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Sampling and processing methods impact microbial community structure and potential activity in a seasonally anoxic fjord: Saanich Inlet, British Columbia

Sampling and processing methods impact microbial community structure and potential activity in a seasonally anoxic fjord: Saanich Inlet, British Columbia
Sampling and processing methods impact microbial community structure and potential activity in a seasonally anoxic fjord: Saanich Inlet, British Columbia
The Scientific Committee on Oceanographic Research (SCOR) Working Group 144 Microbial Community Responses to Ocean Deoxygenation workshop held in Vancouver, B.C on July 2014 had the primary objective of initiating a process to standardize operating procedures for compatible process rate and multi-omic (DNA, RNA, protein, and metabolite) data collection in marine oxygen minimum zones and other oxygen depleted waters. Workshop attendees participated in practical sampling and experimental activities in Saanich Inlet, British Columbia, a seasonally anoxic fjord. Experiments were designed to compare and cross-calibrate in situ versus bottle sampling methods to determine effects on microbial community structure and potential activity when using different filter combinations, filtration methods, and sample volumes. Resulting biomass was preserved for small subunit ribosomal RNA (SSU or 16S rRNA) and SSU rRNA gene (rDNA) amplicon sequencing followed by downstream statistical and visual analyses. Results from these analyses showed that significant community shifts occurred between in situ versus on ship processed samples. For example, Bacteroidetes, Alphaproteobacteria, and Opisthokonta associated with on-ship filtration onto 0.4 μm filters increased fivefold compared to on-ship in-line 0.22 μm filters or 0.4 μm filters processed and preserved in situ. In contrast, Planctomycetes associated with 0.4 μm in situ filters increased fivefold compared to on-ship filtration onto 0.4 μm filters and on-ship in-line 0.22 μm filters. In addition, candidate divisions and Chloroflexi were primarily recovered when filtered onto 0.4 μm filters in situ. Results based on rRNA:rDNA ratios for microbial indicator groups revealed previously unrecognized roles of candidate divisions, Desulfarculales, and Desulfuromandales in sulfur cycling, carbon fixation and fermentation within anoxic basin waters. Taken together, filter size and in situ versus on-ship filtration had the largest impact on recovery of microbial groups with the potential to influence downstream metabolic reconstruction and process rate measurements. These observations highlight the need for establishing standardized and reproducible techniques that facilitate cross-scale comparisons and more accurately assess in situ activities of microbial communities.
microbial ecology, oxygen minimum zone, standards of practice, filtration methods, amplicon sequencing
2296-7745
1-16
Torres-Beltran, Monica
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Mueller, Andreas
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Scofield, Melanie
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Pachiadaki, Maria
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Taylor, Craig
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Tyshchenko, Kateryna
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Michiels, Celine
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Lam, Phyllis
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Ulloa, Osvaldo
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Jürgens, Klaus
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Hyun, Jung-Ho
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Edgcomb, Virginia
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Crowe, Sean
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Hallam, Steven
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Torres-Beltran, Monica
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Mueller, Andreas
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Scofield, Melanie
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Pachiadaki, Maria
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Taylor, Craig
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Tyshchenko, Kateryna
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Michiels, Celine
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Lam, Phyllis
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Ulloa, Osvaldo
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Jürgens, Klaus
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Hyun, Jung-Ho
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Edgcomb, Virginia
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Crowe, Sean
cbfe791e-2505-406f-b97f-5023548ef3c1
Hallam, Steven
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Torres-Beltran, Monica, Mueller, Andreas, Scofield, Melanie, Pachiadaki, Maria, Taylor, Craig, Tyshchenko, Kateryna, Michiels, Celine, Lam, Phyllis, Ulloa, Osvaldo, Jürgens, Klaus, Hyun, Jung-Ho, Edgcomb, Virginia, Crowe, Sean and Hallam, Steven (2019) Sampling and processing methods impact microbial community structure and potential activity in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Frontiers in Marine Science, 6, 1-16. (doi:10.3389/fmars.2019.00132).

Record type: Article

Abstract

The Scientific Committee on Oceanographic Research (SCOR) Working Group 144 Microbial Community Responses to Ocean Deoxygenation workshop held in Vancouver, B.C on July 2014 had the primary objective of initiating a process to standardize operating procedures for compatible process rate and multi-omic (DNA, RNA, protein, and metabolite) data collection in marine oxygen minimum zones and other oxygen depleted waters. Workshop attendees participated in practical sampling and experimental activities in Saanich Inlet, British Columbia, a seasonally anoxic fjord. Experiments were designed to compare and cross-calibrate in situ versus bottle sampling methods to determine effects on microbial community structure and potential activity when using different filter combinations, filtration methods, and sample volumes. Resulting biomass was preserved for small subunit ribosomal RNA (SSU or 16S rRNA) and SSU rRNA gene (rDNA) amplicon sequencing followed by downstream statistical and visual analyses. Results from these analyses showed that significant community shifts occurred between in situ versus on ship processed samples. For example, Bacteroidetes, Alphaproteobacteria, and Opisthokonta associated with on-ship filtration onto 0.4 μm filters increased fivefold compared to on-ship in-line 0.22 μm filters or 0.4 μm filters processed and preserved in situ. In contrast, Planctomycetes associated with 0.4 μm in situ filters increased fivefold compared to on-ship filtration onto 0.4 μm filters and on-ship in-line 0.22 μm filters. In addition, candidate divisions and Chloroflexi were primarily recovered when filtered onto 0.4 μm filters in situ. Results based on rRNA:rDNA ratios for microbial indicator groups revealed previously unrecognized roles of candidate divisions, Desulfarculales, and Desulfuromandales in sulfur cycling, carbon fixation and fermentation within anoxic basin waters. Taken together, filter size and in situ versus on-ship filtration had the largest impact on recovery of microbial groups with the potential to influence downstream metabolic reconstruction and process rate measurements. These observations highlight the need for establishing standardized and reproducible techniques that facilitate cross-scale comparisons and more accurately assess in situ activities of microbial communities.

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Accepted/In Press date: 4 March 2019
Published date: 22 March 2019
Keywords: microbial ecology, oxygen minimum zone, standards of practice, filtration methods, amplicon sequencing

Identifiers

Local EPrints ID: 429424
URI: https://eprints.soton.ac.uk/id/eprint/429424
ISSN: 2296-7745
PURE UUID: ccdddb56-3580-4003-a765-840a4db121c3
ORCID for Phyllis Lam: ORCID iD orcid.org/0000-0003-2067-171X

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Date deposited: 27 Mar 2019 17:30
Last modified: 20 Jul 2019 00:38

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Contributors

Author: Monica Torres-Beltran
Author: Andreas Mueller
Author: Melanie Scofield
Author: Maria Pachiadaki
Author: Craig Taylor
Author: Kateryna Tyshchenko
Author: Celine Michiels
Author: Phyllis Lam ORCID iD
Author: Osvaldo Ulloa
Author: Klaus Jürgens
Author: Jung-Ho Hyun
Author: Virginia Edgcomb
Author: Sean Crowe
Author: Steven Hallam

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