Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

Abstract

Archaea of the phylum Thaumarchaeota are among the most abundant prokaryotes on Earth and are widely distributed in marine, terrestrial, and geothermal environments. All studied Thaumarchaeota couple the oxidation of ammonia at extremely low concentrations with carbon fixation. As the predominant nitrifiers in the ocean and in various soils, ammonia-oxidizing archaea contribute significantly to the global nitrogen and carbon cycles. Here we provide biochemical evidence that thaumarchaeal ammonia oxidizers assimilate inorganic carbon via a modified version of the autotrophic hydroxypropionate/hydroxybutyrate cycle of Crenarchaeota that is far more energy efficient than any other aerobic autotrophic pathway. The identified genes of this cycle were found in the genomes of all sequenced representatives of the phylum Thaumarchaeota, indicating the environmental significance of this efficient CO2-fixation pathway. Comparative phylogenetic analysis of proteins of this pathway suggests that the hydroxypropionate/hydroxybutyrate cycle emerged independently in Crenarchaeota and Thaumarchaeota, thus supporting the hypothesis of an early evolutionary separation of both archaeal phyla. We conclude that high efficiency of anabolism exemplified by this autotrophic cycle perfectly suits the lifestyle of ammonia-oxidizing archaea, which thrive at a constantly low energy supply, thus offering a biochemical explanation for their ecological success in nutrient-limited environments.

Keywords: Nitrosopumilus maritimus; autotrophy.

Fig. 1.

Reactions of the crenarchaeal and thaumarchaeal variants of the HP/HB cycle (modified from ref. 19). The reactions determining energy efficiency of the crenarchaeal (M. sedula) cycle are shown in green, and those for the N. maritimus variant are shown in red. Reactions common to both are shown in black. Note that although the two pathways have similar reactions and intermediates, they are significantly different in energy efficiency (Table 4) and evolved independently in Crenarchaeota and Thaumarchaeota (see text). The numbers in square brackets represent moles of high-energy anhydride bonds of ATP required to form 1 mol of the corresponding central precursor metabolites (see also Table 4). Enzymes as numbered in circles are 1, 3-hydroxypropionyl-CoA synthetase (ADP-forming); 2, 3-hydroxypropionyl-CoA synthetase (AMP-forming); 3, 3-hydroxypropionyl-CoA dehydratase; 4, 4-hydroxybutyryl-CoA synthetase (ADP-forming); 5, 4-hydroxybutyryl-CoA synthetase (AMP-forming); 6, 4-hydroxybutyryl-CoA dehydratase; 7, crotonyl-CoA hydratase; 8, succinyl-CoA synthetase (ADP-forming); 9, succinic semialdehyde dehydrogenase; 10, pyruvate-phosphate dikinase; and 11, pyruvate-water dikinase.

Fig. 2.

Phylogenetic trees of N. maritimus HP/HB cycle enzymes identified in this study and of the key enzyme of the cycle, 4-hydroxybutyryl-CoA dehydratase. (A) Homologs of 3-hydroxypropionyl-CoA synthetase from Nmar_1309. (B) Homologs of the 4-hydroxybutyryl-CoA synthetase (Nmar_0206). (C) Homologs of 3-hydroxypropionyl-CoA dehydratase/crotonyl-CoA hydratase (Nmar_1308). (D) Homologs of 4-hydroxybutyryl-CoA dehydratase (Nmar_0207). Thaumarchaeal sequences are shown in red, crenarchaeal in green, euryarchaeal in blue, eukaryotic in brown, and bacterial in black. The tree is based on amino acid sequence analysis. Tree topology and evolutionary distances are given by the neighbor-joining method with Poisson correction. (Scale bars: a difference of 0.1 substitutions per site.) For details of the tree construction, see SI Appendix, Figs. S6 and S10–S12. The accession numbers of the sequences used for the construction of the tree are listed in SI Appendix, Table S4. A. fulg., A. fulgidus; Caldisph., Caldisphaera.