The upwelling of nutrient-rich waters along the Namibian coast sustains some of the highest rates of primary production in oceans, involving key nitrification steps in the nitrogen (N) cycle. Microbial oxidation of oceanic N changes the state of N electron acceptors such as nitrate (NO3–) available to other organisms. However, the ecology of microbes, particularly nitrifiers, at different depths in this Oxygen Minimum Zone (OMZ) is not well-studied. Using multiplex sequencing of 16S rRNA amplicons (~250bp), complemented by temperature, dissolved oxygen, and N2O stable isotope concentration measurements, we profiled the microbiota at 10m, 25m, 100m, 130m, and 250m depths. The diversity and abundance of ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB), and nitrite oxidizing bacteria (NOB), which oxidize ammonium (NH4+) sequentially to NO3–, and anammox-capable bacteria, which reduce NH4+ to dinitrogen (N2), were accessed after retrieving, analyzing and tallying sequences placed in monophyletic groups encompassing these taxa. Our data indicate that the AOA are the dominant nitrifying microbes at 100m and below, where oxygen becomes depleted, and AOA diversity and abundances are correlated to increased biologically-produced N2O concentration. AOA abundances and diversity far exceed that of other nitrifying bacteria, and anammox bacteria only constituted 1% of the microbiota (or less) at all depths. This study indicates that AOA show evidence of biogeography, are the dominant microbial components in this ecosystem, and are mainly responsible for transformations of NH4+ and N2O production.
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