Addressing a Flat‐Out Problem: Environmental DNA ( eDNA ) Exposes Silent Infestations of Acropora ‐Eating Flatworms ( Prosthiostomum acroporae ) in Coral Aquaculture

ABSTRACT Captive culturing of coral is required to supply a burgeoning aquarium trade and potentially supply populations to replenish reefs that have been degraded globally due to anthropogenic impacts. High‐density coral propagation can be compromised by pests that reduce broodstock and offspring health. Acropora ‐eating flatworms ( Prosthiostomum acroporae ) are parasitic polyclads that often evade visual detection and feed on tissues of branching coral species of the genus Acropora , which are key targets for coral aquaculture production. We developed a highly sensitive and specific droplet digital PCR (ddPCR) assay to detect environmental DNA (eDNA) of P. acroporae from water samples, with the limit of detection of 2.3 copies of the mitochondrial cytochrome c oxidase subunit I gene per ddPCR reaction. Validation was performed using water samples of aquaria holding Acropora corals suspected to be affected by P. acroporae, and the sequence identity of ddPCR amplicons confirmed by Sanger sequencing. P. acroporae eDNA was detected in some cases without visual confirmation of P. acroporae , indicating this assay can detect early infestations of P. acroporae that are not evident through visual monitoring. This study demonstrates that the ddPCR assay can be a valuable tool for monitoring pests in coral aquaculture systems and subclinical detection of parasitic infestations.