A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Area of Science:

• Microbiology
• Space Science
• Planetary Protection

Background:

• Spacecraft clean rooms, like those at NASA's Jet Propulsion Laboratory (JPL) Space Assembly Facility (SAF), undergo rigorous cleaning but are not sterile.
• These environments select for microorganisms with tolerance to cleaning methods, posing potential risks for exoplanetary research and human health.
• Current methods for identifying microbial contamination in clean rooms lack standardization and struggle to detect low-abundance organisms.

Purpose of the Study:

• To develop and implement a comprehensive metagenomic framework for characterizing microorganisms in cleanroom environments relevant to planetary protection.
• To identify microbes with traits potentially enabling survival during spaceflight and assess their risk.
• To establish a standardized workflow for analyzing microbial contamination in spaceflight hardware.

Main Methods:

• Developed a metagenomic framework applicable to various cleanroom classifications (ISO-5 to ISO-8.5) and sample types (surfaces, filters, vacuum debris).
• Sequenced and analyzed 51 metagenomic samples from SAF clean rooms to identify microbes with spaceflight-survival potential.
• Conducted auxiliary testing to ensure the repeatability and validity of the developed analytical techniques.

Main Results:

• Identified microbes in JPL clean rooms possessing traits advantageous for spaceflight, including psychrophilia, biofilm formation, spore-forming capacity, radiation resistance, and desiccation resistance.
• Found that higher-standard cleanrooms (ISO-5) exhibited lower microbial diversity but still contained a measurable microbial load.
• The developed framework successfully characterized microbial communities and identified potentially problematic organisms for space missions.

Conclusions:

• Quantifying microbial thresholds and detecting resilient organisms are vital for achieving Planetary Protection goals.
• The findings provide a biological baseline for cleanroom facilities and inform future space mission planning.
• A standardized metagenomic approach is essential for robust microbial contamination assessment in spaceflight hardware.