cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17882/95601
title: Dataset used to assess the spatio-temporal dynamic of macrobenthic communities on submarine sand dunes

description: The present dataset has been used to assess how macrobenthic communities vary depending on (i) the type of dune, (ii) the position within the dune and (iii) the season. It has been combined with a biological traits dataset [Robert Alexandre Elie, Quillien Nolwenn, Bacha Mahmoud, Caulle Clémence, Nexer Maëlle, Parent Briz, Garlan Thierry, Desroy Nicolas (2021). Biological traits of macroinvertebrates associated with subtidal sandy beforms. SEANOE. https://doi.org/10.17882/80785] and results from this analysis have been published in Marine Pollution Bulletin in 2021 [Alexandre Elie Robert, Nolwenn Quillien, Mahmoud Bacha, Clémence Caulle, Maëlle Nexer, Briz Parent, Thierry Garlan, Nicolas Desroy, Sediment migrations drive the dynamic of macrobenthic ecosystems in subtidal sandy bedforms, Marine Pollution Bulletin, Volume 171, 2021, 112695, ISSN 0025-326X, https://doi.org/10.1016/j.marpolbul.2021.112695.
DOI: 10.17882/95359
title: Stable isotope ratios of C, N and S in fauna sampled at the Vestbrona Carbonate Field (Norway)

description: This dataset contains stable isotope ratios of C, N and S in several macrofaunal taxa sampled at the Vestbrona carbonate field, a methane seep are off the coast of Norway. All details about sampling and analyses can be found in the article "Lack of detectable chemosynthesis at a sponge dominated subarctic methane seep" by Melina Sinner, Wei Li Hong, Loïc N. Michel, Sunil Vadakkepuliyambatta, Jochen Knies and Arunima Sen (currently under revision for Frontiers in Marine Sciences). A full term description of the terms used in the dataset is available at https://doi.org/10.17882/76595.
DOI: 10.17882/95337
title: Dissolved Zinc in the western Bering Sea and near Kamchatka Strait

description: This dataset describes the distribution of dissoved zinc in the western Bering Sea and near Kamchatka Strait. Seawater samples were collected using R/V Professor Multanovskiy during cruise Mu18 between August and October 2018. Trace metal clean procedures were employed for sample collection. Dissolved zinc concentration was determined by high resolution inductively coupled plasma mass spectrometry following pre-concentration using chelating resin column. Reference seawaters GEOTRACES GS and GD were measured using our method, which produced results similar to consensus values. Dissolved Zn showed nutrient type distributions in the western Bering Sea and near Kamchatka Strait. Distinctive kink in the zinc-silicate relationship similar to that in the subarctic Pacific was also observed in our study area. Our data shows that zinc may be supplied from coastal sources and subsequently transported to the subarctic Pacific as zinc-rich particulates.
DOI: 10.17882/95173
title: Outputs from a coupled physical-biogeochemical numerical ocean model of the Hauraki Gulf in Aotearoa New Zealand.

description: This dataset contains NetCDF output from several model runs of a coupled physical biogeochemical model of the Hauraki Gulf in Aotearoa, New Zealand. These model outputs were used in the paper: Macdonald, Helen Skye, Charine Collins, David Plew, John Zeldis, and Niall Broekhuizen. "Modelling the biogeochemical footprint of rivers in the Hauraki Gulf, New Zealand." Frontiers in Marine Science 10: 1041. The model simulations are performed using the Regional Ocean Modelling system with the Fennel model activated to include biogeochemical interactions. The horizontal grid spacing is 750 m with 30 vertical grid cells. Model runs span the time interval between January 2004 to December 2013. Outputs are 12-hourly averages that are divided up into files of approximately 6 months in length. These files are labelled sequentially from 1 to 20. Model simulations were performed which varied the riverine inputs: time-varying riverine inputs (called varying), a constant average riverine input (called fixed) and no riverine inputs (called no_river). This was done for both physics and biological parameters. Several different outputs are included in this dataset: Timeseries of temperature and salinity are included for a point source (175.29 OE, -36.77 OE) for all simulations (varying, fixed, no_river). Timeseries of all model state variables and advective fluxes for stations along 2 transects for the time-varying river. These transects are marked on the figure (red lines labelled “T1” and “T2”). Each station in the transect is labelled by the number of the grid-cell. For T1 this is 70-110 with numbers increasing west to east and for T2 this is 119 to 172 with numbers increasing north to south. Geospatial time series of Bottom denitrification fluxes. Timeseries of chlorophyll, NO3 and NH4 for 13 stations along a 3rd transect (marked as a black line with dots indicating individual stations in the figure) for the time-varying river. These stations are labelled A through O for stations from south to north. Geospatial time series of surface and near bottom fields for temperature, salinity and velocities for simulations with and without riverine inputs (varying and no_river folders respectively). Geospatial time series of surface and near bottom fields for NO3, NH4 and chlorophyll (biological variables) for simulations with and without riverine inputs (varying and no_river folders respectively). Average surface and near bottom dye concentrations from a dye tracer continuously released in 3 main rivers (The Waihou, Piako and Kaueranga Rivers, marked as red * in the figure). These rivers are located in the southern end of the Hauraki Gulf (the Firth on Thames). The average surface and near bottom concentration of a dye released from all other rivers in this region is also included. All files are in NetCDF format and contain information on the position, time and units of each data point.
DOI: 10.17882/95125
title: Response of Benthic Tropical Marine Macroalgae to Ocean Acidification

