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

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.

doi:10.1186/s40168-021-01106-w

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

Journal Article · Tue Jul 20 00:00:00 EDT 2021 · Microbiome

DOI:https://doi.org/10.1186/s40168-021-01106-w· OSTI ID:1813410

^[1]; Tian, Funing ^[1]; Roux, Simon ^[2]; Gazitúa, M. Consuelo ^[1]; Solonenko, Natalie E. ^[1]; Li, Yueh-Fen ^[1]; Davis, Mary E. ^[1]; Van Etten, James L. ^[3]; Mosley-Thompson, Ellen ^[1]; Rich, Virginia I. ^[1]; Sullivan, Matthew B. ^[1]; Thompson, Lonnie G. ^[1]

The Ohio State Univ., Columbus, OH (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Nebraska, Lincoln, NE (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Science Foundation (NSF)

Grant/Contract Number:: AC02-05CH11231; 1502919; 3790

OSTI ID:: 1813410

Journal Information:: Microbiome, Vol. 9, Issue 1; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 1 of Glacier ice archives nearly 15,000-year-old microbes and phages Zhong, Zhi-Ping; Tian, Funing; Roux, Simon https://doi.org/10.6084/m9.figshare.15020417 The current record is supplemented by this dataset	dataset	January 2021
Additional file 2 of Glacier ice archives nearly 15,000-year-old microbes and phages Zhong, Zhi-Ping; Tian, Funing; Roux, Simon https://doi.org/10.6084/m9.figshare.15020420.v1 The current record is supplemented by this text	text	January 2021
Additional file 2 of Glacier ice archives nearly 15,000-year-old microbes and phages Zhong, Zhi-Ping; Tian, Funing; Roux, Simon https://doi.org/10.6084/m9.figshare.15020420 The current record is supplemented by this text	text	January 2021

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

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