Articles | Volume 19, issue 5
https://doi.org/10.5194/gmd-19-2137-2026
© Author(s) 2026. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-19-2137-2026
© Author(s) 2026. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model description paper
| 
16 Mar 2026
Model description paper |
| 16 Mar 2026
| 16 Mar 2026
The BiogeochemicAl Model for Hypoxic and Benthic Influenced areas: BAMHBI v1.0
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Luc Vandenbulcke
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Séverine Chevalier
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Mathurin Choblet
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Ilya Drozd
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Jean-François Grailet
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Evgeny Ivanov
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Loïc Macé
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Polina Verezemskaya
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Haolin Yu
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Lauranne Alaerts
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Ny Riana Randresihaja
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Victor Mangeleer
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Guillaume Maertens de Noordhout
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Arthur Capet
ECOMOD, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
B-Geosys, Université Libre de Bruxelles, Brussels, Belgium
Catherine Meulders
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Anne Mouchet
MAST-FOCUS, Astrophysics, Geophysics and Oceanography Department, University of Liège, B5 Sart-Tilman, 4000 Liège, Belgium
Guy Munhoven
LPAP–SPHERES Astrophysics, Geophysics and Oceanography Department, University of Liège, 4000 Liège, Belgium
Karline Soetaert
Estuarine and Delta System, NIOZ, Yerseke, the Netherlands
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State Planet, 1-osr7, 2, https://doi.org/10.5194/sp-1-osr7-2-2023, https://doi.org/10.5194/sp-1-osr7-2-2023, 2023
Matteo Willeit, Tatiana Ilyina, Bo Liu, Christoph Heinze, Mahé Perrette, Malte Heinemann, Daniela Dalmonech, Victor Brovkin, Guy Munhoven, Janine Börker, Jens Hartmann, Gibran Romero-Mujalli, and Andrey Ganopolski
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This study gives an assessment of bottom trawling on physical, chemical, and biological characteristics in a location known for its strong currents and variable habitats. Although trawl gears only removed the top 1 cm of the seabed surface, impacts on reef-building tubeworms significantly decreased carbon and nutrient cycling. Lighter trawls slightly reduced the impact on fauna and nutrients. Tubeworms were strongly linked to biogeochemical and faunal aspects before but not after trawling.
Alice E. Webb, Didier M. de Bakker, Karline Soetaert, Tamara da Costa, Steven M. A. C. van Heuven, Fleur C. van Duyl, Gert-Jan Reichart, and Lennart J. de Nooijer
Biogeosciences, 18, 6501–6516, https://doi.org/10.5194/bg-18-6501-2021, https://doi.org/10.5194/bg-18-6501-2021, 2021
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The biogeochemical behaviour of shallow reef communities is quantified to better understand the impact of habitat degradation and species composition shifts on reef functioning. The reef communities investigated barely support reef functions that are usually ascribed to conventional coral reefs, and the overall biogeochemical behaviour is found to be similar regardless of substrate type. This suggests a decrease in functional diversity which may therefore limit services provided by this reef.
Estrella Olmedo, Verónica González-Gambau, Antonio Turiel, Cristina González-Haro, Aina García-Espriu, Marilaure Gregoire, Aida Álvera-Azcárate, Luminita Buga, and Marie-Hélène Rio
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2021-364, https://doi.org/10.5194/essd-2021-364, 2021
Revised manuscript not accepted
Short summary
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We present the first dedicated satellite salinity product in the Black Sea. We use the measurements provided by the European Soil Moisture and Ocean Salinity mission. We introduce enhanced algorithms for dealing with the contamination produced by the Radio Frequency Interferences that strongly affect this basin. We also provide a complete quality assessment of the new product and give an estimated accuracy of it.
Chiu H. Cheng, Jaco C. de Smit, Greg S. Fivash, Suzanne J. M. H. Hulscher, Bas W. Borsje, and Karline Soetaert
Earth Surf. Dynam., 9, 1335–1346, https://doi.org/10.5194/esurf-9-1335-2021, https://doi.org/10.5194/esurf-9-1335-2021, 2021
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Shells are biogenic particles that are widespread throughout natural sandy environments and can affect the bed roughness and seabed erodibility. As studies are presently lacking, we experimentally measured ripple formation and migration using natural sand with increasing volumes of shell material under unidirectional flow in a racetrack flume. We show that shells expedite the onset of sediment transport, reduce ripple dimensions and slow their migration rate.
