A compendium of multi-omic sequence information from the Saanich Inlet water column
Abstract
Microbial communities play vital roles in earth’s geochemical cycles. Within marine oxygen minimum zones (OMZs) gradients of oxygen, nitrate and sulfide create redox gradients that drive biogeochemical cycling of carbon, nitrogen and sulphur. Climate-change induced expansion and intensification of OMZs and associated biogeochemical activities has significant implications for green house gas production i.e. nitrous oxide and methane. Next generation sequencing technologies have enabled observations of changes in microbial community structure and expression of RNA and protein along these redox gradients within OMZs. Here, we present a multi-omic time series dataset from Saanich Inlet spanning six years, including high spatial resolution small subunit ribosomal RNA tags, metagenomes, metatranscriptomes, and metaproteomes. As a result, this compendium provides paired multi-omic datasets over multiple time points providing a basis for exploring shifts in microbial community interactions and regulation of metabolic activities both along redox gradients and over time with implications for global climate models.
- Authors:
-
[1];
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- Univ. of British Columbia, Vancouver, BC (Canada)
- Georgetown Univ., Washington, DC (United States)
- Concordia Univ., Montreal, QC (Canada)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- 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. https://doi.org/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. https://doi.org/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 = {Microbial communities play vital roles in earth’s geochemical cycles. Within marine oxygen minimum zones (OMZs) gradients of oxygen, nitrate and sulfide create redox gradients that drive biogeochemical cycling of carbon, nitrogen and sulphur. Climate-change induced expansion and intensification of OMZs and associated biogeochemical activities has significant implications for green house gas production i.e. nitrous oxide and methane. Next generation sequencing technologies have enabled observations of changes in microbial community structure and expression of RNA and protein along these redox gradients within OMZs. Here, we present a multi-omic time series dataset from Saanich Inlet spanning six years, including high spatial resolution small subunit ribosomal RNA tags, metagenomes, metatranscriptomes, and metaproteomes. As a result, this compendium provides paired multi-omic datasets over multiple time points providing a basis for exploring shifts in microbial community interactions and regulation of metabolic activities both along redox gradients and over time with implications for global climate models.},
doi = {10.1038/sdata.2017.160},
journal = {Scientific Data},
number = ,
volume = 4,
place = {United States},
year = {Tue Oct 31 00:00:00 EDT 2017},
month = {Tue Oct 31 00:00:00 EDT 2017}
}
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Cited by: 16 works
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Figures / Tables:
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 »
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Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients
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Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone
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