description: Macroalgae can modify coral reef ecosystem structure and function through a variety of mechanisms, including mediation of biogeochemistry through photosynthesis and the associated production of dissolved organic carbon (DOC). Although DOC plays a critical role in sponge and microbial loops and coastal carbon cycling, high concentrations can be detrimental to corals and have negative consequences for reef assemblages. Ocean and coastal acidification have the potential to fuel photosynthesis and may alter macroalgal DOC production, but this has not been widely studied across taxa and regions. We exposed fleshy (Dictyota spp.) and calcifying (Halimeda tuna) macroalgae to ambient and low seawater pH for 25 days in an outdoor experimental system in the Florida Keys. We quantified algal growth, calcification, photophysiology, and DOC production across pH treatments. We observed no significant differences in the growth or photophysiology of either species between treatments, except for lower chlorophyll b concentrations in Dictyota spp. in response to low pH. The tolerance of Dictyota and Halimeda to near-future seawater carbonate chemistry and stability of photophysiology, suggests that acidification alone is unlikely to change biogeochemical processes associated with algal photosynthesis in these species. Additional research is needed to fully understand how fleshy and calcifying macroalgae that exist across a range of environmental conditions regulate photosynthesis (via carbon uptake strategies) and how this influences their DOC production. Once we understand the physiological responses of macroalgae to current and future ocean change, then we can more accurately model and infer the indirect impacts of macroalgae on future coral health and reef ecosystem processes.
DOI: 10.17882/95124
title: Ocean carbon uptake in simulations with Bern3D-LPX with different starting dates

description: The simulated ocean carbon sink in each year in Earth System Models depends on the starting year of the simulation and the atmospheric partial pressure at that year. Simulations of the last decades and the next century, such as in the Global Carbon Budget or the Coupled Model Intercomparison Project Phase 5 (CMIP5) and 6 (CMIP6) often start in the middle of the 19th century to save computational time, although atmospheric CO2 already started to increase due to anthropogenic activity since 1765. If a simulation starts in 1850, for example, the spin-up simulation is performed with the higher atmospheric partial pressure in 1850. In these simulations, old water masses in the ocean contain more carbon compared to a simulations that would have started in 1765. The difference in the carbon content of deep ocean water masses affects the amount of carbon that is taken up throughout the entire simulation period when these water masses continously come back to the ocean surface, resulting in a too small simulated ocean carbon sink in simulations that start in 1850. However, the magnitude of this difference remains uncertain. Here, I made two sets of simulations with the Earth System Model Bern3D-LPX, one set starts in 1765 and the other one starts in 1850 to quantify this difference. Each set contains 9 different configurations of Bern3D-LPX with different ocean mixing rates and climate sensitivites to cover the wide range of ESMs in CMIP. The model forcing setup is described in detail in Terhaar et al. (2023) (Environ. Res. Lett. 18 (2023) 024033, https://doi.org/10.1088/1748-9326/acaf91). Only output until 2020 should be used.
DOI: 10.17882/94772
title: python SAR processor for level-1 SLC product

