cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25850/nioz/7b.b.fd
title: Marine nitrogen cycling dynamics under altering redox conditions: insights from deposition of sapropels S1 and the ambiguous S2 in the Eastern Mediterranean Sea

description: The eastern Mediterranean Sea (EMS) sedimentary record is periodically interspersed with organic- rich ?sapropel? layers. Sapropels are characteristic of basin-wide anoxic events, triggered by precession-forced insolation maxima. Relatively subdued insolation maxima, however, are not always expressed as distinct sapropel events. The EMS sedimentary record hereby allows anoxia and nitrogen (N) cycling tipping points to be investigated, which may act as analogues for modern deoxygenation. To this end, we investigated a ~68 kyr EMS sedimentary record, containing the well-established sapropel S1 (deposited in two phases: S1a [~10.5?8.5 ka BP] and S1b [~7.8?6.1 ka BP]) and sediments timed to the ambiguous S2 sapropel (~53 ka BP). We focus on lipid biomarkers of microorganisms to reconstruct key components of the N cycle: (1) anaerobic ammonium oxidation (anammox) using ladderanes and a stereoisomer of bacteriohopanetetrol (BHT-x), (2) dinitrogen gas (N2) fixation using heterocyte glycolipids (HGs), and (3) nitrification by Thaumarchaeota using crenarchaeol. During S1, export-productivity (indicated by the barium to aluminum ratio) and anoxia (indicated by redox-sensitive trace elements and benthic foraminifer assemblages) are enhanced. Thaumarchaeota are most abundant in S1a, while anammox is enhanced throughout S1. N2-fixation (indicated by bulk sedimentary ?15N) occurs throughout S1, while the highest heterocyte cyanobacteria abundance is at the S1a termination and S1 interval. Ladderane presence suggests additional episodes of bioavailable N removal between ~69 to 39 cal ka BP. These episodes correspond to brief periods of water column deoxygenation, with anoxia occurring at the sediment-water interface in sediments timed to S2 (53?51 cal ka BP). During these episodes, ladderanes co-occur with the BHT-34R stereoisomer, but not BHT-x. Compound-specific ?13CBHT-34R indicates an anammox source. Our results highlight various modes of operation of the N cycle during the different deoxygenation events. During S1a, a combination of N-loss and P-supply may have reinforced anoxia, by favoring diatom-diazotroph symbiotic consortia. Conversely, a coupling between N2-fixation and anammox was not observed during S1b and the S2-timed interval, either because loss of bioavailable N was insufficient or diazotrophs were nutrient limited. During these periods, anammox may have provided negative feedback on anoxia by quenching primary production.
DOI: 10.25850/nioz/7b.b.vd
title: Monitoring of a sediment plume produced by a deep-sea mining test in shallow water, Malaga Bight, Alboran Sea (southwestern Mediterranean Sea) - Dataset 2018

description: In this study different experimental designs for monitoring of sediment plumes produced by deep-sea mining are presented. Plumes of sediment stirred up from the seabed by mining machines are considered to represent a major environmental pressure which may extend far beyond the actual mining area. Two industry field tests with the scaled mining vehicle Apollo II of Royal IHC conducted in a relatively shallow setting offshore southern Spain provided valuable insights for anticipated monitoring of nodule mining activities in the deep Pacific. Although the tests were performed in only 300 m water depth, much less than the depth where future deep-sea mining will take place, the weakly stratified bottom water, tide-dominated near-bed currents with mean magnitude of around 5-10 cm s-1, and gently sloping seabed covered with fine muddy sediment provide a good analogue to operational conditions in the deep sea. The plume of suspended sediment mobilised by the mining vehicle was monitored with turbidity sensors deployed on a ship-operated CTD system and on a static array of moored sensors and monitored visually using a ship-operated ROV. It was found that the generated sediment plume extended not more than 2 m above the seabed close to the source (100 m) but increased in height at greater distance. Furthermore, turbidity values decreased rapidly with increasing distance to the source. Even though plume monitoring suffered interference from bottom trawling activities in neighbouring areas, a distinct turbidity signal generated by the mining equipment could still be distinguished above background turbidity at 350 m away from the source. From the experience gained in shallow water, recommendations are made on how a combination of sensors operated from moving and moored platforms may be a suitable and successful strategy for monitoring man-made sediment plumes in the deep sea.
DOI: 10.25850/nioz/7b.b.tc
title: Monitoring Verzuring Noordzee dataset v10

