Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review

Abstract

Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.

Keywords: Methane; Methane monooxygenase; Methylocapsa; Methylocella; Methylocystis; biogeochemical cycling; facultative methanotrophs.

Fig. 1.

Summary of natural and anthropogenic methane sources to the atmosphere. A proportion of coal bed methane is of biogenic origin [179]. The magnitude of each source as a percentage of the total (736 Tg CH₄ y⁻¹) is shown in parentheses. Data from reference [1].

Fig. 2.

Phylogeny, based on 16S rRNA genes, of alphaproteobacterial methanotrophs (in bold) together with other closely related non-methanotrophic representatives. Facultative strains are identified with red diamonds. The tree was drawn using the maximum-likelihood method in mega7 [183], with bootstrap values (500 replications) greater than 90 or 50 % shown as circles or diamonds, respectively, at the nodes. The tree is drawn to scale and the scale bar indicates substitutions per site. There were a total of 1524 positions in the final dataset.

Fig. 3.

Genetic potential of facultative methanotrophs with determined genome sequences. The presence of a gene or genes encoding a reaction or pathway is shown as black squares. Whole-genome nucleotide sequences were searched with representative protein query sequences using TBLASTN [184]. BL2, Methylocella silvestris BL2; TVC, Methylocella silvestris TVC; PC1, Methylocella tundrae PC1; PC4, Methylocella tundrae PC4; T4, Methylocella tundrae T4; H2, Methylocystis heyeri H2; S285, Methylocystis bryophila S285; SB2, Methylocystis sp. SB2; CSC1, Methylocystis hirsuta CSC1; KYG, Methylocapsa aurea KYG; R-67164, Methyloceanibacter methanicus R-67174. MmoX, soluble methane monooxygenase; PmoA, particulate methane monooxygenase; BmoX, butane monooxygenase; PrmA, propane monooxygenase; MxaF, Ca-dependent methanol dehydrogenase; XoxF, lanthanide-dependent methanol dehydrogenase; ExaF, lanthanide-dependent ethanol dehydrogenase; MauA, methylamine dehydrogenase; NMG, N-methylglutamate pathway; Serine, serine cycle; RuMP, ribulose monophosphate pathway; CBB, Calvin–Benson–Bassham pathway; ActP, acetate-specific permease; ICL, isocitrate lyase; MS, malate synthase; ECM, ethylmalonyl-CoA pathway; NarGHJI, respiratory nitrate reductase; NapAB, periplasmic nitrate reductase; NirK, copper-containing nitrite reductase; NirS, multi-haem nitrite reductase; cNorB, cytochrome c-dependent nitric oxide reductase; NosZ, nitrous oxide reductase; Nif, nitrogenase; PufLM, photosynthetic reaction centre; Hhy-5, high-affinity group 5 hydrogenase; CODH, carbon monoxide dehydrogenase.

Fig. 4.

Relationship of the α-subunits of the sMMOs and sMMO-like proteins from facultative methanotrophs (indicated with red diamonds) and other representative strains. The sequences at the bottom of the figure, which form a group with BmoX (butane monooxygenase) of Thauera butanivorans, are from non-methanotrophs, except for those from Methylocella tundrae strains PC1 and PC4. The tree was drawn using the maximum-likelihood method in mega7 [183], with bootstrap values (500 replications) greater than 75 % shown as solid circles at the nodes. The tree is drawn to scale and the scale bar indicates substitutions per site. There were a total of 540 amino acid residues in the final dataset.

Fig. 5.

The Methylocella PrmA (propane monooxygenase α-subunit) sequences (shown in bold), group with those of diverse strains not known for propane oxidation, distinct from the propanotrophs in SDIMO groups 5 and 6. The tree was drawn using the maximum-likelihood method in mega7 [183], with bootstrap values (500 replications) greater than 75 % shown as solid circles at the nodes. The tree is drawn to scale and the scale bar indicates substitutions per site. There were a total of 440 amino acid residues in the final dataset.