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The CARBO-ACID research cruise (EUROFLEETS+ SEA02_10) was carried out on the RV Ramón Margalef between August 2nd and August 11st, with departing from Vigo – Spain and ending in Lisbon – Portugal. The main objective of this cruise was to collect data and samples to study the potential effects of ocean acidification on carbonate marine organisms (coccolithophores, pteropods, planktonic and benthic foraminifera, and corals) along the Iberian margin. With this objective, oceanographic data and water samples, plankton, cold-water corals and sediment samples were collected during an upwelling season, along two transects coinciding with the two persistent upwelling filaments off the Iberia Margin: the Cape Finisterra and the Cape Roca. In this dataset is guiven all the acquired data recollected onboad. During the CARBO-ACID cruise we did a total of 7 stations, 4 stations along the Cape Finisterra transect (from W to E: CA3, CA2, CA7, CA8) and 3 stations at the Cape Roca (from W to E: CA6, CA5, CA4) transect (Fig). At each station we usually started with a multibeam survey, a CTD and Rosette cast. These initial operations allowed to identify the different water masses present in this area, characterize their physical properties and to recover seawater samples at specific depth levels. The seawater samples were onboard subsampled, preserved in cold conditions or with chemicals and/ or filtered for several further analysis in the shore-based laboratories: DNA, chlorophyll, fitoplankton, coccolithophores, pH, alkalinity, stable isotopic composition, trace elements concentration and Suspend Particulate Matter. Subsequently to these operations, at each station, two vertical tows with a plankton multinet (with 5 nets) were done on the top 700 m of the water column to sample the planktonic communities of the different water depths. After this, sediment samples were recovered with a box-corer to study the past oceanographic conditions, between the pre-industrial Era and the Present, with multi-proxies used in paleoceanography and sedimentology. A total of 10 box-cores were recollected and each of them was onboard sub-sampled for eDNA, enzymes and benthic foraminifera. Fifteen shipek grab samples were recollected at the Fontanelas seamount (Estremadura Spur), station CA6, to characterize the sedimentary cover and to evaluate the presence of deep cold-water corals. Preliminary results show that the stations CA7, CA8 and CA4, located close to the coast, as expected, are the most influenced by the coastal upwelling, exhibiting colder surface water, higher values of fluorescence, and more zooplankton content reflecting higher phyto-zooplankton concentrations, as typical of the upwelling waters. At station CA4 temperature was higher and fluorescence showed lower values, indicative of less phytoplankton, and interpreted as indicating a different upwelling source water from that upwelled further north. Based on the CTD data, the Cape Roca transect is more influenced by the subtropical East North Atlantic Central Water (ENACWst), while the Cape Finisterra transect is more under the influence of the subpolar branch (ENACWsp). Seafloor sediment samples showed significant differences between the stations. Along the northern transect (Cape Finisterra) the seafloor sediments show an increase in grain size from the offshore to the coast. The offshore stations CA3 and CA2 revealed finer grained sediments, CA8 were composed of coarser sand and the station CA7, the shallowest station 77 m, presented the sediment composed mainly of shell fragments and coarse grain sand. Along the southern transect (Cape Roca), the offshore station CA6 (Fontanelas seamount) has coarser sandy sediments with rock clasts and cold-water coral fragments, and the stations CA5 and CA4 with fine sand to muddy sediments. The detailed CA6 bathymetry allowed to verify the existence of small plateaus on the slope of the Fontanelas seamount, where the fossil cold-water corals fragments were found, suggesting that this area is a very interesting system deserving further study with a ROV, and to characterize the corals fields and verify if there are live corals. These recollected data and samples will allow not only to reconstruct the pH variability under different environmental conditions, but also to estimate the biogeochemical changes along the coastal ocean waters as the anthropogenic influence increases. These results will contribute to better understand and model the effects on the biota under the future expected oceans pH changes.

