Description: Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits in trophic interactions between sharks found in different habitats. We show that populations of shelf-dwelling sharks derive a substantial proportion of their carbon from regional pelagic sources, but contain individuals that forage within additional isotopically diverse local food webs, such as those supported by terrestrial plant sources, benthic production and macrophytes. In contrast, oceanic sharks seem to use carbon derived from between 30° and 50° of latitude. Global-scale compilations of stable isotope data combined with biogeochemical modelling generate hypotheses regarding animal behaviours that can be tested with other methodological approaches.

Description: The dataset contains carbon (C) and nitrogen (N) stable isotope compositions analysed in the muscle tissue of 15 meso- to bathypelagic species sampled in the twilight zone (deep pelagic area) of the Bay of Biscay, North-East Atlantic. The species included 4 crustacean species (Pasiphaea sivado, Sergia robusta, Systellaspis debilis, Ephyrina figueirai) and 11 fish species (Xenodermichthys copei, Searsia koefoedi, Myctophum punctatum, Notoscopelus kroeyeri, Lampanyctus crocodilus, Argyropelecus olfersii, Arctozenus risso, Stomias boa, Serrivomer beanii, Chauliodus sloani, Aphanopus carbo). Specimens were collected during a single fishery in a canyon of the slope of the Bay of Biscay in October 2017, during the EVHOE fishery survey (“Evaluation Halieutique de l'Ouest de l'Europe”; https://doi.org/10.17600/17002300) conducted each autumn by the “Institut Français de Recherche pour l'Exploitation de la Mer” (Ifremer) on R/V Thalassa. A total of 266 individuals belonging to the 15 species were collected at night using a 25 m vertical opening pelagic trawl in the deep scattering layer (ca. 800 m depth in the water column; 1330 m bottom depth). All organisms were collected during one haul of 60 min, at a speed of approximately 4 knots (geographical coordinates at the beginning of the turn/end of the fishing: 45.103°N, -3.543° W). For small fish and crustaceans, organisms belonging to the same species were pooled by individuals of similar sizes. The size of each individual (total length for fish, cephalothorax length for crustaceans, in mm) as well as the total fresh weight of individuals or pools (to the nearest 0.5 g wet mass) were determined on board, and the individuals were rinsed with ultrapure water before storage. Mean individual sizes and fresh wet weights are here reported for each sample constituted by a pool of individuals. Samples (individuals or pools of individuals, N=39 in total) were finally stored at -20°C until further treatment in the laboratory. In clean and contamination-free conditions of the laboratory, whole organisms were briefly thawed and a small piece of white muscle (typically 〈3% of individual total weight) was collected from each individual. The muscle tissue is indeed generally recommended in the literature for food web studies inferred from stable isotope analyses (Pinnegar and Polunin, 1999). After collection, muscle subsamples were frozen again at -20°C, freeze-dried and homogenised manually into a fine powder. An aliquot of this powder (0.40 ± 0.05 mg dry mass) was weighed in tin cups. Analyses were finally performed with an isotope ratio mass spectrometer (Delta V Advantage with a Conflo IV interface, Thermo Scientific) coupled to an elemental analyser (Flash EA 2000, Thermo Scientific). The results are presented in the usual δ notation relative to the deviation from international standards (Vienna Pee Dee Belemnite for δ13C values, and atmospheric nitrogen for δ15N values), in parts per thousand (‰). Based on replicate measurements of USGS-61 and USGS-62 used as laboratory internal standards, experimental analytical precision was 〈0.10‰ and 〈0.15‰ for δ13C and δ15N, respectively. With the elemental analyser, bulk C:N ratios in muscle could be also determined as a proxy of the lipid content or body condition of organisms (Hoffman et al., 2015; Post et al., 2007). Samples were thus untreated (not lipid-extracted) before analyses in order to have access to bulk (untreated) C:N ratios. However, lipids are highly depleted in 13C relative to other tissue components (DeNiro and Epstein, 1977) and significant variations in lipids (especially between species) can affect δ13C signatures even if trophic sources are similar. Before using data as trophic markers, we thus recommend to mathematically correct δ13C values for the potential effect of lipids according to the formula proposed by Post et al. (2007) using bulk C:N ratios (δ13C (corrected) = δ13C (bulk) – 3.32 + 0.99 x C:N ratio). Alternatively, δ15N values do not need to be corrected.

