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Title: A compendium of multi-omic sequence information from the Saanich Inlet water column

Abstract

Marine oxygen minimum zones (OMZs) are widespread regions of the ocean that are currently expanding due to global warming. While inhospitable to most metazoans, OMZs are hotspots for microbial mediated biogeochemical cycling of carbon, nitrogen and sulphur, contributing disproportionately to marine nitrogen loss and climate active trace gas production. Our current understanding of microbial community responses to OMZ expansion is limited by a lack of time-resolved data sets linking multi-omic sequence information (DNA, RNA, protein) to geochemical parameters and process rates. Here, we present six years of time-resolved multi-omic observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique multi-omic framework for studying microbial community responses to ocean deoxygenation along defined geochemical gradients in OMZ waters.

Authors:
ORCiD logo [1];  [1];  [2];  [3];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [4];  [5];  [5];  [5];  [4];  [1];  [4] more »;  [1] « less
  1. Univ. of British Columbia, Vancouver, BC (Canada)
  2. Georgetown Univ., Washington, DC (United States)
  3. Concordia Univ., Montreal, QC (Canada)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1527025
Alternate Identifier(s):
OSTI ID: 1416682
Report Number(s):
[PNNL-SA-121885]
[Journal ID: ISSN 2052-4463]
Grant/Contract Number:  
[AC02-05CH11231; AC05-76RL01830]
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Data
Additional Journal Information:
[ Journal Volume: 4]; Journal ID: ISSN 2052-4463
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; Environmental Molecular Sciences Laboratory

Citation Formats

Hawley, Alyse K., Torres-Beltrán, Mónica, Zaikova, Elena, Walsh, David A., Mueller, Andreas, Scofield, Melanie, Kheirandish, Sam, Payne, Chris, Pakhomova, Larysa, Bhatia, Maya, Shevchuk, Olena, Gies, Esther A., Fairley, Diane, Malfatti, Stephanie A., Norbeck, Angela D., Brewer, Heather M., Pasa-Tolic, Ljiljana, del Rio, Tijana Glavina, Suttle, Curtis A., Tringe, Susannah, and Hallam, Steven J. A compendium of multi-omic sequence information from the Saanich Inlet water column. United States: N. p., 2017. Web. doi:10.1038/sdata.2017.160.
Hawley, Alyse K., Torres-Beltrán, Mónica, Zaikova, Elena, Walsh, David A., Mueller, Andreas, Scofield, Melanie, Kheirandish, Sam, Payne, Chris, Pakhomova, Larysa, Bhatia, Maya, Shevchuk, Olena, Gies, Esther A., Fairley, Diane, Malfatti, Stephanie A., Norbeck, Angela D., Brewer, Heather M., Pasa-Tolic, Ljiljana, del Rio, Tijana Glavina, Suttle, Curtis A., Tringe, Susannah, & Hallam, Steven J. A compendium of multi-omic sequence information from the Saanich Inlet water column. United States. doi:10.1038/sdata.2017.160.
Hawley, Alyse K., Torres-Beltrán, Mónica, Zaikova, Elena, Walsh, David A., Mueller, Andreas, Scofield, Melanie, Kheirandish, Sam, Payne, Chris, Pakhomova, Larysa, Bhatia, Maya, Shevchuk, Olena, Gies, Esther A., Fairley, Diane, Malfatti, Stephanie A., Norbeck, Angela D., Brewer, Heather M., Pasa-Tolic, Ljiljana, del Rio, Tijana Glavina, Suttle, Curtis A., Tringe, Susannah, and Hallam, Steven J. Tue . "A compendium of multi-omic sequence information from the Saanich Inlet water column". United States. doi:10.1038/sdata.2017.160. https://www.osti.gov/servlets/purl/1527025.
@article{osti_1527025,
title = {A compendium of multi-omic sequence information from the Saanich Inlet water column},
author = {Hawley, Alyse K. and Torres-Beltrán, Mónica and Zaikova, Elena and Walsh, David A. and Mueller, Andreas and Scofield, Melanie and Kheirandish, Sam and Payne, Chris and Pakhomova, Larysa and Bhatia, Maya and Shevchuk, Olena and Gies, Esther A. and Fairley, Diane and Malfatti, Stephanie A. and Norbeck, Angela D. and Brewer, Heather M. and Pasa-Tolic, Ljiljana and del Rio, Tijana Glavina and Suttle, Curtis A. and Tringe, Susannah and Hallam, Steven J.},
abstractNote = {Marine oxygen minimum zones (OMZs) are widespread regions of the ocean that are currently expanding due to global warming. While inhospitable to most metazoans, OMZs are hotspots for microbial mediated biogeochemical cycling of carbon, nitrogen and sulphur, contributing disproportionately to marine nitrogen loss and climate active trace gas production. Our current understanding of microbial community responses to OMZ expansion is limited by a lack of time-resolved data sets linking multi-omic sequence information (DNA, RNA, protein) to geochemical parameters and process rates. Here, we present six years of time-resolved multi-omic observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique multi-omic framework for studying microbial community responses to ocean deoxygenation along defined geochemical gradients in OMZ waters.},
doi = {10.1038/sdata.2017.160},
journal = {Scientific Data},
number = ,
volume = [4],
place = {United States},
year = {2017},
month = {10}
}

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Figures / Tables:

Figure 1 Figure 1: Summary of multi-omic samples collected in Saanich Inlet time series. (a) Oxygen concentration contour for CTD data (February 2008 onward)35 indicating 16 sampling depths for water column geochemistry and high-resolution (HR) DNA samples for SSU libraries (small black dots) and six major depths for large volume (LV) samplesmore » for meta-genomics, -transcriptomics, -proteomics and LV SSU libraries (large black dots). (b) Sample inventory from February 2006 to October 2014 indicating multi-omic datasets included in this manuscript (solid black), in previous publications (gray) and accompanying datasets currently undergoing processing and analysis (open gray).« less

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    Works referencing / citing this record:

    Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone
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      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.