Microorganisms Genome Enrichment and Amplification Sequencing (MGEAS)

Recent evidence shows that the Space Assembly Facility (SAF) of Jet Propulsion Laboratory environments, such as floors and hardware surfaces, could harbor various microorganisms, and a comprehensive metagenomics framework to characterize organisms relevant to planetary protection is needed. Sequencing-based approaches, especially whole genome non-targeted metagenomics techniques, are preferred ways of microbial detection for planetary protection due to its fast turnaround time and ability to detect a broader spectrum of viable organisms. Current practices for microbe detection in low biomass samples generally do not fit well with NASA needs, due to high requirements in DNA concentration, small sample processing volumes, variability, and high predictive errors. In this project, we will tackle the problems through three modules (1) A sampling or filtration unit that process larger volumes of input solutions, (2) DNA preparations, enrichment, and amplifications followed by NGS sequencing, (3) Bioinformatics pipeline optimizations for error handling, assembly, and annotations, as well as integration with culture-based data for better risk modeling. The core technological contribution would be to validate or compare the use of two recent library preparation techniques 2bRAD-M and TruePrime MDA methods for microbiome diversity estimates. The technology is superior to 16S rRNA in the ability to detect a broader scope of microbes including virus, archaea, bacteria and fungi and other eukaryotes. This would be the first use of these technologies in JPL low biomass samples. The resulting microbe taxa estimates can guide risk-assessment modeling parameterization of planetary protection practices.