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Article Reference The BiogeochemicAl Model for Hypoxic and Benthic Influenced areas: BAMHBI v1.0
This paper describes the ocean BiogeochemicAl Model for Hypoxic and Benthic Influenced areas (BAMHBI). BAMHBI is a moderate complexity marine biogeochemical model that describes the cycling of carbon, nitrogen, phosphorus, silicon and oxygen through the marine foodweb. It involves 22 state variables, extends from bacteria up to mesozooplankton and includes three phytoplankton functional types (PFTs), two zooplankton size-classes, a microbial loop with several classes of detritic materials. Five optional modules are available allowing to extend the model with the explicit modelling of Chlorophyll a (Chl a) in each PFT, benthic degradation, gelatinous dynamics, particles aggregation and the carbonate system. BAMHBI describes the degradation of organic matter according to oxygenation conditions using an approach similar to that used in the sediment to simulate early diagenesis. The model is particularly appropriate for modelling low oxygen environments and the generation of sulfidic waters. An optional benthic module solves the degradation of sedimentary organic matter and the benthic-pelagic fluxes of solutes using an efficient formulation based on meta-modelling. This paper describes in details model formulations, implementation and coupling with the physics. BAMHBI's code is written in Fortran and can be coupled with many hydrodynamical models. Two case studies of application of BAMHBI in the Black Sea are described. One describes the application of BAMHBI to simulate the biogeochemical dynamics of the northwestern shelf during the eutrophication period. In particular, the ability of BAMHBI to simulate the oxygen dynamics at seasonal and interannual scales is assessed with a focus on the simulation of bottom hypoxia. We highlight the results of the benthic modelling module and its ability to represent benthic-pelagic fluxes. The second case study compares the BAMHBI simulated Chl a, oxygen and nitrate dynamics in the deep sea with respect to biogeochemical Argo.
Located in Library / RBINS Staff Publications 2026
Article Reference Local and landscape effects on ant functional and taxonomic compositions across green spaces of a tropical metropolis
Urbanization is one of the main processes driving environmental transformation, altering the structure and functioning of biological communities across multiple spatial scales. In this study, we evaluated the effects of local and landscape variables on the taxonomic and functional composition of ants in different types of urban green spaces in the city of Salvador, Brazil. A total of 62 sampling points were surveyed across forest fragments, squares, streets medians, and vacant lots, using specific methods for both ground-dwelling and arboreal strata. We recorded 93 ant species distributed among 20 functional groups. Our results indicated that, at the local scale, leaf litter depth was the primary explanatory factor for both taxonomic and functional richness, as well as for functional composition. At the landscape scale, human population density and vegetation cover surrounding the sampling points influenced the distribution of species and functional groups, revealing contrasting patterns between specialist and generalist species. While arboreal, hypogeic, and fungivorous ants were more dependent on structurally complex and conserved habitats, epigeic, omnivorous, and some predatory species were favored in more simplified and heterogeneous environments. These findings highlight that biodiversity conservation in urban areas depends on integrated strategies across multiple scales, encompassing management practices that ensure local structural complexity alongside planning that promotes habitat heterogeneity at the landscape level. Overall, the study demonstrates that the arrangement and quality of urban green spaces play a central role in maintaining both taxonomic and functional diversity of ant communities in tropical cities.
Located in Library / RBINS Staff Publications 2026
Article Reference Threshold values on environmental chemical contaminants in seafood in the European Economic Area
Seafood safety regulation within the European Economic Area has been strongly harmonised, including uniformisation of maximum levels on contaminants and toxins in seafood. Nevertheless, individual countries still have national limit values for different contaminant groups. This publication summarizes currently existing maximum levels on environmental chemical contaminants in seafood and seaweed that are established within the European Economic Area at international or national level. Maximum levels are compared to legal thresholds in other North Atlantic countries that are member of the International Council for the Exploration of the Seas (ICES), i.e. US, Canada and Russia, as well as the international food standards of the Codex Alimentarius. The identification of seafood safety regulatory differences allows to identify current challenges, associated to different topics: (1) contaminants in seafood, (2) contaminants in seaweed and (3) natural aquatic toxins. It can be concluded that increased harmonisation within and between geographical regions e.g. on seaweed regulations, can be beneficial from both a health and economic perspective. Constantly evolving knowledge on contaminants of emerging concern and new or emerging toxins triggers a continuous process of updating seafood regulations. Due to the health benefits of seafood consumption, a balance between risks and benefits is essential, as considered in EFSA seafood consumption advice.
