Unexpected versatility in the metabolism and ecophysiology of globally relevant nitrite-oxidizing Nitrotoga bacteria

Abstract

Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution from freshwater systems by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies revealed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using enrichment methods and genomic sequencing, we identified four novel Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome assembly revealed highly conserved 16S rRNA gene sequences, but a surprisingly broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggest that Nitrotoga can metabolize in low oxygen or anaerobic conditions, which may support a previously unrecognized environmental niche. An array of antibiotic and metal resistance genes likely allows Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses reveal a deeply divergent nitrite oxidoreductase alpha subunit (NxrA) not represented in any other NOB, suggesting a novel evolutionary trajectory for Nitrotoga. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments. This work considerably expands our knowledge of the Nitrotoga genus and improves our understanding of their role in the global nitrogen cycle.