Environmental DNA Marine France LaPerouse 2019

Fish environmental DNA data set collected in the shallow seamount of La Pérouse located between Madagascar and Réunion Island

In 2019, we sampled the shallow seamount of La Pérouse, located between Madagascar and Réunion Island in the WIO. La Pérouse is an extinct volcano with a summit depth at 60 m below the sea surface. The plateau of the summit has a maximum length of 12 km and a maximum width of 4 km. One side of the seamount might have collapsed in the past, leading to a less common crescent-shaped summit. The abyssal plains that surround this isolated pinnacle are at a depth of 5000 m. Despite its proximity to Réunion Island (160 km northwest), La Pérouse and its surroundings are still poorly studied.

To sample eDNA in this location we used a submersible pump (Subspace, Geneva, Switzerland; nominal flow of ~ 1.0 L/min) to collect samples at various depths during close circuit rebreather dives. The pump has an internal battery and can be activated underwater allowing in situ filtration directly at the targeted habitat and depth. The filtration lasted for 30 min to collect a total water volume of ~ 30 L. During close circuit rebreather dives, water samples from various depths, ranging from 60 to 140 m below the sea surface, were collected using only the Submersible method (eight stations: no replicates). Out of the eight water samples, six were collected during the day, while two were collected at night (IS2_1 at 62 m and IS7_1 at 100–125 m). We applied this filtration protocols to collect and filter water throughout a VigiDNA® 0.2 μM cross-flow filtration capsule (SPYGEN, le Bourget du Lac, France) using disposable sterile tubing for each filtration capsule. After the filtration process, the remaining water in the capsules was emptied. The capsules were then filled with 80 ml of lysis conservation buffer (CL1 buffer SPYGEN, le Bourget du Lac, France) and stored at room temperature in the dark. At La Pérouse, a total of eight water samples were collected during the MONT LA PÉROUSE expedition (https://gombessa-expeditions.com/mont-la-perouse/) on board the ship La Curieuse to the seamount La Pérouse from October 27th to November 5th 2019. We followed a strict contamination control protocol in both field and laboratory stages. 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)

• Internal Funding ELE group (ETHZ/WSL)
• Andromede Oceanologie (Grant/Award: GOMBESSA 5)
• ANR labcom 2 (Grant/Award: InToSea (Innovative Tools under the Sea) joint laboratory)
• Manufacture de Haute Horlogerie Suisse Blancpain and Blancpain Ocean Commitment
• Prince Albert II de Monaco Foundation
• Société des explorations de Monaco
• French Water Agency
• Galaxea
• Ministry of Overseas France (Grant/Award: Convergence and Transformation Contract 2019-2022, measure 3.5.1.1 of the “Resilient Territories” section)
• Vie Océane, Aquarium de La Réunion, Comité Régional d'Etudes et de Sports sous-marins de La Réunion, Inset, O Sea Bleu, Fondation du Crédit Agricole Réunion Mayotte, Fondation d'Entreprises des Mers Australes, Air France, Odyssée Créateur de voyages, Entropie. The financial partners of Andromède Océanologie and Gombessa Expéditions are: Blancpain, Ocean Commitment Blancpain, RGBlue, Keldan, Topstar, Bigblue, Ap Diving, Molecular, Subspace, Nikon, Aqualung, Seacam
• ARTE, INPP (Institut National de Plongée Professionnelle), Les Gens Bien Production, Région Sud, Fondation IRIS, Fondation Véolia, Agence Française pour la Biodiversité, CNC, Métropole Nice Côte d'Azur, Parc National des Calanques, Océanopolis Brest, Ushuaïa TV, AP divig, Aqualung, Nikon, Syera, HE2B ISEK, Molecular, Seacam, Bigblue, Keldan, Neotek, enlaps, RG Blue, Azoth Systems, Subspace pictures, Topstar

Muff, Marion, et al. "Environmental DNA highlights fish biodiversity in mesophotic ecosystems." Environ. DNA, vol. 5, no. 1, 1 Jan. 2023, pp. 56-72, doi:10.1002/edn3.358.