Glacier ice archives nearly 15,000-year-old microbes and phages
Abstract 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 fun...
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ftdoajarticles:oai:doaj.org/article:a9617b6e1de14164b9d93705305848b3 2023-05-15T16:38:21+02:00 Glacier ice archives nearly 15,000-year-old microbes and phages Zhi-Ping Zhong Funing Tian Simon Roux M. Consuelo Gazitúa Natalie E. Solonenko Yueh-Fen Li Mary E. Davis James L. Van Etten Ellen Mosley-Thompson Virginia I. Rich Matthew B. Sullivan Lonnie G. Thompson 2021-07-01T00:00:00Z https://doi.org/10.1186/s40168-021-01106-w https://doaj.org/article/a9617b6e1de14164b9d93705305848b3 EN eng BMC https://doi.org/10.1186/s40168-021-01106-w https://doaj.org/toc/2049-2618 doi:10.1186/s40168-021-01106-w 2049-2618 https://doaj.org/article/a9617b6e1de14164b9d93705305848b3 Microbiome, Vol 9, Iss 1, Pp 1-23 (2021) Guliya ice cap Mountain glacier ice Surface decontamination Ice microbes Ice viruses Methylobacterium Microbial ecology QR100-130 article 2021 ftdoajarticles https://doi.org/10.1186/s40168-021-01106-w 2022-12-31T06:40:48Z Abstract 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 ... Article in Journal/Newspaper Ice cap ice core Directory of Open Access Journals: DOAJ Articles Microbiome 9 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Guliya ice cap Mountain glacier ice Surface decontamination Ice microbes Ice viruses Methylobacterium Microbial ecology QR100-130 |
spellingShingle |
Guliya ice cap Mountain glacier ice Surface decontamination Ice microbes Ice viruses Methylobacterium Microbial ecology QR100-130 Zhi-Ping Zhong Funing Tian Simon Roux M. Consuelo Gazitúa Natalie E. Solonenko Yueh-Fen Li Mary E. Davis James L. Van Etten Ellen Mosley-Thompson Virginia I. Rich Matthew B. Sullivan Lonnie G. Thompson Glacier ice archives nearly 15,000-year-old microbes and phages |
topic_facet |
Guliya ice cap Mountain glacier ice Surface decontamination Ice microbes Ice viruses Methylobacterium Microbial ecology QR100-130 |
description |
Abstract 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 ... |
format |
Article in Journal/Newspaper |
author |
Zhi-Ping Zhong Funing Tian Simon Roux M. Consuelo Gazitúa Natalie E. Solonenko Yueh-Fen Li Mary E. Davis James L. Van Etten Ellen Mosley-Thompson Virginia I. Rich Matthew B. Sullivan Lonnie G. Thompson |
author_facet |
Zhi-Ping Zhong Funing Tian Simon Roux M. Consuelo Gazitúa Natalie E. Solonenko Yueh-Fen Li Mary E. Davis James L. Van Etten Ellen Mosley-Thompson Virginia I. Rich Matthew B. Sullivan Lonnie G. Thompson |
author_sort |
Zhi-Ping Zhong |
title |
Glacier ice archives nearly 15,000-year-old microbes and phages |
title_short |
Glacier ice archives nearly 15,000-year-old microbes and phages |
title_full |
Glacier ice archives nearly 15,000-year-old microbes and phages |
title_fullStr |
Glacier ice archives nearly 15,000-year-old microbes and phages |
title_full_unstemmed |
Glacier ice archives nearly 15,000-year-old microbes and phages |
title_sort |
glacier ice archives nearly 15,000-year-old microbes and phages |
publisher |
BMC |
publishDate |
2021 |
url |
https://doi.org/10.1186/s40168-021-01106-w https://doaj.org/article/a9617b6e1de14164b9d93705305848b3 |
genre |
Ice cap ice core |
genre_facet |
Ice cap ice core |
op_source |
Microbiome, Vol 9, Iss 1, Pp 1-23 (2021) |
op_relation |
https://doi.org/10.1186/s40168-021-01106-w https://doaj.org/toc/2049-2618 doi:10.1186/s40168-021-01106-w 2049-2618 https://doaj.org/article/a9617b6e1de14164b9d93705305848b3 |
op_doi |
https://doi.org/10.1186/s40168-021-01106-w |
container_title |
Microbiome |
container_volume |
9 |
container_issue |
1 |
_version_ |
1766028618711957504 |