# First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples

Christina Pavloudi, Ioulia Santi, Iñigo Azua, Zuriñe Baña, Mauro Bastianini, Caroline Belser, Jone Bilbao, Julie Bitz-Thorsen, Caroline Broudin, Mathieu Camusat, et al.

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To cite this version:

Christina Pavloudi, Ioulia Santi, Iñigo Azua, Zuriñe Baña, Mauro Bastianini, et al. First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples. Biodiversity Data Journal, 2025, 13, pp.e143585. 10.3897/BDJ.13.e143585. cea-05046943

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First release of the European marine omics
biodiversity observation network (EMO BON)
shotgun metagenomics data from water and
sediment samples

Christina Pavloudi‡, Ioulia Santi‡,§, Iñigo Azua¹, Zuriñe Baña¹, Mauro Bastianini¶, Caroline Belser#, Jone Bilbaoª, Julie Bitz-Thorsen“, Caroline Broudin”, Mathieu Camusat”, Ibon Cancio“, Louis Caray-Counil”, Raffaella Casotti¹, Jade Castel”, Thierry Comtet’, Cymon J Cox’, Claire Daguin’, Oihane Díaz de Cerio“, Katrina Exter¢, Cécile Fauvelotℓ, Miguel J. Frada³, Pierre E Galand⁵, Laurence Garczarek, Jose González Fernándezª, Laure Guillou’, Pascal I. Hablützel¢,², Hanneloor Heynderickx¢, Céline Houbin”, Anne Emmanuelle Kervella‡, Apostolos Krystallas§, Rune Lagaisse¢, Arnaud Laroquette‡, Lyvia LescureP, Eva LopesF, Melina Loulakaki§, Bruno Louro’, Catarina MagalhaesF, Maria Maidanou§, Francesca MargiottaT, Marina Montresor¹, Fabrice Not’, Estefanía ParedesA,N, Isabella PercopoT, Erwan Pérup, Julie Poulain#, Kim Præbel“, Fabienne Rigaut-Jalabert”, Sarah Romac’, Melanthia Stavroulaki§, Jesús Souza TroncosoA,N, Eric ThiébautK, Wilfried Thomas”, Andrzej Tkacz’, Anna Chiara TranoT, Patrick Wincker#, Nicolas Pade‡

‡ European Marine Biological Resource Centre (EMBRC-ERIC), Paris, France

§ Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece

| Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Biscay, Spain

¶ CNR-National Research Council, ISMAR - Institute of Marine Sciences, Venice, Italy

# Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France

Department of Plant Biology and Ecology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Biscay, Spain

« Norwegian College of Fishery Science,UiT The Arctic University of Norway, Tromsø, Norway

» Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, 29680, Roscoff, France

^ Department of Zoology and Animal Cell Biology, Faculty of Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology, Plentziako itsas Estazioa (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Biscay, Spain

Sorbonne University, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France

Integrative Marine Ecology Department, Stazione Zoologica Anton Dorn, Naples, Italy

Sorbonne Université, CNRS, Adaptation et Diversité en Milieu Marin, AD2M, 29680, Roscoff, France

Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal

Flanders Marine Institute [Vlaams Instituut voor de Zee (VLIZ)], Ostend, Belgium

UMR ENTROPIE (IRD, Université de La Réunion, CNRS, IFREMER, Université de la Nouvelle-Calédonie), Villefranche-sur-Mer, France and Sorbonne University, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
⁴ Department of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel and The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel

P Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France

A Centro de Investigación Mariña, Universidade de Vigo, Estación de Ciencias Mariñas de Toralla, Vigo, Spain

Vrije Universiteit Brussel, Brussel, Belgium

F CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal, Department of Biology, FCUP-Faculty of Sciences of the University of Porto, Porto, Portugal

† Stazione Zoologica Anton Dohrn, Naples, Italy

N Department of Ecology and Animal Biology, ECOCOST group, Marine Sciences Faculty, University of Vigo, Vigo, Spain

K Sorbonne Université, CNRS, OSU STAMAR, Station Biologique de Roscoff, 29680, Roscoff, France