Species distribution models (SDMs) are becoming an important tool for marine conservation and management. Yet while there is an increasing diversity and volume of marine biodiversity data for training SDMs, little practical guidance is available on how to leverage distinct data types to build robust models. We explored the effect of different data types on the fit, performance and predictive ability of SDMs by comparing models trained with four data types for a heavily exploited pelagic fish, the blue shark (Prionace glauca), in the Northwest Atlantic: two fishery-dependent (conventional mark-recapture tags, fisheries observer records) and two fishery-independent (satellite-linked electronic tags, pop-up archival tags). We found that all four data types can result in robust models, but differences among spatial predictions highlighted the need to consider ecological realism in model selection and interpretation regardless of data type. Differences among models were primarily attributed to biases in how each data type, and the associated representation of absences, sampled the environment and summarized the resulting species distributions. Outputs from model ensembles and a model trained on all pooled data both proved effective for combining inferences across data types and provided more ecologically realistic predictions than individual models. Our results provide valuable guidance for practitioners developing SDMs. With increasing access to diverse data sources, future work should further develop truly integrative modeling approaches that can explicitly leverage strengths of individual data types while statistically accounting for limitations, such as sampling biases.  Please see the README document ("README.md") and the accompanying published article: Braun, C. D., M. C. Arostegui, N. Farchadi, M. Alexander, P. Afonso, A. Allyn, S. J. Bograd, S. Brodie, D. P. Crear, E. F. Culhane, T. H. Curtis, E. L. Hazen, A. Kerney, N. Lezama-Ochoa, K. E. Mills, D. Pugh, N. Queiroz, J. D. Scott, G. B. Skomal, D. W. Sims, S. R. Thorrold, H. Welch, R. Young-Morse, R. Lewison. In press. Building use-inspired species distribution models: using multiple data types to examine and improve model performance. Ecological Applications. Accepted. DOI: < article DOI will be added when it is assigned >

Whether marine fish will grow differently in future high pCO2 environments remains surprisingly uncertain. Long-term and whole-life cycle effects are particularly unknown, because such experiments are logistically challenging, space demanding, exclude long-lived species, and require controlled, restricted feeding regimes—otherwise increased consumption could mask potential growth effects. Here, we report on repeated, long-term, food-controlled experiments to rear large populations (>4,000 individuals total) of the experimental model and ecologically important forage fish Menidia menidia (Atlantic silverside) under contrasting temperature (17°, 24°, and 28°C) and pCO2 conditions (450 vs. 2,200 μatm) from fertilization to a third of this annual species' life span. Quantile analyses of trait distributions showed mostly negative effects of high pCO2 on long-term growth. At 17°C and 28°C, but not at 24°C, high pCO2 fish were significantly shorter [17°C: -5 to -9%; 28°C: -3%] and weighed less [17°C: -6 to -18%; 28°C: -8%] compared to ambient pCO2 fish. Reductions in fish weight were smaller than in length, which is why high pCO2 fish at 17°C consistently exhibited a higher Fulton's k (weight/length ratio). Notably, it took more than 100 days of rearing for statistically significant length differences to emerge between treatment populations, showing that cumulative, long-term CO2 effects could exist elsewhere but are easily missed by short experiments. Long-term rearing had another benefit: it allowed sexing the surviving fish, thereby enabling rare sex-specific analyses of trait distributions under contrasting CO2 environments. We found that female silversides grew faster than males, but there was no interaction between CO2 and sex, indicating that males and females were similarly affected by high pCO2. Because Atlantic silversides are known to exhibit temperature-dependent sex determination, we also analyzed sex ratios, revealing no evidence for CO2-dependent sex determination in this species. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2020) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2020-12-25.

