cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23641179
title: A high-quality reference genome of male sika deer and annotation results

description: We designed a new assembly strategy, which was used to assemble high-quality reference genome of male sika deer. Detailly, three genomes of <i>Cervus nippon</i> have previously been reported which include one female and two male genomes . However, contiguity and accuracy have greatly difference among three genome and assemble quality lower than new assemble genome, especially the female sika deer genome have mistaken when scaffold into chromosome that bring misunderstands for genomic analysis . Here, we combined two genomes sequencing data of male sika deer which include illuminate short reads 143Gb(~55X) 、Pacbio hifi longs reads 96.4Gb(~37X)、Oxford Nanopore longs reads 161Gb (~64X) and Hi-C paired-end reads 269Gb(~104X) acquired a gap less reference genome of male sika deer which genome sizes is 2.7 Gb, with contig N50 reach to 89Mb and have 13 T2T chromosomes . In addition, compared to the previously assemble, our improved assembly quality based on genome completeness (99.41%) as measured by the proportion of short-reads that map to the assembly: genome coverage (98.73%) and coverage of BUSCO (Benchmarking Universal Single-Copy Orthologs) genes for vertebrata (97.8%). the assembly quality value (QV) was estimated as 43.98 by an approach of reference-free and k-mer–based approach, exceeding the Vertebrate Genome Project standard of QV40. Together, these results indicate that our new assembly genome of male sika deer has higher accuracy, completeness, and contiguity. The resvised genome size is 2.7Gb, the repeat seqence is 44.9% and annotated 23,284 coding protein genes.
DOI: 10.25850/nioz/7b.b.0
title: SupplementaryMaterial_IndividualAngelShark

description: There is a growing call to restore the natural richness of the North Sea, but it is often unclear what this natural richness actually was. Here we review the demise and the historical ecology of an iconic species, the critically endangered Angelshark Squatina squatina in the southern North Sea, using historical books and catch records of 104 individuals brought to the Dutch fish markets. These sources reveal that between 1600 and 1950, Angelsharks were annual visitors to the North Sea, and in some years were fairly commonly observed. The number of recorded individuals peaked in the early 20th century and between 1945-1955, and declining rapidly in the 1960s, with the last recorded observation in 1973. The decline coincides with the introduction of engine-powered fisheries, whereas the full extirpation followed the increased use of diesel-powered beam-trawlers. The recorded observations of Angelsharks were most commonly from the summer season, in accordance with the prevailing notion of Angelsharks migrating to warmer waters in winter. Furthermore, most recorded catches were of newborns and adult females in shallow waters, showcasing the importance of the area for parturition and nursery. Our review exemplifies how a large predator disappeared from a marine food web and shows the importance of historical data to deduce the natural richness of the North Sea.
DOI: 10.25850/nioz/7b.b.gf
title: Supplementary data

description: For nanoSIMS measurements of R. mucilaginosa cells, we analyzed three sample sets: (i) the original inoculum (Control), (ii) after incubation with 13C-labelled polyethylene without and (iii) with UV-treatment. We measured a total of 1144 regions of interest (ROIs, i.e., corresponding to 1144 individual cells). For IRMS and GCMS measurements we measured 3 replicates for the development of ?13C-CO2 values and CO2 concentration in incubations with R. mucilaginosa (RM) and with 13C-polyethylene (PE), with prior UV-treatment (+UV) and without (-UV) as the sole carbon source as well as in incubations with UV-treated 13C-polyethylene (PE) without R. mucilaginosa.
DOI: 10.25850/nioz/7b.b.hb
title: Suspended particulate matter in a submarine canyon (Whittard Canyon, Bay of Biscay, NE Atlantic Ocean): Assessment of commonly used instruments to record turbidity