description: `xsarslc` is a python package that allow to compute SAR cross spectrum and advanced radar parameters from Sentinel-1 SLC products. It handles 3 modes of acquisitions IW , EW and WV. The source code is relying on `xarray` library. https://github.com/umr-lops/xsar_slc documentation is available here: https://cerweb.ifremer.fr/datarmor/sarwave/documentation/processor/sar/xsarslc/html/ It contains an Algorithm Tehcnical Baseline Document (ATBD) section, describing the equations of each processing steps and their rationales.
DOI: 10.17882/94705
title: EOT-NECS Ocean Tide Model

description: EOT-NECS is a regional Empirical Ocean Tide model of the Northwest European Continental Shelf developed at DGFI-TUM. EOT-NECS is created using 16 altimetry missions from 1992 to 2022 based on residual tidal analysis. A total of 43 ocean tidal constituents are provided on a 1/16 degree resolution based on both semi-empirical and empirical estimations. This model was specifically created for use in the DCSM-FM model to improve tidal boundary forcing, with the results being published in the Ocean Dynamics journal.
DOI: 10.17882/94676
title: BioGeoChemical-Argo float data including bio-optical profiles and POC flux at 1000m in the Southern Ocean from 2014 to 2019.

description: These datasets contain measurements from BGC-Argo floats equipped with a transmissometer and which cover the Southern Ocean from 2014 to 2019. The first dataset ("profile_data.csv") includes bio-optical profiles of the particulate backscattering coefficient (BBP in m-1), the concentration of Chlorophyll-a (CHLA in mg m-3), and the particulate beam attenuation coefficient (CP in m-1) with data processing and quality control described in the manuscript entitled “BioGeoChemical-Argo floats reveal stark latitudinal gradient in the Southern Ocean deep carbon flux driven by phytoplankton community composition” submitted to Global Biogeochemical Cycles. In the second file (i.e. "flux_1000m.csv"), we provided attenuance fluxes (in day-1) at 1000m measured by the transmissometer acting as an Optical Sediment Trap. These flux values were then converted to POC fluxes (mg POC m-2 day-1) with the method described in the submitted manuscript.
DOI: 10.17882/94520
title: Outputs from a Regional Ocean Modeling System (ROMS) two-way nested model of the Mid-Atlantic Bight and Delaware Bay for 2009-2015.

description: This is an archive of model output from the Regional Ocean Modeling System (ROMS) with two grids and two-way nesting. The parent grid resolution (referred to as Doppio) is 7 km and spans the Atlantic Ocean off the northeast United States from Cape Hatteras to Nova Scotia. The refinement grid (referred to as Snaildel) focuses on Delaware Bay and the adjacent coastal ocean at 1 km resolution. This ROMS configuration uses turbulence kinetic energy flux and significant wave height from Simulating Waves Nearshore (SWAN) as surface boundary conditions for turbulence closure.Ocean state variables computed are sea level, velocity, temperature, and salinity. Also inclued are surface and bottom stresses, as well as vertical diffusivity of tracer and momentum. The files uploaded here are examples of one time record from each of this dataset. Outputs for the full reanalysis, which comprises 14 Terabytes of data, are made available for download via a THREDDS (Thematic Real-time Environmental Distributed Data Services) web service to facilitate user geospatial or temporal sub-setting. The THREDDS catalog URLs and example filenames available here, for the respective collections, are: - 12 minute snapshots of the Doppio domain 2009-2015: https://tds.marine.rutgers.edu/thredds/roms/snaildel/catalog.html?dataset=snaildel_doppio_history - 12 minute snapshots of the Snaildel domain 2009-2015: https://tds.marine.rutgers.edu/thredds/roms/snaildel/catalog.html?dataset=snaildel_snaildel_history Garwood, J. C., H. L. Fuchs, G. P. Gerbi, E. J. Hunter, R. J. Chant and J. L. Wilkin (2022). "Estuarine retention of larvae: Contrasting effects of behavioral responses to turbulence and waves." Limnol. Oceanogr. 67: 992-1005. Hunter, E. J., H. L. Fuchs, J. L. Wilkin, G. P. Gerbi, R. J. Chant and J. C. Garwood (2022). "ROMSPath v1.0: Offline Particle Tracking for the Regional Ocean Modeling System (ROMS)." Geosci. Model Dev. 15: 4297-4311.
DOI: 10.17882/94472
title: Physiological adaptation of the diatom Pseudo-nitzschia delicatissima under copper starvation

