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Title: Metagenomic analysis of basal ice from an Alaskan glacier

Abstract

Background Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on the microbial community structures and their metabolic potential is very limited. Here, we provide insights into the microbial lifestyle present at the base of the Matanuska Glacier, Alaska. Results DNA and RNA were extracted from samples of the Matanuska Glacier basal ice. Using Illumina MiSeq and HiSeq sequencing, we investigated the microbial diversity with the metagenomic shotgun reads and 16S ribosomal RNA data. We further assembled 9 partial and draft bacterial genomes from the metagenomic assembly, and identified key metabolic pathways such as sulfur oxidation and nitrification. Collectively, our analyses suggest a prevalence of lithotrophic and heterotrophic metabolisms in the subglacial microbiome. Conclusion Our results present the first metagenomic assembly and bacterial draft genomes for a subglacial environment. These results extend our understanding of the chemical and biological processes in subglacial environments critically influenced by global climate change.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [4]
+ Show Author Affiliations
  1. Tsinghua Univ., Beijing (China). School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Lab. of Bioinformatics
  2. Texas A & M Univ., College Station, TX (United States). College of Geosciences
  3. Argonne National Lab. (ANL), Argonne, IL (United States). Biosciences Division; Univ. of Chicago, IL (United States). Microbiome Center, Dept. of Surgery
  4. Tsinghua Univ., Beijing (China). School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Lab. of Bioinformatics
  5. Argonne National Lab. (ANL), Argonne, IL (United States). Biosciences Division; Univ. of Chicago, IL (United States). Microbiome Center, Dept. of Surgery; Marine Biological Lab., Woods Hold, MA (United States). Microbiome Center
  6. Univ. of Florida, Gainesville, FL (United States). Dept. of Microbiology and Cell Science, Biodiversity Inst.
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; Ministry of Science and Technology of the People's Republic of China; National Natural Science Foundation of China (NNSFC); National Aeronautic and Space Administration (NASA)
OSTI Identifier:
1493906
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Microbiome
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2049-2618
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 58 GEOSCIENCES; 54 ENVIRONMENTAL SCIENCES; Microbiome; Metagenomics; Glacier; Basal ice layer

Citation Formats

Kayani, Masood ur Rehman, Doyle, Shawn M., Sangwan, Naseer, Wang, Guanqun, Gilbert, Jack A., Christner, Brent C., and Zhu, Ting F. Metagenomic analysis of basal ice from an Alaskan glacier. United States: N. p., 2018. Web. doi:10.1186/s40168-018-0505-5.
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Kayani, Masood ur Rehman, Doyle, Shawn M., Sangwan, Naseer, Wang, Guanqun, Gilbert, Jack A., Christner, Brent C., & Zhu, Ting F. Metagenomic analysis of basal ice from an Alaskan glacier. United States. doi:https://doi.org/10.1186/s40168-018-0505-5
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Kayani, Masood ur Rehman, Doyle, Shawn M., Sangwan, Naseer, Wang, Guanqun, Gilbert, Jack A., Christner, Brent C., and Zhu, Ting F. Thu . "Metagenomic analysis of basal ice from an Alaskan glacier". United States. doi:https://doi.org/10.1186/s40168-018-0505-5. https://www.osti.gov/servlets/purl/1493906.
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@article{osti_1493906,
title = {Metagenomic analysis of basal ice from an Alaskan glacier},
author = {Kayani, Masood ur Rehman and Doyle, Shawn M. and Sangwan, Naseer and Wang, Guanqun and Gilbert, Jack A. and Christner, Brent C. and Zhu, Ting F.},
abstractNote = {Background Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on the microbial community structures and their metabolic potential is very limited. Here, we provide insights into the microbial lifestyle present at the base of the Matanuska Glacier, Alaska. Results DNA and RNA were extracted from samples of the Matanuska Glacier basal ice. Using Illumina MiSeq and HiSeq sequencing, we investigated the microbial diversity with the metagenomic shotgun reads and 16S ribosomal RNA data. We further assembled 9 partial and draft bacterial genomes from the metagenomic assembly, and identified key metabolic pathways such as sulfur oxidation and nitrification. Collectively, our analyses suggest a prevalence of lithotrophic and heterotrophic metabolisms in the subglacial microbiome. Conclusion Our results present the first metagenomic assembly and bacterial draft genomes for a subglacial environment. These results extend our understanding of the chemical and biological processes in subglacial environments critically influenced by global climate change.},
doi = {10.1186/s40168-018-0505-5},
journal = {Microbiome},
number = 1,
volume = 6,
place = {United States},
year = {2018},
month = {7}
}
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Journal Article:
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DOI:  https://doi.org/10.1186/s40168-018-0505-5
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Cited by: 3 works
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Figures / Tables:

Fig. 1 Fig. 1: Taxonomic classification, abundance, and genome binning of the Matanuska basal ice layer metagenome. Relative abundance of top bacterial families identified by 16S rDNA (a) and rRNA (b) sequencing data. c Top potential metabolically active bacterial OTUs inferred by rRNA to rDNA ratio. d Relative abundance of top bacterialmore » families identified by metagenomic data. e Partial and draft genome quality assessment plot indicating completeness and contamination levels of each GB« less
All figures and tables (2 total)
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Works referenced in this record:

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Glaciohydraulic supercooling: a freeze-on mechanism to create stratified, debris-rich basal ice: I. Field evidence
journal, January 1998

  • Lawson, Daniel E.; Strasser, Jeffrey C.; Evenson, Edward B.
  • Journal of Glaciology, Vol. 44, Issue 148
  • DOI: 10.3189/s0022143000002069

Short-pulse radar wavelet recovery and resolution of dielectric contrasts within englacial and basal ice of Matanuska Glacier, Alaska, U.S.A.
journal, January 1995

  • Arcone, Steven A.; Lawson, Daniel E.; Delaney, Allan J.
  • Journal of Glaciology, Vol. 41, Issue 137
  • DOI: 10.3189/s0022143000017779

Glaciohydraulic supercooling: a freeze-on mechanism to create stratified, debris-rich basal ice: II. Theory
journal, January 1998

  • Alley, Richard B.; Lawson, Daniel E.; Evenson, Edward B.
  • Journal of Glaciology, Vol. 44, Issue 148
  • DOI: 10.3189/s0022143000002070
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Culture-independent molecular techniques for soil microbial ecology
    journal, June 2010

    The basal ice layer of glaciers and ice sheets
    journal, January 1997

    Glaciohydraulic supercooling: a freeze-on mechanism to create stratified, debris-rich basal ice: I. Field evidence
    journal, January 1998

    • Lawson, Daniel E.; Strasser, Jeffrey C.; Evenson, Edward B.
    • Journal of Glaciology, Vol. 44, Issue 148
    • DOI: 10.1017/s0022143000002069

    Glaciohydraulic supercooling: a freeze-on mechanism to create stratified, debris-rich basal ice: II. Theory
    journal, January 1998

    • Alley, Richard B.; Lawson, Daniel E.; Evenson, Edward B.
    • Journal of Glaciology, Vol. 44, Issue 148
    • DOI: 10.1017/s0022143000002070

    Short-pulse radar wavelet recovery and resolution of dielectric contrasts within englacial and basal ice of Matanuska Glacier, Alaska, U.S.A.
    journal, January 1995

    • Arcone, Steven A.; Lawson, Daniel E.; Delaney, Allan J.
    • Journal of Glaciology, Vol. 41, Issue 137
    • DOI: 10.1017/s0022143000017779

    Biogeochemical weathering under ice: Size matters: GLACIAL BIOGEOCHEMICAL WEATHERING
    journal, September 2010

    • Wadham, J. L.; Tranter, M.; Skidmore, M.
    • Global Biogeochemical Cycles, Vol. 24, Issue 3
    • DOI: 10.1029/2009gb003688