Corresponding author: Christina Pavloudi (christina.pavloudi@embrc.eu), Ioulia Santi (ioulia.santi@embrc.eu)

Academic editor: Lyubomir Penev

Received: 04 Dec 2024 | Accepted: 25 Feb 2025 | Published: 12 Mar 2025

Citation: Pavloudi C, Santi I, Azua I, Baña Z, Bastianini M, Belser C, Bilbao J, Bitz-Thorsen J, Broudin C, Camusat M, Cancio I, Caray-Counil L, Casotti R, Castel J, Comtet T, Cox C, Daguin C, Díaz de Cerio O, Exter K, Fauvelot C, Frada MJ, Galand P, Garczarek L, González Fernández J, Guillou L, Hablützel PI, Heynderickx H, Houbin C, Kervella A, Krystallas A, Lagaisse R, Laroquette A, Lescure L, Lopes E, Loulakaki M, Louro B, Magalhaes C, Maidanou M, Margiotta F, Montresor M, Not F, Paredes E, Percopo I, Péru E, Poulain J, Praebel K, Rigaut-Jalabert F, Romac S, Stavroulaki M, Souza Troncoso J, Thiébaut E, Thomas W, Tkacz A, Trano AC, Wincker P, Pade N (2025) First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples. Biodiversity Data Journal 13: e143585. https://doi.org/10.3897/BDJ.13.e143585

## Abstract

The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.
# Introduction

Here we report the first data release from the European Marine Omics Biodiversity Observation Network (EMO BON) (Santi et al. 2023). This release includes data derived from water and sediment samples that were collected between June and September 2021 from the 13 observatories, across European seas and the Red Sea.

# Value of the dataset

This dataset includes raw DNA sequences obtained from shotgun metagenomics sequencing of water and sediment samples from 13 selected observatories across Europe and the Red Sea. The raw sequence data are released in the European Nucleotide Archive (ENA) (Yuan et al. 2024) with metadata associated with the sampling event, sample preparation and sequencing procedures and a diverse set of measured environmental parameters available in the associated BioSamples (Courtot et al. 2021), such as temperature, salinity and nutrient concentrations.

This dataset contributes to the ongoing efforts of the Ocean Biodiversity Information System (OBIS), which aims at filling the gaps in our current knowledge on biodiversity of the world's oceans. Processed data will be published in OBIS and in the Global Biodiversity Information Facility (GBIF), using the DNA extension of the Darwin Core format. In addition, processed data, once available in OBIS and GBIF, will be incorporated in the European Marine Observation and Data Network (EMODnet) and the European Digital Twin of the Ocean (EuropeanDTO) initiatives.

# Methods

## Sampling

Sample collection was conducted under the standard operating procedures of the EMO BON Handbook (Santi et al. 2021). Water samples were collected and processed according to the "Water Column Standard Operating Procedures 1 – WaSOP 1 (basic)": subsurface seawater was collected from the water column sampling site of each observatory, pre-filtered (> 200 µm) and concentrated by sequential filtration on polycarbonate (PC) membrane filters of 142 mm in diameter and pore sizes 3 µm and 0.2 µm. This resulted in two different plankton size fractions: 3-200 µm and 0.2-3 µm. After filtration, each filter membrane was cut into two pieces by a sterile scalpel and each filter piece was considered to represent one replicate. In total, four replicates were collected from each sampling, since two separate sequential filtrations were conducted at each sampling site. Subsequently, membranes (replicates 1 and 2) were placed in individual containers with the DNA/RNA shield preservative (Zymo Research), flash frozen in liquid nitrogen and stored at -80°C until shipment to the sequencing facility. Filter membranes that were collected for biobanking (replicates 3 and 4) were preserved in cryotubes without the addition of DNA/RNA Shield and stored at -80°C.
Sediment samples were collected and processed, based on all the three proposed protocols. Briefly, observatories NRMCB and RiaFormosa used the 'Soft Substrate Standard Operating Procedures 1 – SoSOP 1 (intertidal sediments)', while OOB and ROSKOGO used the "Soft substrate Standard Operating Procedures 2 – SoSOP 2 (coastal sediments by diving)" and BPNS used "Soft substrate Standard Operating Procedures 3 – SoSOP 3 (coastal sediments by research vessel)". Regardless of the choice of protocol, the steps regarding collection of sediment for microbial community assessment include the use of sediment cores and the subsequent slicing of the top 5 cm layer. As for the water samples, four replicates are collected for the sediment sampling; DNA/RNA shield was added in two of the replicates, which were the ones shipped for sequencing.

