Data_Sheet_3_Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.XLSX
Microorganisms in glacier ice provide tens to hundreds of thousands of years archive for a changing climate and microbial responses to it. Analyzing ancient ice is impeded by technical issues, including limited ice, low biomass, and contamination. While many approaches have been evaluated and advanc...
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ftfrontimediafig:oai:figshare.com:article/6350546 2023-05-15T16:38:21+02:00 Data_Sheet_3_Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.XLSX Zhi-Ping Zhong Natalie E. Solonenko Maria C. Gazitúa Donald V. Kenny Ellen Mosley-Thompson Virginia I. Rich James L. Van Etten Lonnie G. Thompson Matthew B. Sullivan 2018-05-25T04:09:55Z https://doi.org/10.3389/fmicb.2018.01094.s003 https://figshare.com/articles/Data_Sheet_3_Clean_Low-Biomass_Procedures_and_Their_Application_to_Ancient_Ice_Core_Microorganisms_XLSX/6350546 unknown doi:10.3389/fmicb.2018.01094.s003 https://figshare.com/articles/Data_Sheet_3_Clean_Low-Biomass_Procedures_and_Their_Application_to_Ancient_Ice_Core_Microorganisms_XLSX/6350546 CC BY 4.0 CC-BY Microbiology Microbial Genetics Microbial Ecology Mycology clean low biomass in silico decontamination glacier ice microbial community Dataset 2018 ftfrontimediafig https://doi.org/10.3389/fmicb.2018.01094.s003 2018-05-30T22:57:37Z Microorganisms in glacier ice provide tens to hundreds of thousands of years archive for a changing climate and microbial responses to it. Analyzing ancient ice is impeded by technical issues, including limited ice, low biomass, and contamination. While many approaches have been evaluated and advanced to remove contaminants on ice core surfaces, few studies leverage modern sequencing to establish in silico decontamination protocols for glacier ice. Here we sought to apply such “clean” sampling techniques with in silico decontamination approaches used elsewhere to investigate microorganisms archived in ice at ∼41 (D41, ∼20,000 years) and ∼49 m (D49, ∼30,000 years) depth in an ice core (GS3) from the summit of the Guliya ice cap in the northwestern Tibetan Plateau. Four “background” controls were established – a co-processed sterile water artificial ice core, two air samples collected from the ice processing laboratories, and a blank, sterile water sample – and used to assess contaminant microbial diversity and abundances. Amplicon sequencing revealed 29 microbial genera in these controls, but quantitative PCR showed that the controls contained about 50–100-times less 16S DNA than the glacial ice samples. As in prior work, we interpreted these low-abundance taxa in controls as “contaminants” and proportionally removed them in silico from the GS3 ice amplicon data. Because of the low biomass in the controls, we also compared prokaryotic 16S DNA amplicons from pre-amplified (by re-conditioning PCR) and standard amplicon sequencing, and found the resulting microbial profiles to be repeatable and nearly identical. Ecologically, the contaminant-controlled ice microbial profiles revealed significantly different microorganisms across the two depths in the GS3 ice core, which is consistent with changing climate, as reported for other glacier ice samples. Many GS3 ice core genera, including Methylobacterium, Sphingomonas, Flavobacterium, Janthinobacterium, Polaromonas, and Rhodobacter, were also abundant in previously ... Dataset Ice cap ice core Frontiers: Figshare |
institution |
Open Polar |
collection |
Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Microbiology Microbial Genetics Microbial Ecology Mycology clean low biomass in silico decontamination glacier ice microbial community |
spellingShingle |
Microbiology Microbial Genetics Microbial Ecology Mycology clean low biomass in silico decontamination glacier ice microbial community Zhi-Ping Zhong Natalie E. Solonenko Maria C. Gazitúa Donald V. Kenny Ellen Mosley-Thompson Virginia I. Rich James L. Van Etten Lonnie G. Thompson Matthew B. Sullivan Data_Sheet_3_Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.XLSX |
topic_facet |
Microbiology Microbial Genetics Microbial Ecology Mycology clean low biomass in silico decontamination glacier ice microbial community |
description |
Microorganisms in glacier ice provide tens to hundreds of thousands of years archive for a changing climate and microbial responses to it. Analyzing ancient ice is impeded by technical issues, including limited ice, low biomass, and contamination. While many approaches have been evaluated and advanced to remove contaminants on ice core surfaces, few studies leverage modern sequencing to establish in silico decontamination protocols for glacier ice. Here we sought to apply such “clean” sampling techniques with in silico decontamination approaches used elsewhere to investigate microorganisms archived in ice at ∼41 (D41, ∼20,000 years) and ∼49 m (D49, ∼30,000 years) depth in an ice core (GS3) from the summit of the Guliya ice cap in the northwestern Tibetan Plateau. Four “background” controls were established – a co-processed sterile water artificial ice core, two air samples collected from the ice processing laboratories, and a blank, sterile water sample – and used to assess contaminant microbial diversity and abundances. Amplicon sequencing revealed 29 microbial genera in these controls, but quantitative PCR showed that the controls contained about 50–100-times less 16S DNA than the glacial ice samples. As in prior work, we interpreted these low-abundance taxa in controls as “contaminants” and proportionally removed them in silico from the GS3 ice amplicon data. Because of the low biomass in the controls, we also compared prokaryotic 16S DNA amplicons from pre-amplified (by re-conditioning PCR) and standard amplicon sequencing, and found the resulting microbial profiles to be repeatable and nearly identical. Ecologically, the contaminant-controlled ice microbial profiles revealed significantly different microorganisms across the two depths in the GS3 ice core, which is consistent with changing climate, as reported for other glacier ice samples. Many GS3 ice core genera, including Methylobacterium, Sphingomonas, Flavobacterium, Janthinobacterium, Polaromonas, and Rhodobacter, were also abundant in previously ... |
format |
Dataset |
author |
Zhi-Ping Zhong Natalie E. Solonenko Maria C. Gazitúa Donald V. Kenny Ellen Mosley-Thompson Virginia I. Rich James L. Van Etten Lonnie G. Thompson Matthew B. Sullivan |
author_facet |
Zhi-Ping Zhong Natalie E. Solonenko Maria C. Gazitúa Donald V. Kenny Ellen Mosley-Thompson Virginia I. Rich James L. Van Etten Lonnie G. Thompson Matthew B. Sullivan |
author_sort |
Zhi-Ping Zhong |
title |
Data_Sheet_3_Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.XLSX |
title_short |
Data_Sheet_3_Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.XLSX |
title_full |
Data_Sheet_3_Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.XLSX |
title_fullStr |
Data_Sheet_3_Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.XLSX |
title_full_unstemmed |
Data_Sheet_3_Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.XLSX |
title_sort |
data_sheet_3_clean low-biomass procedures and their application to ancient ice core microorganisms.xlsx |
publishDate |
2018 |
url |
https://doi.org/10.3389/fmicb.2018.01094.s003 https://figshare.com/articles/Data_Sheet_3_Clean_Low-Biomass_Procedures_and_Their_Application_to_Ancient_Ice_Core_Microorganisms_XLSX/6350546 |
genre |
Ice cap ice core |
genre_facet |
Ice cap ice core |
op_relation |
doi:10.3389/fmicb.2018.01094.s003 https://figshare.com/articles/Data_Sheet_3_Clean_Low-Biomass_Procedures_and_Their_Application_to_Ancient_Ice_Core_Microorganisms_XLSX/6350546 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmicb.2018.01094.s003 |
_version_ |
1766028633445498880 |