DNA/RNA Preservation in Glacial Snow and Ice Samples
International audience The preservation of nucleic acids for high-throughput sequencing is an ongoing challenge for field scientists. In particular, samples that are low biomass, or that have to be collected and preserved in logistically challenging environments (such as remote sites or during long...
Published in: | Frontiers in Microbiology |
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Main Authors: | , , , , , , , |
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Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2022
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Online Access: | https://hal.science/hal-03827594 https://hal.science/hal-03827594/document https://hal.science/hal-03827594/file/fmicb-13-894893.pdf https://doi.org/10.3389/fmicb.2022.894893 |
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HAL Lyon 1 (University Claude Bernard Lyon 1) |
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ftunivlyon1 |
language |
English |
topic |
[SDV]Life Sciences [q-bio] |
spellingShingle |
[SDV]Life Sciences [q-bio] Trivedi, Christopher Keuschnig, Christoph Larose, Catherine Rissi, Daniel Vasconcelos Mourot, Rey Bradley, James Winkel, Matthias Benning, Liane DNA/RNA Preservation in Glacial Snow and Ice Samples |
topic_facet |
[SDV]Life Sciences [q-bio] |
description |
International audience The preservation of nucleic acids for high-throughput sequencing is an ongoing challenge for field scientists. In particular, samples that are low biomass, or that have to be collected and preserved in logistically challenging environments (such as remote sites or during long sampling campaigns) can pose exceptional difficulties. With this work, we compare and assess the effectiveness of three preservation methods for DNA and RNA extracted from microbial communities of glacial snow and ice samples. Snow and ice samples were melted and filtered upon collection in Iceland, and filters were preserved using: (i) liquid nitrogen flash freezing, (ii) storage in RNAlater, or (iii) storage in Zymo DNA/RNA Shield. Comparative statistics covering nucleic acid recovery, sequencing library preparation, genome assembly, and taxonomic diversity were used to determine best practices for the preservation of DNA and RNA samples from these environments. Our results reveal that microbial community composition based on DNA was comparable at the class level across preservation types. Based on extracted RNA, the taxonomic composition of the active community was primarily driven by the filtered sample volume (i.e., biomass content). In low biomass samples (where <200 ml of sample volume was filtered) the taxonomic and functional signatures trend toward the composition of the control samples, while in samples where a larger volume (more biomass) was filtered our data showed comparable results independent of preservation type. Based on all comparisons our data suggests that flash freezing of filters containing low biomass is the preferred method for preserving DNA and RNA (notwithstanding the difficulties of accessing liquid nitrogen in remote glacial field sites). Generally, RNAlater and Zymo DNA/RNA Shield solutions work comparably well, especially for DNA from high biomass samples, but Zymo DNA/RNA Shield is favored due to its higher yield of preserved RNA. Biomass quantity from snow and ice samples ... |
author2 |
German Research Centre for Geosciences - Helmholtz-Centre Potsdam (GFZ) Ampère, Département Bioingénierie (BioIng) Ampère (AMPERE) École Centrale de Lyon (ECL) Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Freie Universität Berlin |
format |
Article in Journal/Newspaper |
author |
Trivedi, Christopher Keuschnig, Christoph Larose, Catherine Rissi, Daniel Vasconcelos Mourot, Rey Bradley, James Winkel, Matthias Benning, Liane |
author_facet |
Trivedi, Christopher Keuschnig, Christoph Larose, Catherine Rissi, Daniel Vasconcelos Mourot, Rey Bradley, James Winkel, Matthias Benning, Liane |
author_sort |
Trivedi, Christopher |
title |
DNA/RNA Preservation in Glacial Snow and Ice Samples |
title_short |
DNA/RNA Preservation in Glacial Snow and Ice Samples |
title_full |
DNA/RNA Preservation in Glacial Snow and Ice Samples |
title_fullStr |
DNA/RNA Preservation in Glacial Snow and Ice Samples |
title_full_unstemmed |
DNA/RNA Preservation in Glacial Snow and Ice Samples |