Located in Library / RBINS Staff Publications 2022
Article Reference Enhanced removal of warfare agent tri-nitro-toluene by a <i>Methylophaga</i>-dominated microbiome
Historical exposure of the marine environment to 2,4,6-trinitrotoluene (TNT) happened due to the dumping of left-over munitions. Despite significant research on TNT decontamination, the potential of marine microbiome for TNT degradation remains only little explored. In this study, TNT degradation experiments were conducted with sediment located near the World War I munition dumpsite – Paardenmarkt in the Belgian part of North Sea. A slow removal was observed using TNT as sole source of C and N, which could be enhanced by adding methanol. Degradation was reflected in nitro-reduced metabolites and microbial growth. 16S Illumina sequencing analysis revealed several enriched genera that used TNT as a sole source of C and N - Colwellia, Thalossospira, and Methylophaga. Addition of methanol resulted in increased abundance of Methylophaga, which corresponded to the rapid removal of TNT. Methanol enhanced the degradation by providing additional energy and establishing syntrophic association between methanol-utilizing and TNT-utilizing bacteria.
Located in Library / RBINS Staff Publications 2023
Article Reference Evaluating the toxicity of sea-dumped conventional and chemical munition degradation products to fish and human cells using a combination of cell viability assays
The disposal of munitions in marine coastal areas after World Wars I and II has raised significant concerns about environmental contamination and human health risks. This study investigates the acute cytotoxicity of munition-related chemicals commonly detected near marine dumpsites, focusing on degradation products of explosives and related compounds (E&RC) and degradation products of chemical warfare agents and related compounds (CWA&RC). The research examines three CWA&RC (1,4-oxathiane, 1,4-dithiane, thiodiglycol) and four E&RC (2,4,6-trinitrotoluene, tetryl, 1,3-dinitrobenzene, picric acid) using the RTgill-W1 cell line (rainbow trout gill cells) as a proxy for fish toxicity and human cell lines (Caco2 and HepG2) to model potential human exposure via contaminated seafood. The results indicate low acute cytotoxicity of CWA&RC, while E&RC exhibit significantly higher toxicity. Notably, the EC10 and EC50 values for tetryl and 1,3-DNB in RTgill-W1 align with concentrations detected near North American dumpsites, reflecting environmentally relevant conditions. The study also reveals inter-species and inter-organ variability in toxicity mechanisms, identifying potential adverse outcome pathways such as AOP 220. These findings highlight the need for further research into chronic exposure scenarios at environmentally realistic concentrations and contribute crucial data to understanding the risks posed by the degradation products of these chemicals to aquatic life and human health.
Located in Library / RBINS Staff Publications 2025
Article Reference Diagnosing the Flocculation–Transport Dynamics of Suspended Particulate Matter Using a Two-Class Population Balance Model and Bayesian Calibration
Abstract The dynamics of suspended particulate matter (SPM) plays a crucial role in determining water quality, sediment transport, and biogeochemical cycles in inland, estuarine, and coastal water resources. Flocculation processes strongly influence the SPM dynamics via aggregation and breakage under various hydrodynamic and biogeochemical conditions. This study introduces a mechanistic and diagnostic framework that combines a two-class population balance equation (TCPBE) model with Bayesian calibration to simulate flocculation?transport behavior in both laboratory- (time-dependent batch) and field-scale (one-dimensional vertical) systems. Laboratory experiments with biopolymer?clay and microalgae?clay mixtures and field observations from an estuarine turbidity maximum zone are used to derive a comprehensive data set for model validation. Bayesian inference enables the estimation of uncertain model parameters while characterizing their statistical properties, thus supporting the mechanistic interpretation of flocculation dynamics. By quantifying how ionic strength and microbial physiology regulate flocculation kinetics and elucidating the turbulence-driven coupling between flocculation kinetics and sediment transport over tidal cycles, the framework demonstrates its suitability as a process-based diagnostic tool capable of effectively capturing SPM dynamics under various conditions. This framework has strong potential to advance the understanding of flocculation dynamics and support a range of applications in inland and estuarine sediment-laden water systems, including river, reservoir, esturine and coastal waters.
