Interactions between phytoplankton and bacteria play critical roles in shaping marine ecosystems, yet the intricate relationships within these communities - particularly in extreme and rapidly changing environments like the coastal Southern Ocean - remain poorly understood. Here, we apply targeted methods to directly characterize the microbiome associated with individual colonies of Phaeocystis antarctica, a keystone phytoplankton species in the Southern Ocean, for the first time. By comparing the microbiomes of colonies isolated from distinct geographical locations with just a few days between sampling events and again after prolonged laboratory culture, we demonstrate the consistency of the colony microbiome across space while also revealing significant shifts when subjected to laboratory conditions for a year. The bacterial orders Alteromonadales, Oceanospirillales, and Sphingomonadales dominated all field-collected colony microbiomes, regardless of sampling location, whereas Caulobacterales, Cellvibrionales, and Rhodobacterales dominated cultured-colony microbiomes. The shift in microbiome structure emphasizes the importance of in situ field-based studies to capture the complexity of microbial interactions, especially for polar species originating from environments that are difficult to replicate in culture conditions. Furthermore, the relative abundances of bacterial taxa comprising the majority of field-collected colony microbiome - e.g., Paraglaciecola sp. (Alteromonadales) and Nitrincolaceae (Oceanospirillales) - were strongly associated with Phaeocystis abundance in surface waters, highlighting their potential roles in bloom dynamics and carbon cycling. This research provides valuable insights into the ecological significance of microbial interactions with key phytoplankton species and underscores the necessity of considering these dynamics in the context of climate-driven shifts in marine ecosystems.