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 (OMZs) 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 5-fold 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 5-fold 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.
Highlights
Among the many environmental perturbations associated with global climate change is a decrease in dissolved oxygen (O2) concentrations in coastal and interior regions of the ocean
We evaluated microbial community structure using 521 timeseries samples traversing the Saanich Inlet (SI) water column (Supplementary Figure 2) and 29 samples collected during the workshop using rDNA pyrotag sequences to compare and cross-calibrate in situ sampling with the McLane Phytoplankton Sampler (PPS) system and bottle sampling methods
Based on non-metric multidimensional scaling (NMDS) and Hierarchical cluster analysis (HCA) results, we focused on changes in operational taxonomic units (OTUs) relative abundance and taxon identity between groups
Summary
Among the many environmental perturbations associated with global climate change is a decrease in dissolved oxygen (O2) concentrations in coastal and interior regions of the ocean. The expansion of OMZs shifts energy away from higher trophic levels, impacting ecosystem functions and services through changes in food web structure and biodiversity (Diaz and Rosenberg, 2008; Stramma et al, 2010; Gruber, 2011; Bijma et al, 2013; Levin and Breitburg, 2015; Gallo and Levin, 2016) These changes are reflected in an increasing role for microbial metabolism in nutrient and energy cycling through the use of alternative terminal electron acceptors (TEAs) including nitrate (NO−3 ), sulfate (SO24−), and carbon dioxide (CO2) (Diaz and Rosenberg, 2008). Marine microbial responses at the individual, population and community levels to OMZ expansion, and the concomitant impact of these responses on global-scale nutrient and energy cycling remain poorly constrained due in part to inconsistent, and perhaps inadequate sampling methods that limit cross-scale comparisons between locations and may cloud our view of in situ microbial processes
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