description: This dataset contains the data used in the manuscript "Physiological adaptation of the diatom Pseudo-nitzschia delicatissima under copper starvation" accepted for publication in April 2023 in Marine Environmental Research. In the open ocean and particularly in iron (Fe)-limited environment, copper (Cu) deficiency might limit the growth of phytoplankton species. Cu is an essential trace metal used in electron-transfer reactions, such as respiration and photosynthesis, when bound to specific enzymes. Some phytoplankton species, such as the diatom Pseudo-nitzschia spp. can cope with Cu starvation through adaptative strategies. This dataset contains the data collected during the experimental starvation of a strain of the diatom P. delicatissima under laboratory controlled conditions.
DOI: 10.17882/94461
title: Satellite Altimetry and Hydrodynamic Model derived Accurate Dynamic Topography utilizing Marine Geoid Model In Baltic Sea (2017-2019)

description: Accurate determination of dynamic topography (DT) is expected to quantify a realistic sea surface, with respect to its vertical datum, and in identifying sub-mesoscale features of ocean dynamics. This dataset contains DT derived using satellite altimetry (SA) along-track data from Sentinel- 3A (S3A), Sentinel-3B (S3B), and Jason-3 (JA3) for the period 2017‒2019 over the Baltic Sea with respect to a high-resolution marine geoid model (NKG2015). To assess the SA-derived DT accuracy they have been compared with DT derived from a tide gauge (TG) corrected hydrodynamic model (HDM). The HDM model contains the Nemo-Nordic NS01 data assimilated model developed by the Swedish Meteorological and Hydrological Institute (SMHI www.smhi.se) which has been corrected at the time and location of each SA pass and cycle utilizing hourly observation of 73 tide gauge stations over the Baltic Sea using the methodology described in "" paper by Mostafavi M. et al., (2023). The DT can alternatively be converted to Sea Surface Height (SSH) by adding the geoid height value derived from the NKG2015 geoid model available in the dataset. Please refer to readme.txt for a full description.
DOI: 10.17882/94303
title: Benthic categories analyzed by the photoquadrat/CPCe method - impact of the New Coastal Road, Reunion Island

description: In order to study the impact of the New Coastal Road on benthic communities, Biotope use photoquadrat/CPCe method (Coral Point Count with excel extension). CPCe is a visual basic software designed to calculate statistical coral coverage over a specified area. These images are being assigned with spatial random points for user’s further identification. It can also perform both image calibration and area analysis of the benthic features, and has the ability to automatically generate analysis in Microsoft Excel. Customization options include user-specified coral/substrate codes and data point shape, size, and color. For this study, 130 benthic categories are analyzed and they are described into this file. Datas are stored in the french database "BD Recif" (developped by the french Institute : Ifremer). This file allows not only to list the benthic categories sought but also to transcribe the correspondences between datas provided by CPCe and datas stored in BD Recif
DOI: 10.17882/94263
title: Microsatellites and mitochondrial dataset for the vesicomyid bivalve Christineconcha regab

description: Distribution of five mitochondrial haplotypes among 176 individuals , and multilocus genotypes at the eight microsatellite loci analysed for a total of 177 individuals, obtained for the vesicomyid bivalve Christineconcha regab from chemiosynthetic sites of the West African Equatorial margin.
DOI: 10.17882/94189
title: IBER-BAS Coastal marine waters quality monitoring Burgas Bay, Bulgaria, 07.2009-06.2011

description: Coastal marine waters quality monitoring in the southern section of the Burgas Bay, Bulgarian Black Sea coast. Monitoring was carried out in the period 07.2009-06.2011 by the Laboratory of Marine Ecology, IBER-BAS. Dataset already available in the Emodnet Chemistry portal under the following link: https://cdi-chemistry.seadatanet.org/search/welcome.php?query=2228&query_code={D2062C8A-7576-4184-8C24-6E0DE4E1AD15}
DOI: 10.17882/94046
title: Projected cross-shore changes in upwelling induced by offshore wind farm development along the California coast

description: In California offshore waters, sustained northwesterly winds have been identified as a key resource that can contribute substantially to renewable energy goals. However, the development of large-scale offshore wind farms can reduce the wind stress at the sea surface, which could affect wind-driven upwelling, nutrient delivery, and ecosystem dynamics. Here we examine changes to upwelling using atmospheric and ocean circulation numerical models together with a hypothetical upper bound buildout scenario of 877 turbines spread across three areas of interest. Wind speed changes are found to reduce upwelling on the inshore side of windfarms and increase upwelling on the offshore side. These changes, when expressed in terms of widely used metrics for upwelling volume transport and nutrient delivery, show that while the net upwelling in a wide coastal band changes relatively little, the spatial structure of upwelling within this coastal region can be shifted outside the bounds of natural variability.
DOI: 10.17882/94008
title: Temperature, conductivity and salinity data of the RADIALES Program, Vigo, 1987-2020