Guy Munhoven
Geosci. Model Dev., 14, 4225–4240, https://doi.org/10.5194/gmd-14-4225-2021, https://doi.org/10.5194/gmd-14-4225-2021, 2021
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SolveSAPHE (Munhoven, 2013) was the first package to calculate pH reliably from any physically sensible pair of total alkalinity (AlkT) and dissolved inorganic carbon (CT) data and to do so in an autonomous and efficient way. Here, we extend it to use CO2, HCO3 or CO3 instead of CT. For each one of these pairs, the new SolveSAPHE calculates all of the possible pH values (0, 1, or 2), again without any prior knowledge of the solutions.
Guy Munhoven
Geosci. Model Dev., 14, 3603–3631, https://doi.org/10.5194/gmd-14-3603-2021, https://doi.org/10.5194/gmd-14-3603-2021, 2021
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Sea-floor sediments play an important role in biogeochemical cycling of elements (e.g. carbon, silicon, nutrients) in the ocean. Realistic sediment modules are, however, not yet commonly used in global ocean biogeochemical models. Here we present MEDUSA, a model of the processes taking place in the surface sea-floor sediments which control the interaction between the sediments and the ocean. MEDUSA can be configured to meet the exact needs of any given ocean biogeochemical model.
Emil De Borger, Justin Tiano, Ulrike Braeckman, Adriaan D. Rijnsdorp, and Karline Soetaert
Biogeosciences, 18, 2539–2557, https://doi.org/10.5194/bg-18-2539-2021, https://doi.org/10.5194/bg-18-2539-2021, 2021
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Bottom trawling alters benthic mineralization: the recycling of organic material (OM) to free nutrients. To better understand how this occurs, trawling events were added to a model of seafloor OM recycling. Results show that bottom trawling reduces OM and free nutrients in sediments through direct removal thereof and of fauna which transport OM to deeper sediment layers protected from fishing. Our results support temporospatial trawl restrictions to allow key sediment functions to recover.
Cited articles
Aumont, O., Ethé, C., Tagliabue, A., Bopp, L., and Gehlen, M.: PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies, Geosci. Model Dev., 8, 2465–2513, https://doi.org/10.5194/gmd-8-2465-2015, 2015. a, b
Billen, G. and Fontigny, A.: Dynamics of a phaeocystis-dominated spring bloom in belgian coastal waters. II. Bacterio-plankton dynamics, Marine Ecology Progress Series, 37, 249–257, 1987. a
Butenschön, M., Clark, J., Aldridge, J. N., Allen, J. I., Artioli, Y., Blackford, J., Bruggeman, J., Cazenave, P., Ciavatta, S., Kay, S., Lessin, G., van Leeuwen, S., van der Molen, J., de Mora, L., Polimene, L., Sailley, S., Stephens, N., and Torres, R.: ERSEM 15.06: a generic model for marine biogeochemistry and the ecosystem dynamics of the lower trophic levels, Geosci. Model Dev., 9, 1293–1339, https://doi.org/10.5194/gmd-9-1293-2016, 2016. a, b
Capet, A., Beckers, J.-M., and Grégoire, M.: Drivers, mechanisms and long-term variability of seasonal hypoxia on the Black Sea northwestern shelf – is there any recovery after eutrophication?, Biogeosciences, 10, 3943–3962, https://doi.org/10.5194/bg-10-3943-2013, 2013. a, b, c, d
Capet, A., Meysman, F. J. R., Akoumianaki, I., Soetaert, K., and Grégoire, M.: Integrating sediment biogeochemistry into 3D oceanic models : A study of benthic-pelagic coupling in the Black Sea, Ocean Modelling, 101, 83–100, https://doi.org/10.1016/j.ocemod.2016.03.006, 2016. a, b, c
Choblet, M.: mchoblet/benthic_model_assessment: GMD paper figure, Zenodo [code], https://doi.org/10.5281/zenodo.18684398, 2026. a
