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 NO2–) and inhibition
thresholds (0.932 mM vs 2.450 mM NO2–) 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.