An examination of seasonal variation in taxonomic richness and community composition using eDNA on a tropical coral reef

Small volumes of water containing environmental DNA (eDNA) are increasingly combined with metabarcoding to generate biodiversity data for specific fractions of marine flora and fauna. To date, however, few studies have utilized this technique to assess how well it captures seasonal patterns in coral reef communities or how environmental or methodological factors influence eDNA detections. In our study, we used three eDNA metabarcoding assays primarily targeting bony fish, elasmobranchs, as well as cnidarians and sponges (Cnidaria/Porifera) combined with monthly seawater sampling to 1) investigate temporal variation in taxonomic detections and 2) statistically test the potential effect of season, sea surface temperature, timing of spawning (using moon phase as a proxy), and sample preservation on taxon detection across a 12-month period in a model coral reef system (Big Vicki’s Reef, Lizard Island, Great Barrier Reef, Australia). Species-level fish and genus-level scleractinian coral det..., Laboratory processing
DNA was extracted from half of each filter membrane (including filtration controls) within six months of collection using the DNeasy Blood and Tissue Kit (QIAGEN) in the TrEnD Laboratory at Curtin University in Western Australia with the following modifications: 540 µl of ATL lysis buffer, 60 µl of Proteinase K, and a 3-hr digest at 56°C. An extraction blank was processed in parallel with every set of eleven samples to detect any cross-contamination. Three previously published primer sets (16S Fish, CoralITS2, and CoralITS2_acro; Table 1) were employed in this study to amplify primarily teleost fish and scleractinian coral taxa, respectively. Quantitative PCR (qPCR) was carried out in 25 μl containing the following concentrations: 1X AmpliTaq Gold® PCR buffer (Life Technologies, Massachusetts, USA), 2 mM MgCl2 (Fisher Biotec, Australia), 0.4μM dNTPs, 0.1mg BSA (Fisher Biotec, Australia), 0.4 μM each of forward and reverse primers (Integrated DNA Technologies, Austr..., We here provide the demultiplexed 16S Fish (read 1 only), as well as the Coral ITS2 (CP1) and Coral ITS2_acros (CP2; read 1 and read 2) assay sequence data in .fastq format, along with an excel spreadsheet listing the metadata associated with each seawater sample collected at Lizard Island, Australia. These sequences and metadata were used in the following paper:
DiBattista, J.D., West, K.M., Ceccarelli, D.M., Hoggett, A.K., Vail, L.L., Garcia, R., and Richards, Z.T. (in press) An examination of seasonal variation in taxonomic richness and community composition using eDNA on a tropical coral reef. Coral Reefs. https://doi.org/10.1007/s00338-024-02594-6, # An examination of seasonal variation in taxonomic richness and community composition using eDNA on a tropical coral reef

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## Description of the data and file structure

We here provide the raw demultiplexed 16S Fish (read 1 only), as well as the paired-end Coral ITS2 (CP1) and Coral ITS2_acros (CP2) assay sequence data in .fastq format. These files contain sequence data seperated into their individual sample replicates for each genetic assay. For file naming nomenclature, each file name begins with the acronym for Lizard Island Research Station (LIRS), followed by the date of sampling, followed by the replicate number, followed by the genetic assay, and in the case of paired-end sequencing runs/assays (i.e. CP1 and CP2), whether it is the read 1 set of sequences (R1) or the read 2 set of sequences (R2). For example, LIRS_12_01_20_1_16S_Fish.fastq are the DNA sequen...