13.3: Carbon dioxide

Microorganisms can produce and consume carbon dioxide and thus help determine carbon dioxide concentrations within their environments. Microorganisms that can help lower carbon dioxide levels include autotrophs, which form organic carbon from carbon dioxide in biosynthesis reactions (Section 4.3), as well as acetogens and methanogens that use carbon dioxide as an electron acceptor (Section 5.1.3 and 5.1.4). Note that methanogens also produce methane, which is itself a potent greenhouse gas. In contrast, microorganisms that can cause carbon dioxide levels to increase in their environments include chemoorganotrophs, which oxidize organic carbon and can produce carbon dioxide (Section 4.3).

In addition to these direct impacts on carbon dioxide levels, microorganisms also influence carbon dioxide concentrations in water indirectly by affecting pH (Kirk et al., 2013). Specifically, as illustrated by Figure \(13.5\), microbial reactions that consume hydrogen ions can help drive the following reactions forward, converting dissolved carbon dioxide into bicarbonate and then carbonate: \[\begin{align} & \text{CO}_{2} \ (aq) + \text{H}_{2} \text{O} \longleftrightarrow \text{H}^{+} + \text{HCO}_{3}^{-} \\ & \text{HCO}_{3}^{-} \longleftrightarrow \text{H}^{+} + \text{CO}_{3}^{2-} \end{align}\]

In pushing the reactions forward, microorganisms help store inorganic carbon in aqueous solutions as bicarbonate and carbonate, which do not partition into a gas phase like carbon dioxide. Moreover, bicarbonate and carbonate can also react with other ions and precipitate as carbonate minerals, thus sequestering inorganic carbon as a solid. Conversely, microbial reactions that produce hydrogen ions can cause carbonate minerals to dissolve and push the reactions above in the opposite direction, increasing carbon dioxide concentrations.

By affecting the carbon dioxide content of their environments, microorganisms can influence how much carbon dioxide is taken up or lost to the atmosphere. This impact is a possibility even if the environment hosting the microbes is not physically connected to the atmosphere because transport can bridge the gap between the microbe’s environment and the atmosphere. This relationship also applies to the other gases considered in this chapter.

To place these relationships in an environmental context, we first consider the fate of carbon dioxide generated in soils. Large amounts of carbon dioxide are produced in soils by plant respiration and microbial degradation of organic matter, which we can collectively refer to as soil respiration. The carbon dioxide that is produced can diffuse out of soil aggregates into macropores that connect to the atmosphere. Partial pressures of carbon dioxide in soil gas are often 10 to 100 times higher than the atmosphere (Brook et al., 1983; Macpherson, 2009). As such, it is commonly favorable for them to emit carbon dioxide to the atmosphere. Much of the carbon dioxide produced in soils can also be transported into the subsurface during groundwater recharge (Fig. \(13.6\)). A recent study at the Santa Catalina Mountains-Jemez River Basin Critical Zone Observatory, for example, found that two-thirds of the carbon dioxide from soil respiration was transported into the subsurface (Sanchez-Canete et al., 2018).

As carbon dioxide from soil makes its way through the subsurface, a portion is consumed by chemical and microbial reactions. Some is typically consumed by mineral weathering (Section 11.4.2). Significant quantities can also be fixed by autotrophs. A recent study by Overholt et al., (2022), for example, concluded that carbon fixation rates by microorganisms in carbonate aquifers are similar to those measured in low-nutrient marine surface waters. In addition to carbon fixation, microorganisms can also affect carbon dioxide concentration by using it as an electron acceptor (e.g., methanogenesis, acetogenesis) and by catalyzing reactions that produce or consume hydrogen ions and thus affect dissolved inorganic carbon speciation (reactions \(\PageIndex{1}\) and \(\PageIndex{2}\)).

If the groundwater eventually discharges into a stream or some other surface water body, some of the remaining soil carbon dioxide that is moving with it may then be lost to the atmosphere. Alternatively, surficial aquatic habitats can also take in carbon dioxide from the atmosphere. Major factors that determine whether it is favorable for an aquatic habitat to be a source or a sink for carbon dioxide include the concentration of dissolved carbon dioxide \(\left(\text{CO}_{2} \ (aq)\right)\) in the water, the partial pressure of carbon dioxide in the gas phase in contact with the water \(\left(\text{CO}_{2} \ (g)\right)\), and the temperature of the water (see Box \(13.1\) for more on gas solubility). If the water contains a higher dissolved carbon dioxide concentration than it would if it were in equilibrium with the gas phase, then it is favorable for the water to emit carbon dioxide gas. In other words, we can say that the water is supersaturated with carbon dioxide relative to the atmosphere. Indeed, water in many streams and rivers is supersaturated with carbon dioxide relative to atmospheric levels (Butman and Raymond, 2011), with groundwater inputs, instream metabolism, and riparian wetlands serving as major carbon dioxide sources (Kirk and Cohen, 2023).

