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Research article2023Peer reviewedOpen access

Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes

Saghai, Aurelien; Pold, Grace; Jones, Christopher M.; Hallin, Sara


Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.Nitrate ammonifiers are poorly known despite their importance for soil nitrogen retention. This study shows that they are phylogenetically diverse and globally distributed across terrestrial biomes and that the outcome of the competition with denitrifiers is controlled by soil nitrate.

Published in

Nature Communications
2023, Volume: 14, number: 1, article number: 8249