Ciliberti, S., Grégoire, M., Staneva, J., Palazov, A., Coppini, G., Lecci, R., Peneva, E., Matreata, M., Marinova, V., Masina, S., Pinardi, N., Jansen, E., Lima, L., Aydoğdu, A., Creti, S., Stefanizzi, L., Azevedo, D., Causio, S., Vandenbulcke, L., Capet, A., Meulders, C., Ivanov, E., Behrens, A., Ricker, M., Gayer, G., Palermo, F., Ilicak, M., Gunduz, M., Valcheva, N., and Agostini, P.: Monitoring and Forecasting the Ocean State and Biogeochemical Processes in the Black Sea: Recent Developments in the Copernicus Marine Service, Journal of Marine Science and Engineering, 9, 1146, https://doi.org/10.3390/jmse9101146, 2021. a
Cossarini, G., Querin, S., Solidoro, C., Sannino, G., Lazzari, P., Di Biagio, V., and Bolzon, G.: Development of BFMCOUPLER (v1.0), the coupling scheme that links the MITgcm and BFM models for ocean biogeochemistry simulations, Geosci. Model Dev., 10, 1423–1445, https://doi.org/10.5194/gmd-10-1423-2017, 2017. a
Daewel, U., Schrum, C., and Macdonald, J. I.: Towards end-to-end (E2E) modelling in a consistent NPZD-F modelling framework (ECOSMO E2E_v1.0): application to the North Sea and Baltic Sea, Geosci. Model Dev., 12, 1765–1789, https://doi.org/10.5194/gmd-12-1765-2019, 2019. a
Dmitriev, E. V., Khomenko, G., Chami, M., Sokolov, A. A., Churilova, T. Y., and Korotaev, G. K.: Parameterization of light absorption by components of seawater in optically complex coastal waters of the Crimea Peninsula (Black Sea), Appl. Opt., 48, 1249–1261, https://doi.org/10.1364/AO.48.001249, 2009. a
Doerffer, R. and Schiller, H.: The MERIS case 2 water algorithm, International Journal of Remote Sensing, 28, 517–535, 2007. a
Droop, M.: 25 years of algal grwth linetics – personal view, Botanica Marina, 26, 99–112, 1983. a
Dutkiewicz, S., Hickman, A. E., Jahn, O., Gregg, W. W., Mouw, C. B., and Follows, M. J.: Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model, Biogeosciences, 12, 4447–4481, https://doi.org/10.5194/bg-12-4447-2015, 2015. a
Gayer, G., Dick, S., Pleskachevsky, A., and Rosenthal, W.: Numerical modeling of suspended matter transport in the North Sea., Ocean Dynamics, 56, 62–77, https://doi.org/10.1007/s10236-006-0070-5, 2006. a
Geider, R., H., M., and Kana, T.: A dynamic regulatory model of phytoplankton acclimation to light, nutrients and temperature, Limnology and Oceanography, 43, 679–694, https://doi.org/10.1016/S0012-8252(00)00004-0, 1998. a
Grégoire, M. and Soetaert, K.: Carbon, nitrogen, oxygen and sulfide budgets in the Black Sea: A biogeochemical model of the whole water column coupling the oxic and anoxic parts, Ecological Modelling, 221, 2287–2301, https://doi.org/10.1016/j.ecolmodel.2010.06.007, 2010. a
Grégoire, M. and Vandenbulcke, L.: BiogeochemicAl Model for Hypoxic and Benthic Influenced areas (BAMHBI) v1.0.1, Zenodo [code], https://doi.org/10.5281/zenodo.16964655, 2025. a
Grégoire, M., Raick, C., and Soetaert, K.: Numerical modeling of the central Black Sea ecosystem functioning during the eutrophication phase, Progress in Oceanography, 76, 286–333, https://doi.org/10.1016/j.pocean.2008.01.002, 2008. a, b, c
Hedges, J., Hu, F., Devol, A., Hartnett, H., Tsamakis, E., and Keil, R.: Sedimentary organic matter preservation: A test for selective degradation under oxic conditions, Am. J. Sci., 299, 529–555, 1999. a
Hersbach, H., Bell, B., Berrisford, P., Hirahara, S., Horányi, A., Muñoz Sabater, J., Nicolas, J., Peubey, C., Radu, R., Schepers, D., Simmons, A., Soci, C., Abdalla, S., Abellan, X., Balsamo, G., Bechtold, P., Biavati, G., Bidlot, J., Bonavita, M., and Thépaut, J.-N.: The ERA5 global reanalysis, Q. J. R. Meteorol. Soc., https://doi.org/10.1002/qj.3803, 2020. a
Ho, D. T., Law, C. S., Smith, M. J., Schlosser, P., Harvey, M., and Hill, P.: Measurements of air-sea gas exchange at high wind speeds in the Southern Ocean: implications for global parameterizations, Geophys. Res. Lett., 33, 16611, https://doi.org/10.1029/2006GL026817, 2006. a
