Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes

Grace Pold, Aurélien Saghaï, Christopher M. Jones and Sara Hallin ()
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Grace Pold: Swedish University of Agricultural Sciences
Aurélien Saghaï: Swedish University of Agricultural Sciences
Christopher M. Jones: Swedish University of Agricultural Sciences
Sara Hallin: Swedish University of Agricultural Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Diverse microorganisms can execute one or more steps in denitrification, during which nitrate or nitrite is successively reduced into nitric oxide, nitrous oxide, and ultimately dinitrogen. Many of the best-characterized denitrifiers are complete denitrifiers capable of executing all steps in the pathway, but their dominance in natural communities and what metabolic traits and environmental factors drive the global distribution of complete vs. partial denitrifiers are unclear. To address this, we conducted a comparative analysis of denitrification genes in 61,293 genomes, 3991 metagenomes, and 413 terrestrial and aquatic metatranscriptomes. We show that partial denitrifiers outnumber complete denitrifiers and the potential to initiate denitrification is more common than the potential to terminate it, particularly in nutrient rich environments. Our results further indicate that complete denitrifiers tend to be fast-growing organisms, favoring organic acid over sugar metabolism, and encoding the ability to oxidize and reduce a broader range of organic and inorganic compounds compared to partial denitrifiers. This suggests complete denitrifiers are metabolically flexible opportunists. Together, our results indicate an environmental footprint on the presence of denitrification genes which favors the genomic potential for partial over complete denitrification in most biomes and highlight that completion of the denitrification pathway is a community effort.

Date: 2025
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DOI: 10.1038/s41467-025-65319-5

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