Field deployable automated nucleic acid extraction system enables rapid on-site measurement of microbial diversity of Yellowstone National Park hot springs

Abstract

Background: Microbial diversity estimation relies heavily on the extraction of nucleic acids from complex sample matrixes, regardless of the location of the laboratory used to recover the DNA, including those on Earth or in space. Nucleic acid sample preparation steps are labor intensive and require the effective lysis of cells and recovery of pure inhibitor free purification prior to downstream applications. An automated system is desirable for field deployment because easy of use and autonomous rapid results. This extends to use in remote filed locations by NASA for the in situ measurements of life. The goal of this study was to setup a field-deployable lab in a remote setting with limited resources and demonstrate the ability to process and sequence nucleic acid samples on-site. Microbial mat and sediment samples were collected from several hot springs in Yellowstone National Park (YNP), targeting the Five Sister Springs (FSS), spring LNN010, and Octopus Spring (OS). Samples were processed on site and analyzed for microbial diversity using the field-deployable lab instrument. Results: Microbial diversity measured with both the Illumina (short reads) and Oxford Nanopore Technology (ONT; long reads) sequencing systems was highly similar. In general, for both the FSS and OS hot spring sites, bacteria (>90%) dominated over archaea (<10%). Metagenomic results were binned to existing databases such that the taxonomic ID represents the closest known organism with a sequenced genome. With this caveat the presence of, the most common archaeal community member in both the mat and sediment was related to Candidatus Caldiarchaeum subterraneum. Among the bacterial members, Roseiflexus sp. RS-1 was found to be highly abundant in the mat environment, as already reported. Notably, however, organisms related to Bacterium HR17 was abundant several FSS/OS mat samples. The detection of this novel bacterial community member warrants additional research. Conclusion: This is the first study to deploy an automated nucleic acid extraction system in YNP) to rapidly (~8 to 9 hrs) measure the environmental microbiome of hot springs. The demonstration of a field deployable system for nucleic acids extraction from complex materials (mats and sediments) highlights its utility not only in extreme environments on Earth but its potential benefit to NASA and deployment in space, once performance under microgravity is refined. The benefits of this new field-deployable lab include sample processing (extracting nucleic acids), shotgun metagenome library preparation, and sequencing utilizing the space-tested Nanopore sequencing platform.