Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation

Abstract

Nitrite-dependent anaerobic methane oxidation (n-DAMO) has been demonstrated to play important roles in the global methane and nitrogen cycle. However, despite diverse n-DAMO bacteria widely detected in environments, little is known about their physiology for microbial niche differentiation. Here, we show the microbial niche differentiation of n-DAMO bacteria through long-term reactor operations combining genome-centered omics and kinetic analysis. With the same inoculum dominated by both species "Candidatus Methylomirabilis oxyfera" and "Candidatus Methylomirabilis sinica", n-DAMO bacterial population was shifted to "Ca. M. oxyfera" in a reactor fed with low-strength nitrite, but shifted to "Ca. M. sinica" with high-strength nitrite. Metatranscriptomic analysis showed that "Ca. M. oxyfera" harbored more complete function in cell chemotaxis, flagellar assembly, and two-component system for better uptake of nitrite, while "Ca. M. sinica" had a more active ion transport and stress response system, and more redundant function in nitrite reduction to mitigate nitrite inhibition. Importantly, the half-saturation constant of nitrite (0.057 mM vs 0.334 mM NO 2 − ) and inhibition thresholds (0.932 mM vs 2.450 mM NO 2 − ) for "Ca. M. oxyfera" vs "Ca. M. sinica", respectively, were highly consistent with genomic results. Integrating these findings demonstrated biochemical characteristics, especially the kinetics of nitrite affinity and inhibition determine niche differentiation of n-DAMO bacteria.

Evidence for Nitrous Oxide Emissions by Nitrite-Dependent Anaerobic Methane Oxidizing Bacteria

“…In fact, while not completely oxidizing nitrite to N 2 , the reduction of nitrite to N 2 O with methane as electron donor by n-DAMO bacteria, shown in eqs S1 and S2, is also thermodynamically feasible. In this current study, the higher rates of nitrite reduction and higher expression levels of nirS when residual nitrite was available were consistent with the kinetics of nitrite affinity determined previously, reflecting that n-DAMO bacteria were more active under nitrite exposure. In this case, the production of N 2 O as an alternative metabolic route for n-DAMO bacteria would not only produce energy but also avoid the accumulation of toxic intermediate NO.…”

Revisiting the Engineering Roadmap of Nitrate/Nitrite-Dependent Anaerobic Methane Oxidation

“…However, after long-term operation, an enriched n-DAMO bacteria culture could only remove nitrite at a rate of 33 to 77 mg N L –1 d –1 , − which is far below the practically useful rate. To enhance the nitrogen removal activity of n-DAMO bacteria, the environmental condition and growth factors were optimized, which could contribute to the engineering application of n-DAMO bacteria. − By cultivating a highly efficient biofilm capable of accumulating biomass, nitrite removal by n-DAMO bacteria achieved a rate of 0.99 kg N L –1 d –1 , which demonstrated the great application potential of such a process for nitrogen removal NH 4 + + 1.5 normalO 2 → NO 2 − + normalH 2 normalO + 2 normalH + NH 4 + + 1.5 normalO 2 + 0.375 CH 4 + → normalH + + 0.375 CO 2 + 0.5 normalN 2 + 2.25 normalH 2 normalO …”