Nitrous oxide produced by denitrifying pseudomonads inhibits the growth of rhizosphere bacteria by inactivating the cobalamin-dependent methionine synthase

Microbial communities are shaped by complex metabolic interactions, whereby the byproducts of one organism influence the physiology of others. This is exemplified in the microbial nitrogen cycle, where diffusion of free intermediates can drastically reshape the chemical landscape of the environment. One such intermediate, nitrous oxide (N₂O), is often overlooked as biologically inert. However, emerging evidence suggests this gas may inhibit the activity of some cobalamin-dependent enzymes through a reaction with the cofactor. This raises the possibility that, through such an interaction, N₂O-producing organisms may shape the microbial communities in which they reside, selecting against organisms that rely on these sensitive cobalamin enzymes. At the plant root, a hotspot of microbial activity, the impact of such interactions may be especially important. To investigate this, we focused on microbial N₂O production and its effect on methionine biosynthesis, a ubiquitous bacterial process carried out by cobalamin-dependent (MetH) or independent (MetE) methyltransferases. In this study, we show that deleting <i>metE</i> and forcing reliance on MetH sensitizes the denitrifier <i>Pseudomonas aeruginosa</i> to exogenous and self-produced N₂O. We extend these findings to plant-associated bacteria, where we find that a significant portion of an <i>Arabidopsis thaliana</i> rhizosphere culture collection relies exclusively on cobalamin-dependent methionine synthases and experimentally demonstrate their sensitivity to N₂O. Finally, we show that the growth of one MetH-reliant rhizosphere isolate is suppressed in co-culture with N₂O-producing <i>P. aeruginosa</i>. Together, these findings suggest that N₂O producers can shape microbial ecology at the plant root.IMPORTANCEMicrobes that live on plant roots can make important contributions to plant health and often exist in tight-knit communities held together by chemical exchanges. This study investigates an interaction between two such metabolites: the climate-active gas nitrous oxide (N₂O) and cobalamin. N₂O can become toxic through a reaction with methionine synthase enzymes that use cobalamin as a cofactor. We asked whether the production of N₂O by some bacteria curtails the growth of others that rely on these enzymes. Using genetic mutants of a model bacterium and natural isolates from the roots of the plant <i>Arabidopsis thaliana,</i> we showed that N₂O-producing microbes suppress growth of their sensitive neighbors and that N₂O sensitivity is common in rhizosphere bacteria. As natural and agricultural soils periodically experience bursts of N₂O, our results suggest that exposure to this gas may shape the assembly of plant-beneficial microbial communities.