Who’s doing what? A metaproteomic survey of Southern Ocean microbes near Antarctica.
The ocean around Antarctica is not just cold, it’s also dark for a large part of the winter. This means that carbon fixation by photosynthesis is inhibited during the polar winter. We used metaproteomics to reconstruct the ecology of microbes at the surface of the Southern Ocean near the Antarctic Peninsula, for both winter and summer seawater samples. Metagenomics (community genomics) tells us what kinds of genes are present. Metaproteomics goes a step further and determines which proteins (including enzymes) are actively being produced by microbes within a community. Therefore, we can use this approach to reconstruct microbial processes used for carbon fixation, nutrient acquisition, and other metabolic pathways. We found that ammonia-oxidising archaea were dominant at the Southern Ocean in winter, with the detected proteins indicating that they had a major role in ‘dark’ (light-independent) carbon fixation at the surface. In summer, by contrast, these autotrophic archaea were undetectable at the ocean surface, when photosynthesis by algae was the major route of carbon fixation. SAR11 bacteria (Pelagibacter spp.) were prevalent in both winter and summer, and detected proteins indicate that ATP-dependent uptake was important for the acquisition of nutrients by these heterotrophs, including simple organic compounds such as amino acids and taurine. Flavobacteria (especially Polaribacter) were more prevalent in summer, and the detected proteins show that these heterotrophic bacteria use exoenzymes to target complex biomolecules (polypeptides, polysaccharides) released from decaying algae. Overall, metaproteomics of the Southern Ocean surface has allowed us to identify the similarities and differences between winter and summer microbial communities, as well as which particular nutrients are being targeted by individual groups of bacteria and archaea.