Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean

Abstract

Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 10¹³ to ∼2 × 10¹³ mol of C per year globally through the flux of ∼1 × 10¹⁴ to ∼2 × 10¹⁴ mol of N per year of the two steps of oxidation throughout the dark ocean.

Keywords: carbon fixation; dark ocean; homeostasis; nitrification; nitrogen flux.

Fig. 1.

Activity parameters of selected AOA and NOB strains determined under controlled laboratory conditions. Additionally, three marine AOA strains (Nitrosopumilus ureaphilus PS0, N. cobalaminigenes HCA1, and N. oxyclinea HCE1) determined in a previous study are added (24). Means ± SDs are given. The error bars represent SDs of biological replicates (n = 3). One square representing Nitrospina has no SDs, as culture volumes are very small, and biological replicates are not available. Stoichiometric relationships (type I regression) between cell-specific ammonia and nitrite oxidization and DIC-fixation rates are obtained. The two blue dashed lines indicate the theoretical predictions of efficiencies from Zakem et al. (25) (with a slope threefold lower than the red regression line) and the thermodynamic free energy (with a slope fourfold lower).

Fig. 2.

Michaelis–Menten kinetics of nitrite oxidation. Nitrite-oxidation rates were measured at different substrate concentrations at five depths between 75 and 200 m of site S6 in the SCS. Measured rates were obtained from the slope of the linear regression of six independent time-course bottles (SI Appendix, Materials and Methods). Error bars represent the SE of the regression coefficient. The solid lines were fitted by using the Michaelis–Menten equation. R², coefficients (V_max and K_s) of the best fit, and their SEs are shown. (Left) Shows all the data; (Right) shows the range 0 to 500 nM NO₂⁻ concentration.

Fig. 3.

Ammonia affinities of AOA and ammonia-oxidizing bacteria (AOB) and nitrite affinities of NOB. K_m (K_s) values of members of the genera Ca. Nitrosoglobus (upper left triangle) (19), Nitrosomonas (upper right triangles) (, ‒54), Nitrosospira (lower left triangles) (19, 55, 56), Nitrosococcus (lower right triangle) (19), Nitrospira (comammox) (circles) (19), Ca. Nitrosotenuis (down-pointing triangles) (19), Nitrososphaera (ellipses) (19), Nitrosarchaeum (stars) (19), and Nitrosopumilus (pentacle) (10), and in situ communities (squares) from the ETSP (15), Puget Sound Hood Canal (16), Sargasso Sea (17), SCS (18), and the WP (this study is marked in bold; the error bar represents the SE of the estimated coefficient) for ammonia oxidation are shown on the left; K_m (K_s) values of members of the genera Nitrospina (hexagon) (20), Nitrococcus (diamond) (20), Nitrospira (circles) (–21), Nitrotoga (fork) (21), Nitrobacter (triangles) (20, 21), Nitrolancea (cross) (22), and in situ communities (squares) from the ETNP (23) and the SCS (this study is marked in bold; error bars represent the SE of the estimated coefficient) for nitrite oxidation are shown on the right. Cultures were derived from ocean (dark blue), oceanic oxygen-deficient water (black), freshwater (light blue), activated sludge (green), soil (orange), biofilm (yellow), bioreactor (purple), and hot spring/well water (red). Filled symbols indicate pure culture; open symbols indicate mixed culture/enrichment or in situ community. Ca., Candidatus. The values obtained from refs. and are also from references in the two articles. −, the error bars are obtained from references.

Fig. 4.

Gene transcription in AOA and NOB. Relative transcript abundances of phylogenetic taxa and of genes encoding enzymes involved in the N cycle, C metabolism, and sulfur cycle in metatranscriptomes are shown. For the C-fixation pathway, dark circles indicate relative transcript abundances of genes encoding essential/key enzymes (SI Appendix, Table S2); light circles indicate relative transcript abundances of all genes encoding enzymes involved in each pathway. Amo, ammonia monooxygenase; Apr, adenylylsulfate reductase; CBB, Calvin Benson Basham cycle; CysC, adenylyl-sulfate kinase; CysH, phosphoadenosine phosphosulfate reductase; Dsr, dissimilatory sulfite reductase; Nir, nitrite reductase; Nxr, nitrite oxidoreductase; Sat, sulfate adenylyltransferase; Sir, sulfite reductase; SOB, sulfur-oxidizing bacteria.