description: Monitoring programme of the Dutch Ministry of Infrastructure and Water Management to improve the understanding of dynamics and trends in ocean acidification parameters in the Dutch sector of the North Sea. This dataset (version 10) contains all measurements from the first 10 batches of analysis.
DOI: 10.25850/nioz/7b.b.wd
title: Monitoring of a sediment plume produced by a deep-sea mining test in shallow water, Malaga Bight, Alboran Sea (southwestern Mediterranean Sea) - Dataset 2019

description: In this study different experimental designs for monitoring of sediment plumes produced by deep-sea mining are presented. Plumes of sediment stirred up from the seabed by mining machines are considered to represent a major environmental pressure which may extend far beyond the actual mining area. Two industry field tests with the scaled mining vehicle Apollo II of Royal IHC conducted in a relatively shallow setting offshore southern Spain provided valuable insights for anticipated monitoring of nodule mining activities in the deep Pacific. Although the tests were performed in only 300 m water depth, much less than the depth where future deep-sea mining will take place, the weakly stratified bottom water, tide-dominated near-bed currents with mean magnitude of around 5-10 cm s-1, and gently sloping seabed covered with fine muddy sediment provide a good analogue to operational conditions in the deep sea. The plume of suspended sediment mobilised by the mining vehicle was monitored with turbidity sensors deployed on a ship-operated CTD system and on a static array of moored sensors and monitored visually using a ship-operated ROV. It was found that the generated sediment plume extended not more than 2 m above the seabed close to the source (100 m) but increased in height at greater distance. Furthermore, turbidity values decreased rapidly with increasing distance to the source. Even though plume monitoring suffered interference from bottom trawling activities in neighbouring areas, a distinct turbidity signal generated by the mining equipment could still be distinguished above background turbidity at 350 m away from the source. From the experience gained in shallow water, recommendations are made on how a combination of sensors operated from moving and moored platforms may be a suitable and successful strategy for monitoring man-made sediment plumes in the deep sea.
DOI: 10.6084/m9.figshare.21313181.v1
title: Estimating the spectral density at frequencies near zero

description: Estimating the spectral density function <i>f</i>(<i>w</i>) for some w∈[−π,π] has been traditionally performed by kernel smoothing the periodogram and related techniques. Kernel smoothing is tantamount to local averaging, i.e., approximating <i>f</i>(<i>w</i>) by a constant over a window of small width. Although <i>f</i>(<i>w</i>) is uniformly continuous and periodic with period 2π, in this paper we recognize the fact that <i>w</i> = 0 effectively acts as a boundary point in the underlying kernel smoothing problem, and the same is true for w=±π. It is well-known that local averaging may be suboptimal in kernel regression at (or near) a boundary point. As an alternative, we propose a local polynomial regression of the periodogram or log-periodogram when <i>w</i> is at (or near) the points 0 or ±π. The case <i>w</i> = 0 is of particular importance since <i>f</i>(0) is the large-sample variance of the sample mean; hence, estimating <i>f</i>(0) is crucial in order to conduct any sort of inference on the mean.
DOI: 10.25850/nioz/7b.b.1
title: Monitoring Verzuring Noordzee dataset v6.1

description: Monitoring programme of the Dutch Ministry of Infrastructure and Water Management to improve the understanding of dynamics and trends in ocean acidification parameters in the Dutch sector of the North Sea. This dataset (version 6) contains all measurements from the first 6 batches of analysis.
DOI: 10.25850/nioz/7b.b.kg
title: Netherlands North Sea ocean acidification monitoring programme dataset v2023.10

description: Monitoring programme of the Dutch Ministry of Infrastructure and Water Management to improve the understanding of dynamics and trends in ocean acidification parameters in the Dutch sector of the North Sea. This dataset (version 2023.10) contains all measurements from all batches of analysis up to and including October 2023 for which auxiliary variables (temperature, salinity and nutrients) were available from Rijkswaterstaat at the time of publication, specifically, 982 measurements of dissolved inorganic carbon, 981 of total alkalinity and 983 of pH, from 22 January 2018 to 22 March 2023. This dataset is a replacement for the previous version (v10; doi:10.25850/nioz/7b.b.tc). All data that appear in both this and the previous version are identical except for 49 DIC measurements which have been adjusted by up to 3 ?mol/kg due to an improved calibration and 3 measurements of nutrients which have changed almost negligibly due to updated auxiliary data from Rijkswaterstaat.
DOI: 10.6084/m9.figshare.22266744
title: Introduction: Infrastructuring Value

