A nirK–cbb3 genomic region links SAR11 to nitrogen loss in the northern Benguela Upwelling System

Denitrification leads to nitrogen loss from marine oxygen minimum zones. The complete metabolic pathway for denitrification reduces nitrate to dinitrogen gas in four sequential steps. Many facultatively anaerobic bacteria are capable of the initial step of nitrate reduction to nitrite. Far fewer contribute to nitrogen loss by reducing nitrite to nitric oxide, nitrous oxide or dinitrogen gas. We sequenced the genomes of 24 bacteria isolated from low-oxygen waters (23 µM) in the northern Benguela Upwelling System (nBUS) to identify species with the genetic potential for denitrification. Most isolates have the genetic potential for partial denitrification, including ten SAR11 strains with a genomic region that codes for a copper-containing nitrite reductase (NirK) and a high-affinity cbb3-type cytochrome c oxidase. Evidence that nBUS SAR11 have the potential to respire nitrite in low-dissolved-oxygen waters suggests that they could have a more direct role in marine nitrogen loss.