## Geographic range

The dataset's geographical range includes 14 locations (13 observatories) across eight ecoregions, based on the Marine Ecoregions of the World (MEOW), proposed by Spalding et al. (2007) (Table 1; Fig. 1); details are also provided regarding the locality of the observatories, from the broader (ocean/sea) to the regional and the local scale.

<caption>Table 1.</caption>

Locality and coordinates of the sampling stations.

<table><thead><tr><th>Observatory</th><th>Coordinates</th><th>Marine Ecoregion of the World (MEOW)</th><th>Ocean/Sea</th><th>Region</th><th>Location</th><th>Water sampling</th><th>Sediment sampling</th><th>Number of collected samples</th><th>Number of successfully sequenced samples</th></tr></thead><tbody><tr><td>AAOT</td><td>45.31417 N; 12.508333 E</td><td>Adriatic Sea</td><td>Mediterranean Sea - Eastern Basin</td><td>Adriatic Sea</td><td>Gulf of Venice</td><td>Yes</td><td></td><td>8</td><td>7</td></tr><tr><td>BPNS</td><td>51.43333 N; 2.808331 E</td><td>North Sea</td><td>North Atlantic Ocean</td><td>North Sea</td><td>Belgian part of the North Sea</td><td>Yes</td><td>Yes</td><td>12</td><td>11</td></tr><tr><td>EMT21</td><td>42.20194 N; -8.798500 E</td><td>South European Atlantic Shelf</td><td>Atlantic Ocean</td><td>North Atlantic Ocean</td><td>Vigo Seamount</td><td>Yes</td><td></td><td>4</td><td>4</td></tr><tr><td>ESC68N</td><td>68.92589 N; 17.125619 E</td><td>Northern Norway and Finnmark</td><td>Arctic Ocean</td><td>Norwegian Sea</td><td>Norwegian part of the Norwegian Sea</td><td>Yes</td><td></td><td>4</td><td>4</td></tr><tr><td>HCMR-1</td><td>35.34662 N; 25.278761 E</td><td>Aegean Sea</td><td>Mediterranean Sea - Eastern Basin</td><td>Aegean Sea</td><td>Crete Sea</td><td>Yes</td><td></td><td>12</td><td>5</td></tr></tbody></table>
<table><thead><tr><th>Observatory</th><th>Coordinates</th><th>Marine Ecoregion of the World (MEOW)</th><th>Ocean/Sea</th><th>Region</th><th>Location</th><th>Water sampling</th><th>Sediment sampling</th><th>Number of collected samples</th><th>Number of successfully sequenced samples</th></tr></thead><tbody><tr><td>IUIEilat</td><td>29.50000 N; 34.916667 E</td><td>Northern and Central Red Sea</td><td>Indian Ocean</td><td>Gulf of Eilat</td><td>Gulf of Eilat</td><td>Yes</td><td></td><td>4</td><td>4</td></tr><tr><td>NRMCB</td><td>40.80014 N; 14.250000 E</td><td>Western Mediterranean</td><td>Mediterranean Sea - Western Basin</td><td>Tyrhenian Sea</td><td>Naples Gulf</td><td>Yes</td><td>Yes</td><td>18</td><td>13</td></tr><tr><td>OOB</td><td>42.48417 N; 3.135278 E</td><td>Western Mediterranean</td><td>Mediterranean Sea - Western Basin</td><td>Gulf of Lion</td><td>Bay of Banyuls-sur-Mer</td><td></td><td>Yes</td><td>3</td><td>1</td></tr><tr><td>OSD74</td><td>41.14653 N; -8.666639 E</td><td>South European Atlantic Shelf</td><td>Atlantic Ocean</td><td>North Atlantic Ocean</td><td>Porto Valley</td><td>Yes</td><td></td><td>3</td><td>3</td></tr><tr><td>PiEGetxo</td><td>43.33858 N; -3.014639 E</td><td>South European Atlantic Shelf</td><td>North Atlantic Ocean</td><td>Bay of Biscay</td><td>Abra de Bilbao</td><td>Yes</td><td></td><td>6</td><td>6</td></tr><tr><td>RFormosa</td><td>37.00564 N; -7.969250 E</td><td>South European Atlantic Shelf</td><td>Atlantic Ocean</td><td>North Atlantic Ocean</td><td>Ria Formosa</td><td>Yes</td><td>Yes</td><td>6</td><td>6</td></tr><tr><td>ROSKOGO</td><td>48.70833 N; -3.866000 E</td><td>Celtic Seas</td><td>North Atlantic Ocean</td><td>English Channel</td><td>French part of the English Channel</td><td></td><td>Yes</td><td>2</td><td>2</td></tr><tr><td>ROSKOGO</td><td>48.77167 N; -3.968333 E</td><td>Celtic Seas</td><td>North Atlantic Ocean</td><td>English Channel</td><td>French part of the English Channel</td><td></td><td>Yes</td><td>8</td><td>6</td></tr><tr><td>VB</td><td>43.68300 N; 7.317000 E</td><td>Western Mediterranean</td><td>Mediterranean Sea - Western Basin</td><td>Villefranche Bay</td><td>Villefranche Bay - Point B</td><td></td><td>Yes</td><td>8</td><td>8</td></tr></tbody></table>