description: Exploring infrastructure has much to offer for economic anthropology. Inspired by the convergence of literatures on value and infrastructure in studies of financialisation, we develop the analytics of ‘infrastructures of value’ on old terrain: agriculture. Infrastructure facilitates valuation practices and enables valorisation as fixed capital. Material networks emerging from practices of infrastructuring also mediate value by facilitating, channelling, or hindering the circulation – movement and metamorphoses – of objects, people and ideas. Shifting attention from the social life of things to the infrastructure undergirding their circulation fills a major gap in David Graeber’s theory of value: it directs attention to how actions become incorporated into larger wholes. Various infrastructures and the frictions between them shape value by connecting producers and consumers, separating contents, and communicating evidence of qualities of food. Ethnographic attention to this material relationality of value invigorates dialogue between new and historical materialism and challenges binaries in economic thought.
DOI: 10.6084/m9.figshare.22266744.v1
title: Introduction: Infrastructuring Value

description: Exploring infrastructure has much to offer for economic anthropology. Inspired by the convergence of literatures on value and infrastructure in studies of financialisation, we develop the analytics of ‘infrastructures of value’ on old terrain: agriculture. Infrastructure facilitates valuation practices and enables valorisation as fixed capital. Material networks emerging from practices of infrastructuring also mediate value by facilitating, channelling, or hindering the circulation – movement and metamorphoses – of objects, people and ideas. Shifting attention from the social life of things to the infrastructure undergirding their circulation fills a major gap in David Graeber’s theory of value: it directs attention to how actions become incorporated into larger wholes. Various infrastructures and the frictions between them shape value by connecting producers and consumers, separating contents, and communicating evidence of qualities of food. Ethnographic attention to this material relationality of value invigorates dialogue between new and historical materialism and challenges binaries in economic thought.
DOI: 10.6084/m9.figshare.22641112
title: Supplementray Figures and Supplementary Data 1

description: <b>Figure S1</b>. The mechanical diagram of the study.A mechanistic diagram of PPARγ signaling regulating hypoxia-induced ferroptosis in HTR-8/Svneo cells with/without rosiglitazone intervention was built by Figdraw software.<b>Figure S2. </b>Uncropped blots.<b>Figure S3</b>. Pearson correlation analysis.Correlation analysis of PPARγ with Nrf2 levels and ferroptosis-related indicators in PE was performed.<b>Figure S4</b>. Expression verification of GPx4, ACSL4, FASN, ACC1, and SCD1.(a) GPx4 mRNA and protein levels. *P&lt;0.05 vs the NC group, one-way ANOVA. (b) PPARγ binding to SREBP1 and Nrf2 was predicted using the online software STRING. (c) ACSL4 protein levels. (d) FASN, ACC1, and SCD1 levels. (n=3). *P&lt;0.05 vs the NC group, &P&lt;0.05 vs the Hypoxia group, and @P&lt;0.05 vs the Hyp + si-SREBP1 group, two-way ANOVA.<b>Supplementary Data 1.</b> Raw data and original images of this study.
DOI: 10.25850/nioz/7b.b.cc
title: NIOZ jetty hourly data for temperature and salinity for 2018

description: NIOZ jetty LON=4.789E LAT=53.002N, using EXO sensor at depth of -1.5 meter NAP. Derived product from 10 second calibrated data. Separate calibration measurement at 2 week intervals.
DOI: 10.25850/nioz/7b.b.dc
title: NIOZ jetty hourly data for temperature and salinity for 2019

description: NIOZ jetty LON=4.789E LAT=53.002N, using EXO sensor at depth of -1.5 meter NAP. Derived product from 10 second calibrated data. Separate calibration measurement at 2 week intervals.
DOI: 10.25850/nioz/7b.b.vb
title: NIOZ jetty hourly values temperature and salinity for 2002

description: NIOZ jetty LON=4.789E LAT=53.002N , depth of sensors -1.5 meter NAP. Derived product from 10 second calibrated data.
DOI: 10.25850/nioz/7b.b.rc
title: NIOZ jetty Marsdiep high water selected dates for Amaral-Zettler publication Water Research 2021 117289

