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
- microbial ecology; oxygen minimum zone; standards of practice; filtration methods; amplicon sequencing
- Issue Date
- Frontiers Media S.A.
- FRONTIERS IN MARINE SCIENCE , v. 6, Article no. UNSP 132
- 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 mm filters increased fivefold compared to on-ship in-line 0.22 mm filters or
0.4 mm filters processed and preserved in situ. In contrast, Planctomycetes associated
with 0.4 mm in situ filters increased fivefold compared to on-ship filtration onto 0.4 mm
filters and on-ship in-line 0.22 mm filters. In addition, candidate divisions and Chloroflexi
were primarily recovered when filtered onto 0.4 mm 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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