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The multi-species ecosystem model SS-DBEM integrates a species based model (DBEM) with the spectrum approach (SS). This model includes a large number of mechanisms and ecological processes such as population growth, movement, and dispersal of adults and larvae, as well as the ecophysiological effects of temperature, oxygen, and pH on body size, growth, mortality, and reproduction. The SS-DBEM model provides spatially (at a 0.5x0.5º resolution) and temporally (yearly) resolved predictions of changes in species’ size, abundance and biomass with consideration of competition. The competition algorithm describes the resource allocation between different species co-occurring in a spatial unit (thereafter cell) by comparing the flux of energy (in biomass) that can be supported (estimated with the SS model) with the energy demanded by the species predicted to inhabit that cell (estimated with the DBEM model). In addition, the environmental conditions are considered in the mechanisms and since there are different environmental conditions that are provided by the biogeochemical models, species responses are also different spatially. See readme.txt for scientific publications developing and using the model.

Three high resolution multicore records have been collected at three sites in the western Mediterranean with a MC400-Multicorer system during the MedSeA cruise (Mediterranean Sea Acidification in a changing climate) on 2 May to 2 June 2013 onboard the R/V Angeles Álvarino. Core MedSeA-S3-c1 was retrieved in the Alboran basin (Lat. 36.0746° N, Long. 04.11040° W) at a water depth of 1137 m, with a core length of 33 cm. Core MedSeA-S23-c1 was recovered at a water depth of 1156 m in the Balearic basin offshore Barcelona (Lat. 41.1121° N, Long. 2.38200° E) with a core length of 43 cm. MedSeA-S7-c2 was collected at the Strait of Sicily (Lat. 37.7080° N, Long. 12.40553° E) at a water depth of 263 m, with a core length of 46.5 cm. All three cores have been analyzed for changes in size normalized weight (SNW) and stable carbon isotopes (δ13C), measured in planktic foraminiferal clacite shells of the two species Globigerina bulloides and Globigerinoides elongatus. Boron (δ11B) isotopes have been measured in tests of Globigerinoides elongatus at the Alboran site, and in Globigerinoides ruber albus at the Strait of Sicily. Complementary data for the Strait of Sicily record has been obtained, including a 210Pb based age depth model, sea surface temperatures (SST), alkenone concentrations and planktic foraminiferal assemblage changes. The Strait of Sicily record (MedSeA-S7-c2) covers around the last 200 a, describing environmental changes throughout the Industrial Era (IE) at high temporal resolution. The Alboran (MedSeA-S3-c1) and Balearic Sea (MedSeA-S23-c1) records spanning the last about 1 ka at lower temporal resolution, displaying oceanographic changes throughout the transition from the pre-industrial era to present, as discussed in (Pallacks et al., 2021; doi:10.1016/j.gloplacha.2021.103549). Data has been collected to investigate the response of marine calcifiers to the combined effects of climate change stressors on decadal to centennial timescales, caused by anthropogenic CO2 emissions.

gCube Catalogue (gCat) API is a library containing classes shared across gcat* components. gCube is an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments, such as the D4Science Infrastructure, by favouring the realisation of reuse-oriented policies. gCube has been used to successfully build and operate infrastructures and virtual research environments for application domains ranging from biodiversity to environmental data management and cultural heritage. gCube offers components supporting typical data management workflows including data access, curation, processing, and visualisation on a large set of data typologies ranging from primary biodiversity data to geospatial and tabular data. D4Science is a Hybrid Data Infrastructure combining over 500 software components and integrating data from more than 50 different data providers into a coherent and managed system of hardware, software, and data resources. The D4Science infrastructure drastically reduces the cost of ownership, maintenance, and operation thanks to the exploitation of gCube. The source code of this software version is available at: https://code-repo.d4science.org/gCubeSystem/gcat-api/releases/tag/v2.3.0

gCube Catalogue (gCat) Service allows any client to publish on the gCube Catalogue. gCube is an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments, such as the D4Science Infrastructure, by favouring the realisation of reuse-oriented policies. gCube has been used to successfully build and operate infrastructures and virtual research environments for application domains ranging from biodiversity to environmental data management and cultural heritage. gCube offers components supporting typical data management workflows including data access, curation, processing, and visualisation on a large set of data typologies ranging from primary biodiversity data to geospatial and tabular data. D4Science is a Hybrid Data Infrastructure combining over 500 software components and integrating data from more than 50 different data providers into a coherent and managed system of hardware, software, and data resources. The D4Science infrastructure drastically reduces the cost of ownership, maintenance, and operation thanks to the exploitation of gCube. The source code of this software version is available at: https://code-repo.d4science.org/gCubeSystem/gcat/releases/tag/v2.4.1

gCube Catalogue (gCat) Client is a library designed to interact with REST API exposed by the gCat Service. gCube is an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments, such as the D4Science Infrastructure, by favouring the realisation of reuse-oriented policies. gCube has been used to successfully build and operate infrastructures and virtual research environments for application domains ranging from biodiversity to environmental data management and cultural heritage. gCube offers components supporting typical data management workflows including data access, curation, processing, and visualisation on a large set of data typologies ranging from primary biodiversity data to geospatial and tabular data. D4Science is a Hybrid Data Infrastructure combining over 500 software components and integrating data from more than 50 different data providers into a coherent and managed system of hardware, software, and data resources. The D4Science infrastructure drastically reduces the cost of ownership, maintenance, and operation thanks to the exploitation of gCube. The source code of this software version is available at: https://code-repo.d4science.org/gCubeSystem/gcat-client/releases/tag/v2.0.0