description: NIOZ jetty (LON=4.789E, LAT=53.002N) Marsdiep biological time series. 40 samples a year, weekly in growing season, biweekly outside of growing season. Secchi depth and bucket sample of surface water at high tide (North Sea waters) with subsequent analysis of T, S, TSM, TP, PO4, NO3, NO2, NH4, Si, DIC, Chla.
DOI: 10.25850/nioz/7b.b.nc
title: NIOZ jetty Marsdiep high water time series data for 2019

description: NIOZ jetty (LON=4.789E, LAT=53.002N) Marsdiep biological time series. 40 samples a year, weekly in growing season, biweekly outside of growing season. Secchi depth and bucket sample of surface water at high tide (North Sea waters) with subsequent analysis of T, S, TSM, TP, PO4, NO3, NO2, NH4, Si, DIC, Chla.
DOI: 10.25850/nioz/7b.b.9f
title: NIOZ jetty Marsdiep high water time series data for 2022

description: NIOZ jetty (LON= 4.789028 E, LAT=53.001806 N) Marsdiep biological time series. 40 samples a year, weekly in growing season, biweekly outside of growing season. Secchi depth and bucket sample of surface water at high tide (North Sea waters) with subsequent analysis of T, S, TSM, TP, PO4, NO3, NO2, NH4, Si, DIC, Chla.
DOI: 10.25850/nioz/7b.b.lf
title: Nodosarids_dataset2023

description: This the the excel file containing the data-set for the publication: Element/Ca ratios in Nodosariida (Foraminifera) and their potential application for paleoenvironmental reconstructions.
DOI: 10.25850/nioz/7b.b.rf
title: Nutrient release by sediment erosion

description: Intertidal coastal sediments are important centers for nutrient transformation, regeneration, and storage. Sediment resuspension, due to wave action or tidal currents, can induce nutrient release to the water column and fuel primary production. Storms and extreme weather events are expected to increase due to climate change in coastal areas, but little is known about their effect on nutrient release from coastal sediments. We have conducted in-situ sediment resuspension experiments, in which erosion was simulated by a stepwise increase in current velocities, while measuring nutrient uptake or release in field flumes positioned on intertidal areas of a tidal bay (Eastern Scheldt) and an estuary (Western Scheldt). In both systems, the water column concentration of ammonium (NH4+) and nitrite (NO2?) increased predictably with greater erosion as estimated from pore water dilution and erosion depth. In contrast, the phosphate (PO43?) dynamics were different between systems, and those of nitrate (NO3?) were small and variable. Notably, sediment resuspension caused a decrease in the overlying water PO43? concentration in the tidal bay, while an increase was observed in the estuarine sediments. Our observations showed that the concentration of PO43? in the water column was more intensely affected by resuspension than that of NH4 + and NO2 ?. The present study highlights the differential effect of sediment resuspension on nutrient exchange in two contrasting tidal coastal environments.
DOI: 10.6084/m9.figshare.22641112.v8
title: Supplementray Figures and Supplementary Data 1

description: <b>Figure S1</b>. The mechanical diagram of the study.A mechanistic diagram of PPARγ signaling regulating hypoxia-induced ferroptosis in HTR-8/Svneo cells with/without rosiglitazone intervention was built by Figdraw software.<b>Figure S2. </b>Uncropped blots.<b>Figure S3</b>. Pearson correlation analysis.Correlation analysis of PPARγ with Nrf2 levels and ferroptosis-related indicators in PE was performed.<b>Figure S4</b>. Expression verification of GPx4, ACSL4, FASN, ACC1, and SCD1.(a) GPx4 mRNA and protein levels. *P&lt;0.05 vs the NC group, one-way ANOVA. (b) PPARγ binding to SREBP1 and Nrf2 was predicted using the online software STRING. (c) ACSL4 protein levels. (d) FASN, ACC1, and SCD1 levels. (n=3). *P&lt;0.05 vs the NC group, &P&lt;0.05 vs the Hypoxia group, and @P&lt;0.05 vs the Hyp + si-SREBP1 group, two-way ANOVA.<b>Supplementary Data 1.</b> Raw data and original images of this study.
DOI: 10.25850/nioz/7b.b.6f
title: OHGDGT global surface sediments data

