Abstract
Global climate change intensifies the water cycle and makes freshest waters become fresher and vice‐versa. But how this change impacts phytoplankton in coastal, particularly harmful algal blooms (HABs), remains poorly understood. Here, we monitored a coastal bay for a decade and found a significant correlation between salinity decline and the increase of Karenia mikimotoi blooms. To examine the physiological linkage between salinity decreases and K. mikimotoi blooms, we compare chemical, physiological and multi‐omic profiles of this species in laboratory cultures under high (33) and low (25) salinities. Under low salinity, photosynthetic efficiency and capacity as well as growth rate and cellular protein content were significantly higher than that under high salinity. More strikingly, the omics data show that low salinity activated the glyoxylate shunt to bypass the decarboxylation reaction in the tricarboxylic acid cycle, hence redirecting carbon from CO 2 release to biosynthesis. Furthermore, the enhanced glyoxylate cycle could promote hydrogen peroxide metabolism, consistent with the detected decrease in reactive oxygen species. These findings suggest that salinity declines can reprogram metabolism to enhance cell proliferation, thus promoting bloom formation in HAB species like K. mikimotoi , which has important ecological implications for future climate‐driven salinity declines in the coastal ocean with respect to HAB outbreaks.