Located in Library / RBINS Staff Publications 2026
Article Reference The importance of long-time series of benthic data for science and management
Benthic organisms are important ecological receptors, playing fundamental roles across seafloor ecosystems, delivering some of the most important functions in the marine environment. Some of these key benthic functions include nutrient cycling, food provision for higher trophic levels, and carbon storage. Over the past 6 years, benthic monitoring has faced growing complexity, driven by diminishing funding and the constraints imposed by the COVID-19 pandemic. These challenges underscore the pressing need to recognize the enduring value of benthic time series in supporting monitoring, management, and modelling efforts. These long-term data sets have been critical to advance our current understanding into the areas of cumulative effects, conservation, management of Marine Protected Areas (MPAs), development of indicators, and assessment of climate-driven changes in marine ecosystems. Ongoing expert group discussions consistently affirm both the relevance and necessity of continuing to collect these vital data sets. However, the focus on emerging technologies and so-called ‘cutting-edge’ approaches sometimes leads to the undervaluation and compromising some of these long-term series. We contend that a comprehensive understanding of benthic ecology, essential for robust marine management, reliable numerical analysis, and taxonomic consistency, cannot be achieved without the continuity provided by long-term data. Such time series are indispensable for tracking patterns of change and assessing responses across diverse human activities and seafloor ecosystems. While our research has concentrated on soft sediment environments, many of the key principles and recommendations outlined here are broadly applicable to other ecosystem types.
Located in Library / RBINS Staff Publications 2026
Inproceedings Reference Unveiling the biogeochemical role of bat guano in shaping cave morphology in the Madingou region, Republic of the Congo
Located in Library / RBINS Staff Publications 2025
Article Reference At-sea distribution of seals on the Northwest European Shelf: Towards transboundary conservation and management
Quantifying and mitigating transboundary effects of anthropogenic activity is a key challenge in environmental management, particularly for wide-ranging species such as large predators, fish and migratory birds, relying on habitats across multiple national jurisdictions. This challenge is especially complex in marine ecosystems, where the movement of species and impacts across borders is largely unobserved. Central-place foragers, such as pinnipeds and seabirds, exemplify this complexity: abundance is typically assessed on local (regional or national) scales on land, yet at-sea movements and drivers of abundance occur on broader transboundary scales. Resolving this mismatch is critical to effective conservation, especially in areas such as the Northwest European Shelf (NWES), which features globally important predator populations (including two pinniped species) alongside growing anthropogenic pressures and a mosaic of national maritime borders. We model an unprecedented GPS dataset from 236 grey (Halichoerus grypus) and 606 harbour seals (Phoca vitulina) tracked in waters of seven countries across the NWES (United Kingdom, Ireland, France, Belgium, Netherlands, Germany and Denmark). Using regional habitat association models, we generate at-sea distribution estimates for both species at 5 km resolution, scaled to haulout counts, producing country-specific and NWES-wide density maps. Analysis of the extent to which seals making foraging trips from one country occupy the Exclusive Economic Zones (EEZs) of other countries revealed substantial transboundary overlap, particularly for grey seals, and harbour seals in the southern North Sea. A case study apportioning grey seal density within three adjacent offshore marine protected areas in different EEZs revealed that, where total density in a given area is required, overlooking transboundary distribution can underrepresent numbers by an order of magnitude. Synthesis and applications. This study provides the first comprehensive, regionally scalable distribution estimates for pinnipeds across the NWES and its constituent countries. The modelling framework is adaptable to other central-place and migratory species, supporting transboundary biodiversity assessments and international conservation policy. We discuss common limitations and misconceptions of species distribution estimates, highlight priorities for future work and underscore the need for transboundary efforts to manage wide-ranging species, providing a foundation for future ecological modelling and decision-making across shared ecosystems.
Located in Library / RBINS Staff Publications 2026
Article Reference An integrated study of dark earth from the alluvial valley of the Senne river (Brussels, Belgium).
The present article discusses the integration of urban geoarchaeological and archaeobotanical data of a series of Dark Earth deposits situated in the alluvial valley of the Senne River in Brussels, Belgium. Due to their homogeneous character, their interpretation is a huge challenge for archaeologists. Through a caseby-case approach, a detailed picture of the sequence of different activities and (semi-) natural events, leading to the build up of Dark Earth at each individual site has been obtained. Among the activities, agricultural practices and waste management, which are rarely archaeologically recorded in urban contexts, have been identified. Despite being situated in a valley context, none of the sites presented an excellent preservation of the organic plant remains. However, through the integration of geoarchaeological and botanical data, the taphonomical history of the botanical remains could better be understood, allowing us to document the evolution of the environment surrounding the sites. Additionally, it has been demonstrated that the botanical study of Dark Earth units can also provide valuable information on vegetal consumption, in particular fruits. On a broader scale, this integrated geoarchaeologial and archaeobotanical study sheds some light on the process of urbanisation of the Senne alluvial valley between the 11the12th and the 16th century AD.
Located in Library / RBINS Staff Publications 2017