Differences in Prokaryotic Community Composition Between Two Climatically Contrasting Years in an Arctic Fjord Ecosystem

Kongsfjorden, a glaciated fjord in the Arctic, is shaped by Atlantic water inflow and seasonal glacier melt. This study compared prokaryotic community dynamics during spring and summer in two contrasting years, 2019 and 2020. In spring 2019, warmer Atlantic water increased temperatures and nutrients, supporting a Phaeocystis pouchetii ‐dominated bloom. In contrast, spring 2020 was colder, with extensive sea ice and a bloom succession from diatoms to P. pouchetii . Summer surface waters showed strong glacier runoff influence and low‐biomass, flagellate‐dominated phytoplankton. Greater prokaryotic diversity was observed in 2019, particularly at the surface, which was supported by network analysis revealing fewer interactions among prokaryotes in surface waters during 2020 compared to 2019. Prokaryotic community composition clearly differed between the 2 years, showing vertically homogeneous communities and higher cyanobacterial abundance in 2019, while in 2020 communities were more vertically heterogeneous and potentially locally adapted. These patterns reflect greater Atlantic water influence in 2019 versus more stratified Arctic conditions in 2020. Surface and bottom communities showed contrasting trends, shaped by depth‐specific environmental conditions. Our findings highlight the sensitivity of Arctic microbial communities to shifts in hydrography and bloom dynamics and provide important perspectives on the ecological stability and dynamics of Arctic microbial communities under changing environmental conditions.