description: Nepheloid layers with elevated concentrations of suspended particulate matter (SPM) are found throughout the world???s oceans, generated by both natural processes, involving resuspension of seabed sediment by bottom currents, and anthropogenic sediment resuspension due to bottom trawling, dredging and in the future potentially due to deep-sea mining. These nepheloid layers represent pathways of lateral SPM transport, including lithogenic and biogenic sediment, organic matter, (trace) metals, organic pollutants and plastics. For assessment of the dispersion of these materials, it is essential that SPM concentrations can be accurately quantified. However, this is not straightforward as the detected turbidity signal not only depends on the concentration of particles, but also on physical characteristics of these particles, such as particle size. Here we present a comparative study of turbidity data to assess the potential implications different sensors have on the estimates of SPM concentration. Optical backscatter sensors (OBSs), transmissometers and both low- and high-frequency ADCPs were deployed simultaneously in the Whittard Canyon, and water samples were collected for quantification of SPM concentration and ex-situ particle size analysis. We found that SPM concentrations inferred from the transmissometer are easily overestimated in the biologically productive surface layer due to increased light absorption. Furthermore, we observed that depending on sensor type some particles are not, or less well, detected. This is due to differences in particle size sensitivities of these sensors towards the diverse range of particle sizes found in the Whittard Canyon. Whereby the low-frequency ADCP was most sensitive for coarse-grained material and the high-frequency ADCP and OBSs most sensitive for fine-grained material. In future studies, we suggest to use a combination of different sensors as it enabled us to identify a recurring cycle of resuspension, involving aggregation and disaggregation of SPM in the Whittard Canyon.
DOI: 10.25850/nioz/7b.b.7f
title: Temperature records for sediment cores from Prydez Bay (Co1010), Chilean Margin (ODP 1235) and Angola Margin (ODP 1078)

description: This file contains temperature records based on TEX86, TEX86OH, %OH, RI-OH, RI-OH', OHC, UK'37 from three sediment cores. Sediment core Co1010 was retrived from the Prydez Bay, ODP 1235 from the Chilean margin and ODP 1078 from Angola margin. This dataset is related to the study 'Evaluating isoprenoidal hydroxylated GDGT-based temperature proxies in surface sediments from the global ocean'.
DOI: 10.6084/m9.figshare.23641179.v1
title: A high-quality reference genome of male sika deer and annotation results

description: We designed a new assembly strategy, which was used to assemble high-quality reference genome of male sika deer. Detailly, three genomes of <i>Cervus nippon</i> have previously been reported which include one female and two male genomes . However, contiguity and accuracy have greatly difference among three genome and assemble quality lower than new assemble genome, especially the female sika deer genome have mistaken when scaffold into chromosome that bring misunderstands for genomic analysis . Here, we combined two genomes sequencing data of male sika deer which include illuminate short reads 143Gb(~55X) 、Pacbio hifi longs reads 96.4Gb(~37X)、Oxford Nanopore longs reads 161Gb (~64X) and Hi-C paired-end reads 269Gb(~104X) acquired a gap less reference genome of male sika deer which genome sizes is 2.7 Gb, with contig N50 reach to 89Mb and have 11 T2T chromosomes . In addition, compared to the previously assemble, our improved assembly quality based on genome completeness (99.41%) as measured by the proportion of short-reads that map to the assembly: genome coverage (98.73%) and coverage of BUSCO (Benchmarking Universal Single-Copy Orthologs) genes for vertebrata (97.8%). the assembly quality value (QV) was estimated as 43.98 by an approach of reference-free and k-mer–based approach, exceeding the Vertebrate Genome Project standard of QV40. Together, these results indicate that our new assembly genome of male sika deer has higher accuracy, completeness, and contiguity. The resvised genome size is 2.7Gb, the repeat seqence is 44.9% and annotated 23,284 coding protein genes.
DOI: 10.25850/nioz/7b.b.7d
title: Temporal dynamics of heatwaves are key drivers of sediment mixing by bioturbators

