Probably the most intensely investigated factor regulating methane uptake is soil nitrogen. Nitrogen fertilization is usually inhibitory to atmospheric methane oxidation. Inhibition mechanisms are complex, and are outlined briefly in this chapter. However, in some cases nitrogen fertilization is not inhibitory, and in rare instances it even stimulates methane oxidation. Nitrogen is an essential nutrient that is frequently limiting in soils. In rice paddies, where methane concentrations are high and rice plants efficiently compete with bacteria for nitrogen, methanotrophs are nitro gen-limited and their activity is stimulated by fertilization (Bodelier et al., 2000). In aerobic upland soils where less methane is available than in rice paddies, nitrogen limitation is probably less intense. However, both stimulatory and inhibitory effects of nitrogen have been observed, the balance of which is specific to the site, fertilizer dosage and fertilizer type. The vast number of studies on these effects are too numerous to list here, and the reader is referred to the review of Bodelier and Laanbroek (2004).
Fertilizers can inhibit methanotrophs through non-specific salt effects (Nesbit and Breitenbeck, 1992; Adamsen and King, 1993; Dunfield and Knowles, 1995; Gulledge and Schimel, 1998b; Saari et al., 2004), but ammonia (NH3) has a more specific effect as well. Ammonia is a structural analogue of methane and competes for the active site of the methane monooxygenase (MMO) enzyme. Typical competitive inhibition patterns have been observed in pure cultures of methanotrophic bacteria (O'Neill and Wilkinson, 1977; Carlsen et al., 1991) and in soil (Dunfield and Knowles, 1995). The major inhibitory form is NH3 rather than NH+, so the degree of inhibition depends on pH (O'Neill and Wilkinson, 1977; Carlsen et al., 1991). Competition for the MMO active site is obviously relieved as soon as the offending NH3 is nitrified or removed from soil, but inhibition of methane oxidation often persists (Bodelier and Laanbroek, 2004). Active-site competition therefore does not completely explain observed patterns of inhibition. King and Schnell (1994a) proposed that the inhibitory effect of NH3 in soils is primarily due to the production of nitrite (NO-). Ammonia is oxidized by methanotrophs to NO- via hydroxylamine (NH2OH). NO- is a general toxin and additions of NO2- inhibit CH4 oxidation in soil and in methanotroph cultures (O'Neill and Wilkinson, 1977; King and Schnell, 1994b; Schnell and King, 1994; Dunfield and Knowles, 1995). The bacteria recover poorly from NO2- toxicity (King and Schnell, 1994b; Schnell and King, 1994). With this model, enzyme competition is the root but not the direct cause of inhibition by ammonium fertilizers.
As ammonium fertilizers include a counteranion to NH+, the effect of the fertilizer is a combined result of competitive ammonia oxidation plus a non-competitive salt effect (Gulledge and Schimel, 1998b). Generally, because of the competitive effect, ammonia is the most inhibitory form of fertilizer nitrogen, but this is not always the case. Nitrate is a more potent inhibitor than ammonia in some soils, perhaps via NO-produced from nitrate reduction (Wang and Ineson, 2003; Reay and Nedwell, 2004).
A study of the Broadbalk wheat experiment in the UK found a decreased soil methane oxidation potential after 140 years of NH4NO3 applications, but no significant effect of a single fertilization event (Hutsch et al., 1993). In long-term experiments, organic nitrogen additions are often less inhibitory than inorganic nitrogen additions, or may even stimulate methane oxidation (Hutsch et al., 1993; Willison et al., 1996). These studies show that inhibition by nitrogen fertilizers is mediated not only by immediate effects on methanotrophic bacteria, but also by long-term changes in soil chemistry, microbial populations or ecological interactions.
Different experiments show different patterns: methane oxidation may be stimulated, unaffected, inhibited immediately after fertilization or only after several years of fertilization (Bodelier and Laanbroek, 2004). There are considerable study-specific and site-specific factors that determine the effects of nitrogen, including amount of fertilizer applied, type of fertilizer, degree of NH+ fixation on soil minerals, degree of nitrogen limitation, rate of nitrogen uptake by plants, nitrification and denitrification rates, depth to which the fertilizer penetrates, cation exchange capacity and soil pH. Theoretically, the pattern of inhibition may also depend on the particular methanotrophic species present. Gulledge and Schimel (1998b) proposed that different inhibition patterns observed in several soils were an indication that different meth-anotrophic species were present. It now appears that there are indeed several different species of atmospheric methane oxidiz-ers (Section 10.5).
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