description: This file contains surface sediment data from the global ocean used in the study 'Evaluating isoprenoidal hydroxylated GDGT-based temperature proxies in surface sediments from the global ocean'. The excel sheet contains information regarding the surface sediments, their location, enivironmental parameters from each location extracted from WOA database, peak area of iso-GDGTs and OH-isoGDGTs, proxy indices discussed in the study and references for previously published data.
DOI: 10.6084/m9.figshare.22801796
title: Exploring Students’ Performance Using Lingua Franca in Learning Science

description: The uploaded data were the raw data, statistical analysis and test questions used in the study.
DOI: 10.25850/nioz/7b.b.bb
title: Only a few key prey species fuel a temperate coastal fish food web

description: The food web structure of a coastal fish community (western Dutch Wadden Sea) was studied based on stomach content data from samples collected from 2010 to 2018. In total 54 fish species were caught and 72 different prey items were identified. Fish species had consumed from a few up to more than 30 different prey species, suggesting the presence of both opportunistic and more specialized feeders. No significant differences between years nor switches in food source with fish size were found. The trophic positions of the Wadden Sea fish community ranged between 2.0 and 4.7, with most trophic positions above 3.0. In the past, (near)-resident species were the most abundant functional group in spring and juvenile marine migrants in autumn. Nowadays, all functional groups are present in almost similar but low abundances. The (near)-resident community consisted of about 20 species which especially were feeding on amphipod crustaceans, brown shrimps and juvenile herring. There was only a slight overlap in diet with the group of marine juvenile migrants (5 species of juvenile flatfishes and clupeids), whose preferred preys were copepods, polychaetes and brown shrimps. About 15 species of marine seasonal visitors showed an overlap in diet with both the (near)-resident and the marine juvenile migrant especially for brown shrimps and to a lesser extent herring and gobies. Our results illustrate (1) the pivotal position of a few key prey species for the coastal Wadden Sea fishes: amphipod crustaceans, brown shrimps, juvenile herring and gobies, and that (2) the substantial prey overlap in the diet of some predators cannot exclude some intra- and inter-specific competition for some predators.
DOI: 10.6084/m9.figshare.22801796.v2
title: Exploring Students’ Performance Using Lingua Franca in Learning Science

description: The uploaded data were the raw data, statistical analysis and test questions used in the study.
DOI: 10.25850/nioz/7b.b.s
title: Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge

description: Hydrothermal vent fields found at mid-ocean ridges emit hydrothermal fluids which disperse as neutrally buoyant plumes. From these fluids seafloor massive sulfides (SMS) deposits are formed which are being explored as possible new mining sites for (trace) metals and rare earth elements (REE). It has been suggested that during mining activities large amounts of suspended matter will appear in the water column due to excavation processes, and due to discharge of mining waste from the surface vessel. Understanding how hydrothermal plumes can be characterised by means of geochemistry and microbiology as they spread away from their source and how they affect their surrounding environment may help in characterising the behaviour of the dilute distal part of chemically enriched mining plumes. This study on the extensive Rainbow hydrothermal plume, observed up to 25 km downstream from the vent site, enabled us to investigate how microbial communities and (trace) metal composition change in a natural plume with distance. The (trace) metal and REE content of suspended particulate matter (SPM) was determined using HR-ICP mass spectrometry and the microbial communities of the neutrally buoyant plume, above plume-, below plume-, and near-bottom water and sediment were characterised by using 16S rRNA amplicon sequencing methods. Both vertically in the water column and horizontally along the neutrally buoyant plume, geochemical and biological changes were evident as the neutrally buoyant plume stood out by its enrichments in (trace) metals and REEs as e.g. Fe, Cu, V, Mn and REE were enriched by factors of up to ~80, ~90, ~52, ~2.5 and ~40 respectively, compared to above plume water samples taken at 1000 m water depth. The concentrations of these elements changed as the plume aged shown by the decrease of element/Fe molar ratios of chalcophile elements (Cu, Co, Zn), indicative of rapid removal from the hydrothermal plume or removal from the solid phase. Conversely, increasing REE/Fe molar ratios imply uptake of REE from the ambient seawater onto Fe-oxyhydroxides. This was also reflected in the background pelagic system as Epsilonproteobacteria started to dominate and univariate microbial biodiversity declined with distance away from the Rainbow hydrothermal vent field. The Rainbow hydrothermal plume provides a geochemically enriched natural environment, which is a heterogeneous, dynamic habitat that is conducive to ecological changes in a short time span. This study of a hydrothermal plume provides a baseline study to characterize the natural plume before the interference of deep-sea mining.