Description: The dataset contains energy density values and concentrations in 19 elements analysed in whole bodies of 15 meso- to bathypelagic species sampled in the twilight zone (deep pelagic area) of the Bay of Biscay, North-East Atlantic. The species included 4 crustacean species (Pasiphaea sivado, Sergia robusta, Systellaspis debilis, Ephyrina figueirai) and 11 fish species (Xenodermichthys copei, Searsia koefoedi, Myctophum punctatum, Notoscopelus kroeyeri, Lampanyctus crocodilus, Argyropelecus olfersii, Arctozenus risso, Stomias boa, Serrivomer beanii, Chauliodus sloani, Aphanopus carbo). The elements included 6 major constitutive elements (macro-minerals) and 13 trace elements among which 9 essential (micro-nutrients) and 4 non-essential elements (undesirables, with no know biological function). Specimens were collected during a single fishery in a canyon of the slope of the Bay of Biscay in October 2017, during the EVHOE fishery survey (“Evaluation Halieutique de l'Ouest de l'Europe”; https://doi.org/10.17600/17002300) conducted each autumn by the “Institut Français de Recherche pour l'Exploitation de la Mer” (Ifremer) on R/V Thalassa. A total of 266 individuals belonging to the 15 species were collected at night using a 25 m vertical opening pelagic trawl in the deep scattering layer (ca. 800 m depth in the water column; 1330 m bottom depth). All organisms were collected during one haul of 60 min, at a speed of approximately 4 knots (geographical coordinates at the beginning of the turn/end of the fishing: 45.103°N, -3.543° W). For small fish and crustaceans, organisms belonging to the same species were pooled by individuals of similar sizes. The size of each individual (total length for fish, cephalothorax length for crustaceans, in mm) as well as the total fresh weight of individuals or pools (to the nearest 0.5 g wet mass) were determined on board, and the individuals were rinsed with ultrapure water before storage. Mean individual sizes and fresh wet weights are here reported for each sample constituted by a pool of individuals. Samples (individuals or pools of individuals, N=39 in total) were finally stored at -20°C until further treatment in the laboratory. In clean and contamination-free conditions of the laboratory, whole organisms were briefly thawed and the digestive tracts of fish (i.e. stomachs and intestines) were emptied and put back in individuals. Whole individuals were then cut into small pieces and a first fresh grinding of individuals (or pools of individuals for small fish and crustaceans) was carried out using an Ultra Turrax® type grinder with stainless steel arms. Samples were finally refrozen at -20° C in acid pre-cleaned and calcined (450°C) glass jars, lyophilized during 72 h, and ground again into a fine and homogeneous powder using a stainless-steel knife mill. If necessary, this was completed by ball milling (MM400 Retsch®) using bowls and marbles with zirconium oxide coating. Each material was conscientiously rinsed with a succession of ultrapure water/ethanol/ultrapure water between each sample. Energy density was estimated on dried homogenised samples following Spitz et al. (2010), using a Parr® 1266 semi-micro-oxygen bomb calorimeter and an adiabatic bomb-calorimetry in which gross energy is determined by measuring heat of combustion. Values are presented in kJ/g dry weight and are means of duplicate determination (deviation between two assays 〈2%). Total concentrations of calcium (Ca), potassium (K), magnesium (Mg), sodium (Na), phosphorus (P) and strontium (Sr), as major constitutive chemical elements (macro-minerals) in biological organisms, were determined by inductively coupled plasma atomic emission spectrometry (ICP-OES, Vista-Pro Varian) according to an in-laboratory approved method. Briefly with this method, aliquots of samples (~250 mg dry mass of homogenised powder) were digested using a 6:2 (v/v) mixture with nitric acid (HNO3 69%, Trace Metal Grade®, FisherScientific) and hydrochloric acid (HCl, 34%, Trace Metal Grade®, FisherScientific). Acidic digestion of the samples was performed overnight at room temperature and then in a microwave oven (START-D, Milestone). The digests were finally diluted to 50 mL with ultrapure water before analyses with ICP-OES. Total concentrations of 9 essential – arsenic (As), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), molybdenum (Mo), selenium (Se), vanadium (V), zinc (Zn) – and 4 non-essential – silver (Ag), cadmium (Cd), lead (Pb) – trace elements were determined by inductively coupled plasma mass spectrometry (ICP-MS, ICAP-Qc ThermoFisher) according to an in-laboratory approved method. Briefly with this method, aliquots of samples (~200 mg of homogenised powder) were placed in Teflon bombs and mineralized with a mixture of ultrapure HNO3 acid (PlasmaPure Plus grade, SCP Science®) and ultrapure water using a microwave (ETHOS-UP, Milestone). The digests were then diluted to 50 ml with ultrapure water before analyses with ICP-MS. Finally, total mercury (Hg) concentrations (a non-essential-element) were determined by atomic absorption spectrophotometry using an Advanced Mercury Analyser (ALTEC AMA-254, Altec Ltd), on aliquots of homogenised powder (50 ± 5 mg), according to the standard operating procedure described in the US-EPA method N°7473 (U.S. Environmental Protection Agency, 1998). The quality assurance of all metal analyses relied on blank and internal standard controls, and on the accuracy and reproducibility of data relative to the certified reference materials (CRMs) used in each analytical run. Blank values were systematically below the detection limits and CRM values concurred with certified concentrations. All elemental concentrations given on a dry weight basis can be converted on a wet weight basis according to the percentage of moisture measured for each sample.