Tides significantly affect polar coastlines by modulating ice shelf melt and modifying shelf water properties through transport and mixing. However, the effect of tides on the marine carbonate chemistry in such regions, especially around Antarctica, remains largely unexplored. We address this topic with two case studies in a coastal polynya in the south-eastern Weddell Sea, neighbouring the Ekström Ice Shelf. The case studies were conducted in January 2015 (PS89) and January 2019 (PS117), capturing semi-diurnal oscillations in the water column. These are pronounced in both physical and biogeochemical variables for PS89. During rising tide, advection of sea ice meltwater from the north-east created a fresher, warmer, and more deeply mixed water column with lower dissolved inorganic carbon (DIC) and total alkalinity (TA) content. During ebbing tide, water from underneath the ice shelf decreased the polynya's temperature, increased the DIC and TA content, and created a more stratified water column. The variability during the PS117 case study was much smaller, as it had less sea ice meltwater input during rising tide and was better mixed with sub-ice shelf water. The contrasts in the variability between the two case studies could be wind and sea ice driven, and they underline the complexity and highly dynamic nature of the system. The variability in the polynya induced by the tides results in an air–sea CO2 flux that can range between a strong sink (−24 mmol m−2 d−1) and a small source (3 mmol m−2 d−1) on a semi-diurnal timescale. If the variability induced by tides is not taken into account, there is a potential risk of overestimating the polynya's CO2 uptake by 67 % or underestimating it by 73 %, compared to the average flux determined over several days. Depending on the timing of limited sampling, the polynya may appear to be a source or a sink of CO2. Given the disproportionate influence of polynyas on heat and carbon exchange in polar oceans, we recommend future studies around the Antarctic and Arctic coastlines to consider the timing of tidal currents in their sampling strategies and analyses. This will help constrain variability in oceanographic measurements and avoid potential biases in our understanding of these highly complex systems.

Since 2000, and for the following 20 years, hydrological data of the Mediterranean Sea, with a particular focus on the western and central Mediterranean sub-basins, have been acquired to study the hydrodynamics at both coastal and open sea scales. In total, 1468 hydrological casts were realized in 29 oceanographic cruises planned due to scientific purposes linked with funding research projects but were also sometimes driven by sea conditions and type of vessel. After accurate quality assurance and control, following standard procedures, all hydrological data were included in four online public open-access repositories in SEANOE (SEA scieNtific Open data Edition), available from https://doi.org/10.17882/87567 (Ribotti et al., 2022). Hydrological and dissolved oxygen data are always present in all of the datasets, whereas pH, fluorescence, turbidity, and chromophoric dissolved organic matter (CDOM) are available just for some cruises. Samplings were carried out mainly along transects, with some repetition over the years. The results of two data analyses, i.e., staircase systems in the Tyrrhenian Sea and in the Algero-Provençal sub-basin and spreading of the Western Mediterranean Transient, are mentioned.

We report the results of an aquaria-based experiment testing the effects of suspended particles generated during potential mining activities, on a common habitat-building coral species in the Azores, Dentomuricea aff. meteor. Corals were collected from the summit of Condor Seamount (Azores, NE Atlantic) at depths between 185-210 m in August 2014. Coral fragments were maintained in 10-L aquaria and exposed to three experimental treatments for a period of four weeks at the DeepSeaLab aquaria facilities (Okeanos-University of the Azores): (1) control conditions (no added sediments); (2) suspended polymetallic sulphide (PMS) particles; (3) suspended quartz particles. PMS particles were obtained by grinding PMS inactive chimney rocks collected at the hydrothermal vent field Lucky Strike. Both particle types were delivered at a concentration of 25 mg L-1. The putative effects of PMS particles were evaluated through measurements of the coral physiological responses at the levels of the organism (oxygen consumption, ammonium excretion), tissue (bioaccumulation of metals) and cell (enzyme activity and gene expression).

Robust estimates of marine species vulnerability to ongoing climate change require realistic stressor experiments. Here, we subjected an important coastal predator, the sea star Asterias rubens, to projected warming and ocean acidification over an annual seasonal cycle. Warming and, less so, acidification, had strongly season-specific impacts on animal energy budgets. Specifically, simulated future summer temperatures caused >95% sea star mortality, reduced feeding rate and body mass loss. Additional acute experiments demonstrated that respiratory oxygen flux was preferentially directed to support high summer metabolism at the expense of feeding-related processes. Using 15 years of field temperature data and end of century warming projections, we estimate that potentially lethal summer heat waves will occur in 20% of future years. Our study demonstrates the importance of assessing stress responses along seasonal thermal cycles and the high selective force that future summer heat waves likely can exert on coastal marine animal populations.

This data set collection provides quality controlled temperature, conductivity and pressure measurements from moored instrumentation (Seabird Microcat) in the Denmark Strait. Practical salinity was calculated from the measured quantities and is provided as well. Temporal resolution of the time series is 10 to 20 minutes. The data was collected between 2005 to 2015 at the location of mooring DS2. This mooring is part of the Denmark Strait Overflow array and maintained by the Institute of Oceanography, University Hamburg. The purpose of the array is to monitor the properties and variability of the dense Denmark Strait Overflow.