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Eh and methanogenesis


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Using GWB software, I’m trying to reproduce the in-situ transition of functional microbial communities with thermodynamic ladder.

According to the existing advices in this forum, I have started trial under the simplified condition.

I attached the React file for the trial.


The main concept of the trial is to reproduce the decrease of Eh with consumption of O2(aq) by aerobes in closed chamber.

Next is that carbonate and hydrogen are used as resources for hydrogenotrophic methanogenesis.

Analysis time was basically for 5 days (besides, 1 day, 5 month, and so on).

Thermo.com.V8.R6+.dat was used with the decoupling of Lactic_acid(aq)/HCO3-, H2(aq)/H+, and Methane(aq)/HCO3-..

Lactic_acid(aq) was swapped to Lactate.


Results were as below:

- The decrease of Eh was not observed in the result of the above simulation although O2(aq) concentration and Lactic_acid(aq) concentration decreased until zero with the increase of Aerobe biomass. Rather, the Eh acutely increased.

- Though HCO3- and H+ were provided to the system, they seemed to be used by methanogen.


I have several questions.

Concerning the decrease of Eh in the system and the consistency between change of Eh and methanogenesis.


I think that the ‘Eh’ in the Gtplot seems to reflect ‘Eh(O2(aq)/H2O)’ only, without reflecting other redox couplings, for example ‘Eh(H+/H2(aq)’, ‘Eh(Lactic_acid(aq)/Methane(aq)’, and so on. I hope to express the anaerobic condition (around -250 mV) for methanogenesis after O2(aq) is completely consumed. How should I revise the React setting? In addition, what does the ‘Eh’ in the Gtplot represent? Mixed potential or Eh(O2(aq)/H2O) only?


I expect that the methanogenesis which needs extremely low Eh (around -250 mV) starts after all of O2 is consumed. However, methanogen didn’t start after O2 consumption in the simulation. On the other hand, when I input larger value of H2(aq) (ex. 1e-5), methanogenesis have started in spite of the fact that there remained O2(aq) in the system and Eh value was so high (around +700 mV). Could anyone give me advices regarding the decrease of Eh in the system and the consistency between change of Eh and methanogenesis?


In this case, can the helper function in rate law option on the Kinetic microbe-Aerobe be available for solving this problem? If so, could you give me any example of rate raw available for this case?


Concerning the consumption of H2(aq) or H+.


Hydrogenotrophic methanogenesis is shown by the equation as below.

HCO3- + 4*H2(aq) + H+ -> Methane(aq) + 3*H2O

However, hydrogen released from Aerobic respiration seems not to be used in methanogenesis in the simulation. Because H+ in fluid didn’t decrease and H2(aq) concentration was constant for any analysis time. Of course, biomass of methanogen decreased according to only decay constant.

Even if I set hydrogen of equation by unifying in either H2(aq) or H+ in the all kinetics for microbes, it results in charge imbalance.

How should I handle Basis and Reactants to describe hydrogenotrophic methanogenesis?


Thank you for your consideration.


Best regards,




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Hi Maki,


In Gtplot, "Eh" generally refers to the "Master Eh" of the system. In an equilibrium model, you might set an overall oxidation state for your initial system (i.e. DO, Eh, O2(g) fugacity, aSO4--/aHS-, ...). This will affect all coupled redox pairs. When you start decoupling redox pairs, however, these are considered separately from the "Master Eh". Since you've decoupled Lactate, CH4, and H2, there are no more coupled redox reactions in your system, and Eh becomes identical to the Eh(O2(aq)/H2O).


Keep in mind that Eh is relative to pH (try comparing the slanted lines of an Eh-pH diagram with the flat lines of a log f O2-pH diagram). Your system is becoming more acidic with reaction progress, so even though oxygen fugacity is decreasing, the "Eh" actually goes up a little. If you look at O2 fugacity, you'll see the decrease in oxidation state, though not by the amount you expect. Although most of the oxidant O2(aq) has been removed from your system, you don't have enough reductant to drive the redox state down to very low values.


