Glacier ice archives nearly 15,000-year-old microbes and phages

• Published in: Microbiome
• Main Authors: Zhong, Zhi-Ping, Tian, Funing, Roux, Simon, Gazitúa, M. Consuelo, Solonenko, Natalie E., Li, Yueh-Fen, Davis, Mary E., Van Etten, James L., Mosley-Thompson, Ellen, Rich, Virginia I., Sullivan, Matthew B., Thompson, Lonnie G.
• Format: Text
• Language: English
• Published: BioMed Central 2021
• Subjects: Research; ice core
• Online Access: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8290583/; http://www.ncbi.nlm.nih.gov/pubmed/34281625; https://doi.org/10.1186/s40168-021-01106-w

BACKGROUND: Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approaches, more challenging metagenomic approaches, which provide access to functional, genome-resolved information and viruses, are under-utilized, partly due to low biomass and potential contamination. RESULTS: We expand existing clean sampling procedures using controlled artificial ice-core experiments and adapted previously established low-biomass metagenomic approaches to study glacier-ice viruses. Controlled sampling experiments drastically reduced mock contaminants including bacteria, viruses, and free DNA to background levels. Amplicon sequencing from eight depths of two Tibetan Plateau ice cores revealed common glacier-ice lineages including Janthinobacterium, Polaromonas, Herminiimonas, Flavobacterium, Sphingomonas, and Methylobacterium as the dominant genera, while microbial communities were significantly different between two ice cores, associating with different climate conditions during deposition. Separately, ~355- and ~14,400-year-old ice were subject to viral enrichment and low-input quantitative sequencing, yielding genomic sequences for 33 vOTUs. These were virtually all unique to this study, representing 28 novel genera and not a single species shared with 225 environmentally diverse viromes. Further, 42.4% of the vOTUs were identifiable temperate, which is significantly higher than that in gut, soil, and marine viromes, and indicates that temperate phages are possibly favored in glacier-ice environments before being frozen. In silico host predictions linked 18 vOTUs to co-occurring abundant bacteria (Methylobacterium, Sphingomonas, and Janthinobacterium), indicating that these phages infected ice-abundant bacterial groups before being archived. Functional genome annotation revealed four virus-encoded auxiliary metabolic genes, particularly two motility genes suggest viruses ...