biostudies-literatureGirard EBH2020 European Institute of Innovation and TechnologyDutch Research Council (NWO)e9549https://www.ebi.ac.uk/biostudies/studies/S-EPMC9682090biostudies-literatureUnknown12(11)Monitoring community composition of Foraminifera (single-celled marine protists) provides valuable insights into environmental conditions in marine ecosystems. Despite the efficiency of environmental DNA (eDNA) and bulk-sample DNA (bulk-DNA) metabarcoding to assess the presence of multiple taxa, this has not been straightforward for Foraminifera partially due to the high genetic variability in widely used ribosomal markers. Here, we test the correctness in retrieving foraminiferal communities by metabarcoding of mock communities, bulk-DNA from coral reef sediment samples, and eDNA from their associated ethanol preservative using the recently sequenced cytochrome c oxidase subunit 1 (COI) marker. To assess the detection success, we compared our results with large benthic foraminiferal commuEcology and evolutionCOI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies.PMC968209016.161.301813360Macher JNJompa JRenema WGirard EBfalseCOI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies.Monitoring community composition of Foraminifera (single-celled marine protists) provides valuable insights into environmental conditions in marine ecosystems. Despite the efficiency of environmental DNA (eDNA) and bulk-sample DNA (bulk-DNA) metabarcoding to assess the presence of multiple taxa, this has not been straightforward for Foraminifera partially due to the high genetic variability in widely used ribosomal markers. Here, we test the correctness in retrieving foraminiferal communities by metabarcoding of mock communities, bulk-DNA from coral reef sediment samples, and eDNA from their associated ethanol preservative using the recently sequenced cytochrome c oxidase subunit 1 (COI) marker. To assess the detection success, we compared our results with large benthic foraminiferal commu2022-01-01T00:00:00Z2022 Nov2026-07-14T17:32:21.362Z2025-04-05T18:22:35.885ZS-EPMC96820903644031310.1002/ece3.9549