## DNA extraction, library preparation and sequencing

DNA extraction was performed at Genoscope, which was the chosen centralised facility to minimise biases and follow the same standardised procedures. For DNA extraction of the water column filter samples, the same protocol as described by Alberti et al. (2017) was used. The procedure consisted of a first step of cell disruption by cryogenic grinding of membrane filters followed by chemical lysis and then nucleic acid purification using
NucleoSpin RNA kits, combined with the NucleoSpin RNA/DNA buffer set (Macherey-Nagel, Düren, Germany). For sediment samples, DNA extraction was performed using the commercially available DNeasy PowerSoil Pro Kit (Qiagen) with slight modifications.

<figure><img src="image_4.png" /><figcaption>Figure 1.</figcaption></figure>

Map of the observatories collecting:

a: sediment samples; doi

b: water samples. doi

Sequencing was also performed at Genoscope. Metagenome libraries were constructed according to the available DNA: 10 to 100 ng of genomic DNA were sonicated to obtain fragments of around 350 bp, using the Covaris E220 instrument (Covaris, Woburn, MA, USA). Fragments were repaired, 3'-adenylated and NEXTflex PCR freebarcodes adapters (Bioo Scientific, Austin, TX, USA) were added using the NEBNext® Ultra II DNALibrary prep kit for Illumina (New England Biolabs, Ipswich, MA, USA). Ligation products were purified by AMPure XP beads 0:8 volume (Beckmann Coulter, Brea, CA, USA). DNA fragments (> 200 bp) were amplified by PCR (2 PCR reactions, 14 cycles) using Illumina adapter-specific primers and NEBNext® Ultra II Q5 Master Mix (NEB). All libraries were subjected to size profile analysis conducted by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and to qPCR quantification using the KAPA Library Quantification Kit for Illumina Libraries (KapaBiosystems, Wilmington, MA, USA). All metagenomic libraries validated by the quality-control were sequenced using 151-bp pairwise read chemistry on an Illumina NovaSeq6000 sequencer, using S4 Flowcells (Illumina, San Diego, CA, USA). A minimum of 40,000 million useful paired-end reads were obtained per sample. Short Illumina reads were bioinformatically post-processed sensu Alberti et al. (2017) to filter out low-quality data. First, low-quality nucleotides (Q < 20) were discarded from both read ends. Then the remaining Illumina sequencing adapters and primer sequences were removed and only reads ≥ 30 nucleotides were retained. These filtering steps were done using in-house-designed software, based on the FastX package (Engelen and Aury 2016). Finally, read pairs mapping to the phage phiX genome were identified and discarded using SOAP aligner (Li et al. (2008), default parameters) and the Enterobacteria phage PhiX174 reference sequence (GenBank: NC_001422.1).
## Biodiversity scope

