Most cultivated methanotrophs can oxidize atmospheric methane. However, most species lose this ability within a few days when exposed to only 1.7 ppmv methane (Roslev and King, 1994; Schnell and King, 1995; Knief and Dunfield, 2005). Presumably, as long as cells have recently seen high methane (or methanol) concentrations, they have sufficient reductant to use as a co-substrate for MMO function. However, because atmospheric methane does not supply enough maintenance energy, the amount of reducing power decreases with time and cells become inactive. The minimum methane mixing ratio needed for maintenance ranges from 10 to more than 1000 ppmv, but there are differences among species (Knief and Dunfield, 2005). The most oligotrophic methanotrophs known are some strains of Methylocystis. These have the highest specific affinity, need only about 10-100 ppmv methane for growth and oxidize atmospheric methane for several months without loss of activity (Knief and Dunfield, 2005). Presumably the reductant for
MMO during atmospheric methane oxidation comes from storage compounds. Methylocystis therefore fit the 'flush feeder' profile described in Section 10.5.2.
Some cultivated Methylocystis can therefore theoretically contribute to atmospheric methane oxidation in soils. These bacteria are most likely to be important in soils such as wet gleysols where ephemeral methanogene-sis occurs. In some gleysols, population sizes of Methylocystis are sufficient to account for atmospheric methane oxidation rates (Horz et al., 2002; Knief et al., 2005b). Methylocystis can also display a pseudo high-affinity activity similar to that observed in situ in these soils (Dunfield and Conrad, 2000). However, Methylocystis need additional energy sources for long-term survival, and populations of this bacterium in many forest soils are too low to account for measured activity (Knief and Dunfield, 2005; Kolb et al., 2005). They may be important in some sites, but in forest soils with high methane oxidation rates uncultivated methanotrophs such as USCa and USCg are probably more important.
so there may be other, undetected groups of methanotrophs in soils. Many unidentified phylogenetic groups of pmoA that are distant from any cultivated species have already been detected in various soils (Holmes et al., 1999; Henckel et al., 2000; Knief et al., 2003; Knief et al., 2005b). Because of primer biases, these may be more abundant than expected based on their rare detection. As an example of the importance of primer bias, an alternative pmoA gene present in most type II methano-trophs was only recently discovered, because it was less easily PCR-amplified than the known pmoA gene (Dunfield et al., 2002).
It has recently been discovered that some crenarchaea are capable of autotrophic ammonia oxidation, and possess an amoA gene (Konneke et al., 2005; Treusch et al., 2005). Perhaps discoveries of yet-unknown methane oxidizers will also be made. These could possess pMMO or sMMO, or evolu-tionarily unrelated methane monooxygen-ases. It cannot be ruled out that completely unexpected species are involved in atmospheric methane oxidation.
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