Continual eDNA detectability amidst diel reef species fluctuations on diver transects

This eDNA sequence data was collected as part of a collaborative project between CSIRO and the University of Tasmania examining diel reef activity fluctuations observed by underwater visual census (diver transects) on eDNA detectability across a 24-hr period. eDNA sequence data is provided in the form of fastq files - these files are demultiplexed and primer trimmed, but have not yet been quality filtered.\nLineage: Seawater samples for eDNA analyses were collected from Fortescue Bay, Tinderbox Marine Reserve and Waubs Bay, Bicheno in Tasmania, Australia, in the summer months of November 2021, February and March 2022. These samples were collected in tandem with Reef Life Survey diver transects every six-hours (four times within a 24-hr period; time-points: 10 am, 4 pm, 10 pm, 4 am) at the three sites (see manuscript supplementary information). The 10 am and 4 pm time-points were within daylight hours; the 10 pm and 4 am time points were during the night.\n\nFive eDNA seawater samples were collected by divers adjacent to the seafloor (depth of 5 m) at the start and end of the transects using bleach-sterilised Nalgene bottles (total 10 x 1 L eDNA samples per time point, per site). Seawater eDNA samples were then individually filtered across 0.45 µm 47 mm MF-Millipore® mixed cellulose ester (MCE) membranes using a Masterflex® L/S® Variable-Speed Digital Drive pump within one hour of collection. A 10% bleach solution was used to clean filtration equipment between time points at a site, followed by a rinse in Milli-Q® (MilliporeSigma) water. A one-litre sample of the Milli-Q rinse water was filtered between the day and night intervals at each site, to serve as a filtration control and detect any carry over contamination. At the conclusion of sampling, filtrate membranes were kept cool at ~5°C and transported to CSIRO Marine Laboratories in Hobart, Tasmania, then stored at -80°C until extracted.\n\nDNA was extracted from each filter membrane within two months of collection using the DNeasy Blood and Tissue Kit (QIAGEN) with modifications. Fish and macroinvertebrate DNA was specifically amplified using two previously published PCR assays (16S Fish and COI Leray) from our mixed seawater samples (see manuscript for more information). The resulting library was sequenced on an Illumina NovaSeq 6000 platform (SP flow cell: 500 cycle, 2 x 250 bp) at the Australian Genome Research Facility. \n\nSequencing reads were demultiplexed and trimmed in Cutadapt (v4.5; Martin, 2011) and quality filtered and denoised in R (v3.5.3; RStudio Team, 2015) using the DADA2 (v1.10.1) bioinformatics package (Callahan et al., 2016).\n\nWe have uploaded demultiplexed and primer trimmed (NOT quality filtered) eDNA data for public use. Each sample file is in a fastq format; with sample names corresponding to site/replicate numbers (see eDNA_fastq_READ_ME.txt in Supporting Documentation).