Description: The dataset contains carbon (C) and nitrogen (N) stable isotope compositions analysed in the muscle tissue and energy density values and concentrations of 19 elements analysed in whole bodies of 15 meso- to bathypelagic species sampled in the twilight zone (deep pelagic area) of the Bay of Biscay, North-East Atlantic. The species included 4 crustacean species (Pasiphaea sivado, Sergia robusta, Systellaspis debilis, Ephyrina figueirai) and 11 fish species (Xenodermichthys copei, Searsia koefoedi, Myctophum punctatum, Notoscopelus kroeyeri, Lampanyctus crocodilus, Argyropelecus olfersii, Arctozenus risso, Stomias boa, Serrivomer beanii, Chauliodus sloani, Aphanopus carbo). The elements included 6 major constitutive elements (macro-minerals) and 13 trace elements among which 9 essential (micro-nutrients) and 4 non-essential elements (undesirables, with no know biological function). Specimens were collected during a single fishery in a canyon of the slope of the Bay of Biscay in October 2017, during the EVHOE fishery survey (“Evaluation Halieutique de l'Ouest de l'Europe”; https://doi.org/10.17600/17002300) conducted each autumn by the “Institut Français de Recherche pour l'Exploitation de la Mer” (Ifremer) on R/V Thalassa. A total of 266 individuals belonging to the 15 species were collected at night using a 25 m vertical opening pelagic trawl in the deep scattering layer (ca. 800 m depth in the water column; 1330 m bottom depth). All organisms were collected during one haul of 60 min, at a speed of approximately 4 knots (geographical coordinates at the beginning of the turn/end of the fishing: 45.103°N, -3.543° W).

Description: The dataset contains the concentrations of 11 essential elements (micro-nutrients) analysed in whole bodies of 78 forage species sampled on the continental shelf or in the canyons of the Bay of Biscay, North-East Atlantic. The species encompass jellyfish, crustaceans, cephalopods, cartilaginous and bony fish from coastal to oceanic and deep-sea waters. The elements include two macro-minerals (nitrogen and phosphorous) and nine trace elements (arsenic, cobalt, chromium, copper, iron, manganese, nickel, selenium, and zinc). Most of the specimens were collected during the annual EVHOE fishery campaigns (“Evaluation Halieutique de l'Ouest de l'Europe”; https://doi.org/10.18142/8) conducted each autumn by the “Institut Français de Recherche pour l'Exploitation de la Mer” (Ifremer) on R/V Thalassa, between 2002 and 2008, by benthic trawling with marge vertical opening or by pelagic trawling. Some species were additionally sampled during the same period from opportunistic fishing boats. As far as possible, the size range of these forage species was selected to match published prey sizes for cetacean predators in the Bay of Biscay. All the material was frozen immediately after collection and kept at –20°C until being processed. In the laboratory, whole organisms were briefly thawed. To reduce inter-individual variability, few to hundreds of individuals (depending on the size of species) were grouped for each species (i.e. constitution of pools) and homogenized using a stainless-steel knife mill, carefully rinsed with ultrapure water between each sample. These pools of whole specimens (corresponding to analytical samples) were frozen again –20°C, freeze-dried and reduced into fine powder until further analyses. A total of 115 samples was finally analysed. The process of organisms and samples (brief thawing, homogenization, freeze-dried and reduction into powder) was done within a maximum of two years after at-sea collection, and the samples (powders) were stored in a clean and dry place until analyses. Total element analyses on samples were then all conducted at the same date (in 2016). Total nitrogen (N) concentrations were determined following the Kjeldahl method (AOAC, 1990). Briefly, this method consists in digesting the samples with sulfuric acid to transform all N present into ammonium sulfate. The solution is then alkalized and the resulting ammonia is determined by distillation into a known volume of boric acid, the excess of which (corresponding to the amount of nitrogen in samples) is finally determined by titration. For all other elements, aliquots of samples (~200 mg dry weight of homogenised powder) were digested using a 6:2 (v/v) mixture with nitric acid (HNO3 69%, Trace Metal Grade®, FisherScientific) and hydrochloric acid (HCl, 34%, Trace Metal Grade®, FisherScientific). Acidic digestion of the samples was performed overnight at room temperature and then in a microwave oven (START-D, Milestone). Total concentrations of the micro-mineral phosphorus (P) and of the essential trace elements arsenic (As), cobalt (Co), chromium (Cr), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), selenium (Se) and zinc (Zn) were determined by inductively coupled plasma atomic emission spectrometry (ICP-OES, Vista-Pro Varian) and/or mass spectrometry (ICP-MS, X Series 2 Thermofisher Scientific). The quality assurance of these elemental analyses relied on blank and internal standard controls, and on the accuracy and reproducibility of data relative to the certified reference materials (CRMs) used in each analytical run. The CRMs used were TORT-3 (lobster hepatopancreas, National Research Council of Canada/NRCC) and DOLT-4 (dogfish liver, NRCC). Blank values were systematically below the detection limits and CRM values concurred with certified concentrations, with recovery rates ranging between 83% and 116% depending on the elements and on the CRM. Limits of quantification (LOQ) were calculated for each sample, depending on the mass of the aliquot analysed. The few concentrations below LOQ were replaced by half of the LOQ for each sample of concern. Specifically, this concerned 19 and 2 samples out of the 115 analysed for Cr and Ni respectively, corresponding to about 15% of values (for Cr) or much less than 15% (for Ni), in which cases this method of replacing non-detects by half the LOQ may be applied for data analysis (U.S. Environmental Protection Agency, 2000). All elemental concentrations given on a dry weight basis can be converted on a wet weight basis according to the average percentages of moisture given for each species.

