Fermentative nitrite ammonifiers are abundant in soils and ecologically distinct from NrfA-dependent ammonifiers

Abstract Microorganisms can use different enzymes to perform nitrite ammonification, the reduction of nitrite to ammonium, an important process to retain nitrogen in soils. Yet, the organisms mediating this process and their distribution in terrestrial ecosystems remain poorly resolved. Here, we determined the phylogenetic diversity of bacteria performing fermentative nitrite ammonification via the NAD(P)H-dependent nitrite reductase NirB, assessed their distribution across terrestrial ecosystems, and identified their environmental preferences. We found that these organisms are broadly distributed, spanning 29 phyla including Bacillota, Pseudomonadota and Actinomycetota. Screening 1,587 globally distributed soil metagenomes using a phylogeny-based approach revealed that fermentative nitrite ammonifiers are ubiquitous across biomes and particularly abundant in Mediterranean forests and desert soils. In these ecosystems, they outnumbered NrfA-dependent ammonifiers, the best characterized ammonifier group to date, suggesting distinct ecological niches for the two groups. Consistent with this, random forest modelling revealed a negative relationship between fermentative nitrite ammonifiers and the carbon-to-nitrate ratio, which contrasts with a preference for high carbon-to-nitrate conditions in NrfA-dependent ammonifiers. However, moisture and salinity emerged as the strongest predictors of the abundance of fermentative nitrite ammonifiers, indicating a high tolerance to osmotic stress in this group. Overall, our results demonstrate that fermentative nitrite ammonifiers are both phylogenetically diverse and environmentally widespread, calling for future efforts to determine the conditions under which they contribute to nitrogen retention in soils.