| 20 Oct 2025
A mechanistic model of hypoxia-driven benthic carbon cycling integrating microbial energetics and faunal mortality
Abstract. Hypoxia reduces the mineralization of organic detritus and increases mortality in benthic fauna, both of which alter carbon storage through complex changes in organic matter and calcium carbonate (CaCO₃) dynamics. To mechanistically assess these processes, we developed a new model that links oxic, suboxic, and anoxic mineralization pathways to microbial ATP production efficiency. This formulation was incorporated into the benthic–pelagic coupled model EMAGIN-B.C., resulting in an extended version designated EMAGIN-B.C.-MR (MR: mineralization rate). The model also includes revised mortality and metabolic suppression functions for benthic fauna under oxygen-deficient conditions and explicitly couples suspension-feeding benthos biomass with CaCO₃ production and burial fluxes. We applied EMAGIN-B.C.-MR to Tokyo Bay, a eutrophic coastal system prone to seasonal hypoxia, to simulate long-term changes in carbon cycling under hypoxic (0 mg L⁻¹) and non-hypoxic (5 mg L⁻¹) summer conditions. Results showed that hypoxia enhanced detritus storage and burial by both suppressing microbial degradation and reducing bioturbation and grazing due to suspension-feeding benthos mortality. Conversely, CaCO₃ production and burial declined owing to inhibited shell formation. These dynamics revealed that total carbon storage is shaped by interacting biogeochemical and ecological feedbacks, resulting in nonlinear trajectories under repeated hypoxic stress over decadal timescales. By integrating microbial energetics and oxygen-sensitive faunal responses, the EMAGIN-B.C.-MR model provides a mechanistic framework for assessing benthic carbon cycling under deoxygenation. This framework offers biogeochemical insights into the regulation of organic and inorganic carbon burial balance by oxygen availability – with implications for coastal carbon budgets, blue carbon management, and climate feedbacks – and is applicable to other oxygen-deficient environments such as eutrophic estuaries and semi-enclosed seas.
In this manuscript, the authors apply an *improved* model of benthic carbon cycling to estimate sedimentary carbon cycling and storage in Tokyo Bay. The authors claim to present a novel formulation of detritus mineralization that is based on ATP production efficiency of microbes performing oxic, suboxic and anoxic mineralization. This they argue is an improvement over other formulations that assume simple first-order kinetics.
While the paper makes a lot of claims to improve a model, it is very difficult to assess whether this is so. First of all, the model itself is very crudely explained, if at all: one has to assemble bits and pieces to deduce that the benthic model is probably a biogeochemical (early diagenetic?) model, but it is not stated which processes this model describes (e.g. which physical processes?). Units of parameters are rarely given, the parameter values are lacking, tables do not use proper symbols for parameters or variables, and so on. With so much information lacking in this manuscript, it is difficult to interpret the results.
The text has many inconsistencies. For instance, it is said that the model introduces ATP production rates and microbial biomass dynamics, so one would assume that microbes must die else their biomass would only increase - but this is unexplained. Also, based on the Figure 2, it appears that bacterial biomass is set as a fixed fraction of total detritus instead (equation 5), but how this is deduced is unclear.
From figure 2, equation 5, it appears that in this *new* formulation the detritus mineralisation is (again) first – order to detritus. So, as far as I can see, the new formulation is the same as the formulation that it replaces, i.e. first-order mineralisation. What is then the point?
The formalism is very non-standard, e.g. the use of the delta in figure 2 (to represent a derivative or what?). There is inconsistent use of symbols (e.g. T which is used for time is also used for temperature. Many things are unexplained, e.g. what is the “oxygen-nitrate concentration dependent function” in table 1, and so on. Based on all this, the underlying manuscript is not of sufficient quality to be admissible for publication.