel (Cy3 labeled, not shown).