DNA/RNA Preservation in Glacial Snow and Ice Samples

• Published in: Frontiers in Microbiology
• Main Authors: Christopher B. Trivedi, Christoph Keuschnig, Catherine Larose, Daniel Vasconcelos Rissi, Rey Mourot, James A. Bradley, Matthias Winkel, Liane G. Benning
• Format: Article in Journal/Newspaper
• Language: English
• Published: Frontiers Media S.A. 2022
• Subjects: DNA/RNA preservation; glacial microbiology; metagenomics; metatranscriptomics; RNAlater; Zymo DNA/RNA Shield; Microbiology; QR1-502; Iceland
• Online Access: https://doi.org/10.3389/fmicb.2022.894893; https://doaj.org/article/955d62e9434e410681202a8aae3b5ba1

The preservation of nucleic acids for high-throughput sequencing is an ongoing challenge for field scientists. In particular, samples that are low biomass, or that have to be collected and preserved in logistically challenging environments (such as remote sites or during long sampling campaigns) can pose exceptional difficulties. With this work, we compare and assess the effectiveness of three preservation methods for DNA and RNA extracted from microbial communities of glacial snow and ice samples. Snow and ice samples were melted and filtered upon collection in Iceland, and filters were preserved using: (i) liquid nitrogen flash freezing, (ii) storage in RNAlater, or (iii) storage in Zymo DNA/RNA Shield. Comparative statistics covering nucleic acid recovery, sequencing library preparation, genome assembly, and taxonomic diversity were used to determine best practices for the preservation of DNA and RNA samples from these environments. Our results reveal that microbial community composition based on DNA was comparable at the class level across preservation types. Based on extracted RNA, the taxonomic composition of the active community was primarily driven by the filtered sample volume (i.e., biomass content). In low biomass samples (where <200 ml of sample volume was filtered) the taxonomic and functional signatures trend toward the composition of the control samples, while in samples where a larger volume (more biomass) was filtered our data showed comparable results independent of preservation type. Based on all comparisons our data suggests that flash freezing of filters containing low biomass is the preferred method for preserving DNA and RNA (notwithstanding the difficulties of accessing liquid nitrogen in remote glacial field sites). Generally, RNAlater and Zymo DNA/RNA Shield solutions work comparably well, especially for DNA from high biomass samples, but Zymo DNA/RNA Shield is favored due to its higher yield of preserved RNA. Biomass quantity from snow and ice samples appears to be the most ...