Hofmann, A. F., Meysman, F. J. R., Soetaert, K., and Middelburg, J. J.: A step-by-step procedure for pH model construction in aquatic systems, Biogeosciences, 5, 227–251, https://doi.org/10.5194/bg-5-227-2008, 2008. a
Khalil, K., Rabouille, C., Gallinari, M., Soetaert, K., DeMaster, D., and Ragueneau, O.: Constraining biogenic silica dissolution in marine sediments: A comparison between diagenetic models and experimental dissolution rates, Marine Chemistry, 106, 223–238, 2007. a
Kowalczuk, P., Cooper, W. J., Whitehead, R. F., Durako, M. J., and Sheldon, W.: Characterization of CDOM in an organic-rich river and surrounding coastal ocean in the South Atlantic Bight, Aquatic Sciences, 65, 384–401, 2003. a
Kremer, P.: Respiration and excretion by the ctenophore Mnemiopsis leidyi, Marine Biology, 44, 20–43, 1977. a
Lancelot, C., Staneva, J., Van Eeckhout, D., Beckers, J., and Stanev, E.: Modelling the Danube-influenced North-western Continental Shelf of the Black Sea. II: Ecosystem Response to Changes in Nutrient Delivery by Danube River after its damming in 1972, Estuarine, Coastal and Shelf Science, 54, 473–499, 2002. a, b
Laws, E. and Wong, D.: Studies on carbon andnitrogen metabolism by three marine phytoplankton species in nitrate-limited continuous culture, Journal of Phycology, 14, 406–416, 1978. a
Lee, Z.-P., Du, K.-P., and Arnone, R.: A model for the diffuse attenuation coefficient of downwelling irradiance, Journal of Geophysical Research, 110, C02016, https://doi.org/10.1029/2004JC002275, 2005. a, b
Lenstra, W. K., Hermans, M., Séguret, M. J. M., Witbaard, R., Behrends, T., Dijkstra, N., van Helmond, N. A. G. M., Kraal, P., Laan, P., Rijkenberg, M. J. A., Severmann, S., Teaca, A., and Slomp, C. P.: The shelf-to-basin iron shuttle in the Black Sea revisited, Chem. Geol., 511, 314–341, https://doi.org/10.1016/j.chemgeo.2018.10.024, 2019. a, b
Lewis, E. and Wallace, D. W. R.: Program Developed for CO2 System Calculations, ORNL/CDIAC-105. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, https://doi.org/10.15485/1464255, 1998. a
Lichtschlag, A., Donis, D., Janssen, F., Jessen, G. L., Holtappels, M., Wenzhöfer, F., Mazlumyan, S., Sergeeva, N., Waldmann, C., and Boetius, A.: Effects of fluctuating hypoxia on benthic oxygen consumption in the Black Sea (Crimean shelf), Biogeosciences, 12, 5075–5092, https://doi.org/10.5194/bg-12-5075-2015, 2015. a, b
Macé, L., Vandenbulcke, L., Brankart, J.-M., Brasseur, P., and Grégoire, M.: Characterisation of uncertainties in an ocean radiative transfer model for the Black Sea through ensemble simulations, Biogeosciences, 22, 3747–3768, https://doi.org/10.5194/bg-22-3747-2025, 2025a. a
Macé, L., Vandenbulcke, L., Brankart, J.-M., Grailet, J.-F., Brasseur, P., and Grégoire, M.: Three-stream modelling of radiative transfer for the simulation of Black Sea biogeochemistry in a NEMO framework, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2025-4973, 2025b. a
Mague, T., Friberg, E., Hughes, D., and Morris, I.: Extracellular release of carbon by marine phytoplankton: a physiological approach., Limnology and Oceanography, 25, 262–279, 1980. a
Mee, L., Friedrich, J., and Gomoiu, M.-T.: Restoring the Black Sea in times of uncertainty, Oceanography, 18, 32–43, 2005. a
Middelburg, J. and Meysman, F.: Burial at Sea, Science, 18, 1775–1810, https://doi.org/10.1126/science.1144001, 2007. a
Mishonov, A. V., Boyer, T. P., Baranova, O. K., Bouchard, C. N., Cross, S. L., Garcia, H. E., Locarnini, R. A., Paver, C. R., Reagan, J. R., Wang, Z., Seidov, D., Grodsky, A. I., and Beauchamp, J. G.: World Ocean Database 2023, National Centers for Environmental Information (U.S.), https://doi.org/10.25923/z885-h264, 2024. a, b, c, d, e, f
Muramoto, J., Honjo, S., Fry, B., Hay, B., Howarth, R., and Cisne, J.: Sulfur, iron and organic carbon fluxes in the Black Sea : sulfur isotopic evidence for origin of sulfur fluxes, Deep Sea Research II, 38, 1151–1188, 1991. a
