This study aims to explore the structure and function of planktonic communities in the Amundsen Sea, a crucial and climate-sensitive area in the Southern Ocean, using environmental DNA metabarcoding. Given the Amundsen Sea's significant role in global carbon cycles, the research focuses on understanding the microbial food web dynamics in relation to nutrient availability and environmental changes. By analyzing seawater samples from polynya, sea ice, and ice-free regions, the study identifies spatial variations in microbial diversity, nutrient dynamics, and the distribution of functional genes linked to nitrogen cycling and sulfur compound degradation. Key findings include interactions among primary producers, bacteria, and zooplankton, emphasizing the importance of nitrogen and sulfur cycles in maintaining ecosystem balance. These insights highlight the potential impact of rapid environmental changes on planktonic food web dynamics, biodiversity, and ecosystem functioning in the Antarctic.