A Pilot Application of Sedimentary DNA to Reveal Long-Term Fish Diversity Dynamics in an Urbanized Estuary and Adjacent Waters

Estuaries and adjacent waters are highly productive ecosystems, but are increasingly stressed by urbanization and climate change. Understanding long-term shifts in fish communities is critical for sustainable management, yet remains limited by scarce historical data. Here, we applied quality-controlled sedimentary DNA (sedDNA) metabarcoding, combining contamination prevention, stringent data filtering, and statistical calibration, to reconstruct <i>ca</i>. 100 years of fish diversity dynamics in the Pearl River Estuary (PRE) area, southern China. The monitored sedDNA data sets revealed that changes in fish communities in the PRE can be categorized into four distinct historical phases: the 1930s-1950s, 1950s-1970s, 1970s-1990s, and 1990s-2020s. Taxonomic and functional richness peaked around the 1970s but declined sharply thereafter. Small-bodied and omnivorous species gradually gave way to larger-bodied and warm-water species, reflecting a shift in trophic and habitat preferences over time. Invasive species, such as <i>Oreochromis niloticus</i> and <i>Coptodon zillii</i>, became increasingly dominant, whereas indigenous species markedly declined. Multivariate analyses showed that urbanization primarily affected taxonomic diversity, while climate drivers shaped functional traits and community structure, with invasive species acting as key mediators of ecological disruption. Overall, these results offer new insights into the century-scale fish diversity dynamics under compounded urbanization and climatic pressures, and highlight sedDNA as a powerful tool for reconstructing historical biomonitoring records.