title_sort |
dna/rna preservation in glacial snow and ice samples |
publisher |
HAL CCSD |
publishDate |
2022 |
url |
https://hal.science/hal-03827594 https://hal.science/hal-03827594/document https://hal.science/hal-03827594/file/fmicb-13-894893.pdf https://doi.org/10.3389/fmicb.2022.894893 |
genre |
Iceland |
genre_facet |
Iceland |
op_source |
ISSN: 1664-302X EISSN: 1664-302X Frontiers in Microbiology https://hal.science/hal-03827594 Frontiers in Microbiology, 2022, 13, ⟨10.3389/fmicb.2022.894893⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.3389/fmicb.2022.894893 hal-03827594 https://hal.science/hal-03827594 https://hal.science/hal-03827594/document https://hal.science/hal-03827594/file/fmicb-13-894893.pdf doi:10.3389/fmicb.2022.894893 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.3389/fmicb.2022.894893 |
container_title |
Frontiers in Microbiology |
container_volume |
13 |
_version_ |
1766042986804674560 |
spelling |
ftunivlyon1:oai:HAL:hal-03827594v1 2023-05-15T16:52:37+02:00 DNA/RNA Preservation in Glacial Snow and Ice Samples Trivedi, Christopher Keuschnig, Christoph Larose, Catherine Rissi, Daniel Vasconcelos Mourot, Rey Bradley, James Winkel, Matthias Benning, Liane German Research Centre for Geosciences - Helmholtz-Centre Potsdam (GFZ) Ampère, Département Bioingénierie (BioIng) Ampère (AMPERE) École Centrale de Lyon (ECL) Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Freie Universität Berlin 2022-05-23 https://hal.science/hal-03827594 https://hal.science/hal-03827594/document https://hal.science/hal-03827594/file/fmicb-13-894893.pdf https://doi.org/10.3389/fmicb.2022.894893 en eng HAL CCSD Frontiers Media info:eu-repo/semantics/altIdentifier/doi/10.3389/fmicb.2022.894893 hal-03827594 https://hal.science/hal-03827594 https://hal.science/hal-03827594/document https://hal.science/hal-03827594/file/fmicb-13-894893.pdf doi:10.3389/fmicb.2022.894893 info:eu-repo/semantics/OpenAccess ISSN: 1664-302X EISSN: 1664-302X Frontiers in Microbiology https://hal.science/hal-03827594 Frontiers in Microbiology, 2022, 13, ⟨10.3389/fmicb.2022.894893⟩ [SDV]Life Sciences [q-bio] info:eu-repo/semantics/article Journal articles 2022 ftunivlyon1 https://doi.org/10.3389/fmicb.2022.894893 2023-04-07T11:11:28Z International audience The preservation of nucleic acids for high-throughput sequencing is an ongoing challenge for field scientists. In particular, samples that are low biomass, or that have to be collected and preserved in logistically challenging environments (such as remote sites or during long sampling campaigns) can pose exceptional difficulties. With this work, we compare and assess the effectiveness of three preservation methods for DNA and RNA extracted from microbial communities of glacial snow and ice samples. Snow and ice samples were melted and filtered upon collection in Iceland, and filters were preserved using: (i) liquid nitrogen flash freezing, (ii) storage in RNAlater, or (iii) storage in Zymo DNA/RNA Shield. Comparative statistics covering nucleic acid recovery, sequencing library preparation, genome assembly, and taxonomic diversity were used to determine best practices for the preservation of DNA and RNA samples from these environments. Our results reveal that microbial community composition based on DNA was comparable at the class level across preservation types. Based on extracted RNA, the taxonomic composition of the active community was primarily driven by the filtered sample volume (i.e., biomass content). In low biomass samples (where <200 ml of sample volume was filtered) the taxonomic and functional signatures trend toward the composition of the control samples, while in samples where a larger volume (more biomass) was filtered our data showed comparable results independent of preservation type. Based on all comparisons our data suggests that flash freezing of filters containing low biomass is the preferred method for preserving DNA and RNA (notwithstanding the difficulties of accessing liquid nitrogen in remote glacial field sites). Generally, RNAlater and Zymo DNA/RNA Shield solutions work comparably well, especially for DNA from high biomass samples, but Zymo DNA/RNA Shield is favored due to its higher yield of preserved RNA. Biomass quantity from snow and ice samples ... Article in Journal/Newspaper Iceland HAL Lyon 1 (University Claude Bernard Lyon 1) Frontiers in Microbiology 13 |