Metabarcoding of sedimentary ancient DNA reveals centuries of species turnover and introductions of non-indigenous species in a highly urbanised estuary

Understanding how anthropogenic pressures shape ecosystems over time is crucial for managing both biodiversity and bioinvasion risk. Despite recent research efforts focussing on temporal community changes as a result of human impacts, little is known about such changes over periods exceeding a century. Here, we reconstructed long-term community changes and non-indigenous species (NIS) dynamics by using sedimentary ancient DNA (sedaDNA) metabarcoding and geochemical analysis of sediment cores samples collected from a temperate estuary (Southampton Water, southern British Isles) subject to significant human impacts for centuries. We detected 73 species of Metazoa and Plantae and classified them by their status (native, cryptogenic and NIS). Our results revealed sporadic detection of NIS (both failed and continuously successful NIS introductions) throughout the entire sedimentary record. Notably, some NIS were detected as early as the 18th century, indicating the presence of NIS introductions in pre-industrial times. We found a continuous overall decline in native species richness since the 19th century. In addition, we found distinct peaks in copper and zinc concentrations reflecting recent periods of intensified industrial and port activity, highlighting the role of human activities in shaping biodiversity patterns and NIS dynamics. Our findings demonstrate how metabarcoding of sedaDNA archives can reveal trends in the distribution of NIS and wider biodiversity over centuries. The integrated approach used here provides new insights into biodiversity changes through time, unravels key information for biodiversity conservation management and biosecurity policy, and shows the potential that sedaDNA metabarcoding has for investigating intrinsic attributes of NIS introductions.