Search publications of the members of the Royal Belgian institute of natural Sciences
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Iron and sulfur cycling in the cGENIE.muffin Earth system model (v0.9.21)
- The coupled biogeochemical cycles of iron and sulfur are central to the long-term biogeochemical evolution of Earth’s oceans. For instance, before the development of a persistently oxygenated deep ocean, the ocean interior likely alternated between states buffered by reduced sulfur (“euxinic”) and buffered by reduced iron (“ferruginous”), with important implications for the cycles and hence bioavailability of dissolved iron (and phosphate). Even after atmospheric oxygen concentrations rose to modern-like values, the ocean episodically continued to develop regions of euxinic or ferruginous conditions, such as those associated with past key intervals of organic carbon deposition (e.g. during the Cretaceous)and extinction events (e.g. at the Permian–Triassic boundary). A better understanding of the cycling of iron and sulfur in an anoxic ocean, how geochemical patterns in the ocean relate to the available spatially heterogeneous geological observations, and quantification of the feedback strengths between nutrient cycling, biological productivity, and ocean redox requires a spatially resolved representation of ocean circulation together with an extended set of (bio)geochemical reactions. Here, we extend the “muffin” release of the intermediate complexity Earth system model cGENIE to now include an anoxic iron and sulfur cycle (expanding the existing oxic iron and sulfur cycles), enabling the model to simulate ferruginous and euxinic redox states as well as the precipitation of reduced iron and sulfur minerals (pyrite, siderite, greenalite) and attendant iron and sulfur isotope signatures, which we describe in full. Because tests against present-day (oxic) ocean iron cycling exercises only a small part of the new code, we use an idealized ocean configuration to explore model sensitivity across a selection of key parameters. We also present the spatial patterns of concentrations and d56Fe and d34S isotope signatures of both dissolved and solid-phase Fe and S species in an anoxic ocean as an example application. Our sensitivity analyses show that the first-order results of the model are relatively robust against the choice of kinetic parameter values within the Fe–S system and that simulated concentrations and reaction rates are comparable to those observed in process analogues for ancient oceans (i.e. anoxic lakes). Future model developments will address sedimentary recycling and benthic iron fluxes back to the water column, together with the coupling of nutrient (in particular phosphate) cycling to the iron cycle.
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End-Permian marine extinction due to temperature-driven nutrient recycling and euxinia
- Extreme warming at the end-Permian induced profound changes in marine biogeochemical cycling and animal habitability, leading to the largest metazoan extinction in Earth’s history. However, a causal mechanism for the extinction that is consistent with various proxy records of geochemical conditions through the interval has yet to be determined. Here we combine an Earth system model with global and local redox interpretations from the Permian/Triassic in an attempt to identify this causal mechanism. Our results show that a temperature-driven increase in microbial respiration can reconcile reconstructions of the spatial distribution of euxinia and seafloor anoxia spanning the Permian–Triassic transition. We illustrate how enhanced metabolic rates would have strengthened upper-ocean nutrient (phosphate) recycling, and thus shoaled and intensified the oxygen minimum zones, eventually causing euxinic waters to expand onto continental shelves and poison benthic habitats. Taken together, our findings demonstrate the sensitive interconnections between temperature, microbial metabolism, ocean redox state and carbon cycling during the end-Permian mass extinction. As enhanced microbial activity in the ocean interior also lowers subsurface dissolved inorganic carbon isotopic values, the carbon release as inferred from isotope changes in shallow subsurface carbonates is likely overestimated, not only for this event, but perhaps for many other carbon cycle and climate perturbations through Earth’s history.
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A series of two Workshops to develop a suite of management options to reduce the impacts of bottom fishing on seabed habitats and undertake analysis of the trade-offs between overall benefit to seabed habitats and loss of fisheries revenue (WKTRADE3)
- WKTRADE3 developed methods and data flows that allow the assessment of seabed abrasion, economic value, weight of landings and impact on the seabed of mobile bottom-contacting gears in European waters by MSFD broad habitat type and métier. This report provides regional-specific assessments of pressure and impact of bottom-contacting fishing gears on the seabed and of trade-offs between fisheries and seafloor habitat protection. We also present an analysis of spatial and temporal variation in core fishing grounds, and review and evaluate any potential consequences to the ecosystem that could arise, if greater areas of seabed are left undisturbed by bottom fishing. An attempt was made to disaggregate variable costs from the STECF Annual Economic Report out on VMS data. The assessment covers four MSFD (sub)regions, 22 sub-divisions and four countries from Mediterranean and Black Sea. It is spanning from Norway and Finland in the North to Bulgaria in the south. For all areas, the surface abrasion data were avail-able for at least one year. For the Greater North Sea and Baltic Sea, it was possible to perform a complete analysis, while in the other regions data availability was more limited and it was not possible to assess the seabed impact. The impact of mobile bottom-contacting gears (MBCG) on seabed biota was assessed using two different methods and the percentage unfished c-squares was used as an indicator of fishing pressure. The average fishing intensity varies widely between habitat types and regions. Landings per swept area, and landings per unit impact also vary be-tween métiers by an order of magnitude. Effort reductions resulted in different responses between the two impact indicators and the fishing pressure indicator. For PD, the reduction of effort resulted in proportional reductions between benthic impact and fisheries value. For the two other indicators, L1 and percentage area unfished, the relationship between the weight/value and the indicators was not linear, meaning that larger improvements in the indicators could be obtained at small decreases in fisheries landings. There are many other direct and indirect benefits to eco-system and ecosystem services that could result from a reduction in MBCG, but currently the methods and data are not available to quantify these at the required spatial scale. Collectively, ICES expert groups produce many valuable reports each year. Some of these are very long (up to 1000 pp.). As much of the target audience will not have time to read the whole of each document, it is imperative that reports start with a clear, succinct, and factual executive summary that presents the key issues addressed in the main report.
