Nutrient Variables Regulate the Southern Ocean Microbiota Along the Water Column

Understanding the ecological patterns of microbiomes in natural ecosystems is fundamental for predicting their responses to global change. In the productivity-limited Southern Ocean (SO), microbial ecosystem services, including the biogeochemical cycling of carbon, are strongly shaped by environmental variables including temperature, salinity, oxygen, and the availability of nutrients, such as nitrogen, phosphorus, and silicate. However, we lack mechanistic insights regarding the effects of these variables on microbial communities, their functions, interactions, and potential feedback on carbon sequestration. To reduce this knowledge deficit regarding SO microbiomes, we used flow cytometry to estimate the total number of prokaryotes, and 16S rRNA gene amplicon analysis of bacteria and archaea to assess the putative interactions of microbiota throughout the water column, along a 2,800 km transect, spanning all the major SO fronts. As part of a seasonal experiment focused on understanding biological contributions to carbon sequestration, we complemented our microbe data with nutrient measurements to assess the importance of environmental factors on community dynamics. Between winter and spring, prokaryotic abundances increased significantly, likely due to a rise in primary productivity. In both seasons, the diversity and structure of bacterial and archaeal communities were shaped by depth, latitudinal differences, and water mass characteristics. Environmental variables played a strong role in shaping microbial communities in spring and were less important in winter when conditions throughout the water column were homogenous. Our analysis shows that bacterial keystone taxa differed between the seasons in the euphotic zone, while archaeal keystone taxa were primarily influenced by seasonal changes in aphotic waters. Together, our results shed new light on the structure of and interactions among Southern Ocean microbial communities in response to environmental changes and nutrient availability in winter and spring.