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Data and Codes: Restoring ecosystem services in mature salt marshes through topsoil removal
No full textThis repository provides the complete dataset and analysis workflow underpinning the manuscript “Restoring ecosystem services in mature salt marshes through topsoil removal” (Grandjean et al. submitted). The study evaluates topsoil removal as a rejuvenation measure in a mature salt marsh (Zuidgors, Western Scheldt, The Netherlands) and quantifies biotic and abiotic responses over four years following intervention (2021–2024), including sediment accretion, soil properties and consolidation, tidal inundation and flow dynamics, vegetation succession, and model-based assessment of wave attenuation under normative storm conditions.
All materials are organised by figure and corresponding research component, with figure-specific raw data, processed datasets, and scripts provided in separate, clearly labelled folders. This structure enables full reproducibility of all reported results and visualisations (Figures 1–6 and Appendix Figure 1), including statistical outputs (e.g., Mann–Kendall trend tests, correlation analyses, PERMANOVA). The data and methods for Figure 7 and Appendix Table 2 are available upon request to the authors from Deltares (Jasper Dijkstra, Joana van Nieuwkoop, Madelief Doeleman)
Oyster microhabitat study 2023-2024, data for "Thermal buffering by intertidal oyster reefs on mudflats in the European Wadden Sea"
No full textIntertidal organisms are exposed to extreme temperatures especially during heatwaves, that are increasing in frequency and severity due to climate change. Habitat-forming species may buffer extreme temperatures creating a more hospitable environment for their conspecifics and other organisms. Pacific oysters (Magallana gigas) are known to have such temperature buffering capacity on rocky shore systems but their thermal effects on mudflat ecosystems has not been investigated before. We filled this gap by recording temperatures in oyster-formed microhabitats (crevices and oyster-created tidal pools) and comparing them to temperatures on surrounding plain mud flats in the European Wadden Sea. The measurements were conducted over a one-year period using biomimetic temperature loggers. The temperature buffering effect was most pronounced in the summer, when mean temperatures were 0.3-0.4 °C lower in crevices between oysters than on plain mud. The difference was also present, albeit less pronounced, for cumulative heat exposure hours, while a difference in day maximum temperatures occurred only in one of the two locations. These results show that oyster reefs provide thermal buffering also in temperate intertidal mudflat systems with the effect being less pronounced than on tropical rocky shores where the temperature difference is approximately six degrees around the year
De Westerscheldenatuur: Een mooie toekomst vraagt keuzes nu!
No full textDe Westerschelde onder druk
De antropogene ontwikkeling van het Scheldebekken, met onder andere inpolderingen, vaargeulverdiepingen (--> verruiming) en het bagger- en stortbeheer, heeft vanaf 1300 geresulteerd in geleidelijke maar ingrijpende veranderingen in de Westerschelde. Inmiddels zijn de morfologische veranderingen in de Westerschelde dusdanig duidelijk, waaronder de recent sterk zichtbare verschorring, dat een inschatting van de langetermijnontwikkeling van de natuurwaarden dringend noodzakelijk is. Het doel van dit rapport is dan ook om de maatschappij en haar bestuurders inzicht te geven in deze ontwikkeling.
Ontwikkeling van ecotopen
Analyses van publiek beschikbare bodemhoogtedata (1955–heden) en ecotoopkaarten (1996–heden) tonen een structurele verschuiving van intergetijdengebieden naar hogere ecotopen. Het areaal hoogdynamisch slik neemt gestaag af, terwijl laagdynamisch slik, pionierzone en schor toenemen. Deze langetermijntrend duidt op een systematische opwaartse ontwikkeling die een ecologische cascade in gang zet. Deze verschuiving vormt een risico voor het behouden van de Natura 2000-doelstellingen.
Oorzaken van structurele veranderingen
Substantiële veranderingen in de hoogteontwikkeling vallen samen met de eerste verdieping (1973–1976) en de sterke toename van het jaarlijkse baggervolume: van minder dan 0.5 miljoen m³ vóór 1950 tot circa 7–10 miljoen m³ per jaar sinds de eerste verdieping. Hoewel slikhoogte-toename vaak wordt toegeschreven aan autonome processen, wijzen onze analyses erop dat een Westerschelde-brede autonome ophogingstrend veel beperkter is dan vaak wordt aangenomen. De lokale toename in slikhoogte toont echter een sterke correlatie met het nabij gestorte baggervolume. Dit duidt erop dat bagger- en stortbeheer een belangrijke sturende rol spelen in de recente morfologische ontwikkeling, in tegenstelling tot de vaak genoemde historische effecten van inpoldering. De verdiepingen hebben daarmee gezorgd voor een blijvende verstoring van de sedimentbalans.
