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Water
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Marine Biogeochemical Modeling
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Marine Biogeochemical Modeling

A special issue of Water (ISSN 2073-4441). This special issue belongs to the section "Oceans and Coastal Zones".

Deadline for manuscript submissions: closed (30 April 2021) | Viewed by 22536

Special Issue Editors

Dr. Evgeniy V. Yakushev

E-Mail Website
Guest Editor
Section for Marine Biogeochemistry and Oceanography, Norwegian Institute for Water Research (NIVA), Oslo, Norway
Interests: chemical oceanography; marine biogeochemistry; oxygen depletion processes; aquatic environment
Dr. Oleg P. Savchuk

E-Mail Website
Guest Editor
Baltic Nest Institute, Stockholm University Baltic Sea Centre, Sweden
Interests: mathematical modeling; marine ecosystems; biogeochemical cycles

Special Issue Information

Dear Colleagues,

Marine biogeochemistry studies the interactions of physical, chemical, biological, and geological variables and processes that take place in the water body and sediments underneath. The complexity of such interactions, including their simultaneous occurrence on multiple scales, requires the implementation of a system approach involving mathematical modelling as its major tool. Depending on the objectives, the useful models can be analytical or numerical and be used for the exploration of new interactions or the simulation of specific sites and events according to well-established designs. This Special Issue calls for works that both introduce new methods and apply simulation modelling for specific tasks related to marine biogeochemistry.

Dr. Evgeniy V. Yakushev
Dr. Oleg P. Savchuk
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Water is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biogeochemical modeling
  • eutrophication
  • pollution
  • de-oxygenation
  • acidification

Published Papers (7 papers)