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Subtidal Natural Hard Substrate Quantitative Habitat Mapping: Interlinking Underwater Acoustics and Optical Imagery with Machine Learning
- Subtidal natural hard substrates (SNHS) promote occupancy by rich benthic communities that provide irreplaceable and fundamental ecosystem functions, representing a global priority target for nature conservation and recognised in most European environmental legislation. However, scientifically validated methodologies for their quantitative spatial demarcation, including information on species occupancy and fine-scale environmental drivers (e.g., the effect of stone size on colonisation) are rare. This is, however, crucial information for sound ecological management. In this investigation, high-resolution (1 m) multibeam echosounder (MBES) depth and backscatter data and derivates, underwater imagery (UI) by video drop-frame, and grab sediment samples, all acquired within 32 km2 of seafloor in offshore Belgian waters, were integrated to produce a random forest (RF) spatial model, predicting the continuous distribution of the seafloor areal cover/m2 of the stones’ grain sizes promoting colonisation by sessile epilithic organisms. A semi-automated UI acquisition, processing, and analytical workflow was set up to quantitatively study the colonisation proportion of different grain sizes, identifying the colonisation potential to begin at stones with grain sizes Ø ≥ 2 cm. This parameter (i.e., % areal cover of stones Ø ≥ 2 cm/m2) was selected as the response variable for spatial predictive modelling. The model output is presented along with a protocol of error and uncertainty estimation. RF is confirmed as an accurate, versatile, and transferable mapping methodology, applicable to area-wide mapping of SNHS. UI is confirmed as an essential aid to acoustic seafloor classification, providing spatially representative numerical observations needed to carry out quantitative seafloor modelling of ecologically relevant parameters. This contribution sheds innovative insights into the ecologically relevant delineation of subtidal natural reef habitat, exploiting state-of-the-art underwater remote sensing and acoustic seafloor classification approaches.
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The first lower jaw of a ctenacanthid shark from the Late Devonian (Famennian) of Belgium
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The erroneous chondrichthyan egg case assignments from the Devonian: implications for the knowledge on the evolution of the reproductive strategy within chondrichthyans
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First Detections of Culiseta longiareolata (Diptera: Culicidae) in Belgium and the Netherlands
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Abeilles de Belgique et des régions limitrophes (Insecta: Hymenoptera: Apoidea) Famille Halictidae
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Diversity of bone microstructure in mammals
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Effects of elevational range shift on the morphology and physiology of a carabid beetle invading the sub-Antarctic Kerguelen Islands
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Skilled in camouflage: Barbary sheep in the elite cemetery
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Samenvatting v.d. volledige milieuvergunningsprocedure in de vorm v.e. flow-chart
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The new stick insect genus Medauromorpha gen. nov. with one new species from Vietnam and notes on Medauroidea Zompro, 2000 (Phasmida: Phasmatidae: Clitumninae)
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The Picasso stick insect. A striking new species of Calvisia from Vietnam with notes on captive breeding and new methods for incubation of eggs (Phasmida: Diapheromeridae: Necrosciinae)
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Assessing the radiocarbon freshwater reservoir effect for a Northwest-European river system (the Schelde basin, Belgium)
- The freshwater reservoir effect (FRE) for the Schelde basin (Belgium) is assessed for the Roman, Medieval and early Post-medieval periods by comparing historical and archaeological dates from individual archaeological deposits with radiocarbon dates on the remains of freshwater fish and terrestrial mammals from those same deposits. This is the first time such an assessment has been attempted for the Schelde basin. The FRE offsets prove to be substantial for the historical periods considered. They also differ markedly between fish species and between size classes of a single species. These observations have implications for the evaluation of radiocarbon dates obtained on archaeological remains of humans (and animals) with a substantial amount of freshwater fish into their diet. The data obtained in this study suggest that it will not be easy to correct for any FRE.