If you look at FD and TPF for the methanogen, you'll see that these are very close to zero (the reaction is limited both kinetically and thermodynamically). This is why your methanogen is not active. You need more H2(aq) in your system. Although reaction is possible at H2(aq) = 1e-5 molal, it won't proceed very far since that is still very little H2(aq). The overall Eh (or Eh(O2(aq)/H2O) in this model) has no effect in the model on the H2(aq)/H+ redox state, so that's why it is possible for the methanogen to be active even in the presence of oxygen.


If the methanogen should be inhibited by oxygen physiologically, you could probably use a rate law script. For example, something like:


IF molality"O2(aq)" > 0.001, THEN 20 ELSE 40

20: rate = 0

40: rate = rate_con * ...


You are correct that H+ is produced by the lactate oxidation. The methanogen could use this H+, along with HCO3- and H2(aq) to drive its metabolism. However, 1e-20 molal H2(aq) is simply not enough for this to be possible. The way you've written the reaction for the methanogen looks correct. You just need a source of H2(aq) in your system.


Hope this helps,


Brian Farrell

Aqueous Solutions LLC

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Thank you for your detailed reply.



I’m complicated with the problem in relation to decoupling of redox pair and Basis setting. I understand that decoupled redox pair is considered separately from the “Master Eh”. In the case, however, I think that users cannot set the related Basis (for example Lactic_acid(aq)) for microbial kinetics in the initial system.

How do I handle their setting in the case that I would like to set the microbial kinetics and I would like to consider electron donor or acceptor for Master Eh value at the same time? Or should I adopt the Eh value of specific redox couple (Eh(Lactic_acid(aq)/Methane(aq)) in my example) as Master Eh?



I have tried the rate law script as below.

IF molality ("O2(aq)") > 0.00001 THEN 20 ELSE 40

20: rate = 0.0


40: rate = rate_con * biomass * FD * FA * TPF

60: RETURN rate

Unfortunately, the calculation didn’t converge with the message “N-R didn't converge after 400 its., maximum residual = 3.97e+119, Xi = 0.0243”.

Even if I exchanged the value of O2(aq) molality many times, neither that worked.


If the script or input values has any problem, could you point out it?


Best regards,



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Hi Maki,


If you'd like to independently constrain the initial concentrations of species in various redox states, you'll need to decouple the appropriate redox pair(s). For example, if both lactic acid and HCO3- are present in your system, but not at equilibrium with the "Master Eh," then you'll need to decouple the Lactic_acid(aq)/HCO3- redox pair. Setting a "Master Eh" (O2(aq), Eh, pe, etc.) will have no effect on the distribution of mass between lactic acid and HCO3-. Only a kinetic rate law (redox or microbial) will control the manner in which a chemical species is transformed from one redox state to another.


Because the Master Eh will only affect those redox couples which remain coupled, it doesn't really have meaning for decoupled redox pairs. You should probably track the Eh of the redox pairs that you are interested in.




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  • 2 weeks later...

Hi Brian,


Sorry for delay reply.


I understand that “Master Eh” (O2(aq), Eh, pe) constrains coupled redox pairs only.


On the other hand, what decides “Master Eh” after reaction?

In many cases, “Master Eh” seems to have equaled to “Eh (O2(aq)/H2O)” in the Xtplot and Gtplot even if any or no redox couples are decoupled.


Does this fact mean that although “Master Eh” in GWB constrains the distribution of oxidant and reductant in each of redox pairs, the distribution of oxidant and reductant in each of redox pairs doesn’t control “Master Eh” even after kinetic reaction is carried out, and only “Eh (O2(aq)/H2O)” is cosidered in “Master Eh”?

If I set the kinetic sulfate reduction (Acetate + SO4-- -> 2*HCO3- + HS-) under the condition which O2(aq) concentration is given and I don’t decouple HS-/SO4--, is “Master Eh” calculated by considering “Eh(HS-/SO4--)”?

Though I can track the Eh of the redox pairs that I am interested in as you suggested, can I track “Master Eh” which is calculated based on redox pairs?


If my explanation is not clear, could you let me know?


Best regards,



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