Abstract: The Northern Gannet Morus bossanus is an avian sentinel; the largest breeding seabird in Ireland and an obligate piscivore. Gannet eggs were collected from two island colonies off the east coast of Ireland, approximately 150km from each other, in locations with divergent history of industrialization (n = 10-20). Levels of potentially harmful contaminants including Polychlorinated biphenyls (PCBs), Polybrominated diphenyl ethers (PBDEs), Organochlorine pesticides (OCs), heavy metals and mercury were measured and differences of contaminant concentrations between different colonies compared. This is the first such study of contaminant levels in Gannet, or in any seabird egg in Ireland. Stable isotopes of carbon (d13C) and nitrogen (d15N) were measured in each egg to understand the influence of diet in contaminant levels detected. Significantly higher levels of PCBs, PBDEs and mercury were detected near Dublin (Ireland's industrialized capital city and location of its largest port) compared to Wexford. No differences were observed in levels of OCs and heavy metals between the two colonies. Stable isotope analysis demonstrated that Gannets in both locations occupy the same dietary niche excluding a difference in diet as the driver of differing contaminant levels in the two feeding areas. Though Gannets travel significant distances when foraging for food (~200km) tracking studies have shown that Gannets colonies maintain exclusive feeding areas with little overlap between neighbouring colonies. Differences between colonies within the feeding range of Gannets can therefore be detected despite Gannet's high dispersal ability. These results are in concurrence with elevated levels of contaminants in lower trophic level organisms that have been found in Dublin Bay compared to the rest of Ireland, indicating potential for Gannets as a higher trophic level indicator - though variability in their diet, including feeding on fishing discard, may lead to unacceptable levels of variability for an indicator species. Authors: Andrew Power��, Philip White��, Brendan McHugh��, Sinead Murphy��, Simon Berrow��, Moira Schlingermann��, Stephen Newton��, Linda O'Hea��, Brian Boyle��, Marissa Tannian��, Denis Crowley��, Evin McGovern��, Ian O'Connor�� ��Galway Mayo Institute of Technology, ��Marine Institute, ��BirdWatch Ireland

Ambient conditions shape microbiome responses to both short- and long-duration environment changes through processes including physiological acclimation, compositional shifts, and evolution. Thus, we predict that microbial communities inhabiting locations with larger diel, episodic, and annual variability in temperature and pH should be less sensitive to shifts in these climate-change factors. To test this hypothesis, we compared responses of surface ocean microbes from more variable (nearshore) and more constant (offshore) sites to short-term factorial warming (+3 °C) and/or acidification (pH -0.3). In all cases, warming alone significantly altered microbial community composition, while acidification had a minor influence. Compared with nearshore microbes, warmed offshore microbiomes exhibited larger changes in community composition, phylotype abundances, respiration rates, and metatranscriptomes, suggesting increased sensitivity of microbes from the less-variable environment. Moreover, while warming increased respiration rates, offshore metatranscriptomes yielded evidence of thermal stress responses in protein synthesis, heat shock proteins, and regulation. Future oceans with warmer waters may enhance overall metabolic and biogeochemical rates, but they will host altered microbial communities, especially in relatively thermally stable regions of the oceans. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2019) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2020-10-20.

Project: GCOS Earth Heat Inventory - A study under the Global Climate Observing System (GCOS) concerted international effort to update the Earth heat inventory (EHI), and presents an updated international assessment of ocean warming estimates, and new and updated estimates of heat gain in the atmosphere, cryosphere and land over the period from 1960 to present. Summary: The file “GCOS_EHI_1960-2020_Earth_Heat_Inventory_Ocean_Heat_Content_data.nc” contains a consistent long-term Earth system heat inventory over the period 1960-2020. Human-induced atmospheric composition changes cause a radiative imbalance at the top-of-atmosphere which is driving global warming. Understanding the heat gain of the Earth system from this accumulated heat – and particularly how much and where the heat is distributed in the Earth system - is fundamental to understanding how this affects warming oceans, atmosphere and land, rising temperatures and sea level, and loss of grounded and floating ice, which are fundamental concerns for society. This dataset is based on a study under the Global Climate Observing System (GCOS) concerted international effort to update the Earth heat inventory published in von Schuckmann et al. (2020), and presents an updated international assessment of ocean warming estimates, and new and updated estimates of heat gain in the atmosphere, cryosphere and land over the period 1960-2020. The dataset also contains estimates for global ocean heat content over 1960-2020 for different depth layers, i.e., 0-300m, 0-700m, 700-2000m, 0-2000m, 2000-bottom, which are described in von Schuckmann et al. (2022). This version includes an update of heat storage of global ocean heat content, where one additional product (Li et al., 2022) had been included to the initial estimate. The Earth heat inventory had been updated accordingly, considering also the update for continental heat content (Cuesta-Valero et al., 2023).

