COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies.

Area of Science:

• Marine Ecology
• Molecular Ecology
• Protistology

Background:

• Foraminifera (single-celled protists) are vital indicators of marine ecosystem health.
• Traditional methods for monitoring Foraminifera are labor-intensive.
• DNA metabarcoding offers efficient multi-taxa assessment but faces challenges with Foraminifera due to high genetic variability in ribosomal markers.

Purpose of the Study:

• To evaluate the effectiveness of DNA metabarcoding using the cytochrome c oxidase subunit 1 (COI) marker for retrieving Foraminifera communities.
• To compare the performance of bulk-DNA and environmental DNA (eDNA) metabarcoding for Foraminifera detection.
• To assess the accuracy of the COI marker against known Foraminifera communities.

Main Methods:

• Metabarcoding analysis of mock communities, bulk-DNA from coral reef sediment, and eDNA from ethanol preservatives.
• Utilized the cytochrome c oxidase subunit 1 (COI) gene marker for Foraminifera identification.
• Compared metabarcoding results with previously reported large benthic foraminiferal data from the same sites.

Main Results:

• Mock community metabarcoding successfully detected most target Foraminifera species.
• Bulk-DNA metabarcoding revealed significantly higher species richness compared to eDNA.
• Bulk-DNA metabarcoding identified additional species not previously reported at the sampling sites.

Conclusions:

• The COI marker provides accurate retrieval of Foraminifera diversity and community composition via DNA metabarcoding.
• Bulk-DNA metabarcoding using the COI marker is a powerful tool for assessing Foraminifera communities.
• The COI marker's lower variability compared to 18S rRNA enhances its utility, provided an adequate reference database is available.