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

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:
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:
Report Number(s):
PNNL-SA-121885
Journal ID: ISSN 2052-4463; 47981; KP1704020
Grant/Contract Number:
AC05-76RL01830
Type:
Accepted Manuscript
Journal Name:
Scientific Data
Additional Journal Information:
Journal Volume: 4; Journal ID: ISSN 2052-4463
Publisher:
Nature Publishing Group
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; Environmental Molecular Sciences Laboratory
OSTI Identifier:
1416682

Hawley, Alyse K., Torres-Beltran, Monica, 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., Web. doi:10.1038/sdata.2017.160.
Hawley, Alyse K., Torres-Beltran, Monica, 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-Beltran, Monica, 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.. 2017. "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/1416682.
@article{osti_1416682,
title = {A compendium of multi-omic sequence information from the Saanich Inlet water column},
author = {Hawley, Alyse K. and Torres-Beltran, Monica 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 = {2017},
month = {10}
}

Works referenced in this record:

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
  • DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
  • Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
  • DOI: 10.1128/AEM.03006-05