description: Heatwaves affect tidal flat ecosystems by altering the bioturbating behavior of benthic species, with potential consequences for sediment oxygenation, particle mixing, and erodibility. Although the frequency and duration of heatwaves are expected to increase under global warming scenarios, we lack insights into how heatwaves' temporal dynamics affect bioturbating behaviors. Using the widely distributed bioturbator Cerastoderma edule as model species, we quantified how heatwaves with identical heat-sum but different temporal dynamics (i.e., 3-day vs. 6-day heating and normal temperature cycles) affect bioturbating behaviors and the sediment mixing processes in tidal mesocosms. Our results show that short but frequent 3-day heatwave cycles increased the magnitude of bioturbating behaviors, thereby resulting in more bio-mixed sediment than observed under infrequent prolonged 6-day heatwave cycles. This unexpected result could be ascribed to the weakening health condition indicated by a high death rate (47.37%) under 6-day heatwave cycles than in 3-day and no-heatwave control cycles. Present findings reveal that the impact of heatwaves on sediment bioturbation will strongly depend on the temporal dynamics of future heatwaves: bioturbation will be enhanced unless the heatwave duration exceeds species resistance and increases mortality.
DOI: 10.6084/m9.figshare.23716134
title: The contig level assembly result of male sika deer genome

description: Here, we upload two contig level genomes of male sika deer, which used hifi long reads and ONT long reads assembled respectively.
DOI: 10.6084/m9.figshare.23716134.v1
title: The contig level assembly result of male sika deer genome

description: Here, we upload two contig level genomes of male sika deer, which used hifi long reads and ONT long reads assembled respectively.
DOI: 10.25850/nioz/7b.b.cb
title: The intertidal mudflats of Barr Al Hikman, Sultanate of Oman, as feeding, reproduction and nursery grounds for brachyuran crabs

description: Brachyuran crabs are an important ecological and economical, yet often unstudied aspect of intertidal mudflats of the Arabian Peninsula. Here we provide baseline density estimates of crabs at the relatively pristine intertidal mudflats of Barr Al Hikman (Sultanate of Oman) and provide information on their life cycle and habitat preference. Across the winters of 2012???2015 crabs were sampled on a grid covering the entire intertidal depth gradient. 29 species were found and average densities varied between 12 and 54 crabs/m2. Deposit-feeding and herbivorous crabs were the most abundant species across all winters. Size frequency data and the presence of ovigerous females show that most crabs species reproduce in the intertidal area. P. segnis, the most important crab for local fisheries, was found to use the intertidal area as a nursery ground. We analysed the relationship between the two most abundant crab species, Macrophthalmus sulcatus and Thalamita poissonii and the environmental variables: seagrass density, tidal elevation, median grain size and sediment depth using Random Forest models. The predictive capacity of the models and the relative importance of the environmental predictors varied between years, but crab densities in general were positively associated with seagrass density, presumably because seagrass offers feeding habitat.
DOI: 10.25850/nioz/7b.b.zd
title: Tissue- and diet-dependent stable carbon and nitrogen isotope discrimination: a calibration study in a captive shorebird species

description: In ecology, stable-isotope ratios are widely used to determine diets of organisms and reconstruct food webs. This is usually done by analyzing the stable-isotope ratios of nitrogen (?15N), which increase with increasing trophic level, and those of carbon (?13C), which correlate with the ?13C value of food source(s) and generally differ between terrestrial and marine food sources. Assimilation of food changes stable-isotope ratios, resulting in different values between the food source and its consumer. These differences are known as isotope trophic discrimination factors and, if known, can be used to determine from the stable-isotope ratios in the consumer?s tissue what the consumer has been eating. What is often ignored is that discrimination factors can differ between consumer?s food sources and also between tissue types. Therefore, we performed a controlled feeding study in red knots Calidris canutus to determine discrimination factors between different food sources and red knot tissues. We kept two groups of red knots in captivity on a stable diet, one group feeding on mudsnails and the other on Trouvit pellets, for several months, during which the birds molted their feathers. We analyzed ?13C and ?15N in both food sources and in five red knot tissues (blood cells, blood plasma and three feather types) and subsequently calculated the isotope discrimination factors. We confirmed that the discrimination factors differed between tissues, and also between diets. Our values deviated from general averages reported in reviews on a wide range of animals/birds, but were very similar to values from previous red knot and dunlin studies. We therefore think that our discrimination factors can be used in future stable isotope studies, not only on red knots, but also on other marine shorebird species and plea for careful consideration of using the right discrimination factors.
DOI: 10.6084/m9.figshare.23804452
title: Metabolomics analysis of mycelial exudates provides insights into fungal antagonists of <i>Armillaria</i>