Nakamura, Y.: Growth and grazing of a large heterotrophic dinoflagellate, Noctiluca scintillans, in laboratory cultures, Journal of Plankton Research, 20, 1711–1720, 1998. a
Raick, C., Delhez, E., Soetaert, K., and Gregoire, M.: Study of the seasonal cycle of the biogeochemical processes in the Ligurian Sea using an 1D interdisciplinary model, Journal of Marine Systems, 55, 177–203, https://doi.org/10.1016/j.jmarsys.2004.09.005, 2005. a
Raick, C., Soetaert, K., and Grégoire, M.: Model complexity and performance: how far can we simplify?, Progress in Oceanography, 70, 27–57, https://doi.org/10.1016/j.pocean.2006.03.001, 2006. a
Ricour, F., Capet, A., D'Ortenzio, F., Delille, B., and Grégoire, M.: Dynamics of the deep chlorophyll maximum in the Black Sea as depicted by BGC-Argo floats, Biogeosciences, 18, 755–774, https://doi.org/10.5194/bg-18-755-2021, 2021. a
Smith, C. and Tett, P.: A depth–resolving numerical model of physically forced microbiology at the European shelf edge, Journal of Marine Systems, 26, 1–36, 2000. a
Soetaert, K., Herman, P. M. J., Middelburg, J. J., Heip, C., Smith, C. L., Tett, P., and Wild-Allen, K.: Numerical modelling of the shelf break ecosystem: reproducing benthic and pelagic measurements, Deep Sea Research Part II: Topical Studies in Oceanography, 48, 3141–3177, https://doi.org/10.1016/S0967-0645(01)00035-2, 2001. a, b
Soulsby, R.: Dynamics of marine sands: a manual for practical applications, Oceanographic Literature Review, 9, 947, ISBN 978-0-7277-2584-X, 1997. a
Stanev, E. and Kandilarov, R.: Sediment dynamics in the Black Sea: numerical modelling and remote sensing observations, Ocean dynamics, 62, 533–553, https://doi.org/10.1007/s10236-012-0520-1, 2012. a, b
Tett, P.: Parameterising a microplankton model, Napier University, ISBN 0 902703 60 9, 1998. a
Van Cappellen, P., Dixit, S., and van Beusekom, J.: Biogenic silica dissolution in the oceans: reconciling experimental and field-based dissolution rates, Global Biogeochemical Cycles, 16, 1075, https://doi.org/10.1029/2001GB001431, 2002. a
Vandenbulcke, L. and Grailet, J.-F.: BAMHBI stable, GitLab repository [code], https://gitlab.uliege.be/ESPECES/MAST/bamhbi-stable (last access: 19 February 2026), 2025. a
Wanninkhof, R.: Relationship between wind speed and gas exchange over the ocean, Journal of Geophysical Research, 97, 7373–7382, 1992. a
Wijsman, J., Herman, P., Middelburg, J. J., and Soetaert, K. E.: A model for early diagenetic processes in sediments of the continental shelf of the Black Sea, Estuarine Coastal and Shelf Science, 54, 403–421, https://doi.org/10.1006/ecss.2000.0655, 2002. a, b
Williams, P.: The importance of losses duringn microbial growth: commentary on the physiology, measurement and ecology of the release of dissolved organic material, Marine Microbial Food Webs, 4, 175–206, 1990. a
Wolf-Gladrow, D. and Riebesell, U.: Diffusion and reactions in the vicinity of plankton: a refined model for inorganic carbon transport, Marine Chemistry, 59, 17–34, https://doi.org/10.1016/S0304-4203(97)00069-8, 1997. a
Xu, J., Hood, R. R., and Chao, S.-Y.: A simple empirical optical model for simulating light attenuation variability in a partially mixed estuary, Estuaries, 28, 572–580, 2005. a
Zaitsev, Y.: Impact of eutrophication on the Black Sea fauna, General Fisheries Council for the Mediterranean, Tech.Rep., FAO, Rome, vol. 64, 63–86, 1993. a
Short summary
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. BAMHBI is a stand-alone biogeochemical model that can be coupled to any hydrodynamical model and is particularly appropriate for modelling low oxygen environments and the generation of sulfidic waters.
This paper describes the ocean BiogeochemicAl Model for Hypoxic and Benthic Influenced areas...
