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

Autor: Zhong ZP; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.; Department of Microbiology, Ohio State University, Columbus, OH, USA.; Center of Microbiome Science, Ohio State University, Columbus, OH, USA., Tian F; Department of Microbiology, Ohio State University, Columbus, OH, USA.; Center of Microbiome Science, Ohio State University, Columbus, OH, USA., Roux S; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Gazitúa MC; Department of Microbiology, Ohio State University, Columbus, OH, USA., Solonenko NE; Department of Microbiology, Ohio State University, Columbus, OH, USA.; Center of Microbiome Science, Ohio State University, Columbus, OH, USA., Li YF; Department of Microbiology, Ohio State University, Columbus, OH, USA.; Center of Microbiome Science, Ohio State University, Columbus, OH, USA., Davis ME; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA., Van Etten JL; Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA., Mosley-Thompson E; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.; Center of Microbiome Science, Ohio State University, Columbus, OH, USA.; Department of Geography, Ohio State University, Columbus, OH, USA., Rich VI; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.; Department of Microbiology, Ohio State University, Columbus, OH, USA.; Center of Microbiome Science, Ohio State University, Columbus, OH, USA., Sullivan MB; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA. sullivan.948@osu.edu.; Department of Microbiology, Ohio State University, Columbus, OH, USA. sullivan.948@osu.edu.; Center of Microbiome Science, Ohio State University, Columbus, OH, USA. sullivan.948@osu.edu.; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA. sullivan.948@osu.edu., Thompson LG; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA. thompson.3@osu.edu.; Center of Microbiome Science, Ohio State University, Columbus, OH, USA. thompson.3@osu.edu.; School of Earth Sciences, Ohio State University, Columbus, OH, USA. thompson.3@osu.edu.
Jazyk: angličtina
Zdroj: Microbiome [Microbiome] 2021 Jul 20; Vol. 9 (1), pp. 160. Date of Electronic Publication: 2021 Jul 20.
DOI: 10.1186/s40168-021-01106-w
Abstrakt: 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 potentially facilitate nutrient acquisition for their hosts. Finally, given their possible importance to methane cycling in ice, we focused on Methylobacterium viruses by contextualizing our ice-observed viruses against 123 viromes and prophages extracted from 131 Methylobacterium genomes, revealing that the archived viruses might originate from soil or plants.
Conclusions: Together, these efforts further microbial and viral sampling procedures for glacier ice and provide a first window into viral communities and functions in ancient glacier environments. Such methods and datasets can potentially enable researchers to contextualize new discoveries and begin to incorporate glacier-ice microbes and their viruses relative to past and present climate change in geographically diverse regions globally. Video Abstract.
(© 2021. The Author(s).)
Databáze: MEDLINE
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