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Under anaerobic conditions, the final step of the mineralization of organic carbon results in the production of CH₄, which is carried out by a subset of the Archaea called methanogens (Bridgham et al., 2013; Megonigal et al., 2004). Methane emissions to the atmosphere reflect the balance between rates of CH₄ production (methanogenesis) and CH₄ oxidation (methanotrophy). Methane also can be produced abiotically by the burning of vegetation and peat, which can be especially important in years when large peatland fires occur (Kuwata et al., 2016). The last fifteen years have seen reports of aerobic CH₄ production by plants (Bruhn et al., 2012; Keppler et al., 2006), fungi (Lenhart et al., 2012), soil macrofauna (Kammann et al., 2009), and in the water column (Damm et al., 2010; Grossart et al., 2011); the importance of these pathways in wetlands is unknown. Globally, wetlands are the largest source of CH₄ to the atmosphere, with natural wetlands accounting for 30% of all CH₄ emissions (natural + anthropogenic) and paddies associated with rice cultivation adding another 5% to the total (Saunois et al., 2016). Although CH₄ is a powerful greenhouse gas, wetland CH₄ emissions are not contributing to recent climate change, except to the extent that these emissions have changed in the last ~250 years (Section 3.2).

Methanogenesis has the lowest yield of the terminal metabolic pathways so it tends to be most important when other terminal metabolic pathways are limited by low rates of electron acceptor resupply/regeneration and/or when supply rates of acetate, H₂, and other suitable electron donors are high enough to relieve competition with other anaerobic decomposers. The production of CH₄ typically requires anaerobic conditions, such that rates of CH₄ emissions are inversely related to soil O₂ levels (Smyth et al., 2019) and rates of methanogenesis drop sharply in response to decreases in wetland water levels (MacDonald et al., 1998; T. R. Moore & Knowles, 1989). Oxygen inputs can stimulate aerobic respiration (Mueller, Jensen et al., 2016; A. A. Wolf et al., 2007) and/or reoxidize alternate terminal electron acceptors (Laanbroek, 2010; Neubauer, Givler et al., 2005), such that methanogens may be unable to successfully compete for electron donors. Rates of methanogenesis can also be suppressed by the delivery of alternate terminal electron acceptors – largely NO₃^–, Fe(III), and/or SO₄^2– – from saltwater intrusion (L. G. Chambers et al., 2013; Kroeger et al., 2017; Neubauer et al., 2013), fertilizer runoff (Bodelier, 2011; Kim et al., 2015), atmospheric deposition (Gauci et al., 2004; Watson & Nedwell, 1998), and river flooding (Luo et al., 2020).

There is tight coupling between plant activity and CH₄ emissions (Whiting & Chanton, 1993), in part because plants produce low molecular weight organic molecules that can be used by methanogens (Dorodnikov et al., 2011; Megonigal et al., 1999). Plants can also prime the decomposition of soil organic matter (Basiliko et al., 2012; Bernal et al., 2017), thus providing substrates that fuel methanogenesis. Plant species composition affects CH₄ cycling (Kao‐Kniffin et al., 2010) due to differences in the reactivity of carbon supplied by each vegetation type (e.g., Chanton et al., 2008). Humic substances inhibit the production of CH₄, either through direct competition between microbial humic reducers and methanogens or, alternately, by abiotically reoxidizing reduced sulfur compounds and therefore supporting sulfate reducers that outcompete the methanogens (Heitmann et al., 2007; Keller, Weisenhorn et al., 2009). The polyphenol sphagnum acid and the polysaccharide sphagnan, both of which are produced by Sphagnum mosses, can interfere with methanogenic activity (van Breemen, 1995; Bridgham et al., 2013) and help explain why some peatlands have low rates of methanogenesis despite low concentrations of inorganic terminal electron acceptors such as Fe(III) and SO₄^2– (Galand et al., 2010; Keller & Bridgham, 2007; Vile et al., 2003).

Methanotrophy, which oxidizes CH₄ to CO₂, can proceed aerobically using O₂ as the electron acceptor or anaerobically using the entire suite of alternate terminal electron acceptors (Bridgham et al., 2013). Whether a wetland emits gas as CH₄ or CO₂ is unimportant in the context of a wetland’s carbon budget but has large implications for the radiative balance of the wetland. On a global basis, the aerobic oxidation of CH₄ can prevent 40–70% of the CH₄ produced in wetlands from reaching the atmosphere (Megonigal et al., 2004), but it is rare that annual wetland CH₄ oxidation exceeds methanogenesis (that is, very few wetlands are net sinks for CH₄; Bridgham et al., 2006; Harriss et al., 1982; Petrescu et al., 2015). Beyond the first‐order control that the aerobic oxidation of CH₄ requires O₂, the availability of O₂ can regulate methanotrophy when there is a narrow aerobic zone, when CH₄ spends little time in the aerobic zone before being emitted to the atmosphere (as would happen when most CH₄ emissions are via ebullition and/or transport through plants), and/or when rates of CH₄ production are high (Megonigal et al., 2004). Conversely, methanotrophy can be limited by the availability of CH₄ when rates of CH₄ production are low and/or there is a large diffusive aerobic zone (Megonigal & Schlesinger, 2002). High concentrations of ammonium (NH₄⁺) inhibit methane oxidation because both CH₄ and NH₄⁺ compete for the same sites on the enzyme methane monooxygenase (Bodelier & Frenzel, 1999; Crill et al., 1994). However, it is also possible that methanotrophs can be nitrogen limited, such that fertilization increases rates of CH₄ oxidation (Bodelier et al., 2000). Like all biological processes, rates of aerobic methanotrophy increase with increasing temperatures, although methanotrophy is less sensitive to temperature than is methanogenesis (Segers, 1998).

Rates of the anaerobic oxidation of CH₄ can be of the same magnitude as aerobic oxidation (Smemo & Yavitt, 2007) and, globally, may be comparable to the total CH₄ emissions from freshwater wetlands (Segarra et al., 2015). Rates of anaerobic oxidation of CH₄ in wetlands and wet soils are correlated with rates of CH₄ production (Blazewicz et al., 2012; Segarra et al., 2015). The anaerobic oxidation of CH₄ can be coupled with the reduction of NO₃^– or nitrite (NO₂^–) (Hu et al., 2014; Raghoebarsing et al., 2006), Mn(III, IV) and Fe(III) (Beal et al., 2009; Egger et al., 2015), humic acids (Smemo & Yavitt, 2011; Valenzuela et al., 2017), or SO₄^2– (Egger et al., 2015; Knittel & Boetius, 2009). It is not always straightforward to identify which electron acceptors drive the oxidation of CH₄ (Gupta et al., 2013; Segarra et al., 2013), but the electron acceptor likely varies in freshwater vs. saline wetlands, organic vs. mineral soils, and oligotrophic vs. eutrophic sites, as is the case for terminal metabolism (see Anaerobic metabolism in Section 3.3.2).