Abstract
NASA planetary protection (PP) requires an assessment of the biological contamination of the potential microbial burden on spacecraft destined to explore planetary bodies that may harbor signs of life, like Mars and Europa. To help meet these goals, the performance of multiple metagenomic pipelines were compared and assessed for their ability to detect microbial diversity of a low-biomass clean room environment used to build spacecraft destined to these planetary bodies. Four vendors were chosen to implement their own metagenomic analysis pipeline on the shotgun sequences retrieved from environmental surfaces in the relevant environments at NASA’s Jet Propulsion Laboratory. None of the vendors showed the same microbial profile patterns when analyzing same raw dataset since each vendor used different pipelines, which begs the question of the validity of a single pipeline to be recommended for future NASA missions. All four vendors detected species of interest, including spore-forming and extremotolerant bacteria, that have the potential to hitch-hike on spacecraft and contaminate the planetary bodies explored. Some vendors demonstrated through functional analysis of the metagenomes that the molecular mechanisms for spore-formation and extremotolerance were represented in the data. However, relative abundances of these microorganisms varied drastically between vendor analyses, questioning the ability of these pipelines to quantify the number of PP-relevant microorganisms on a spacecraft surface. Metagenomics offers tantalizing access to the genetic and functional potential of a microbial community that may offer NASA a viable method for microbial burden assays for planetary protection purposes. However, future development of technologies such as streamlining the processing of shotgun metagenome sequence data, long read sequencing, and all-inclusive larger curated and annotated microbial genome databases will be required to validate and translate relative abundances into an actionable assessment of PP-related microbes of interest. Additionally, the future development of machine learning and artificial intelligence techniques could help enhance the quality of these metagenomic analyses by providing more accurate identification of the genetic and functional potential of a microbial community.
Highlights
Planetary protection (PP) requires a periodic assessment of the potential biological contamination for microbial burden of space flight hardware destined to or nearby planetary bodies that may or may not have harbored signs of life such as Mars or the Icy Worlds of the outer solar system (COSPAR, 2011)
Concerns regarding the inability of the NASA standard assay (NSA) culture method to detect all microorganisms in a sample has led NASA to look toward state-of-the art molecular methods like shotgun metagenomics to detect a wider range of taxa on spacecraft and associated environments
All four vendors used in this study identified taxa of PP concern in the Jet Propulsion Laboratory (JPL) Spacecraft Assembly Facility (SAF) environment where spacecraft are built, including Acidobacteria, Acinetobacter, Anoxybacillus, Bacillus, Brevundimonas, and Caulobacteraceae, demonstrating that modern metagenomic approaches and computational biology can detect these organisms of concern, unlike NSA culture methods
Summary
Planetary protection (PP) requires a periodic assessment of the potential biological contamination for microbial burden of space flight hardware destined to or nearby planetary bodies that may or may not have harbored signs of life such as Mars or the Icy Worlds of the outer solar system (COSPAR, 2011). Space hardware exploring the possibility of life on a planetary body of interest, such as recent missions to Mars, are required to be cleaned to have less than an average of 300 spores/m2 on spacecraft surfaces and less than 5 × 105 spores at launch (Benardini et al, 2014) For future missions, such as Mars Sample Return, in addition to limiting outbound contamination, the science community has deemed it important to collect an Earth-based assessment of the potential biological and organic contamination that the hardware could have experienced as part of the hardware integration and test operations (Beaty et al, 2018). Heat tolerant microorganisms (80◦C; 15 min) that can grow aerobically in a nutrient rich Tryptic Soy Agar (TSA) medium, incubated at 32◦C, for 72 h are captured by this NSA measurement, but slow growing microorganisms that (i) prefer cooler or hotter temperatures, (ii) are obligate anaerobes, (iii) or have dietary requirements not met by TSA may not be detected by this NSA method
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