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Torres-Beltrán M, Hawley AK, Capelle D, Zaikova E, Walsh DA, Mueller A, Scofield M, Payne C, Pakhomova L, Kheirandish S, Finke J, Bhatia M, Shevchuk O, Gies EA, Fairley D, Michiels C, Suttle CA, Whitney F, Crowe SA, Tortell PD, Hallam SJ. Author Correction: A compendium of geochemical information from the Saanich Inlet water column. Sci Data 2019; 6:1. [PMID: 30647409 PMCID: PMC6333813 DOI: 10.1038/s41597-018-0005-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In Table 3 of this Data Descriptor the units of Mean_N2O and Mean_CH4 are incorrectly stated as "Nanomolar (μM)". This should instead read "Nanomolar (nM)".
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Affiliation(s)
- Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Alyse K Hawley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - David Capelle
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Elena Zaikova
- Department of Biology, Georgetown University, Washington, DC, 20007, USA
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Andreas Mueller
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Chris Payne
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Larysa Pakhomova
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Jan Finke
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Maya Bhatia
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Olena Shevchuk
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Esther A Gies
- Department of Civil Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Diane Fairley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Céline Michiels
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.,Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Frank Whitney
- Department of Fisheries and Oceans Canada, Sidney, British Columbia, V9L 6V9, Canada
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Philippe D Tortell
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.,Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, British Columbia, V6T 1Z2, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada. .,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada. .,Peter Wall Institute for Advanced Studies, University of British Columbia, British Columbia, V6T 1Z2, Canada. .,Genome Science and Technology Program, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. .,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
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2
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Gies EA, LeNoble JL, Noël M, Etemadifar A, Bishay F, Hall ER, Ross PS. Retention of microplastics in a major secondary wastewater treatment plant in Vancouver, Canada. Mar Pollut Bull 2018; 133:553-561. [PMID: 30041349 DOI: 10.1016/j.marpolbul.2018.06.006] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 05/23/2023]
Abstract
Municipal wastewater treatment plants (WWTPs) are conduits through which microplastics (MPs) are released into aquatic environments. However, the technical challenges in working with wastewater sample matrices have precluded reliable particle count budget calculations. We applied newly-adapted methods for MP collection and analysis to a study of a major WWTP serving a population of 1.3 million people near Vancouver, Canada. Suspected MP particles, including fibres, were counted and categorized using light microscopy in influent, primary effluent, secondary effluent, primary sludge and secondary sludge. Fourier Transform Infrared Spectroscopy (FT-IR) confirmed that just 32.4% of the suspected MPs were plastic polymers. Using FT-IR corrected data, we estimate that 1.76 ± 0.31 trillion MPs enter the WWTP annually, with 1.28 ± 0.54 trillion MPs settling into primary sludge, 0.36 ± 0.22 into secondary sludge, and 0.03 ± 0.01 trillion MPs released into the receiving environment. This corresponds to a retention of microplastics of up to 99% in the WWTP.
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Affiliation(s)
- Esther A Gies
- Coastal Ocean Research Institute, Ocean Wise Conservation Association, P. O. Box 3232, Vancouver, BC V6B 3X8, Canada; Environmental and Civil Engineering, University of British Columbia, Canada
| | - Jessica L LeNoble
- Coastal Ocean Research Institute, Ocean Wise Conservation Association, P. O. Box 3232, Vancouver, BC V6B 3X8, Canada
| | - Marie Noël
- Coastal Ocean Research Institute, Ocean Wise Conservation Association, P. O. Box 3232, Vancouver, BC V6B 3X8, Canada
| | - Anahita Etemadifar
- Coastal Ocean Research Institute, Ocean Wise Conservation Association, P. O. Box 3232, Vancouver, BC V6B 3X8, Canada
| | | | - Eric R Hall
- Environmental and Civil Engineering, University of British Columbia, Canada
| | - Peter S Ross
- Coastal Ocean Research Institute, Ocean Wise Conservation Association, P. O. Box 3232, Vancouver, BC V6B 3X8, Canada.
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3
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Hawley AK, Torres-Beltrán M, Zaikova E, Walsh DA, Mueller A, Scofield M, Kheirandish S, Payne C, Pakhomova L, Bhatia M, Shevchuk O, Gies EA, Fairley D, Malfatti SA, Norbeck AD, Brewer HM, Pasa-Tolic L, del Rio TG, Suttle CA, Tringe S, Hallam SJ. A compendium of multi-omic sequence information from the Saanich Inlet water column. Sci Data 2017; 4:170160. [PMID: 29087368 PMCID: PMC5663217 DOI: 10.1038/sdata.2017.160] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/02/2017] [Indexed: 01/08/2023] Open
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.