description: The genus <i>Armillaria</i> has high edible and medical values, with zones of antagonism often occurring when different species are paired in culture on agar media, while the antagonism-induced metabolic alteration remains unclear. Here, the metabolome of mycelial exudates of two Chinese <i>Armillaria</i> biological species, C and G, co-cultured or cultured separately was analysed to discover the candidate biomarkers and the key metabolic pathways involved in <i>Armillaria</i> antagonists. A total of 2,377 metabolites were identified, mainly organic acids and derivatives, lipids and lipid-like molecules, and organoheterocyclic compounds. There were 248 and 142 differentially expressed metabolites between group C-G and C, C-G, and G, respectively, and fourteen common differentially expressed metabolites including malate, uracil, Leu-Gln-Arg, etc. Metabolic pathways like TCA cycle and pyrimidine metabolism were significantly affected by C-G co-culture. Additionally, 156 new metabolites (largely organic acids and derivatives) including 32 potential antifungal compounds, primarily enriched into biosynthesis of secondary metabolites pathways were identified in C-G co-culture mode. We concluded that malate and uracil could be used as the candidate biomarkers, and TCA cycle and pyrimidine metabolism were the key metabolic pathways involved in <i>Armillaria</i> antagonists. The metabolic changes revealed in this study provide insights into the mechanisms underlying fungal antagonists.
DOI: 10.6084/m9.figshare.23804452.v1
title: Metabolomics analysis of mycelial exudates provides insights into fungal antagonists of <i>Armillaria</i>

description: The genus <i>Armillaria</i> has high edible and medical values, with zones of antagonism often occurring when different species are paired in culture on agar media, while the antagonism-induced metabolic alteration remains unclear. Here, the metabolome of mycelial exudates of two Chinese <i>Armillaria</i> biological species, C and G, co-cultured or cultured separately was analysed to discover the candidate biomarkers and the key metabolic pathways involved in <i>Armillaria</i> antagonists. A total of 2,377 metabolites were identified, mainly organic acids and derivatives, lipids and lipid-like molecules, and organoheterocyclic compounds. There were 248 and 142 differentially expressed metabolites between group C-G and C, C-G, and G, respectively, and fourteen common differentially expressed metabolites including malate, uracil, Leu-Gln-Arg, etc. Metabolic pathways like TCA cycle and pyrimidine metabolism were significantly affected by C-G co-culture. Additionally, 156 new metabolites (largely organic acids and derivatives) including 32 potential antifungal compounds, primarily enriched into biosynthesis of secondary metabolites pathways were identified in C-G co-culture mode. We concluded that malate and uracil could be used as the candidate biomarkers, and TCA cycle and pyrimidine metabolism were the key metabolic pathways involved in <i>Armillaria</i> antagonists. The metabolic changes revealed in this study provide insights into the mechanisms underlying fungal antagonists.
DOI: 10.25850/nioz/7b.b.gg
title: Trophic Interactions in the Subtidal Wadden Sea

description: Unravelling the intricate food web in the subtidal regions of the Wadden Sea is crucial for better understanding of the ecosystem. Even basic basic metrics of food web structure are useful indicators of ecosystem complexity compared to other often-used indices. Insight in the food web structure can also aid conservation efforts by pinpointing vulnerabilities and informing sustainable management strategies. However, the overview of the trophic interactions in the ecosystem to base such food webs on was incomplete. Therefore, we constructed a comprehensive interaction matrix that contains trophic interactions of all species we found during a two-year experiment with hard substrate in the Wadden Sea as well as during two subtidal sampling campaigns. The trophic interactions in the matrix are based on literature study. This dataset also contains an example R script that shows how a food web can be constructed and how metrics can be calculated based on this interaction matrix.
DOI: 10.25850/nioz/7b.b.mc
title: Underway surface seawater high-resolution pH time series for R/V Sonne cruise SO279.

