Continental scale metagenomics reveals Microcystis ‐induced synchrony among aquatic taxa is exacerbated by trophic cascades

Harmful Microcystis proliferation severely threatens aquatic ecosystems globally, but its impacts on food‐web stability remain poorly understood. Here, we analyzed 1309 metagenomic samples from freshwater ecosystems across China to investigate how Microcystis abundance affects synchrony among taxa in multi‐trophic food webs (from bacteriophages to piscivorous fish). We found that Microcystis abundance was significantly positively correlated with anthropogenic factors (e.g. GDP, population density, nitrogen and phosphorus emissions), and its proliferation was strongly associated with increased synchrony among aquatic taxa. In contrast, other aquatic taxa (e.g. fish, zooplankton and bacteria) showed no such effects on synchrony. The enhanced synchrony associated with Microcystis proliferation occurred more frequently between consumers and their food resources than among aquatic taxa lacking consumer–resource relationships. Moreover, trophic cascades were more strongly correlated with these synchrony dynamics at middle and high trophic levels, whereas synchrony at low trophic levels was mainly directly affected by Microcystis . Overall, our results reveal that synchrony among aquatic taxa is strongly dependent on trophic linkages. This study provides a pioneering framework for integrating large‐scale metagenomic datasets to improve our understanding of food webs dynamics under Microcystis proliferation pressure across a broad taxonomic range.