description: Pressure, temperature, conductivity, and derived salinity data with their associated quality flags from the Vigo section of the monitoring program "Oceanography Time Series in Northern Spain" (RADIALES; https://www.seriestemporales-ieo.net/), carried out by the Instituto Español de Oceanografía. Data were collected biweekly to monthly from August 1987 to September 2020 in the interior of the Ría de Vigo and its adjacent shelf, at four stations with depths ranging from 29 m to 148 m. Data were acquired using MARK III, Sea-Bird Scientific 19 SeaCAT, SBE 9 Plus and SBE 25 Sealogger CTD (conductivity, temperature, depth) profilers. They were processed using Sea-Bird Scientific's Seasoft software package, and subsequently, quality controlled with both ctdcheck (https://github.com/PabloOtero/CTDChecker) and Ocean Data View software.
DOI: 10.17882/93267
title: Incubation and first feeding of European smelt (Osmerus eperlanus, L.) eggs and larvae using conventional hatchery equipment

description: This dataset contains all information collated during an experimental mass incubation and rearing of European smelt (Osmerus eperlanus, L.) eggs and larvae. The experiment specifically tested (I) whether a technical modification of the egg incubations jars would improve the overall number of surviving eggs, and (II) how first-feeding protocols for larvae could be improved. For more details please see the associated article Reiser et al (2023) in Aquatic Living Resources. The following parameters were recorded: (1) number of incubated eggs, (2) egg survival, (3) hatch success, (4) length-at-age, (5) larval mortality, and (6) larval prey consumption. Data on all six parameters are provided as separate CSV files. In addition, a legend of the abbreviations used in the CSV files is provided. The code for analyzing the data in R is available upon request. Adult European smelt caught in River Weser (Bremen, Germany) at 53.060 (lat) and 8.864 (long). Experimental rearing at Thünen Institute of Fisheries Ecology (Herwigstr 31, 27572 Bremerhaven, Germany) at 53.524 (lat) and 8.581 (long).
DOI: 10.17882/93188
title: Opportunistic macroalgae blooms (green tides) monitoring along the North and Atlantic French coasts since 2008

description: Opportunistic macroalgae blooms (green tides) data are collected during monitoring surveys on the English Channel / Bay of Biscay French coasts since 2008 (Quadrige program code : BLOOMS). Protocols are implemented in the European Water Framework Directive.
DOI: 10.17882/93168
title: Compilation of published data from oceanic drilling that covers the late Miocene and early Pliocene interval for the study of the Late Miocene Biogenic Bloom.

description: Compilation of published ocean drilling (DSDP, ODP and IODP) records of sedimentation rates, CaCO3, opal and terrigenous accumulation rates that cover the late Miocene and early Pliocene interval. We compiled oceanographic data from DSDP, ODP and IODP expeditions that cover the late Miocene and early Pliocene. Data mining was performed by automatically collecting the Pangaea datasets that correspond to the selected time interval and that have at least one of the following variables: sedimentation rate, dry bulk density, mass accumulation rate (MAR), CaCO3 accumulation rate, bSiO2 accumulation rate (biogenic SiO2) , %CaCO3, %bSiO2. The compilation was then improved by manually adding datasets absent from Pangaea but relevant to our study. The data compilation contains 154 datasets (122 are from Pangaea) from 118 different ocean drilling sites. Age-depth models have been calibrated to the GTS2020 time scale in order to perform a temporal comparison of the datasets. This step was performed using the Neptune Sandbox Berlin database (Renaudie et al. 2020, Palaeontologia Electronica, DOI:10.26879/1032). The Meta_Data_Table file is a metadata table with the following information : site number, dataset label, site label, publication, elevation, site coordinates, site paleocoordinates (10 Ma), available variables, variables used for labeling, the time scale used in the original publication, and the web link to the original dataset. The Time_series file is a file that contains the time series of all the variables in all the data sets in this repository. Each file (.csv) contains a dataset and includes the following information: - Site number - Original link of the dataset - Citation - List of ages - List of values for each variable