# Data and code for Does increasing temperature accentuate disease impacts on fisheries species? A meta-analysis [https://doi.org/10.5061/dryad.4j0zpc8jx](https://doi.org/10.5061/dryad.4j0zpc8jx) Update November 12, 2024: Updated colors in TM1R plot*, updated plot labels in Salmoniformes*_figures plot, renamed files to be more reflective of figure descriptions in manuscript. Updated names of files at the end of the READ ME document. ## Description of the data and file structure The attached csv file is the compiled dataset used to perform the meta-analysis described in the manuscript. These data include columns not utilized in the text as these categorical variables were later simplified to increase sample size. These columns were retained in this dataset for transparency purposes. Sources for additional information outside of what was provided in the original studies are described in Appendix S2 and full citations are available in Appendix S4. The column descriptions are as follows: Study: In-text citation for the original manuscript where the mortality data were sourced (See Appendix S2 and S4) Group: the experiment associated with that row of mortality data (see Methods) Temp_C: the temperature at which the experiment was performed in degrees Celsius. Temp_Cent: mean-centered temperature in degrees Celsius. Days_in_study: the duration of the experiment in days. TrueLOR: the calculated log odds ratio from that experiment (see Methods) TrueLORVar: the calculated variance of the log odds ratios (see Methods) Inv_var: inverse of the TrueLORVar variance, used to weight Bayesian model (see Methods) Order: Order of the host species used Class: Class of the host species used Phylum: Phylum of the host species used Superfamily: Superfamily of the host species used Host_mobility: If adult host was mobile in the water column (See Appendix S1) Vertebrae: If adult host has a vertebrae (See Appendix S1) LH_clean: Life stage listed in source paper (See Appendix S1) Temp_zone: Host distribution (See Appendix S1) Salinity: Salinity tolerance of host (See Appendix S1), later simplified into Salinity_simple which was the variable used in the meta-analysis. Parasite_Type: Taxonomic group of Parasite used (See Appendix S1), later simplified into Parasite_Type_simple which was the variable used in the meta-analysis. Host_source: The local source of the experimental animals as described in the paper (See Appendix S1), later simplified into Host_source_simple which was the variable used in the meta-analysis. Motivation_code_2: The motivation of the researchers performing the original study (See Appendix S1). Salinity_simple: Simplified salinity tolerance (See Methods, Table 1, and Appendix S1). LH_simple: Life history of the hosts simplified (See Methods, Table 1, and Appendix S1). Parasite: The parasite used in the study (Appendix S2). Parasite_Type_simple: The simplified parasite taxonomy used in the study (See Methods, Table 1, and Appendix S1). Parasite_transmission3: The mode of transportation of the parasite (See Methods, Table 1, and Appendix S1). Pathogen_type: The life history strategy of the parasite (See Methods, Table 1, and Appendix S1). Parasite_location: If the parasite was an external or internal parasite (See Methods, Table 1, and Appendix S1). Parasite_Transmission_simple: Simplified parasite transmission into single or multiple transmission modes. Not used in the meta-analysis Host_source_simple: Simplified Host source (See Methods, Table 1, and Appendix S1). ## Sharing/Access information Data was derived from the sources listed in Appendix S3 and Appendix S4 in the manuscript. ## Code/Software Attached are R scripts to produce the statistical models and all figures in the manuscript. These were created using R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) Final_mods.R : Script with statistical models referenced in paper Host_taxonomony_mod_figure.R: Script that produces Figure 2 and model estimates listed in Table S1. TM1_R_figures2.R: Script to produce model output in Table S2 and Figure 3. Salmoniformes_figures.R: Script to produce model output in Table S3 and Figure 4. Funnel_plot: Script used to produce Figure S2. We compiled data from experimental studies on fisheries species that compared mortality of parasitized and unparasitized hosts at a static temperature. We defined fisheries species to include both invertebrate and vertebrate species that are harvested commercially or recreationally. In Fall 2019, we searched Web of Science following PRISMA protocols (O’Dea et al. 2021) using key terms that would return papers focused on harvested aquatic species, parasites, and diseases, but would exclude papers that were focused on human, environmental or domestic animal health (see Appendix S1 in Supporting Information). This search yielded 1,201 papers. We then screened the abstracts of these papers, and retained only papers that satisfied four criteria: 1) an experiment was performed that included at least one parasite exposure treatment