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Affiliation(s)
- Alyse K. Hawley
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Elena Zaikova
- Department of Biology, Georgetown University,
Washington, District Of Columbia 20057,
USA
| | - David A. Walsh
- Department of Biology, Concordia University,
Montreal, Quebec, Canada H4B 1R6
| | - Andreas Mueller
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Chris Payne
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Larysa Pakhomova
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Maya Bhatia
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Olena Shevchuk
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Esther A. Gies
- Department of Civil Engineering, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Diane Fairley
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | | | - Angela D. Norbeck
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | - Heather M. Brewer
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | - Ljiljana Pasa-Tolic
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | | | - Curtis A. Suttle
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
- Department of Botany, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Susannah Tringe
- Department of Energy Joint Genome Institute,
Walnut Creek, California 94598, USA
| | - Steven J. Hallam
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
- Peter Wall Institute for Advanced Studies, University of
British Columbia, Canada V6T 1Z2
- Genome Science and Technology Program, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
- Graduate Program in Bioinformatics, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
- ECOSCOPE Training Program, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
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4
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Torres-Beltrán M, Hawley AK, Capelle D, Zaikova E, Walsh DA, Mueller A, Scofield M, Payne C, Pakhomova L, Kheirandish S, Finke J, Bhatia M, Shevchuk O, Gies EA, Fairley D, Michiels C, Suttle CA, Whitney F, Crowe SA, Tortell PD, Hallam SJ. A compendium of geochemical information from the Saanich Inlet water column. Sci Data 2017; 4:170159. [PMID: 29087371 PMCID: PMC5663218 DOI: 10.1038/sdata.2017.159] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/21/2017] [Indexed: 11/13/2022] Open
Abstract
Extensive and expanding oxygen minimum zones (OMZs) exist at variable depths in
coastal and open ocean waters. As oxygen levels decline, nutrients and energy
are increasingly diverted away from higher trophic levels into microbial
community metabolism, resulting in fixed nitrogen loss and production of climate
active trace gases including nitrous oxide and methane. While ocean
deoxygenation has been reported on a global scale, our understanding of OMZ
biology and geochemistry is limited by a lack of time-resolved data sets. Here,
we present a historical dataset of oxygen concentrations spanning fifty years
and nine years of monthly geochemical time series 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 geochemical framework for evaluating long-term
trends in biogeochemical cycling in OMZ waters.
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Affiliation(s)
- Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Alyse K Hawley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - David Capelle
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Elena Zaikova
- Department of Biology, Georgetown University, Washington, DC 20007, USA
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada H4B 1R6
| | - Andreas Mueller
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Chris Payne
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Larysa Pakhomova
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Jan Finke
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Maya Bhatia
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Olena Shevchuk
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Esther A Gies
- Department of Civil Engineering, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Diane Fairley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Céline Michiels
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Frank Whitney
- Department of Fisheries and Oceans Canada, Sidney, British Columbia, Canada V9L 6V9
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Philippe D Tortell
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Peter Wall Institute for Advanced Studies, University of British Columbia, Canada V6T 1Z2
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Peter Wall Institute for Advanced Studies, University of British Columbia, Canada V6T 1Z2.,Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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5
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Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, Levy A, Gies EA, Cheng JF, Copeland A, Klenk HP, Hallam SJ, Hugenholtz P, Tringe SG, Woyke T. High-resolution phylogenetic microbial community profiling. ISME J 2016; 10:2020-32. [PMID: 26859772 PMCID: PMC5029162 DOI: 10.1038/ismej.2015.249] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/24/2015] [Accepted: 11/30/2015] [Indexed: 02/07/2023]
Abstract
Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.
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Affiliation(s)
- Esther Singer
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Brian Bushnell
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Devin Coleman-Derr
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.,USDA-ARS, Albany, CA, USA
| | | | - Robert M Bowers
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Asaf Levy
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Esther A Gies
- University of British Columbia, Vancouver, BC, Canada
| | - Jan-Fang Cheng
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Alex Copeland
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Hans-Peter Klenk
- Newcastle University, School of Biology, Newcastle upon Tyne, UK
| | | | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Susannah G Tringe
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
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