A multi-faceted indirect anticyanobacterial mechanism through cell-free filtrates of Enterobacter cloacae TL3

Cyanobacterial blooms pose a major threat to aquatic ecosystem health and water quality. Anticyanobacterial bacteria are promising for bloom mitigation, yet their time-resolved inhibitory mechanisms in cyanobacteria remain poorly understood. Here, we isolated a potent anticyanobacterial strain, Enterobacter cloacae TL3, from the eutrophic Taihu Lake and systematically elucidated its time-dependent, multi-target inhibitory mechanism against the dominant bloom-forming cyanobacterium Microcystis aeruginosa. By integrating short-term phenotypic assays with time-resolved transcriptomic profiling, we revealed a distinct temporal cascade of cellular disruption triggered by the sterile filtrates of strain TL3. Within 6 h, sterile filtrates of TL3 triggered extensive transcriptional reprogramming in M. aeruginosa, primarily disrupting Photosystem I (PSI) function and cellular defense pathways. After 12 h, microscopic observation revealed severe structural damage, including cell wall rupture, thylakoid membrane disintegration, complete inhibition of PSI inactivation, and a significant decline in the electron transport of Photosystem II (PSII). Cyanobacterial cells exhibited marked stress responses, characterized by enlargement of intracellular poly-β-hydroxybutyrate (PHB) granules associated with osmotic balance. A substantial downregulation of genes was further revealed by transcriptomic analyses in pathways including cell wall biosynthesis (C789_RS10970), PSII structural components (psbC, psbD), as well as pigment production, self-defense, and DNA repair (cmr4, ruvA). Collectively, these multi-layered impairments ultimately led to irreversible cellular collapse. Our study elucidates a previously unrecognized multi-target anticyanobacterial mechanism in E. cloacae TL3, providing new insights for the development of sustainable strategies to mitigate cyanobacterial blooms in eutrophic waters.