Description: Mesopelagic organisms play a critical role in marine ecosystems, channelling energy and organic matter across food webs and serving as the primary prey for many open-ocean predators. Nevertheless, trophic pathways involving mesopelagic organisms are poorly understood and their contribution to food web structure remains difficult to assess (St. John et al., 2016). Existing data to assess mesopelagic feeding interactions and energy transfer are scattered in the literature or remain unpublished, making it difficult to locate and use such datasets. As part of the EU funded project SUMMER - Sustainable Management of Mesopelagic Resources H2020-BG-2018-2, GA: 817806) (https://summerh2020.eu/), we created MesopTroph, a georeferenced database of diet, trophic biogeochemical markers, and energy content of mesopelagic organisms and other marine taxa from the Northeast Atlantic and Mediterranean Sea, compiled from 191 published and non-published sources. MesopTroph includes seven datasets: (i) diet compositions from stomach content analysis, (ii) stable isotopes of carbon and nitrogen (δ13C and δ15N), (iii) fatty acid trophic markers (FATM), (iv) major and trace elements, (v) energy density, (vi) estimates of diet proportions, and (vii) trophic positions. The database contains information from 4918 samples, representing 51119 specimens from 499 species or genera, covering a wide range of trophic guilds and taxonomic groups. Metadata provided for each record include the location, dates and method of sample collection, taxonomic ranks (phylum, class, order, family), number and size (or size range) of sampled organisms, method/model used in data analysis, reference and DOI of the original data source. Compiled data were checked for errors, missing information, and to avoid duplicate entries, and scientific names and taxonomy were standardized.

Description: Bulk stable isotope ratios, primarily of carbon (δ13C) and nitrogen (δ15N), are increasingly used to examine predator-prey interactions and food web structure. We compiled δ13C and δ15N values of marine taxa from 56 published sources to support investigations on trophic interactions in mesopelagic food webs and assess the importance of mesopelagic organisms in the marine ecosystem. A total of 2095 records were collected, representing 8716 individual organisms from 349 unique species or genera sampled across the central and Northeast Atlantic, and the Mediterranean Sea, between 1905 and 2020. Records include 185 benthic and pelagic fish, 47 cephalopods, 31 marine mammals, 30 crustaceans, 26 elasmobranchs, 16 seabirds, 4 marine turtles, 4 jelly fish, 3 copepods, 2 salps, in addition to data from several organisms only identified to higher taxonomic ranks (family or above). The dataset includes isotopic ratios measured in the tissues or in the whole body of individual organisms, or mean values (and standard deviations) from pooled samples. Because lipids have more negative δ13C values relative to other major biochemical compounds in plant and animal tissues (DeNiro & Epstein, 1977), many studies correct for the lipid effect by extracting lipids from samples before analysis, or a posteriori, through mathematical corrections (Post, 2002). Therefore, δ13C values were reported as uncorrected, lipid-extracted, or mathematically-corrected. When available, the total organic carbon to nitrogen ratio (C:N) was included. For each data record, we also provided the sampling location, geographic coordinates, month and year of sample collection, method of sample collection, taxonomic ranks (phylum, class, order, family), number and size (or size range) of sampled organisms, as well as the reference and DOI of the original data source, for further details on the samples analysed and/or the analytical techniques used.