description: This dataset contains a high-resolution (1 measurement every 30 seconds) time series of surface ocean pH in the Azores Region (North Atlantic Ocean) measured with a PyroScience fiber-based pH sensor (PHROBSC-PK8T) and cross-calibrated using discrete carbonate system observations (total alkalinity, dissolved inorganic carbon and nutrients). The measurements were collected during R/V Sonne cruise SO279 in Dec 2020, as part of the NAPTRAM research programme to build an understanding of the transport pathways of plastic and microplastic debris in the North Atlantic. Bad results from technical issues during analysis have been removed from these results, so there are no recognised issues. The data were collected as part of an international effort from the JPI Oceans project HOTMIC and BMBF project PLASTISEA , and forms a joint effort of HOTMIC and PLASTISEA researchers from a range of countries and institutes. The NIOZ created the metadata entry and is responsible for holding master copies of the data.
DOI: 10.6084/m9.figshare.23822784
title: Niche and ecosystem preference of earliest diverging fungi in soils

description: Within the supergroup Rotosphaeromycetes, or “Holomycota”/“Nucletmycea”, there are several well-recognised unicellular clades in the earliest diverging fungi (EDF). However, we know little about their occurrence. Here, we investigated EDF in the rhizosphere and bulk soils from cropland, forest, orchard, and wetland ecosystems around the Beijing-Hebei area, China, to illustrate their niche and ecosystem preference. More than 500 new operational taxonomic units (OTUs) of EDF were detected based on the 18S rRNA genes. Microsporida and Aphelida constitute dominant groups, whereas Rozellosporida was quite rare. Although the EDF community was site-specific, the soil chemical characteristics, vegetation, and other eukaryotic microorganisms were the key factors driving the occurrence of EDF. Moreover, the stochastic process consisted the most of the EDF community assembly.
DOI: 10.25850/nioz/7b.b.cd
title: Vegetation controls on channel network complexity in coastal wetlands - Dataset

description: This is the full dataset that supports the findings of the following manuscript: van de Vijsel, R.C., van Belzen, J., Bouma, T.J., van der Wal, D., Borsje, B.W., Temmerman, S., Cornacchia, L., Gourgue, O., van de Koppel, J. (2023, Nature Communications). Vegetation controls on channel network complexity in coastal wetlands. This dataset is archived and publicly available via https://doi.org/10.25850/nioz/7b.b.cd. The model (SFERE v1.0) introduced and used in this study is available via GitHub (https://github.com/RCvandeVijsel/SFERE) and Zenodo (https://doi.org/10.5281/zenodo.8411955).
DOI: 10.25850/nioz/7b.b.uf
title: Underway surface seawater high-resolution pH time series for R/V Sonne cruise SO289.

description: This dataset contains a high-resolution (1 measurement every 30 seconds) time series of surface ocean pH in the South Pacific Ocean measured with a PyroScience fiber-based pH sensor (PHROBSC-PK8T) and cross-calibrated using discrete carbonate system observations (total alkalinity and dissolved inorganic carbon). The measurements were collected during R/V Sonne cruise SO289 in February-April 2022,as part of the GEOTRACES GP21 research programme to build an understanding of the distribution, origins, and depletions of trace elements and their isotopes (TEIs) in a lesser-explored ocean region. Bad results from technical issues during analysis have been removed from these results, so there are no recognised issues. The NIOZ created the metadata entry and is responsible for holding master copies of the data.
DOI: 10.6084/m9.figshare.23822784.v2
title: Niche and ecosystem preference of earliest diverging fungi in soils

description: Within the supergroup Rotosphaeromycetes, or “Holomycota”/“Nucletmycea”, there are several well-recognised unicellular clades in the earliest diverging fungi (EDF). However, we know little about their occurrence. Here, we investigated EDF in the rhizosphere and bulk soils from cropland, forest, orchard, and wetland ecosystems around the Beijing-Hebei area, China, to illustrate their niche and ecosystem preference. More than 500 new operational taxonomic units (OTUs) of EDF were detected based on the 18S rRNA genes. Microsporida and Aphelida constitute dominant groups, whereas Rozellosporida was quite rare. Although the EDF community was site-specific, the soil chemical characteristics, vegetation, and other eukaryotic microorganisms were the key factors driving the occurrence of EDF. Moreover, the stochastic process consisted the most of the EDF community assembly.