### Target

The target of the dataset was to assess prokaryotic and eukaryotic diversity associated with the collected samples.

### Taxonomic range

Archaea, Bacteria, Eukaryota

## Data Resources

Details for the samples can be found in Suppl. material 1 and their basic metadata can be found in Suppl. material 2. All the raw sequence files of this study were submitted to ENA (Yuan et al. 2024) with the umbrella study accession number [PRJEB51688](https://www.ncbi.nlm.nih.gov/nuccl/). The accession numbers of the component projects under the umbrella study are [PRJEB51662](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51661](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51660](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51659](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51658](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51665](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51664](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51656](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51655](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51654](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51653](https://www.ncbi.nlm.nih.gov/nuccl/), [PRJEB51652](https://www.ncbi.nlm.nih.gov/nuccl/), and [PRJEB50566](https://www.ncbi.nlm.nih.gov/nuccl/). All sampling event and environmental data, linked to the respective accession numbers, are also available to browse and download from [EMO BON's data landing page](https://data.bon.int/).

## Resource 1

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/037/ERR13930537/ERR13930537_1.fastq.gz

### Download URL

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ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/057/ERR13954257/ERR13954257_2.fastq.gz
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**Download URL**

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## Resource 12

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**Resource identifier**

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## Resource 17

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ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/068/ERR13954268/ERR13954268_2.fastq.gz

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## Resource 19

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/070/ERR13954270/ERR13954270_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/070/ERR13954270/ERR13954270_2.fastq.gz
**Resource identifier**

ERR13954270

**Data format**

FASTQ

**Resource 20**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/071/ERR13954271/ERR13954271_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/071/ERR13954271/ERR13954271_2.fastq.gz

**Resource identifier**

ERR13954271

**Data format**

FASTQ

**Resource 21**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/073/ERR13954273/ERR13954273_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/073/ERR13954273/ERR13954273_2.fastq.gz

**Resource identifier**

ERR13954273

**Data format**

FASTQ
## Resource 22

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/074/ERR13954274/ERR13954274_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/074/ERR13954274/ERR13954274_2.fastq.gz

### Resource identifier

ERR13954274

### Data format

FASTQ

## Resource 23

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/075/ERR13954275/ERR13954275_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/075/ERR13954275/ERR13954275_2.fastq.gz

### Resource identifier

ERR13954275

### Data format

FASTQ

## Resource 24

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/076/ERR13954276/ERR13954276_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/076/ERR13954276/ERR13954276_2.fastq.gz
### Resource identifier

ERR13954276

### Data format

FASTQ

## Resource 25

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/079/ERR13954279/ERR13954279_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/079/ERR13954279/ERR13954279_2.fastq.gz

### Resource identifier

ERR13954279

### Data format

FASTQ

## Resource 26

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/080/ERR13954280/ERR13954280_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/080/ERR13954280/ERR13954280_2.fastq.gz

### Resource identifier

ERR13954280

### Data format

FASTQ
## Resource 27

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/081/ERR13954281/ERR13954281_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/081/ERR13954281/ERR13954281_2.fastq.gz

### Resource identifier

ERR13954281

### Data format

FASTQ

## Resource 28

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/082/ERR13954282/ERR13954282_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/082/ERR13954282/ERR13954282_2.fastq.gz

### Resource identifier

ERR13954282

### Data format

FASTQ

## Resource 29

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/083/ERR13954283/ERR13954283_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/083/ERR13954283/ERR13954283_2.fastq.gz
**Resource identifier**