Description: Fractional trophic levels (i.e., trophic positions) describe the position of organisms within food webs and help define their functional roles in ecosystems (Odum & Heald, 1975). Trophic positions are thus critical for characterizing species' diets and energy pathways, investigating food web dynamics and ecosystem functioning, and assessing ecosystem health and resilience (Pauly et al., 1998; Pauly & Watson, 2005; Vander Zanden & Fetzer, 2007). We compiled estimates of trophic positions of marine organisms sampled across North Atlantic and Mediterranean waters between 1974 and 2015, gathered from 33 published and unpublished sources. The dataset comprises 208 unique species or genera, including zooplankton, decapods, cephalopods, pelagic and benthic fish, elasmobranchs, marine mammals, marine turtles, seabirds, as well as detritus. Estimates of trophic position were based on the analyses of stomach contents, bulk nitrogen stable isotopes (δ15N values), or amino acid compound-specific nitrogen isotopic analysis. For each data record, we also provided the sampling location, geographic coordinates, month and year of sample collection, method of sample collection, taxonomic ranks (phylum, class, order, family), number and size (or size range) of sampled organisms, type of analyses and estimation method, as well as the reference and DOI of the original data source, for further details on the samples analysed and/or the analytical techniques used.

Description: Information on the energy density of prey is critical for estimating food requirements and consumption by predators and modelling energy flux through food webs (Van de Putte et al., 2006). We compiled energy density values for 121 marine species or genera from 12 published sources. The dataset encompasses 71 benthic and pelagic fish, 29 crustaceans, 15 cephalopods, 2 elasmobranchs, 2 jelly fish and 1 salp, sampled in the central and Northeast Atlantic and in the Mediterranean Sea between 1992 and 2017. Data were collected from studies that measured energy density directly by bomb calorimetry, and those studies that measured the proximate composition (i.e. the percentage of proteins, lipids and carbohydrates) of sampled tissues and converted these percentages into energy using combustion equivalents reported in the literature. When available, we reported energy density (or mean density, for samples with more than one individual) as a function of dry and wet weight, and the moisture percentage of samples. For each data record, we also provided the sampling location, geographic coordinates, month and year of sample collection, method of sample collection, taxonomic ranks (phylum, class, order, family), number and size (or size range) of sampled organisms, as well as the reference and DOI of the original data source, for further details on the samples analysed and/or the analytical techniques used.

Description: Organisms accumulate major and trace elements (including metals) directly from the external environment and/or indirectly through diet. As such, their elemental composition can help to infer dietary preferences, solve trophic links and/or inform quantitative dietary analysis primarily based on carbon and nitrogen stable isotopes or on fatty acids (Lahaye et al. 2005, Ramos and González-Solís 2012, Soto et al. 2016, Majdi et al. 2018). This dataset reports the total concentrations of 30 major and trace elements analysed in whole bodies or in the muscle tissue of 82 unique species or genera characteristic of meso- to bathypelagic waters (referred as “mesopelagic”) or living on the continental shelf (referred as “other”). The species encompass jellyfish, crustaceans, cephalopods, fish, and were collected in North Atlantic and Mediterranean areas between 1968 and 2018. When available, the sampling method/gear as well as the sampling depth are specified. For the element mercury (Hg), the concentration of organic forms (referred as methyl-Hg) is also given when available, as well the percentage of these organic forms (% methyl-Hg) relative to total Hg. A column specifies whether concentrations are expressed on a dry weight or wet weight basis (weight of the animal tissue after being dried or containing water, respectively). All element concentrations given on a wet weight basis can be converted on a dry weight basis (and vice-versa if necessary) according to the percentages of moisture given for each sample analysed (when available). Data were compiled from 27 published studies/papers for which DOI are indicated, for further details and information on the samples analysed and/or the analytical techniques used.