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Research

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17 pages, 4389 KiB  
Article
Modeling Nickel Leaching from Abandoned Mine Tailing Deposits in Jøssingfjorden
by Svetlana Pakhomova, Evgeniy Yakushev and Morten Thorne Schaanning
Water 2021, 13(7), 967; https://doi.org/10.3390/w13070967 - 31 Mar 2021
Cited by 4 | Viewed by 2465
Abstract
Underwater disposal of mine tailings in lakes and seas has been considered favorable due to the geochemical stability obtained during long-term storage in anoxic sediments. Sulfides are stable in the ore; however, oxidation and transformation of some substances into more soluble forms may [...] Read more.
Underwater disposal of mine tailings in lakes and seas has been considered favorable due to the geochemical stability obtained during long-term storage in anoxic sediments. Sulfides are stable in the ore; however, oxidation and transformation of some substances into more soluble forms may impact bioavailability processes and enhance the risk of toxic effects in the aquatic environment. The goal of this work was to construct a model for simulating the nickel (Ni) cycle in the water column and upper sediments and apply it to the mine tailing sea deposit in the Jøssingfjord, SouthWest Norway. A one-dimensional (1D) benthic–pelagic coupled biogeochemical model, BROM, supplemented with a Ni module specifically developed for the study was used. The model was optimized using field data collected from the fjord. The model predicted that the current high Ni concentrations in the sediment can be a potential source of Ni leaching to the water column until about 2040. The top 10 cm of sediments were classified as being of “poor” environmental state according to the Norwegian Quality Standards. A numerical experiment predicted that with complete cessation of the discharges there would be an improvement in the environmental state of sediment to “good” in about 20 years. On the other hand, doubling of discharge would lead to an increase in the Ni content in the sediment, approaching the boundary of the “very poor” environmental state. The model results demonstrated that Ni leaching from the sea deposits may be increased due to sediment reworking by bioturbation at the sediment–water interface. The model can be an instrument for analysis of different scenarios for mine tailing activities from point of view of reduction of environmental impact as a component of the best available technology. Full article
(This article belongs to the Special Issue Marine Biogeochemical Modeling)
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17 pages, 4348 KiB  
Article
Estimating Nitrogen and Phosphorus Cycles in a Timber Reef Deployment Area
by Jamaluddin Fitrah Alam, Tamiji Yamamoto, Tetsuya Umino, Shinya Nakahara and Kiyonori Hiraoka
Water 2020, 12(9), 2515; https://doi.org/10.3390/w12092515 - 09 Sep 2020
Cited by 2 | Viewed by 2199
Abstract
In an oligotrophic bay, Mitsu Bay, Japan, artificial timber reefs (ATRs) are deployed to increase fish production. In such man-made ecosystems, the biological activities of other organisms as well as the physical structures of ATRs could influence nutrient cycling. A pelagic–benthic coupling model [...] Read more.
In an oligotrophic bay, Mitsu Bay, Japan, artificial timber reefs (ATRs) are deployed to increase fish production. In such man-made ecosystems, the biological activities of other organisms as well as the physical structures of ATRs could influence nutrient cycling. A pelagic–benthic coupling model expressing both phosphorus and nitrogen cycling was developed to investigate seasonal variation in the associated nutrients and their annual budget in the ATR areas and the entire bay system. The model consists of equations representing all the relevant physical and biological processes. The model reproduced the observed seasonal variations in dissolved inorganic P, ammonium, and nitrate concentrations that were low in spring and summer and high in autumn and winter. The internal regeneration rates of the nutrients were two times higher in the ATRs than in the bay area, so that fish production was predicted to be higher in the ATRs than in the bay area. Considering the inflows from the land and precipitation are quite low, nutrient regeneration is an important source of nutrients for the water in Mitsu Bay. ATR deployment could be an important local nutrient source in an oligotrophic bay, and could increase fish production. Full article
(This article belongs to the Special Issue Marine Biogeochemical Modeling)
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22 pages, 6523 KiB  
Article
Understanding the Biogeochemical Impacts of Fish Farms Using a Benthic-Pelagic Model
by Evgeniy V. Yakushev, Philip Wallhead, Paul E. Renaud, Alisa Ilinskaya, Elizaveta Protsenko, Shamil Yakubov, Svetlana Pakhomova, Andrew K. Sweetman, Kathy Dunlop, Anfisa Berezina, Richard G. J. Bellerby and Trine Dale
Water 2020, 12(9), 2384; https://doi.org/10.3390/w12092384 - 25 Aug 2020
Cited by 10 | Viewed by 4145
Abstract
Sustainable development of the salmon farming industry requires knowledge of the biogeochemical impacts of fish farm emissions. To investigate the spatial and temporal scales of farm impacts on the water column and benthic biogeochemistry, we coupled the C-N-P-Si-O-S-Mn-Fe transformation model BROM with a [...] Read more.
Sustainable development of the salmon farming industry requires knowledge of the biogeochemical impacts of fish farm emissions. To investigate the spatial and temporal scales of farm impacts on the water column and benthic biogeochemistry, we coupled the C-N-P-Si-O-S-Mn-Fe transformation model BROM with a 2-dimensional benthic-pelagic transport model (2DBP), considering vertical and horizontal transport in the water and upper 5 cm of sediments along a 10 km transect centered on a fish farm. The 2DBP model was forced by hydrophysical model data for the Hardangerfjord in western Norway. Model simulations showed reasonable agreement with field data from the Hardangerfjord in August 2016 (correlations between the model and observations were significant for most variables, and model biases were mostly <35%). The model predicted significant impacts on seafloor biogeochemistry up to 1 km from the fish farm (e.g., increased organic matter in sediments, oxygen depletion in bottom water and sediments, denitrification, metal and sulfur reduction), as well as detectable decreases in oxygen and increases in ammonium, phosphate and organic matter in the surface water near to the fish farm. Full article
(This article belongs to the Special Issue Marine Biogeochemical Modeling)
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23 pages, 5389 KiB  
Article
Understanding the Role of Organic Matter Cycling for the Spatio-Temporal Structure of PCBs in the North Sea
by Ute Daewel, Evgeniy V. Yakushev, Corinna Schrum, Luca Nizzetto and Elena Mikheeva
Water 2020, 12(3), 817; https://doi.org/10.3390/w12030817 - 14 Mar 2020
Cited by 5 | Viewed by 3258
Abstract
