Table 3.
Gene markers of methanol-utilizing microorganisms for amplicon-based pyrosequencing or as targets for homology screens in metagenome, -trancriptome, or -proteome datasets.
| Methanol utilizers | Enzyme | Function | Gene marker | Primers | Reference | PyroseqD |
|---|---|---|---|---|---|---|
| Proteobacteria | PQQ MDH | MeOH ox. | mxaF | 1003f/1555rE | McDonald and Murrell (1997); Neufeld et al. (2007) | Yes |
| Proteobacteria, Verrucomicrobia | PQQ MDH | Putatively MeOH ox. | xoxF | 1003f/1555rE | McDonald and Murrell (1997); Neufeld et al. (2007) | Yes |
| Burkholderiales | PQQ MDH2 | MeOH ox. | mdh2 | Not availableA | Kalyuzhnaya et al. (2008) | No |
| Various Proteobacteria, non-methylotrophs | FAE | OtherB | fae1 | fae1f/fae1r | Kalyuzhnaya et al. (2004) | Yes |
| MCH | OtherB | mch | mch-2a/mch-3 | Vorholt et al. (1999); Kalyuzhnaya and Chistoserdova (2005) | Yes | |
| Actinobacteria | MDO | MeOH ox. | mdo | Not availableA | Park et al. (2010) | No |
| Bacilli | NAD MDH | MeOH ox. | mdh | Not availableA | Devries et al. (1992); Krog et al. (2013) | No |
| Methylotrophic methanogens | Methanol:CoM methyl-transferase system | MeOH ox. | mtaCC | Not availableA | Hagemeier et al. (2006) | No |
| Methylotrophic acetogens | Methanol:CoM methyl-transferase system-like | MeOH ox. | mtaC-likeC | Not availableA | Das et al. (2007) | No |
| Fungi | FAD AO | MeOH ox. | mod1, mod2, others | Not availableA | Reid and Fewson (1994); Ozimek et al. (2005), Hartner and Glieder (2006); Nakagawa et al. (2006) | No |
MeOH, methanol oxidation.
A
Primers for this group of genes have not designed and tested in environmental surveys.
B
These enzymes do not oxidize methanol, but are involved in formaldehyde oxidation. These enyzmes also occur in methylotrophs that do not use methanol and in non-methylotrophs (Chistoserdova, 2011).
C
Homologs of unknown function are present in methanogens (Ding et al., 2002).
D
Has been used in amplicon pyrosequencing.
E
Detect only mxaF and xoxF-like genes of Proteobacteria.