Harmful cyanobacterial blooms (HCBs) caused by Microcystis
aeruginosa are of great concern as they negatively
affect the aquatic environment and human health. Chemical methods
could rapidly eradicate HCBs and have been used for many decades.
However, many chemical reagents are not recommended to eliminate HCBs
in the long term, given the possible destructive and toxic effects
of the chemicals employed on non-target aquatic organisms. We developed
a new algaecide, 2-((1,3,4-thiadiazol-2-yl)thio)-N-(4-chlorophenyl) acetamide (Q2), to control harmful cyanobacteria
while being environmentally friendly and selective. In our study,
Q2 effectively inhibited cyanobacterial growth, especially of M. aeruginosa, but did not affect eukaryotic algae
in test concentrations. A critical mechanism was revealed by transcriptome
and metagenomic results showing that Q2 affects multiple cellular
targets of cyanobacteria for HCB control, including the destruction
of organelles, damage in the photosynthesis center, as well as inhibition
of gas vesicle growth, and these changes can be highly relevant to
the decrease of quorum-sensing functional KEGG pathways. Furthermore,
Q2 did not affect the microbial composition and could recover the
disrupted aquatic functional pathways in a short period. This is different
from the impact on ecosystem functioning of the traditionally used
harmful algaecide diuron. All these results verified that Q2 could
be friendly to the aquatic environment, providing a new directional
choice in managing HCBs in the future.