Gevolgen en risico’s
Op basis van de resultaten van dit rapport concluderen wij dat de Westerschelde structureel ophoogt en verstart, een ontwikkeling die wordt versterkt door de eerdere verdiepingen en het huidige bagger- en stortbeheer. Hierdoor verschuiven intergetijdengebieden naar hoger gelegen ecotopen, wat leidt tot een ecologische cascade richting verschorring en verlies van belangrijke NATURA-2000 gebieden en vogelfoerageergebieden. Tegelijkertijd wijst literatuur erop dat de geobserveerde afvlakking van het systeem het estuarium gevoeliger maakt voor zeespiegelstijging, waardoor de ecologische veerkracht afneemt.
Beleidsimplicaties en kansen
Onze resultaten tonen aan dat zonder koerswijziging het verlies van natuurwaarden in de Westerschelde een groot risico is. Daarom is het noodzakelijk de sediment- en stortstrategie te herzien, omdat deze, ondanks bestaande ecologische uitgangspunten, in de praktijk leidt tot een ontwikkeling die niet wenselijk is voor de Natuurlijkheid van de Westerschelde. Tegelijkertijd liggen er kansen om het beschikbare sediment te benutten als een strategische hulpbron voor meegroeivermogen van mens en natuur, mits zorgvuldig ingezet. Deze herziening vraagt om doelgerichte keuzes in het heden, met het oog op het veiligstellen van de ecologische en maatschappelijke functies van het estuarium voor de toekomstige generaties Zeeuwen
How Shells of Different Shapes Affect Current-driven Sand Transport [data and code]
No full textThis dataset and code belongs to the manuscript "How Shells of Different Shapes Affect Current-driven Sand Transport".
The seabed rarely consists solely of bare sand: often other materials, such as shells are present. They can influence sand transport by armouring the bed and modifying its roughness. Biogenic shells come in different shapes and sizes, depending on the mollusc species that produce them. To understand how changes in bivalve species composition affect sediment transport, we need a mechanistic understanding of how shell content and shell shape influence the near-bed flow and sand transport. We performed experiments in a racetrack flume, testing the effect of elongated (Ensis leei) versus rounded (Spisula subtruncata) shells on unidirectional current-driven sand transport. For both types of shells, a higher depth-averaged flow velocity was needed for initiation of motion and a decrease in bedload transport of sand was found. At a shell content of 20%, the threshold of motion of sand increased up to 75%, and bedload transport was reduced by up to 50%. These effects are explained by a balance between roughness-induced turbulence and bed armouring. Compared to a bare bed, shells decreased bed roughness by reducing ripple formation; rounded shells lowered roughness more than elongated shells, which formed roughness elements themselves, but also covered a larger fraction of the bed. However, there was no clear difference between round versus elongated shells on the overall sand transport; only shell content was key for the overall effect. Our results imply that sediment transport is likely overpredicted when a high number of shells is present in the seabed
Data and code for "Wait a minute? Hiding behavior of burrowing crabs and an oversized bill explain why crab plovers prefer armored swimming crabs"
No full textIn the Indo-West Pacific biogeographical region a suite of shorebirds searches for crabs as food. While the majority of these shorebirds hunt on burrowing crabs, the endemic crab plover Dromas ardeola additionally feeds on swimming crabs with ‘fast and powerful claws’. Here, we examined the trade-off made by crab plovers between foraging for swimming crabs and burrowing crabs on the intertidal mudflats of Barr Al Hikman in the Sultanate of Oman during four winters (2012-2015). Foraging on burrowing crabs requires waiting for the occupant to emerge, whereas foraging on swimming crabs involves searching and extensive handling. We found that crab plovers strongly preferred swimming crabs. In fact, diet composition was exclusively a function of the densities of swimming crabs, i.e. crab plovers stopped waiting for burrowing crabs above threshold densities of swimming crabs even if burrowing crabs were abundant. Using a two-prey functional response model, we could explain diet composition from an energy-maximization perspective, but only if waiting time was added as an identification phase independent of prey densities. This suggests that crab plovers exhibit selective attention and can only wait for a limited number of burrowing crabs at a time. We conclude that the preference for swimming crabs emerges from both efficient handling of swimming crabs by the crab plover and the long hiding times of the burrowing crabs. Undoubtedly, it is the crab plovers’ specialized bill which makes handling of swimming crabs profitable. We speculate that this bill uniquely evolved in the ‘escalated’ environment of the Indo-West Pacific
ACTNOW project - Fit for purpose datasets Task 1.3
No full textThese are meta-data about mechanistic single species movement responses, mechanistic single species physiological responses, DEB species parameterization, community data, food web and ecosystem models collected from WP2 and WP3 contributors for task 1.3 within the ACTNOW project
CLSM - Temperature Experiment
No full textData related to "The effect of proton pumping on the magnesium content of foraminiferal calcite
Dissolved Fe (DFe) and Fe-binding dissolved organic ligands were analysed during two GEOTRACES cruises in the Mediterranean Sea in May and August 2013 - data
