Full-length 16S rRNA gene sequencing combined with adequate database selection improves the description of Arctic marine prokaryotic communities

When we think about the Arctic, images of endless ice and polar bears usually come to mind. However, beneath the surface of the Arctic Ocean lies an incredible world that plays a vital role in the health of our planet: microbes. These tiny organisms, like bacteria and archaea, live in the cold, dark waters and playing a vital role in the ecosystem.

Despite their importance, scientists have only scratched the surface of understanding which microbes live in the Arctic and what they do. Why? Mostly because of methodology constrains, studies until now have relied on sequencing just small fragments of microbial DNA, making it difficult to identify many species accurately.

This’s where this study comes in. Scientists wanted to test if there were differences between sequencing the full-length 16S rRNA gene and just sequencing short regions of the gene. Also, teste the influence of databases, comparing the commonly used SILVA databased to the more recent Genome Taxonomy Database (GTDB). Researchers thought that sequencing the entire gene and using GTDB for taxonomic assignment would recover a much more complete and accurate view at Arctic microbial communities.

The results? Indeed, using the two tools combined, the researchers were able to identify many more microbial species (Figure 1). Not only did they confirm the presence of known groups, but they also discovered new lineages and better classified many species that had previously been hard to identify to such taxonomic detail.

Figure 1: Percentage of Amplicon sequencing variant/s (ASVs) classified at each taxonomic level. The left panel shows results for the GTDB database and the right panel shows results for the Silva database. For each database, full-length and V4-V5 16S rRNA gene sequencing were compared (orange and blue, respectively).

Why is this important? As the Arctic warms faster than any other region on Earth, understanding how its ecosystems work is more urgent than ever. Microbes are incredibly sensitive to changes in temperature and nutrients and if they change, the effetc can ripple through the entire ecosystem. So, by knowing who these microbes are and how they function, scientists can better monitor/predict how the Arctic is/will respond to climate change.

This study gives us a clearer way to investigate the hidden life of the Arctic Ocean. By using full-length gene sequencing and modern classification tools, researchers identified more species, painting a more detailed picture of Arctic microbial life.

Source: Pascoal, F., Duarte, P., Assmy, P. et al. Full-length 16S rRNA gene sequencing combined with adequate database selection improves the description of Arctic marine prokaryotic communities. Ann Microbiol 74, 29 (2024). https://doi.org/10.1186/s13213-024-01767-6

Author: Lucas Bastos

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