    Molecular and biogeochemical evidence for methane cycling beneath the western margin of the Greenland Ice Sheet
    journal, April 2014

    • Dieser, Markus; Broemsen, Erik L. J. E.; Cameron, Karen A.
    • The ISME Journal, Vol. 8, Issue 11
    • DOI: 10.1038/ismej.2014.59

    Stabilizing feedbacks in glacier-bed erosion
    journal, August 2003

    • Alley, R. B.; Lawson, D. E.; Larson, G. J.
    • Nature, Vol. 424, Issue 6950
    • DOI: 10.1038/nature01839

    A microbial ecosystem beneath the West Antarctic ice sheet
    journal, August 2014

    • Christner, Brent C.; Priscu, John C.; Achberger, Amanda M.
    • Nature, Vol. 512, Issue 7514
    • DOI: 10.1038/nature13667

    Debris-Rich Basal Ice as a Microbial Habitat, Taylor Glacier, Antarctica
    journal, October 2013

    A Comparison of the Pebble Orientations in Ice and Deposits of the Matanuska Glacier, Alaska
    journal, November 1979

    • Lawson, Daniel E.
    • The Journal of Geology, Vol. 87, Issue 6
    • DOI: 10.1086/628457

    Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge
    journal, January 2016

    • Mikucki, J. A.; Lee, P. A.; Ghosh, D.
    • Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 374, Issue 2059
    • DOI: 10.1098/rsta.2014.0290

    Chemolithotrophic Primary Production in a Subglacial Ecosystem
    journal, August 2014

    • Boyd, Eric S.; Hamilton, Trinity L.; Havig, Jeff R.
    • Applied and Environmental Microbiology, Vol. 80, Issue 19
    • DOI: 10.1128/aem.01956-14

    Influence of bedrock mineral composition on microbial diversity in a subglacial environment
    journal, August 2013

    • Mitchell, Andrew C.; Lafrenière, Melissa J.; Skidmore, Mark L.
    • Geology, Vol. 41, Issue 8
    • DOI: 10.1130/g34194.1

    Estuaries beneath ice sheets
    journal, September 2013

    • Horgan, H. J.; Alley, R. B.; Christianson, K.
    • Geology, Vol. 41, Issue 11
    • DOI: 10.1130/g34654.1

    Basal ice formation and deformation: a review
    journal, December 1989

    • Hubbard, Bryn; Sharp, Martin
    • Progress in Physical Geography: Earth and Environment, Vol. 13, Issue 4
    • DOI: 10.1177/030913338901300403

    Structural control of englacial conduits in the temperate Matanuska Glacier, Alaska, USA
    journal, January 2009

    Basal-crevasse-fill origin of laminated debris bands at Matanuska Glacier, Alaska, U.S.A.
    journal, January 2001

    • Ensminger, Staci L.; Alley, Richard B.; Evenson, Edward B.
    • Journal of Glaciology, Vol. 47, Issue 158
    • DOI: 10.3189/172756501781832007

    Microbial Community Structure of Subglacial Lake Whillans, West Antarctica
    journal, September 2016

    • Achberger, Amanda M.; Christner, Brent C.; Michaud, Alexander B.
    • Frontiers in Microbiology, Vol. 7
    • DOI: 10.3389/fmicb.2016.01457

    Diversity of probiotic adhesion genes in the gastrointestinal tract of goats
    journal, February 2019

    • Subramaniyan, Vishnupriya; Gurumurthy, Kalaichelvan
    • Journal of Cellular Biochemistry, Vol. 120, Issue 8
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    Culture independent bacterial diversity of Changme Khang and Changme Khangpu glaciers of North Sikkim, India
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    • Sherpa, Mingma Thundu; Najar, Ishfaq Nabi; Das, Sayak
    • Environmental Sustainability, Vol. 2, Issue 3
    • DOI: 10.1007/s42398-019-00067-z
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