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 compre..., Fusion-tag qPCR
A universal primer set targeting 18S rRNA (V1-3 hypervariable region; 18S_uni_1F: 5’ – GCCAGTAGTCATATGCTTGTCT – 3’; 18S_uni_400R: 5’ – GCCTGCTGCCTTCCTT – 3’; Pochon et al. 2013) was used to maximise detection of the eukaryotic component of marine diversity, hereafter the 18Suni assay. We used a second assay targeting ITS2 (scl58SF: 5’ – GARTCTTTGAACGCAAATGGC – 3’; scl28SR: 5’ – GCTTATTAATATGCTTAAATTCAGCG – 3’; Brian et al. 2019) to increase the taxonomic resolution of identified Anthozoa (Phylum Cnidaria) and Demospongiae (Phylum Porifera) within each environmental sample, hereafter the ITS2 assay (also referred to as “CP1 assay” in Alexander et al. 2020). The former class includes anemones, stony corals, soft corals, and gorgonians, whereas the latter class includes 81% of all sponge species. Both groups play an important role in the functioning of coral reef ecosystems, such as recycling dissolved organic matter (Rix et al. 2016). 
Quantitative PCR (qPCR) experiments f..., We here provide Illumina MiSeq sequences demultiplexed by seawater or gut content sample each in .fastq.gz format. All downstream data quality filtering steps that we used are outlined in the PeerJ publication (https://doi.org/10.7717/peerj.16075).