The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.

The rapid urbanization and industrialization of Kuwait and the consequent effluent discharges into marine environments have resulted in a degradation of water and sediment quality in the coastal marine ecosystems such as in the Kuwait Bay. This study investigates the ecological response of benthic foraminifera (protists) to environmental stress in the Kuwait Bay. The traditional morphological approach was compared to the innovative environmental DNA (eDNA) metabarcoding to evaluate the ecological quality status (EcoQS). Forty-six surface sediment samples were collected from selected stations in the Kuwait Bay. To detect the pollution gradient, environmental parameters from water (e.g., salinity, pH, dissolved oxygen) and sediment (e.g., grain-size, trace metals, total organic carbon, total petroleum hydrocarbons) were measured at each station. Although the foraminiferal assemblages were different in the morphological and molecular datasets, the species turnover was congruent and statistically significant. Diversity-based biotic indices derived from both morphological and metabarcoding approaches, reflect the environmental stress gradient (i.e., organic and metal contaminations) in the Kuwait Bay. The lowest values of EcoQS (i.e., bad to poor) are found in the innermost part (i.e., Sulaibikhat Bay and Ras Kazmah), while higher EcoQS values occur in the outer part of the bay. This study constitutes the first attempt to apply the foraminiferal metabarcoding to assess the EcoQS within the Arabian Gulf and presents its advantages compared to the conventional morphological approach.