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Applied and Environmental Microbiology, October 2009, p. 6559-6567, Vol. 75, No. 20
0099-2240/09/$08.00+0     doi:10.1128/AEM.01073-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Comprehensive Census of Bacteria in Clean Rooms by Using DNA Microarray and Cloning Methods ^,

Myron T. La Duc,^1, Shariff Osman,^2, Parag Vaishampayan,¹ Yvette Piceno,² Gary Andersen,² J. A. Spry,¹ and Kasthuri Venkateswaran^1*

Biotechnology and Planetary Protection Group, National Aeronautics and Space Administration Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109,¹ Lawrence Berkeley National Laboratory, Berkeley, California 85721²

Received 11 May 2009/ Accepted 16 August 2009

A census of clean room surface-associated bacterial populations was derived from the results of both the cloning and sequencing of 16S rRNA genes and DNA microarray (PhyloChip) analyses. Samples from the Lockheed Martin Aeronautics Multiple Testing Facility (LMA-MTF), the Kennedy Space Center Payload Hazard and Servicing Facility (KSC-PHSF), and the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) clean rooms were collected during the various assembly phases of the Phoenix and Mars Science Laboratory (MSL) spacecraft. Clone library-derived analyses detected a larger bacterial diversity prior to the arrival of spacecraft hardware in these clean room facilities. PhyloChip results were in agreement with this trend but also unveiled the presence of anywhere from 9- to 70-fold more bacterial taxa than cloning approaches. Among the facilities sampled, the JPL-SAF (MSL mission) housed a significantly less diverse bacterial population than either the LMA-MTF or KSC-PHSF (Phoenix mission). Bacterial taxa known to thrive in arid conditions were frequently detected in MSL-associated JPL-SAF samples, whereas proteobacterial lineages dominated Phoenix-associated KSC-PHSF samples. Comprehensive bacterial censuses, such as that reported here, will help space-faring nations preemptively identify contaminant biomatter that may compromise extraterrestrial life detection experiments. The robust nature and high sensitivity of DNA microarray technologies should prove beneficial to a wide range of scientific, electronic, homeland security, medical, and pharmaceutical applications and to any other ventures with a vested interest in monitoring and controlling contamination in exceptionally clean environments.

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* Corresponding author. Mailing address: Biotechnology and Planetary Protection, NASA Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 89, Oak Grove Dr., Pasadena, CA 91109. Phone: (818) 393-1481. Fax: (818) 393-4176. E-mail: kjvenkat{at}jpl.nasa.gov

Published ahead of print on 21 August 2009.

Supplemental material for this article may be found at http://aem.asm.org/.

M.T.L.D. and S.O. contributed equally to this work.

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Applied and Environmental Microbiology, October 2009, p. 6559-6567, Vol. 75, No. 20
0099-2240/09/$08.00+0     doi:10.1128/AEM.01073-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.