Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in 15 N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (p372 nM NO 2 À d À1 ) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to B9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO 3 À was re-oxidized back to NO 3 À via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways.

A globally distributed yet previously overlooked marine nitrite oxidizer can reduce nitrate, produce N2O, and oxidize sulfide.

A detailed understanding of gut microbial ecology is essential to engineer effective microbial therapeutics and to model microbial community assembly and succession in health and disease. However, establishing generalizable insights into the functional determinants of microbial fitness in the human gut has been a formidable challenge. Here we employ fecal microbiota transplantation (FMT) as an in natura experimental model to identify determinants of microbial colonization and resilience. Our long-term sampling strategy and high-resolution multi-omics analyses of FMT donors and recipients reveal adaptive ecological processes as the main driver of microbial colonization outcomes after FMT. We also show that high-fitness donor microbial populations are significantly enriched in metabolic pathways that are responsible for the biosynthesis of nucleotides, essential amino acids, and micronutrients, independent of taxonomy. To determine whether such metabolic competence can explain the microbial ecology of human disease states, we analyzed genomes reconstructed from healthy humans and humans with inflammatory bowel disease (IBD). Our data reveal that such traits are also significantly enriched in microbial genomes recovered from IBD patients, linking presence of superior metabolic competence in bacteria to their expansion in IBD. Overall, these findings suggest that the transfer of gut microbes from a healthy donor to a disrupted recipient environment initiates an environmental filter that selects for populations that can self-sustain. Such ecological processes that select for self-sustenance under stress offer a model to explain why common yet typically rare members of healthy gut environments can become dominant in inflammatory conditions without any need for them to be causally associated with, or contribute to, such disease states.