| 04 Jun 2026
Spatial differentiation of carbon-control structures in urban coastal ecosystems under nutrient enrichment
Abstract. Urban coastal ecosystems, which are strongly influenced by human activities and elevated nutrient inputs, can contribute to climate-change mitigation through carbon uptake, fixation, and storage. However, it remains unclear how the underlying carbon-control structures governing these functions respond to nutrient enrichment, owing to the interactions of multiple biogeochemical processes across pelagic and benthic systems. In this study, we applied the benthic–pelagic coupled ecosystem model EMAGIN-B.C. ver. 2 to Tokyo Bay to examine how nutrient loading influences carbon cycling in urban coastal environments. To interpret these responses mechanistically, carbon cycling was organised into three paired flux balances representing carbon uptake (A/R), carbon fixation (F/U), and carbon storage (S/D). These functional pairs were analysed within a conceptual framework of a Dual Carbon Loop consisting of organic and carbonate pathways. Model simulations demonstrate that increased nutrient loading enhances atmospheric CO₂ uptake and pelagic carbon fixation. However, the dominant mechanisms controlling carbon cycling differ substantially across regions. In the estuarine region, nutrient enrichment amplified pelagic primary production, resulting in simultaneous increases in carbon uptake, fixation, and organic carbon burial. In the central bay, production and remineralization are intensified in tandem, indicating strong internal coupling of carbon fluxes. In contrast, tidal flats exhibited a transformation-dominated response wherein externally supplied organic matter was rapidly processed by benthic communities, thereby limiting net pelagic fixation while maintaining relatively stable carbonate storage and producing a system characterised more by transport, transformation, and redistribution than by new production. These contrasting responses indicate that identical nutrient forcing can produce distinct carbon-cycling behaviours depending on the regional ecosystem structure. We interpret these patterns as spatial differentiation of carbon-control structures governed by the relative balance of opposing carbon fluxes within the Dual Carbon Loop system. The proposed framework provides a mechanistic basis for understanding how nutrient management influences climate-mitigation functions in urban coastal ecosystems and offers a perspective for analysing shallow, nutrient-enriched coastal systems characterised by strong benthic–pelagic biogeochemical coupling.
Comments to Authors
This is an interesting paper examines how nutrient loading influences carbon cycling in Tokyo Bay, which is one of the typical examples of eutrophic, urban coastal water in Japan, by using a novel ecological model developed by authors. The authors define three carbon functions as carbon uptake, fixation, and storage and established a conceptual framework of a “Dual Carbon Loop” consisting of organic and carbonate pathways. They analytically demonstrated the dominant mechanisms of carbon cycling differ substantially across three regions: the estuarine regions directly influenced by river discharge, the central bay, and the tidal flat area rich in benthic organisms.
Main results of the contrast response in these regions to nutrient enrichment are remarkable.
Such findings are quite valuable and unique for the general readers of EGUsphere. The manuscript is well written and quite understandable. Thus, the reviewer suggests that this is acceptable, after slightly minor points to be corrected or incorporated as below.
The followings are some major or specific points that are to be considered for further revision.
1. General information of Tokyo Bay
The reviewer supposes that general readers of EGUsphere are unfamiliar with Tokyo Bay. So, its geographical/physical information such as the mean water depth, mean retention time, tidal range, and population of its watershed, as well as biological activity are to be presented in an appropriate place in the manuscript. Especially, the tidal flat information that the bay has relatively large sandy tidal flat rich in bivalve at least up to around 2000 would be important, because it explains why the authors consider tidal-flat region as one of the characteristic regions. It is strongly related to the relative preference of the “carbonate pathway” for the storage function in tidal-flat system, which is one of the most important results of this analysis.
2. Model functional forms and parameters
The authors extended the original EMAGIN-B.C. model with some improvements as shown in Line 139-142. In this manuscript, however, information on functional forms of physicochemical processes and the values of model parameters is not presented. At least, reference would be necessary.
Additionally, the reviewer was not able to catch carbon cycling after mortality of benthos. Flesh of suspension feeders will turn to be labile organic carbon and shell CaCO3 will be produced autonomously?
