Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation

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.