Abstract
BackgroundGlacier 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.ResultsWe 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.ConclusionsTogether, 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.8eoz6b1Gq7e8M2dM_SBXdyVideo
Highlights
Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change
Even with extremely sensitive method, contaminant lambda phage DNA was not detected in the resulting inner ice (Fig. 1c). These results indicate that the decontamination procedure removed contaminants such as bacteria, viruses, and free DNA from the surface ice and left clean inner ice that was free of detectable contaminants for microbial and viral analysis
Microbial profiles potentially differ between the PS and summit core 3 (S3) ice cores Once a clean decontamination procedure was established with both artificial ice cores and authentic ice core sections, we investigated the microbial and viral communities of two ice cores from Guliya ice cap (Fig. 2a, b, c, d)
Summary
Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. The first reports of microbes in glacier ice appeared early in the twentieth century [1] but were largely ignored until the 1980s when microbes were investigated in the deep Vostok ice core [2] and subsequent studies near the end of the 1990s (reviewed in [3,4,5,6]). These studies revealed microbial cell concentrations of 102 to 104 cells ml−1 in most glacier-ice samples [4], which are several orders of magnitude lower than other environments such as seawater or soils [7]. There is currently no direct evidence for in situ activity, some studies have hinted at the possibility of microbial activity in frozen glacier ice based on the detection of some excess gases (e.g., CO2, CH4, and N2O), which may be produced by postdepositional microbial metabolism [24,25,26]
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