The example above considers the fate of carbon dioxide that is produced near the surface, but what about carbon dioxide emanating from deep within the Earth? Microorganisms appear to also play a significant role in affecting the fate of that carbon dioxide as well, effectively forming a biological filter that decreases how much carbon dioxide is able to reach the surface.

As an example, we briefly consider recent studies by Fullerton et al. (2021) and Rodgers et al. (2022) along the Costa Rican convergent margin. There, the Cocos plate is actively subducting beneath the Caribbean plate. As the Cocos plate subducts, large fluxes of carbon dioxide and other volatiles are released into the overlying Caribbean plate, where they make their way upward toward the surface and atmosphere. The researchers considered how these fluids impact the subsurface biosphere by examining the microbiology and geochemistry of hot springs near the convergent margin. Their findings indicate that subsurface chemolithotrophic microorganisms fix large quantities, as much as \(1.4 \times 10^{9}\) mol per year, of slab-derived carbon dioxide in the subsurface, and thus significantly alter fluxes of carbon at the plate margin. This microbial carbon sink operates alongside other sinks at the plate margin, including calcite precipitation, formation of dissolved inorganic carbon species such as bicarbonate and carbonate, and production of dissolved organic carbon (Barry et al., 2019; de Moor et al., 2017).

Box \(13.1\): Henry's Law

Henry’s Law states that the amount of dissolved gas in a solution is proportional to its partial pressure above the solution. Thus, we can use this relationship to understand how much gas will dissolve into water if the water and an adjacent gas phase are allowed to equilibrate. For water that is in contact with the atmosphere, this relationship can tell us whether the water would be a source or sink for atmospheric gases.

For an example calculation, consider the following reaction, which describes dissolution of carbon dioxide in water: \[\text{CO}_{2} \ (g) \longleftrightarrow \text{CO}_{2} \ (aq) \nonumber\]

The equilibrium constant \((K)\) for this reaction, like all reactions, is temperature dependent. The log value of K at \(15^{\circ} \text{C}\) is \(-1.3240\) (see Appendix A). The mass action equation for the reaction at \(15^{\circ} \text{C}\) is as follows: \[-1.3240 = -\log \left[\text{CO}_{2} (g)\right] + \log \left[\text{CO}_{2} (aq)\right] \nonumber\]

Note that brackets indicate activity for dissolved species and fugacity for gases. For a review of these concepts and mass action, please see Chapter 8. If we assume that activity and fugacity are equivalent to molar concentration and partial pressure in atmospheres, respectively, and insert a value for carbon dioxide gas consistent with atmospheric levels \((\sim 0.0004 \ \text{atm})\), then the equation becomes: \[-1.3240 = -\log (0.0004) + \log \left(\text{CO}_{2} (aq)\right) \nonumber\]

Solving for dissolved carbon dioxide concentration gives \[\log \left(\text{CO}_{2} (aq)\right) = -1.3240 + \log (0.0004) = -4.722 \nonumber\]

The antilog value of this result gives a dissolve carbon dioxide concentration of \(1.9 \times 10^{-5} \ \text{M}\) or \(19 \ \mu \text{M}\). Thus, if water at \(15^{\circ} \text{C}\) has a concentration of carbon dioxide that exceeds this level, then the water is supersaturated with carbon dioxide and it is favorable for the water to lose carbon dioxide to the atmosphere. Alternatively, if a water at \(15^{\circ} \text{C}\) has a concentration below this level, then it is undersaturated with carbon dioxide and favorable for the solution to dissolve more from the atmosphere.

Box \(13.2\): Practice Henry's Law

Practice 13.1. For more practice, recalculate the dissolved carbon dioxide concentration that would exist in a solution equilibrated with the atmosphere at \(5^{\circ}\text{C}\) \((\log K = -1.2000)\) and \(25^{\circ} \text{C}\) \((\log K = - 1.4524)\). How does the equilibrium dissolved carbon dioxide concentration change with temperature? Answers are provided at the end of this chapter.

Practice 13.2. How do the solubilities of carbon dioxide and methane compare? Assume a water at \(15^{\circ}\text{C}\) is in equilibrium with a gas phase that contains \(0.0001 \ \text{atm}\) of each gas. What are the dissolved concentrations of each gas in the water? Which gas is more soluble? For the calculation, assume activity equals concentration in molar units and fugacity equals partial pressure in atmospheres. Gas dissolution reactions and information needed to calculate \(\log K\) values at various temperatures are available in Appendix A.

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