Additionally, how to evaluate partial pressure of CO2 in the air appeared in Eq (1). Constant value or seasonally different?
3. Introduction
Description on the historical regulation policy including total volume control for pollutants (TN and TP were added as the target since 2001, the beginning year of the of 5th total volume control) and recent social experiments on artificial seasonal nutrient supply from sewage treatment plants from Line 46 to Line 51 seems unclear. In this study, around the year 2000 was the baseline of the analysis. In this sense, more detailed description would be necessary, in order to make clearer the objectives and target period of this analysis. Also, up to our knowledge, nutrient management plan recently established in Hyogo and Aichi prefectures are not directly aimed to climate-change mitigation as described in Line 53.
For general readers of EGUsphesre, additional description on recent nutrient management policy in Japan would be informative, e.g., Uehara and Hidaka (Ocean and Coastal Management 244 (2023)).
4. Chapt.4: Model validation
In Line 206, the authors describe that “the correlations for PP and POC in the bottom layer are relatively low”. However, PP (Bottom) are missing both for Estuarine region and Central bay region in Figure 5. The reviewer wonders that such discrepancies may lead to inaccurate estimation of the burial rate and storage function.
5. Analysis
In this study, results of a kind of the sensitivity analysis with varying nutrient loading such as DIN and DIP are described precisely. How about organic loadings? They are kept constant in the analysis?
6. Temporal variation of model state variables
Main results of the temporal variations of model variables expressed as 1-day moving average are shown in Figures 11, 14, and 17. Each figure shows almost monthly or semi-monthly variations. Why was such a somewhat regular fluctuating pattern calculated?
Interesting features are found for the carbon storage flux, as shown in Figures 13 (Estuarine region) and 16 (Central-bay region). The amount of “organic carbon storage” seems almost constant temporally, whereas “CaCO3 storage” slightly varies corresponding to the timing of abrupt decline of suspension-feeders and deposit feeders, which may be the results of damages caused by hypoxia. These differences among the two storage pathways may be the results that the total depth of the sediment layer is deep enough for organic carbon distribution, but not for CaCO3. Different characteristics in the seasonal variations of these storage rates are found for the tidal-flat system. Both carbon and CaCO3 burial rates shows seasonal, almost sinusoidal variations as shown in Figure 19. Are these different temporal characteristics are originated from the effect of bio-turbation, or other mechanics?
7. Results of the tidal-flat region
As for carbon fixation function in tidal-flat region, the authors described in Line 772-774 that fixation is affected by hypoxia, as well as in the summary section Line 798-799. However, judging from DO concentration shown in figures 17 and 19, bottom DO seems high enough even in the bottom layer. Therefore, the reviewer does not understand such description. Additionally, the authors summarize that the tidal-flat region is characterized as transformation-dominated type: externally supplied organic matter is transformed and remineralized within the benthic system (Line 834). The reviewer well agreed this kind of general characteristics of sandy tidal flat rich in bivalve. However, the reviewer has difficulty to find out from which part of the manuscript can the authors conclude that the “externally supplied organic matter is transformed” is originated.
8. Minor points
(1) Unit of model variables and parameters
Model state variables and their units are listed in Table 1. However, related units in Figures 10 to 19 are not always the same. For example, units of state variables are in molar basis in Figures 11, 14, and 17, whereas these are in g basis for Table 1. Unification of units would be strongly recommended.
Additionally, units of biomass of benthos are expressed as m-2 in Figure 17, but cm-1 in Figures 16 and 19. These are all in cm-2 units? Please check them carefully.
(2) Section 2.1.4: Fractions of organic matter
Three fractions of organic matter are described, based on their different degradability. The term “Multi-G model for organic carbon degradation” would be more popular.
(3) Fixation-enhancement (-reduction) or Fixation-enhancing (-reducing)
“Fixation-enhancement” or “Fixation-reduction” is used in the semi-headings of 6.2.1 and 6.2.2, whereas “Fixation-enhancing” or “Fixation-reducing” is used in Figure 8. The same mixed terminology is found for Figure 8 and the semi-headings of 6.3.1 and 6.3.2. Please unify the terminology.