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StratigrapheR: making and using lithologs in R
- StratigrapheR is an open-source integrated stratigraphy package. It is available in the free software environment R (https://CRAN.R-project.org/package=StratigrapheR) and is designed to generate lithologs in a semi-automated way, to process stratigraphical information, and to visualize any plot along the lithologs in the R environment. The basic graphical principle behind StratigrapheR is the incremental addition of elements to a drawing: a plot is opened, and graphical elements are successively added. This allows compartmentalisation of the drawing process, as well as the superposition of different plots for comparison. For instance a litholog of a single section can be written as a single function including all the drawing sub-functions, and be integrated in a larger plot, for instance to be correlated to other sections or to show proxy data. The StratigrapheR package is designed for efficient work, and minimum coding, while still allowing versatility. The lithological information of beds (upper and lower boundary, hardness, lithology, etc.) is converted into polygons. All polygons are drawn together using a single function, and each polygon can have its personalised symbology allowing to distinguish lithologies. A similar workflow can be used for plotting proxies while distinguishing each sample by their lithology. Vector graphics can be imported as SVG files, and precisely drawn with the lithologs to serve as symbols or complex elements. Every type of symbol is plotted by calling one single function which repeats the drawing for each occurrence of the represented feature. This illustrates that the amount of work invested to make lithologs using StratigrapheR is related to their complexity rather than their length: a long but monotonous litholog (e.g. of marl-limestone alternations) only takes a few lines of code to generate. The StratigrapheR package also provides a set of functions to deal with selected stratigraphic intervals (for instance in the [0,1[ form): they allow simplification, merging, inversion and visualisation of intervals, as well as identifying the samples included in the given intervals, and characterising the relation of the intervals with each other (overlap, neighbouring, etc.). StratigrapheR includes PDF and SVG generation of plots, of any dimension. The generated PDF can even store multiple plots in a single file (each plot on a different page) to document data processing comprehensively.
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A posteriori verification methodology for astrochronology: a step further to improve the falsifiability of cyclostratigraphy
- Cyclostratigraphy is increasingly used to improve the Geologic Time Scale and our understanding of past climatic systems. However, except in a few existing methodologies, the quality of the results is often not evaluated. We propose a new methodology to document this quality, through a decomposition of a signal into a set of narrow band components from which instantaneous frequency and amplitude can be computed, using the Hilbert transform. The components can be obtained by Empirical Mode Decomposition (EMD), but also by filtering a signal (be it tuned or not) in any relevant way, and by subsequently performing EMD on the signal minus its filtered parts. From that decomposition, verification is performed to estimate the pertinence of the results, based on different concepts that we introduce: Integrity quantifies to what extent the sum of the components is equal to the signal. It is defined as the cumulated difference between (1) the signal, and (2) the summed components of the decomposition. EMD fulfils integrity by design, except for errors caused by floating-decimal arithmetic. Ensemble Empirical Mode Decomposition (EEMD) may fail to satisfy integrity unless noisy realisations are carefully chosen in the algorithm to cancel each other when averaging the realisations. We present such an algorithm implemented in R: “extricate”, which performs EEMD in a few seconds. Parsimony checks that the decomposition does not generate components that heavily cancel out. We propose to quantify it as the ratio between (1) the cumulated absolute values of each component (except the trend), and (2) the cumulated absolute values of the signal (minus the trend). The trend should be ignored in the calculation, because an added trend decreases the parsimony estimation of a similar decomposition. IMF departure (IMFD) quantifies the departure of each component to the definition of intrinsic mode functions (IMF), from which instantaneous frequency can reliably be computed. We define it as the mean of the absolute differences of the base 2 logarithms of frequencies obtained using (1) a robust generalized zero-crossing method (GZC, which simplifies the components into extrema separated by zero-crossings) and (2) a more local method such as the Hilbert Transform. Reversibility is the concept that all initial data points are preserved, even after linear interpolation and tuning. This allows to revert back to the original signal and discuss the significance of each data point. To facilitate reversibility we introduce the concept of quanta (smallest depth or time interval having significance for a given sampling) and an algorithm computing the highest rational common divisor of given values in R: “divisor”. This new methodology allows to check the final result of cyclostratigraphic analysis independently of how it was performed (i.e. a posteriori). Once the above-mentioned concepts are taken into account, the instantaneous frequencies, ratios of frequencies and amplitudes of the components can be computed and used to interpret the pertinence of the analysis in a geologically meaningful way. The instantaneity and independence of frequency and amplitude so obtained open a new way of performing time-series analysis.
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Book review of « Current status of stratigraphic units named from Belgium and adjacent areas »
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State of the art on the “calamine” - type zinc deposits of Belgium
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La carte géologique de Wallonie
