| 10 Feb 2026
Interactive Simulation of Methane and Hydrogen Soil Deposition in ECHAM5/MESSy Atmospheric Chemistry Model (EMAC) v2.55 with the new Submodel BIODEP (v1.0)
Abstract. Methane (CH4) and hydrogen (H2) play critical roles in atmospheric chemistry and climate processes. CH4 is a powerful greenhouse gas, whereas H2, although not a greenhouse gas itself, indirectly affects radiative forcing by modifying the atmosphere's oxidative capacity and therefore the concentrations of CH4, ozone (O3) and stratospheric water vapor. Hydrogen is predominantly removed through microbial uptake in soils, while approximately 6 % of CH4 is taken up by soils, a factor that contributes significantly to its overall atmospheric budget. Soil uptake depends on various soil characteristics, including type, temperature, moisture, and for CH4, nitrogen deposition. Accurately representing these influences requires a detailed understanding of both atmospheric conditions and land surface and hydrological properties. However, many Earth system models currently use fixed soil deposition rates for H2 and CH4, without accounting for variations in soil properties. We present BIODEP, a new biogenic deposition submodel that has been integrated into the ECHAM/MESSy Atmospheric Chemistry model (EMAC). BIODEP dynamically simulates the uptake of CH4 and H2 by soil, based on local meteorological and soil conditions. With BIODEP, the soil sinks of CH4 and H2 are updated online based on the meteorological conditions, atmospheric composition, and land surface properties provided by the EMAC model. The EMAC model is coupled to the JSBACH land surface and vegetation model. This allows for a consistent and interactive treatment of soil sinks within the atmospheric chemistry model. Modeled global mean soil uptakes of 62.7 ± 11.7 Tg yr−1 for H2 and 30.2 ± 4.8 Tg yr−1 for CH4 are consistent with previous studies, and the resulting atmospheric mixing ratios show good agreement with observations from the NOAA GML Carbon Cycle Cooperative Global Air Sampling Network, evaluated over the period 2009–2019. In addition, comparison with column-averaged CH4 (XCH4) observations from the Greenhouse Gases Observing Satellite (GOSAT) demonstrates that EMAC reproduces the global and zonal-scale methane distribution with small mean biases, providing independent support for the accuracy of the simulated soil methane sink. This development makes EMAC a state-of-the-art model to interactively simulate atmospheric chemistry, including both the soil sinks of CH4 and H2. This enables more consistent simulation of trace gas budgets and an improved assessment of the feedbacks between land surface processes, atmospheric composition, and future climate and emission scenarios.
Competing interests: At least one of the (co-)authors is a member of the editorial board of Geoscientific Model Development.
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Review of “Interactive simulation of methane and hydrogen soil deposition in ECHAM5/MESSy Atmospheric Chemistry Model (EMAC) v2.55 with the new submodel BIODEP (v1.0), by Anna Martin et al.
General comments
Results from a new global model which simulates the atmospheric chemistry and land surface fluxes of hydrogen and methane is presented. Some of the equations used in the model are unclear (in particular the units used – see specific comments below). The model does a reasonable job at simulating the global distribution of H2 and CH4, but its seasonality, especially in the Northern Hemisphere, appears less well simulated (although the authors claim otherwise). Although the soil deposition schemes for the two gases are described in some detail, the other main determinant of seasonality (reaction with OH in the atmosphere) is not discussed, and it seems that the relative strengths of these two sinks is perhaps incorrectly described by the model. I think this needs to be investigated before the paper can be accepted.
If the equations describing the model can be clarified, and some extra discussion about the atmospheric sinks, and their interplay with the soil sinks, can be included then this paper should be suitable for publication.
Specific comments
l40 H2 sources (not emissions). Both % values are over-precise, given the uncertainties.
l58 How does the interactive soil moisture compare to ERA5 (and reality)?
P3 I don’t think Table 1 is referred to anywhere in the text.
I’m a bit confused how the COVID-19 pandemic resulted in data gaps before 2020 – but may it is possible if it disrupted data analysis of data collected earlier? Please clarify.
l120 I don’t understand the scaling applied to CH4 emissions – please clarify.
l124 of the Appendix
P6 Equations 1-3 and surrounding text: Units are only partially given (e.g., what are the units of A, B and J?). The units of eq.2 mixes ppbv and mg m-3. Please clarify and make these equations dimensionally balance.
l147 Clarify that GT is (presumably) also dimensionless.
P6 Equation 6: The volumetric soil water must be a fraction, not a %? Please clarify.
l160 Presumably these scaling factors are also dimensionless.
L166 values
L170 Suggest clarify that you mean soil oxidation rate (as opposed to atmospheric oxidation rate, which is more commonly discussed for methane).
L174 Suggest state that the scheme yields an optimum soil moisture content of 0.2.
P8 Equation 12 isn’t dimensionally balanced. Please clarify.
P9 Figure 1b: I was expecting the soil response factor rT to vary between 0-1 (like rSM and rN; and based on equation 7), but it varies from 0-3.5. Please explain.
P9 Figure 1 caption: I am unsure what the “initial bulk density” of 14.7 kg m-3 is, please clarify.
L221 Aeolian.
L228 rate -> velocity
L228 The value in Figure 2 is 0.032 cm, not 0.033 cm
P11 Table 3. I don’t understand what is meant by atmospheric burden “at surface” and “total column”. Surely the atmospheric burden is just the total mass in the atmosphere, and can’t be qualified like that?
L266 4a should be either 3a or 4b?
L269 4b should be 4a?
L270 I disagree that the CH4 seasonal cycle “shows generally good agreement”. In Figure 4a, observations show a summer minimum in the Northern Hemisphere, whilst the model has a late summer maximum. The Southern Hemisphere seasonal cycle is not very clear from Figure 4a (partly due to the poor choice of scale), but is also not great.
I found it surprising that the discussion around Figure 4 and the seasonal cycle didn’t include mention of the atmospheric oxidation of CH4 by OH as a significant driver. Whether atmospheric oxidation or soil uptake dominates the seasonality is a key question, and this probably varies with sites. I’d expect there to be some difference between hemispheres, as there is much less land in the SH, so it is more likely to be more dominated by the atmospheric OH sink. It looks to me that your model simulations do not have quite the right balance between these two drivers of seasonality in CH4.
L273 ‘likely’ – you could check whether outlier stations are having an influence – then you would know one way or the other.
P14 Figure 4a: You have not chosen a good scale to clearly illustrate the seasonal cycle.
P14 Figure 4: Are all the plots averages over 2009-2019?
P14 Figure 4b: Would be clearer if you used different shaped symbols for the model and observations (e.g., cross and circle).
P18 Figure 7: Similarly to CH4, the modelled seasonal cycle of H2 in the NH is nowhere near in phase with the measurements, suggesting something is not right. Again, there is a balance between soil deposition and reaction with OH, but for H2, the soil sink is now dominant. Tardito Chaudhri and Stevenson (2025: https://acp.copernicus.org/articles/25/7369/2025) have also looked at this.
L381 “the model captures the general shape of the observed seasonal cycles”. Maybe it gets the shape, but the phase is shifted several months.