ERR13954283

**Data format**

FASTQ

**Resource 30**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/038/ERR13954638/ERR13954638_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/038/ERR13954638/ERR13954638_2.fastq.gz

**Resource identifier**

ERR13954638

**Data format**

FASTQ

**Resource 31**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/039/ERR13954639/ERR13954639_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/039/ERR13954639/ERR13954639_2.fastq.gz

**Resource identifier**

ERR13954639

**Data format**

FASTQ
## Resource 32

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/040/ERR13954640/ERR13954640_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/040/ERR13954640/ERR13954640_2.fastq.gz

### Resource identifier

ERR13954640

### Data format

FASTQ

## Resource 33

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/041/ERR13954641/ERR13954641_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/041/ERR13954641/ERR13954641_2.fastq.gz

### Resource identifier

ERR13954641

### Data format

FASTQ

## Resource 34

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/042/ERR13954642/ERR13954642_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/042/ERR13954642/ERR13954642_2.fastq.gz
**Resource identifier**

ERR13954642

**Data format**

FASTQ

**Resource 35**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/043/ERR13954643/ERR13954643_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/043/ERR13954643/ERR13954643_2.fastq.gz

**Resource identifier**

ERR13954643

**Data format**

FASTQ

**Resource 36**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/028/ERR13954728/ERR13954728_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/028/ERR13954728/ERR13954728_2.fastq.gz

**Resource identifier**

ERR13954728

**Data format**

FASTQ
## Resource 37

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/029/ERR13954729/ERR13954729_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/029/ERR13954729/ERR13954729_2.fastq.gz

### Resource identifier

ERR13954729

### Data format

FASTQ

## Resource 38

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/030/ERR13954730/ERR13954730_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/030/ERR13954730/ERR13954730_2.fastq.gz

### Resource identifier

ERR13954730

### Data format

FASTQ

## Resource 39

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/031/ERR13954731/ERR13954731_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/031/ERR13954731/ERR13954731_2.fastq.gz
**Resource identifier**

ERR13954731

**Data format**

FASTQ

**Resource 40**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/032/ERR13954732/ERR13954732_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/032/ERR13954732/ERR13954732_2.fastq.gz

**Resource identifier**

ERR13954732

**Data format**

FASTQ

**Resource 41**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/033/ERR13954733/ERR13954733_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/033/ERR13954733/ERR13954733_2.fastq.gz

**Resource identifier**

ERR13954733

**Data format**

FASTQ
## Resource 42

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/034/ERR13954734/ERR13954734_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/034/ERR13954734/ERR13954734_2.fastq.gz

### Resource identifier

ERR13954734

### Data format

FASTQ

## Resource 43

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/035/ERR13954735/ERR13954735_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/035/ERR13954735/ERR13954735_2.fastq.gz

### Resource identifier

ERR13954735

### Data format

FASTQ

## Resource 44

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/036/ERR13954736/ERR13954736_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/036/ERR13954736/ERR13954736_2.fastq.gz
**Resource identifier**

ERR13954736

**Data format**

FASTQ

**Resource 45**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/037/ERR13954737/ERR13954737_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/037/ERR13954737/ERR13954737_2.fastq.gz

**Resource identifier**

ERR13954737

**Data format**

FASTQ

**Resource 46**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/038/ERR13954738/ERR13954738_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/038/ERR13954738/ERR13954738_2.fastq.gz

**Resource identifier**

ERR13954738

**Data format**

FASTQ
## Resource 47

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/039/ERR13954739/ERR13954739_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/039/ERR13954739/ERR13954739_2.fastq.gz

### Resource identifier

ERR13954739

### Data format

FASTQ

## Resource 48

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/040/ERR13954740/ERR13954740_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/040/ERR13954740/ERR13954740_2.fastq.gz

### Resource identifier

ERR13954740

### Data format

FASTQ

## Resource 49

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/013/ERR13954813/ERR13954813_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/013/ERR13954813/ERR13954813_2.fastq.gz
Resource identifier

ERR13954813

Data format

FASTQ

Resource 50

Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/014/ERR13954814/ERR13954814_1.fastq.gz

Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/014/ERR13954814/ERR13954814_2.fastq.gz

Resource identifier

ERR13954814

Data format

FASTQ

Resource 51

Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/015/ERR13954815/ERR13954815_1.fastq.gz

Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/015/ERR13954815/ERR13954815_2.fastq.gz

Resource identifier

ERR13954815

Data format

FASTQ
## Resource 52

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/016/ERR13954816/ERR13954816_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/016/ERR13954816/ERR13954816_2.fastq.gz

### Resource identifier

ERR13954816

### Data format

FASTQ

## Resource 53

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/017/ERR13954817/ERR13954817_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/017/ERR13954817/ERR13954817_2.fastq.gz

### Resource identifier

ERR13954817

### Data format

FASTQ

## Resource 54

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/018/ERR13954818/ERR13954818_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/018/ERR13954818/ERR13954818_2.fastq.gz
**Resource identifier**

ERR13954818

**Data format**

FASTQ

**Resource 55**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/019/ERR13954819/ERR13954819_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/019/ERR13954819/ERR13954819_2.fastq.gz

**Resource identifier**

ERR13954819

**Data format**

FASTQ

**Resource 56**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/020/ERR13954820/ERR13954820_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/020/ERR13954820/ERR13954820_2.fastq.gz

**Resource identifier**

ERR13954820

**Data format**

FASTQ
## Resource 57

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/052/ERR13954852/ERR13954852_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/052/ERR13954852/ERR13954852_2.fastq.gz

### Resource identifier

ERR13954852

### Data format

FASTQ

## Resource 58

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/053/ERR13954853/ERR13954853_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/053/ERR13954853/ERR13954853_2.fastq.gz

### Resource identifier

ERR13954853

### Data format

FASTQ

## Resource 59

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/054/ERR13954854/ERR13954854_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/054/ERR13954854/ERR13954854_2.fastq.gz
**Resource identifier**

ERR13954854

**Data format**

FASTQ

**Resource 60**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/055/ERR13954855/ERR13954855_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/055/ERR13954855/ERR13954855_2.fastq.gz

**Resource identifier**

ERR13954855

**Data format**

FASTQ

**Resource 61**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/056/ERR13954856/ERR13954856_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/056/ERR13954856/ERR13954856_2.fastq.gz

**Resource identifier**

ERR13954856

**Data format**

FASTQ
## Resource 62

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/057/ERR13954857/ERR13954857_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/057/ERR13954857/ERR13954857_2.fastq.gz

### Resource identifier

ERR13954857

### Data format

FASTQ

## Resource 63

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/058/ERR13954858/ERR13954858_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/058/ERR13954858/ERR13954858_2.fastq.gz

### Resource identifier

ERR13954858

### Data format

FASTQ

## Resource 64

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/059/ERR13954859/ERR13954859_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/059/ERR13954859/ERR13954859_2.fastq.gz
**Resource identifier**

ERR13954859

**Data format**

FASTQ

**Resource 65**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/060/ERR13954860/ERR13954860_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/060/ERR13954860/ERR13954860_2.fastq.gz

**Resource identifier**

ERR13954860

**Data format**

FASTQ

**Resource 66**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/061/ERR13954861/ERR13954861_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/061/ERR13954861/ERR13954861_2.fastq.gz

**Resource identifier**

ERR13954861

**Data format**

FASTQ
## Resource 67

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/062/ERR13954862/ERR13954862_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/062/ERR13954862/ERR13954862_2.fastq.gz

### Resource identifier

ERR13954862

### Data format

FASTQ

## Resource 68

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/063/ERR13954863/ERR13954863_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/063/ERR13954863/ERR13954863_2.fastq.gz

### Resource identifier

ERR13954863

### Data format

FASTQ

## Resource 69

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/064/ERR13954864/ERR13954864_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/064/ERR13954864/ERR13954864_2.fastq.gz
### Resource identifier

ERR13954864

### Data format

FASTQ

## Resource 70

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/087/ERR13955087/ERR13955087_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/087/ERR13955087/ERR13955087_2.fastq.gz

