Global climate change intensifies the water cycle and makes freshest waters become
fresher and vice-versa. But how this change impacts phytoplankton in coastal, par-
ticularly harmful algal blooms (HABs), remains poorly understood. Here, we moni-
tored 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 CO2 release to biosynthesis. Furthermore, the
enhanced glyoxylate cycle could promote hydrogen peroxide metabolism, consist-
ent 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.

global climate change, harmful algal blooms (HABs)