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    During three cruises in the Mid Atlantic Ridge area in 2016 and 2017, we collected samples of mesopelagic species down to a depth of 600?m. We studied fish behaviour and identified and quantified the species composition of the catches using HD videos (60 frames/s). For species identification and the estimation of the number of siphonophores/m³ we analysed the videos frame by frame using the tool VLC media player.

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    Mesopelagic fishes experience an extreme body transformation from larvae to adults. DNA barcoding has been useful in establishing phylogenetic relationships among mesopelagic and other deep-sea fishes, however no molecular evidence to confirm the identity of their larvae was available so far. Molecular analyses were conducted to identify the larvae and adults of 18 species of the most abundant and frequent mesopelagic fishes in the western Mediterranean, across 14 genera. For myctophids, 7 of 9 species of the subfamily Lampanyctinae and all species from Myctophinae (6) were analysed. At least 565 nucleotides of the mtDNA CO1 region were sequenced. The 12S rRNA region was selected for C. braueri and C. pygmaea (372 nucleotides). Pairwise nucleotide distances were notably higher inter- than intraspecifically allowing to discern between congeners such as Cyclothone braueri and C. pygmaea, Hygophum benoiti and H. hygomii, Lampanyctus crocodilus and L. pusillus, and Notoscopelus bolini and N. elongatus. The good fit between larvae and adult sequences for each species proved the accuracy of earlier larval descriptions based on morphology and pigmentation characters. A list of the genetic markers used to identify each species with their accession numbers in Genbank is provided here along with their developmental stage, sampling location and depth.

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    The values of natural abundance of stable isotopes were measured in 13 micronekton fish species sampled during the BATHYPELAGIC cruise (North Atlantic, June 2018). This dataset contains the values obtained for carbon and nitrogen in bulk tissues, and nitrogen values in amino acids. Length and biomass data for each individual analyzed are also provided. Fishes were collected using a ''Mesopelagos” net (5x7 m mouth opening, 58 m total lenght) equipped with graded-mesh netting (starting with 30 mm and ending with 4 mm) and a multi-sampler for collecting samples from 5 different depth layers (Olivar et al., 2017). Individual fish were eviscerated, freeze-dried and weighted. Aliquots of muscular tissue (or whole individuals for species of small size) were analyzed in an elemental analyzer (bulk tissues, Olivar et al., 2019) or a gas chromatograph (derivatized amino acids, Mompeán et al., 2016) coupled to isotope-ratio mass spectrometers. Carbon analyses were made before and after removal of lipids with a mixture of trichloromethane:methanol:water.

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    This file contains data on numerical abundance of mesopelagic fishes collected in April 2015 across the tropical and equatorial Atlantic. Twelve stations were visited day and night, from the oligotrophic region close to the Brazilian coast to the more productive region off the western African coast. Hauls were performed with a scientific midwater trawl, the Mesopelagos (designed by Meillat, 2012), which works with a single traction cable. The gear consists of graded-mesh netting starting with 30 mm and ending with 4 mm. At the end of the net, a multi-sampler (designed for the present investigation by one of the co-authors, A. Castellón-CSIC) was installed to obtain samples from 5 different depth layers of the water column. For some stations, where lots of gelatinous organisms, or Sargassum weed occurred, the system could not work and the data presented integrates the water column from 800 m to the surface. The depth of the net was controlled by a SCANMAR system. Samples were identified on board or frozen for a later identification in the laboratory. These data were obtained within the project: "Migrants and Active Flux In the Atlantic Ocean, financed by the Spanish Ministerio de Ciencia e Innovación CTM2012-39587-C04.

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    The present data were collected from two cruises that took place in the Canary Current from September 10 to October 1, 2002 (COCA I) and from May 21 to June 7, 2003 (COCA II). The study was conducted along two zonal sections (21ºN and 26ºN) extending from the coastal upwelling to the open ocean at 26ºW, and focused on the epipelagic (0-200 m) and mesopelagic (200-1000 m) zones. The cruises consisted of a total of 31 hydrographic stations and 10 biogeochemical stations, half of them along each section, which were roughly equidistant. At each hydrographic station, conductivity, temperature and pressure were recorded by means of a Seabird 911+ CTD, mounted on a General Oceanics rosette sampler equipped with 24 10L-Niskin bottles.

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    Daytime acoustic data (nautical area scattering coefficients, in m2/nmi2) integrated over 2 m vertical bins, from 200 to 1000 m depth. Data in each “pixel” is the average of all cleaned and valid data recorded at that depth range, in a time period starting 8 hours before the start of a station (defined as start of the CTD cast) and ending 8 hours after the start of the station, subject to being in the period between 1 hour after local sunrise and 1 hour prior to local sunset (i.e. during local daytime hours, but removing crepuscular periods). The relatively long interval over which data was accepted around each station was chosen due to frequent occurrences of periods of unusable acoustic data. Note that the provided positions correspond to the fixed Malapina station at that date, not the start and end point of the data collection.

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    During three cruises in the Mid Atlantic Ridge area in 2016 and 2017, we collected samples of mesopelagic species down to a depth of 600?m and analysed the chemical composition of the catch samples. We present gross proximate composition (g /100 g fresh weight) and fatty acid composition (% of total fatty acids) in mesopelagic raw material samples (values are mean ± standard deviation of 2–4 samples).

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    Carbon export (from the epipelagic towards the mesopelagic zone) and sequestration (from the mesopelagic towards the bathypelagic zone) in the ocean are reviewed. Particulate organic carbon (POC) flux, and active flux due to migrant zooplankton and micronekton are shown from the epipelagic to the mesopelagic zone, and from the latter to the bathypelagic zone. Values towards the meso- and bathypelagic zones are compared in oligotrophic and productive systems. Zooplankton and prokaryote respiration in the meso- and bathypelagic zones of the ocean are also reviewed for oligotrophic and productive systems. Values were integrated over a depth layer and are given as the flux or respiration under one square meter (in g/m**2/a) between e.g. 100 m and 1000 m depth.

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    This file contains data on numerical abundance of micronekton organisms, mostly decapods, cephalopods, and cnidarians collected in winter (December 2009) and summer (July 2010) in the Balearic Islands region. A relatively small area was repeatedly sampled throughout the day. Samples were obtained by means of a double-warp modified commercial mid-water trawl, with standard pelagic trawl doors (otter boards) and graded-mesh netting to the cod-end (10 mm). Hauls were horizontal and lasted between 30 min and 1 hour, and the depth of the net was controlled by a SCANMAR system. Samples were identified on board or frozen for a later identification in the laboratory. These data were obtained within the project: "Estructura y dinámica del ecosistema bentopelágico de talud en dos zonas oligotróficas del Mediterráneo: una aproximación multidisciplinar y a distintas escalas temporales en las Islas Baleares", financed by the Spanish Ministerio de Ciencia e Innovación CTM2007-65844-C03.