Harmful algal and bacterial blooms linked to deforestation, soil loss and global warming are increasingly frequent in lakes and rivers. We demonstrate that climate changes and deforestation can drive recurrent microbial blooms, inhibiting the recovery of freshwater ecosystems for hundreds of millennia. From the stratigraphic successions of the Sydney Basin, Australia, our fossil, sedimentary and geochemical data reveal bloom events following forest ecosystem collapse during the most severe mass extinction in Earth’s history, the end-Permian event (EPE; c. 252.2 Ma). Microbial communities proliferated in lowland fresh and brackish waterbodies, with algal concentrations typical of modern blooms. These initiated before any trace of post-extinction recovery vegetation but recurred episodically for >100 kyrs. During the following 3 Myrs, algae and bacteria thrived within short-lived, poorly-oxygenated, and likely toxic lakes and rivers. Comparisons to global deep-time records indicate that microbial blooms are persistent freshwater ecological stressors during warming-driven extinction events.

与森林砍伐、土壤流失和全球变暖有关的有害藻类和细菌大量繁殖在湖泊和河流中越来越频繁。我们证明气候变化和森林砍伐会导致微生物反复大量繁殖，从而抑制淡水生态系统的恢复达数百年之久。从澳大利亚悉尼盆地的地层序列中，我们的化石、沉积和地球化学数据揭示了地球历史上最严重的大规模灭绝期间森林生态系统崩溃后的水华事件，即二叠纪末事件（EPE；c. 252.2 Ma）。微生物群落在低地淡水和微咸水体中增殖，藻类浓度是现代水华的典型特征。这些在任何灭绝后恢复植被的踪迹之前就开始了，但在超过 100 kyrs 的时间内偶尔出现。在接下来的 3 Myrs 期间，藻类和细菌在寿命短、缺氧且可能有毒的湖泊和河流中繁衍生息。与全球深度时间记录的比较表明，在变暖驱动的灭绝事件期间，微生物大量繁殖是持续的淡水生态压力源。