Using the North Sea as a case scenario, a combined three-dimensional hydrodynamic-biogeochemical-pollutant model was applied for simulating the seasonal variability of the distribution of hydrophobic chemical pollutants in a marine water body. The model was designed in a nested framework including a hydrodynamic [...] Read more.
Using the North Sea as a case scenario, a combined three-dimensional hydrodynamic-biogeochemical-pollutant model was applied for simulating the seasonal variability of the distribution of hydrophobic chemical pollutants in a marine water body. The model was designed in a nested framework including a hydrodynamic block (Hamburg Shelf Ocean Model (HAMSOM)), a biogeochemical block (Oxygen Depletion Model (OxyDep)), and a pollutant-partitioning block (PolPar). Pollutants can be (1) transported via advection and turbulent diffusion, (2) get absorbed and released by a dynamic pool of particulate and dissolved organic matter, and (3) get degraded. Our model results indicate that the seasonality of biogeochemical processes, including production, sinking, and decay, favors the development of hot spots with particular high pollutant concentrations in intermediate waters of biologically highly active regions and seasons, and it potentially increases the exposure of feeding fish to these pollutants. In winter, however, thermal convection homogenizes the water column and destroys the vertical stratification of the pollutant. A significant fraction of the previously exported pollutants is then returned to the water surface and becomes available for exchange with the atmosphere, potentially turning the ocean into a secondary source for pollutants. Moreover, we could show that desorption from aging organic material in the upper aphotic zone is expected to retard pollutants transfer and burial into sediments; thus, it is considerably limiting the effectiveness of the biological pump for pollutant exports. Full article
(This article belongs to the Special Issue Marine Biogeochemical Modeling)
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26 pages, 11407 KiB  
Article
Effects of Physical Forcing on Summertime Hypoxia and Oxygen Dynamics in the Pearl River Estuary
by Jia Huang, Jiatang Hu, Shiyu Li, Bin Wang, Yongji Xu, Bo Liang and Dehong Liu
Water 2019, 11(10), 2080; https://doi.org/10.3390/w11102080 - 05 Oct 2019
Cited by 13 | Viewed by 3447
Abstract
A validated hydrodynamic-biogeochemical model was applied to investigate the effects of physical forcing (i.e., river discharge, winds, and tides) on the summertime dissolved oxygen (DO) dynamics and hypoxia (DO < 3 mg L−1) in the Pearl River estuary (PRE), based on [...] Read more.
A validated hydrodynamic-biogeochemical model was applied to investigate the effects of physical forcing (i.e., river discharge, winds, and tides) on the summertime dissolved oxygen (DO) dynamics and hypoxia (DO < 3 mg L−1) in the Pearl River estuary (PRE), based on a suite of model sensitivity experiments. Compared with the base model run in 2006 (a wet year), the simulated hypoxic area in the moderate year (with 75% of river discharge of the base run) and the dry year scenario (with 50% of river discharge of the base run) was reduced by ~30% and ~60%, respectively. This is because under the lower river discharge levels, less particulate organic matter was delivered to the estuary that subsequently alleviated the oxygen demand at the water–sediment interface, and in the meantime, the water stratification strength was decreased, which facilitated the vertical diffusion of DO. Regarding the effect of winds, the highly varying and intermittent strong winds had a significant impact on the replenishment of bottom DO by disrupting water stratification and thus inhibiting the development of hypoxia. Sensitivity experiments showed that the hypoxic area and volume were both remarkably increased in the low wind scenario (with a bottom hypoxic zone extending from the Modaomen sub-estuary to the western shoal in Lingdingyang Bay), whereas hypoxia was almost absent in the strong wind scenario. The DO budget indicated that winds altered the bottom DO mostly by affecting the DO flux due to vertical diffusion and horizontal advection, and had a limited influence on the DO consumption processes. Moreover, the DO concentration exhibited remarkable fluctuations over the spring-neap tidal cycles due to the significant differences in vertical diffusion. The results of a tide-sensitivity experiment indicated that without tide forcing, most of the shallow areas (average water depth < 5 m) in the PRE experienced severe and persistent hypoxia. The tides mainly enhanced mixing in the shallow areas, which led to higher vertical diffusion and enhanced replenishment of bottom DO. Full article
(This article belongs to the Special Issue Marine Biogeochemical Modeling)
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22 pages, 5168 KiB  
Article
A 1-Dimensional Sympagic–Pelagic–Benthic Transport Model (SPBM): Coupled Simulation of Ice, Water Column, and Sediment Biogeochemistry, Suitable for Arctic Applications
by Shamil Yakubov, Philip Wallhead, Elizaveta Protsenko, Evgeniy Yakushev, Svetlana Pakhomova and Holger Brix
Water 2019, 11(8), 1582; https://doi.org/10.3390/w11081582 - 30 Jul 2019
Cited by 3 | Viewed by 3945
Abstract
Marine biogeochemical processes can strongly interact with processes occurring in adjacent ice and sediments. This is especially likely in areas with shallow water and frequent ice cover, both of which are common in the Arctic. Modeling tools are therefore required to simulate coupled [...] Read more.
Marine biogeochemical processes can strongly interact with processes occurring in adjacent ice and sediments. This is especially likely in areas with shallow water and frequent ice cover, both of which are common in the Arctic. Modeling tools are therefore required to simulate coupled biogeochemical systems in ice, water, and sediment domains. We developed a 1D sympagic–pelagic–benthic transport model (SPBM) which uses input from physical model simulations to describe hydrodynamics and ice growth and modules from the Framework for Aquatic Biogeochemical Models (FABM) to construct a user-defined biogeochemical model. SPBM coupled with a biogeochemical model simulates the processes of vertical diffusion, sinking/burial, and biogeochemical transformations within and between the three domains. The potential utility of SPBM is demonstrated herein with two test runs using modules from the European regional seas ecosystem model (ERSEM) and the bottom-redox model biogeochemistry (BROM-biogeochemistry). The first run simulates multiple phytoplankton functional groups inhabiting the ice and water domains, while the second simulates detailed redox biogeochemistry in the ice, water, and sediments. SPBM is a flexible tool for integrated simulation of ice, water, and sediment biogeochemistry, and as such may help in producing well-parameterized biogeochemical models for regions with strong sympagic–pelagic–benthic interactions. Full article
(This article belongs to the Special Issue Marine Biogeochemical Modeling)
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Review