### Resource identifier

ERR13955087

### Data format

FASTQ

## Resource 71

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/088/ERR13955088/ERR13955088_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/088/ERR13955088/ERR13955088_2.fastq.gz

### Resource identifier

ERR13955088

### Data format

FASTQ
## Resource 72

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/089/ERR13955089/ERR13955089_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/089/ERR13955089/ERR13955089_2.fastq.gz

### Resource identifier

ERR13955089

### Data format

FASTQ

## Resource 73

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/090/ERR13955090/ERR13955090_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/090/ERR13955090/ERR13955090_2.fastq.gz

### Resource identifier

ERR13955090

### Data format

FASTQ

## Resource 74

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/091/ERR13955091/ERR13955091_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/091/ERR13955091/ERR13955091_2.fastq.gz
**Resource identifier**

ERR13955091

**Data format**

FASTQ

**Resource 75**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/092/ERR13955092/ERR13955092_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/092/ERR13955092/ERR13955092_2.fastq.gz

**Resource identifier**

ERR13955092

**Data format**

FASTQ

**Resource 76**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/093/ERR13955093/ERR13955093_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/093/ERR13955093/ERR13955093_2.fastq.gz

**Resource identifier**

ERR13955093

**Data format**

FASTQ
## Resource 77

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/094/ERR13955094/ERR13955094_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/094/ERR13955094/ERR13955094_2.fastq.gz

### Resource identifier

ERR13955094

### Data format

FASTQ

## Resource 78

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/095/ERR13955095/ERR13955095_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/095/ERR13955095/ERR13955095_2.fastq.gz

### Resource identifier

ERR13955095

### Data format

FASTQ

## Resource 79

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/096/ERR13955096/ERR13955096_1.fastq.gz

### Download URL

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/096/ERR13955096/ERR13955096_2.fastq.gz
**Resource identifier**

ERR13955096

**Data format**

FASTQ

**Resource 80**

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/097/ERR13955097/ERR13955097_1.fastq.gz

**Download URL**

ftp.sra.ebi.ac.uk/vol1/fastq/ERR139/097/ERR13955097/ERR13955097_2.fastq.gz

**Resource identifier**

ERR13955097

**Data format**

FASTQ

**Usage Rights**

CC BY 4.0

**Acknowledgements**

This work used resources provided by the European Marine Omics Biodiversity Observation Network (EMO BON) project, coordinated by the European Marine Biological Resource Centre (EMBRC). For the NRMCB observatory, the captain and crew of RV Vettoria, Ferdinando Tramontano and Carmen Minucci and the NEREA Team (www.nerea-observatory.org) are acknowledged for support to sampling. For the BPNS observatory, captain and crew of RV Simon Stevin are acknowledged for operational support. For the PiEGetxo observatory, we also acknowledge TED2021-132109B-C21 research project funded by MCIN/AEI /10.13039/501100011033 and by the European Union NextGenerationEU/PRTR. For Station Biologique de Roscoff, the captain and crew of RV Neomysis, Stéphanie Cabioch, Noël Guidal, Arnaud Perrey and the Service Mer et Plongée Team are acknowledged for operational support to sampling. This work was supported by the Genoscope, the Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA) and France Génomique (ANR-10-INBS-0009).
Conflicts of interest

The authors have declared that no competing interests exist.

References

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## Supplementary materials

### Suppl. material 1: ENA sample, run, experiment and project accession numbers for the first release of the EMO BON shotgun metagenomics data from water and sediment samples [doi](https://doi.org/10.1093/nar/gkad1067)

**Authors:** Christina Pavloudi

**Data type:** metadata

[Download file](https://doi.org/10.1093/nar/gkad1067) (8.82 kb)

### Suppl. material 2: BioSamples MlxC checklists [doi](https://doi.org/10.1093/nar/gkad1067)

**Authors:** Christina Pavloudi

**Data type:** metadata

[Download file](https://doi.org/10.1093/nar/gkad1067) (37.54 kb)