Long-term trends in aquatic communities of mesotrophic lakes along a land-use gradient in eastern Canada

Increased human development since the Industrial Era has intensified toxic cyanobacterial blooms, which pose significant risks to public health and can cause detrimental effects on lake ecosystems. Mesotrophic lakes are particularly sensitive to nutrient shifts, making them critical systems for understanding bloom dynamics. Sedimentary DNA from paleolimnological archives provides valuable insights into community structure by situating contemporary data within the context of historical dynamics. We analyzed sediment cores from six mesotrophic lakes in Québec and Ontario (Canada) that span a modern human land-use gradient. Cores were analyzed using sedimentary DNA techniques targeting specific cyanobacteria marker genes, including quantitative (q)PCR and 16S rRNA gene sequencing. Cladoceran assemblages from the same cores provided complementary food web data. We detected widespread increases in cyanobacteria abundance across all lakes, with a higher magnitude of increase in lakes located in high intensity land-use catchments. Bloom-forming orders (Nostocales, Chroococcales, Oscillatoriales) increased in relative abundance in some lakes, often replacing unicellular Synechococcales, which tended to dominate less-impacted systems. These cyanobacterial shifts often coincided with compositional changes in cladoceran assemblages, favoring small-bodied and ecologically flexible taxa such as Bosmina and Chydorus brevilabris. Overall, the analyses of paleogenetic records demonstrate that climate change, land-use intensity, and lake-specific traits have driven century-scale cyanobacterial increases and food-web shifts in mesotrophic lakes, with impacts on both bloom dynamics and cladoceran communities. Such long-term analyses are essential for revealing how interacting human and climatic pressures reshape aquatic ecosystems and guiding more effective management.