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In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

Arwyn Edwards, Aliyah R. Debbonaire, Samuel M. Nicholls, Sara M.E. Rassner, Birgit Sattler, Joseph M. Cook, Tom Davy, André Soares, Luis A.J. Mur, Andrew J. Hodson
doi: https://doi.org/10.1101/073965
Arwyn Edwards
1Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DD, UK.
2Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, SY23 3DD, UK.
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  • For correspondence: aye@aber.ac.uk
Aliyah R. Debbonaire
1Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DD, UK.
2Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, SY23 3DD, UK.
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Samuel M. Nicholls
1Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DD, UK.
2Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, SY23 3DD, UK.
3Department of Computer Science, Aberystwyth University, Aberystwyth, SY23 3DB, UK.
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Sara M.E. Rassner
2Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, SY23 3DD, UK.
4Department of Geography & Earth Sciences, Aberystwyth University, Aberystwyth, SY23 3DB, UK.
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Birgit Sattler
5Institute of Ecology, University of Innsbruck, Innsbruck, Austria.
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Joseph M. Cook
6Department of Geography, University of Sheffield, Sheffield, UK.
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Tom Davy
1Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DD, UK.
2Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, SY23 3DD, UK.
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André Soares
2Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, SY23 3DD, UK.
4Department of Geography & Earth Sciences, Aberystwyth University, Aberystwyth, SY23 3DB, UK.
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Luis A.J. Mur
1Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DD, UK.
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Andrew J. Hodson
7Department of Arctic Geology, University Centre in Svalbard (UNIS), Longyearbyen, Svalbard.
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ABSTRACT

In the field of observation, chance favours only the prepared mind (Pasteur). Impressive developments in genomics have led microbiology to its third “Golden Age”. However, conventional metagenomics strategies necessitate retrograde transfer of samples from extreme or remote environments for later analysis, rendering the powerful insights gained retrospective in nature, striking a contrast with Pasteur’s dictum. Here we implement highly portable USB-based nanopore DNA sequencing platforms coupled with field-adapted environmental DNA extraction, rapid sequence library generation and off-line analyses of shotgun metagenome and 16S ribosomal RNA gene amplicon profiles to characterize microbiota dwelling within cryoconite holes upon Svalbard glaciers, the Greenland Ice Sheet and the Austrian Alps. We show in-field nanopore sequencing of metagenomes captures taxonomic composition of supraglacial microbiota, while 16S rRNA Furthermore, comparison of nanopore data with prior 16S rRNA gene V1-V3 pyrosequencing from the same samples, demonstrates strong correlations between profiles obtained from nanopore sequencing and laboratory based sequencing approaches. gene amplicon sequencing resolves bacterial community responses to habitat changes. Finally, we demonstrate the fidelity and sensitivity of in-field sequencing by analysis of mock communities using field protocols. Ultimately, in-field sequencing potentiated by nanopore devices raises the prospect of enhanced agility in exploring Earth’s most remote microbiomes.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 19, 2019.
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In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota
Arwyn Edwards, Aliyah R. Debbonaire, Samuel M. Nicholls, Sara M.E. Rassner, Birgit Sattler, Joseph M. Cook, Tom Davy, André Soares, Luis A.J. Mur, Andrew J. Hodson
bioRxiv 073965; doi: https://doi.org/10.1101/073965
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In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota
Arwyn Edwards, Aliyah R. Debbonaire, Samuel M. Nicholls, Sara M.E. Rassner, Birgit Sattler, Joseph M. Cook, Tom Davy, André Soares, Luis A.J. Mur, Andrew J. Hodson
bioRxiv 073965; doi: https://doi.org/10.1101/073965

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