Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of their reef environment

In tropical marine ecosystems, the coral-based diet of benthic-feeding
reef fishes provides a window into the composition and health of coral
reefs. In this study, for the first time, we compare multi-assay
metabarcoding sequences of environmental DNA (eDNA) isolated from seawater
and partially digested gut items from an obligate corallivore
butterflyfish (Chaetodon lunulatus) resident at coral reef sites in the
South China Sea. We specifically tested the proportional and statistical
overlap of the different approaches (seawater versus gut content
metabarcoding) in characterizing eukaryotic community composition on coral
reefs. Based on 18S rRNA and ITS2 rRNA sequence data, which differed in
their taxonomic sensitivity, we found that gut content detections were
only partially representative of the eukaryotic communities detected in
the seawater. Overall, our results indicate that dietary metabarcoding of
specialized feeders can be complimentary to, but is no replacement for,
more comprehensive environmental DNA assays of reef environments that can
include the processing of different substrates (seawater, sediment,
plankton) or traditional observational surveys. These molecular assays, in
tandem, might be best suited to highly productive but cryptic oceanic
environments (coral reefs, kelp forests, seagrass meadows) that contain an
abundance of organisms that are often small, epiphytic, symbiotic, or
cryptic.