No full textMethod: Competing ligand exchange adsorptive cathodic stripping voltammetry (CLE-aCSV) was performed using two systems consisting of a μAutolab potentionstat (Metrohm Autolab B.V.), a 663 VA stand with a Hg drop electrode (Metrohm) and a 778 sample processor with ancillary pumps and dosimats (Metrohm), all controlled using a consumer laptop running Nova 1.9 (Metrohm Autolab B.V.). The characteristics of Fe-binding dissolved organic ligands, that is both the ligand concentration [Lt] (in nano-equivalents of molar Fe, nEq of M Fe) and the conditional binding constant K′ (M−1) with respect to [Fe3+], commonly expressed as log K′ are determined using 2- (2-Thiazolylazo)-p-cresol (TAC) as an added measuring ligand (Croot and Johansson, 2000). TAC was used with a final concentration of 10 μM, and the complex (TAC)2-Fe was measured after equilibration (> 6 h). The increments of Fe concentrations used in the titration were 0 (2×), 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.5, 2, 2.5, 3, 4, 6, and 8 (2×) nM. Using a non-linear regression of the Langmuir isotherm, the electrical signal recorded in nA (nano-Ampere) was converted into a concentration in nM, and the ligand concentration [Lt] and the binding strength K were estimated (Gerringa et al., 2014). Using [Lt] and K, the concentration of Fe bound to a natural Febinding ligand [FeL], the concentration of inorganic Fe [Fe′] and the concentration of natural unbound ligand [L′] were calculated under the assumption of chemical equilibrium. Since K is log transformed, the standard error (SE) is asymmetric to lower and upper values; therefore two SE values are obtained, one to lower (down) and to upper (up) values
Data and script for "High CO2 emission rates from dredged sediments than global soils: Discerning moisture, temperature, and oxygen responses in carbon release"
No full textUnderstanding carbon emissions from dredged sediments under changing environmental conditions is critical for assessing their environmental impact in large-scale sediment reuse projects. This study investigates the effects of moisture, temperature, and oxygen availability on CO₂ emission rates from dredged sediments collected from the Port of Rotterdam, comparing them with global soil data from nearly 400 laboratory incubations. Sediment incubation experiments revealed that CO₂ emissions increased with higher moisture levels, elevated temperatures, and oxygen exposure. However, the observed optimal moisture (>85% water-filled pore space) and temperature (20–30 °C) differed from transitional biogeochemical model assumptions, indicating a need to revisit these functions. Machine learning analysis using XGBoost suggested that similar moisture and temperature response patterns are widespread in both soils and sediments, whereas oxygen has stronger effect on sediments, likely because organic carbon is better preserved in reducing environments than aerated soils. Notably, under oxic conditions, dredged sediment exhibited higher CO2 emissions rates than many soils, implying the more reactive nature of carbon in dredged sediments. A two-pool model further indicated that carbon emissions in most incubations were dominated by the slow carbon pool, with differences in average emission rates throughout incubation reflecting the carbon reactivity of slow pool. These findings suggest that dredged sediments, if not handled properly, can act as a biochemical carbon bomb upon oxygen exposure. Therefore, carbon-sensitive sediment management strategies are essential to mitigate carbon emissions during sediment dredging, processing, and reuse
Geochemical characteristics of SPM around Piscadera Bay, Curacao
No full textCaribbean coral reefs face rising pressure from coastal development, yet the pathways by which urban pollution reaches these endangered ecosystems remain poorly understood. Bays act as dynamic channels, trapping, transforming, and releasing materials that can impact adjacent reef systems. We investigated the seasonal and spatial variability of suspended particulate matter (SPM)—a key vector for pollutants and nutrients— coming from an urbanized bay in Curaçao and determined its effect on surrounding coral reefs. Using sediment traps deployed across spatial gradients (bay mouth to nearby reefs in the East and West) during the dry (April-May) and wet (October-November) seasons, we measured mass, carbon, and nitrogen fluxes and associated grain-size and geochemical particle composition. Results were compared to environmental conditions (e.g. rain fall, current speed) and revealed a clear spatial gradient of bay influence: the bay mouth showed the strongest terrestrial signal, followed by the eastern reef (sheltered from currents) with elevated SPM fluxes of fine particles enriched in terrigenous elements (Si, Fe, Al, and Mn), while the western reef (exposed to open-ocean flow) exhibited lower fluxes of coarser particles with elevated Ca/Fe, Pb, Cu and Ni. This indicates diminished bay effect and stronger marine influence mixed with localized pollution. During the dry season, differences in SPM fluxes and composition between reef sites were minimal, but wet season conditions amplified spatial patterns, with rainfall-driven runoff locally increasing dissolved and particular matter delivery. This implies that reef vulnerability to bay-derived pollution locally depends on both proximity to source waters and seasonal hydrodynamic variability, with sheltered reefs experiencing the greatest impacts during periods of enhanced terrestrial runoff