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Metatranscriptomics reveals a shift in microbial community composition and function during summer months in a coastal marine environment

View ORCID ProfileBen J. G. Sutherland, Jan F. Finke, Robert Saunders, Snehal Warne, View ORCID ProfileAngela D. Schulze, Jeff H. T. Strohm, View ORCID ProfileAmy M. Chan, View ORCID ProfileCurtis A. Suttle, Kristina M. Miller
doi: https://doi.org/10.1101/2022.01.21.477286
Ben J. G. Sutherland
1Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada V9T 6N7
2Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
3Sutherland Bioinformatics, Lantzville, BC, Canada V0R 2H0
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  • ORCID record for Ben J. G. Sutherland
  • For correspondence: Sutherland.Bioinformatics@protonmail.com
Jan F. Finke
2Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
4Hakai Institute, PO Box 309, Heriot Bay, BC, Canada, V0P 1H0
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  • For correspondence: jfinke@eoas.ubc.ca
Robert Saunders
5RKS Labs, Parksville, BC, Canada V9P 2A2
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Snehal Warne
5RKS Labs, Parksville, BC, Canada V9P 2A2
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Angela D. Schulze
1Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada V9T 6N7
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  • ORCID record for Angela D. Schulze
Jeff H. T. Strohm
1Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada V9T 6N7
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Amy M. Chan
2Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
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  • ORCID record for Amy M. Chan
Curtis A. Suttle
2Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
6Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3
7Department of Botany, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
8Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, BC, Canada, V6T1Z4
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Kristina M. Miller
1Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada V9T 6N7
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Abstract

Temperate coastal marine waters are often thermally stratified from spring through fall, but can be dynamic and disrupted by tidal currents and wind-driven upwelling. These mixing events introduce deeper, cooler water with a higher partial pressure of CO2 (pCO2), and its associated microbial communities to the surface. Anecdotally, there have been concerns that these changes in water quality as well as in microbial composition and activity may be involved in mass mortality events of Pacific oysters (Crassostrea gigas) on the East Coast of Vancouver Island, British Columbia. Therefore, improved understanding of the composition and microbial activity of marine waters associated with seasons and abiotic variables may be useful in managing these mortality events. To characterize both compositional and functional changes associated with abiotic factors, here we generate a reference metatranscriptome from the Strait of Georgia over the representative seasons and analyze metatranscriptomic profiles of the microorganisms present within intake water containing different pCO2 levels at a shellfish hatchery in British Columbia from June through October. Abiotic factors studied include pH, temperature, alkalinity, aragonite, calcite and pCO2. Community composition changes were observed to occur at broad taxonomic levels, and most notably to vary with temperature and pCO2. Functional gene expression profiles indicated a strong difference between early (June-July) and late summer (August-October) associated with viral activity. The taxonomic data suggests this could be due to the termination of cyanobacteria and phytoplankton blooms by viral lysis in the late season. Functional analysis indicated fewer differentially expressed transcripts associated with abiotic variables (e.g., pCO2) than with the temporal effect. Microbial composition and activity in these waters varies with both short-term effects observed alongside abiotic variation as well as long-term effects observed across seasonal changes, as captured in the samples analyzed here. The analysis of both taxonomy and functional gene expression simultaneously in the same samples (i.e., metatranscriptomics) provided a more comprehensive view for monitoring water bodies than either would in isolation.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://doi.org/10.6084/m9.figshare.18128966.v1

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 22, 2022.
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Metatranscriptomics reveals a shift in microbial community composition and function during summer months in a coastal marine environment
Ben J. G. Sutherland, Jan F. Finke, Robert Saunders, Snehal Warne, Angela D. Schulze, Jeff H. T. Strohm, Amy M. Chan, Curtis A. Suttle, Kristina M. Miller
bioRxiv 2022.01.21.477286; doi: https://doi.org/10.1101/2022.01.21.477286
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Metatranscriptomics reveals a shift in microbial community composition and function during summer months in a coastal marine environment
Ben J. G. Sutherland, Jan F. Finke, Robert Saunders, Snehal Warne, Angela D. Schulze, Jeff H. T. Strohm, Amy M. Chan, Curtis A. Suttle, Kristina M. Miller
bioRxiv 2022.01.21.477286; doi: https://doi.org/10.1101/2022.01.21.477286

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