Multi-omics insights into plant-microbe dysbiosis caused by cyanobacterial bloom-affected water

The use of untreated, cyanobacterial bloom-affected river water as a readily available source for crop production is a realistic scenario in many regions, yet its systemic impact on crop health remains poorly defined. Here, we investigate the multifaceted effects of this practice by cultivating lettuce (Lactuca sativa) with bloom-season water from the eutrophic Nakdong River and comparing it to lettuce grown in a nutrient-optimized hydroponic solution. We found that exposure to bloom-affected water severely inhibited plant growth and led to the accumulation of microcystins in edible tissues, with estimated daily intakes exceeding WHO safety thresholds. Multi-omics analyses revealed that this phenotype was driven by a synergistic failure of internal and external support systems: key mitochondrial genes for energy production were downregulated, protective antioxidant flavonoids were depleted, and the aquatic microbiome shifted to a dysbiotic state that favored stress-tolerant taxa while reducing beneficial ones. Together, these results establish how bloom-affected water initiates a vicious cycle of physiological stress and microbial dysbiosis that undermines crop health. This study provides an integrative framework for assessing risks in real-world hydroponic systems and for guiding future investigations into more complex soil-based agriculture.