RÉSUMÉ
In recent years, the region surrounding Sepetiba Bay (SB; SE Brazil) has become a hub of intense urban expansion and economic exploitation in response to ore transport and industrial and port activities. As a result, contaminants have been introduced into the bay, leading to an overall worsening of the environmental quality. The present work applies for the first time a foraminiferal morphology-based approach (M) and eDNA-based metabarcoding sequencing (G), along with geochemical data to assess the ecological quality status (EcoQS) in the SB. Principal component analysis shows that the eDNA and morphospecies diversity as well as most of the taxa relative abundance decline in response to the environmental stress (ES) gradient related to total organic carbon (TOC) and metal pollution. Based on ecological indices, Exp(H'bc) (G), Exp(H'bc) (M), foraminifera ATZI marine biotic index (Foram-AMBI), Foram Stress Index (FSI), and geochemical indices (TOC and Potential Ecological Risk Index), the lowest values of EcoQS (i.e., bad to moderate) are inferred in the innermost part of the SB. Despite minor discrepancies among the six EcoQS indices, an agreement has been found for 63% of the stations. To improve the agreement between the ecological indices, it is necessary to fill the gap in species ecology; information on the ecology of many species is still unknown. This work reinforces the importance of molecular analysis and morphological methods in environmental impact studies and confirms the reliability of foraminiferal metabarcoding in EcoQS assessment. This is the first study evaluating the EcoQS in the South Atlantic by using combined foraminiferal eDNA metabarcoding with morphological data.