Changing Pacific salmon nursery lake ecosystem dynamics over centuries to millennia: insights from sedimentary DNA metabarcoding

Pacific salmon are keystone species to North Pacific freshwater, coastal, and oceanic ecosystems, but many populations have declined or become more variable in recent decades due to anthropogenic impacts and climate change. Long-term records are needed to understand past changes, identify ecosystem stressors, and guide restoration. We used sedimentary DNA (sedDNA), an emerging paleoecological approach offering broader taxonomic information than traditional methods, to reconstruct ecosystem changes across five Pacific salmon nursery lakes in British Columbia (Canada). DNA metabarcoding targeting the 18S ribosomal RNA gene V7 region was used to track shifts in eukaryotic communities including algae and invertebrates over centuries to millennia. Most lakes showed notable algal community shifts over the past two centuries, with declining green algae and rising diatom relative abundances. Chrysophytes and dinoflagellates also increased over the past century in most lakes, likely driven by stronger thermal stratification, which favored these motile and mixotrophic algae that are capable of vertical migration and flexible nutrient acquisition. We contextualized the trajectories of each core through an ordination analysis based on 98 lakes distributed across British Columbia, which identified land-use changes and longer growing seasons as potential drivers. Network analyses of the sedDNA time series revealed decreasing modularity and increasing connection across lakes, suggesting a shift in resilience mechanisms from between-module buffering by compartmentalized specialists to within-guild insurance via functional overlap among generalists. Our findings demonstrate that sedDNA provides taxonomically rich, long-term insights into aquatic ecological dynamics, which are foundational for understanding and protecting Pacific salmon nursery habitats.