paired with an unexposed control group, 2) temperatures were intended to be constant and not intentionally varied, 3) hosts were from species that constitute a fishery, including those in aquaculture, and 4) estimates of survival or mortality were reported for both infected and uninfected hosts at each temperature treatment. This selection process reduced the number of studies to 386 (Appendix S1 and Figure S1). We obtained full versions of 364 papers (22 papers from the original 386 were unobtainable). We then screened the full text of these papers to ensure a match to our four criteria, which reduced the 364 papers to 70. To increase statistical power to estimate the effect of host Order on parasite-induced mortality, we excluded experiments from hosts in Orders with fewer than three effect sizes. This reduced the number of papers included in our study from 70 to 56 and yielded a total of 287 effect sizes from 131 experiments (several papers included more than one experiment; Appendix S1 and S2, Figure S1). At least two people extracted data from each paper to reduce extraction error. If extracted values differed, the data were re-extracted until there was agreement between the two extractors. For data that were displayed in a graphical format only, we used WebPlotDigitizer (Rohatgi 2022) to extract data. Data (which may have been presented as mortality rates, or proportion surviving) were converted to numbers of host individuals that were dead and alive at the end of the experiment. We also extracted information about the paper itself, including the source of the hosts used in the paper and the motivation for conducting the experiment (see Appendix S1). Finally, we collected additional information about host and parasite traits from outside sources (e.g., other peer reviewed papers, government reports) when necessary to obtain moderator variables (Table 1, Appendix S1 and S2). The moderators (Table 1) were used to test a priori hypotheses regarding how host, parasite, and study design traits influenced how temperature affected parasite-induced mortality. Because our focus was on parasite-induced mortality, we used log odds ratios and the variance surrouding log odds ratio as our effect size to compare host survival in the parasitized vs unparasitized treatments. Rapid warming could drastically alter host-parasite relationships, which is especially important for fisheries crucial to human nutrition and economic livelihoods; yet we lack a synthetic understanding of how warming influences parasite-induced mortality in these systems. We conducted a meta-analysis using 287 effect sizes from 56 empirical papers on harvested aquatic species and determined the relationship between parasite-induced host mortality and temperature and how this relationship was altered by host, parasite and study design traits. Overall, temperature increased parasite-induced host mortality; however, the magnitude and sometimes direction of this relationship varied. Hosts from the order Salmoniformes experienced a greater increase in parasite-induced mortality with temperature than average. Opportunistic parasites were correlated with a greater increase in host mortality with temperature than average, while bacterial parasite-induced mortality was lower than average as temperature increased. Thus, parasites will generally increase host mortality as the environment warms; however, this effect will vary among systems.

Current trends in the global climate facilitate the displacement of numerous marine species from their native distribution ranges to higher latitudes when facing warming conditions. In this work, we analyzed occurrences of a circumtropical reef fish, the spotfin burrfish, Chilomycterus reticulatus (Linnaeus, 1958), in the Madeira Archipelago (NE Atlantic) between 1898 and 2021. In addition to available data sources, we performed an online survey to assess the distribution and presence of this species in the Madeira Archipelago, along with other relevant information, such as size class and year of the first sighting. In total, 28 valid participants responded to the online survey, georeferencing 119 C. reticulatus sightings and confirming its presence in all archipelago islands. The invasiveness of the species was screened using the Aquatic Species Invasiveness Screening Kit. Five assessments rated the fish as being of medium risk of establishing a local population and becoming invasive. Current temperature trends might have facilitated multiple sightings of this thermophilic species in the Madeira Archipelago. The present study indicates an increase in C. reticulatus sightings in the region. This underlines the need for updated comprehensive information on species diversity and distribution to support informed management and decisions. The spread of yet another thermophilic species in Madeiran waters provides further evidence of an ongoing tropicalization, emphasizing the need for monitoring programs and the potential of citizen science in complementing such programs.