Fish environmental DNA data set collected in the French Scattered Islands across Surface and Seamount Habitats
During a scientific expedition aboard the R/V Marion Dufresne in April 2019, spanning from the 8th to the 28th, we collected 75 water samples in four French Scattered Islands (Europa, Glorieuse, Juan de Nova, and Tromelin). These samples comprised two types: transect samples of surface water and fixed point samples taken from the surface to deeper waters. Regarding transect sampling, 36 water samples were collected along 18 transects across the four islands (Europa = 6; Glorieuse = 5; Juan de Nova = 4; Tromelin = 3). We conducted filtration replicates in parallel, with filtration tubes positioned a few centimeters below the surface on each side of the boat. Each transect involved a 30-minute filtration of approximately 30 liters. Initial transects were performed close to the shore on shallow reefs. Subsequent transects were conducted at various distances from the initial points, accounting for observed changes in depth. For Europa, transects were carried out at distances of 50, 300, and 600 meters from the initial point due to a gradual decrease in depth extending from the island's northern part. In contrast, depth decreased rapidly from the initial points in Glorieuse and Tromelin. Therefore, transects were performed at distances of 50, 100, and 300 meters from the initial points for Glorieuse, and at distances of 50 and 100 meters for Tromelin, considering the island's small size, sudden depth decrease, and safety concerns (see Figure 1a–d).
Regarding fixed point sampling, eDNA was collected using 12L Niskin bottles from the surface to deeper habitats at various locations (Europa = 2; Glorieuse = 1; Juan de Nova = 1; Tromelin = 1; Canyon = 1; Juan_Mayotte = 1; Seamount = 1; Seamount_near_Tromelin = 1), covering depths from -1 meter to -3000 meters (from 12L, 24L, or 30L bottles).
In both sampling cases the filtration equipment comprised an Athena® peristaltic pump (Proactive Environmental Products LLC, Bradenton, Florida, USA; nominal flow of 1.0 L min-1), a VigiDNA® 0.2 µM cross flow filtration capsule (SPYGEN, le Bourget du Lac, France), and disposable sterile tubing for each filtration capsule. After filtration, capsules were emptied of water, filled with 80 mL of CL1 conservation buffer (SPYGEN, le Bourget du Lac, France), and stored at room temperature in the dark. We followed a strict contamination control protocol in both field and laboratory stages (Valentini et al., 2016). Each water sample processing included the use of disposable gloves and single-use filtration equipment to avoid any risk of contamination. Libraries were prepared with ligation using the MetaFast protocol (Fasteris).
Data content:
* rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences.
* taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata.
* metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)