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31 pages, 9788 KiB  
Review
Accounting for Dissolved Organic Nutrients in an SPBEM-2 Model: Validation and Verification
by Alexey Isaev, Oksana Vladimirova, Tatjana Eremina, Vladimir Ryabchenko and Oleg Savchuk
Water 2020, 12(5), 1307; https://doi.org/10.3390/w12051307 - 05 May 2020
Cited by 4 | Viewed by 2190 | Correction
Abstract
Modern models of the Baltic Sea eutrophication describe only a bioavailable fraction of the nutrient input from land, thus introducing uncertainty into forcing. In order to alleviate this uncertainty, the coupled 3D hydrodynamical-biogeochemical St. Petersburg Eutrophication Model (SPBEM) has been expanded with variables [...] Read more.
Modern models of the Baltic Sea eutrophication describe only a bioavailable fraction of the nutrient input from land, thus introducing uncertainty into forcing. In order to alleviate this uncertainty, the coupled 3D hydrodynamical-biogeochemical St. Petersburg Eutrophication Model (SPBEM) has been expanded with variables representing dissolved organic nutrients. The model modification involves an explicit description of the labile and refractory fractions of dissolved organic nitrogen and phosphorus, in addition to their particulate forms, represented by the detritus variables. The modified SPBEM-2 allows for a full account of the total amounts of nutrients reported in field measurements and presented in environmental documents. Particularly, a model description of detritus, as the only bulk organic matter variable, has been replaced by more realistic parameterizations with adequate rates of settling and mineralization. The extensive validation and verification of the model performance in the Gulf of Finland from 2009 to 2014, based on over 4000 oceanographic stations, shows that SPBEM-2 plausibly reproduces all the major large-scale features and phenomena of the ecosystem dynamics in the Gulf of Finland, especially in its surface productive layer. These demonstrated capabilities of SPBEM-2 make the model a useful tool, both in studies of biogeochemical interactions and in historical and scenario simulations. Full article
(This article belongs to the Special Issue Marine Biogeochemical Modeling)
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