Abstract
Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical, and temporal turnover. Yet, recent studies showed that the Arctic marine ecosystem harbors unique microbial community members that are adapted to harsh environmental conditions, such as near-freezing temperatures and extreme seasonality. The gene for the small ribosomal subunit (16S rRNA) is commonly used to study the taxonomic composition of microbial communities in their natural environment. Several primer sets for this marker gene have been extensively tested across various sample sets, but these typically originated from low-latitude environments. An explicit evaluation of primer-set performances in representing the microbial communities of the Arctic Ocean is currently lacking. To select a suitable primer set for studying microbiomes of various Arctic marine habitats (sea ice, surface water, marine snow, deep ocean basin, and deep-sea sediment), we have conducted a performance comparison between two widely used primer sets, targeting different hypervariable regions of the 16S rRNA gene (V3–V4 and V4–V5). We observed that both primer sets were highly similar in representing the total microbial community composition down to genus rank, which was also confirmed independently by subgroup-specific catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) counts. Each primer set revealed higher internal diversity within certain bacterial taxonomic groups (e.g., the class Bacteroidia by V3–V4, and the phylum Planctomycetes by V4–V5). However, the V4–V5 primer set provides concurrent coverage of the archaeal domain, a relevant component comprising 10–20% of the community in Arctic deep waters and the sediment. Although both primer sets perform similarly, we suggest the use of the V4–V5 primer set for the integration of both bacterial and archaeal community dynamics in the Arctic marine environment.
Highlights
The Arctic Ocean is the most rapidly changing marine region on the planet due to its fast warming causing substantial seaice loss (Peng and Meier, 2018; Dai et al, 2019), as well as increasing pollution (Peeken et al, 2018)
The final datasets consisted of 3,318,649 sequences in the V3–V4 dataset that were assigned to 12,045 amplicon sequence variants (ASVs) and 3,340,628 sequences in the V4–V5 dataset that were assigned to 14,505 ASVs (Supplementary Table 2)
The sediment community richness was significantly higher in the V4–V5 dataset (Wilcoxon signed-rank test; p < 0.01), with up to double the amount of bacterial ASVs compared to the V3–V4 dataset
Summary
The Arctic Ocean is the most rapidly changing marine region on the planet due to its fast warming causing substantial seaice loss (Peng and Meier, 2018; Dai et al, 2019), as well as increasing pollution (Peeken et al, 2018). Throughout the annual cycle, Arctic surface waters bacterial and archaeal communities exhibit pronounced fluctuations of the dominant taxonomic groups (Alonso-Sáez et al, 2008; Wilson et al, 2017; Müller et al, 2018), which are strongly associated with presence of sea ice and the seasonal phytoplankton blooms (Kirchman et al, 2007; Nikrad et al, 2012; Fadeev et al, 2018; Cardozo-Mino et al, 2020). As well as under ice-covered conditions, the communities are dominated by the bacterial classes Alphaproteobacteria (mainly the SAR11 clade), Dehalococcoidia (mainly SAR202 clade), and the archaeal class Nitrososphaeria (Alonso-Sáez et al, 2008; Wilson et al, 2017; Müller et al, 2018). Differences between ice-covered and icefree communities affect the microbial diversity of the deep ocean and the seafloor via alterations of microbial communities on marine snow (Fadeev et al, 2020)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
