Nitrification in the OMZ of the Arabian Sea (OMG!)

A review of: Newell SE, Babbin AR, Jayakumar A, Ward BB (2011) Ammonia oxidation rates and nitrification in the Arabian Sea. Global Biogeochemical Cycles, 25: 1-10.

A major rate limiting nutrient in the marine environment is nitrogen and oxidation of ammonia derived from organic matter is postulated to support 12-32% of primary production globally. The involvement of ammonia oxidising archaea (AOA) from the phylum Crenarcheota in nitrogen recyling was a relatively recent discovery. It was previously thought that ammonia oxidation was restricted to groups of β and γ proteobacteria (AOB), however more recent studies reveal AOA numbers that are considerably higher than AOB. The rates of archaea and bacteria ammonia oxidation in the oceans have not been quantified separately and archaea metabolism in the mesopelagic zone is yet to be fully elucidated. The Arabian Sea oxygen minimum zone (OMZ) is the largest in the world and the nitrogen cycle within this body of water has been the focus of many recent studies. The aim of the investigation by Newell et al (2011) was to explore the factors that influence the rates of ammonia oxidation and the abundance of AOA and AOB on the surface of the Arabian Sea, in low oxygen regions and in the mesopelagic zone below the OMZ.

Specific primers to identify the gene that encodes the ammonia monooxygenase enzyme (amoA) were used to estimate abundance of AOA and AOB using qPCR. Bacteria and archaea amoA genes were detected at every sampling depth in three locations, revealing AOA to be 35 to 216 times more abundant than AOB. Ammonia oxidation rates ranged from undetectable to 21.1 ± 0.1 nmol l^-1 d^-1; with the highest measurement near the surface layer (40 to 80 m in depth). The rates of ammonia oxidation within the oxycline (95-136 m in depth) above the OMZ were between 1.5 ± 0.2 and 4.6 ± 0.4 nmol l^-1 d^-1, while a low average of 0.07 ± 0.05 nmol l^-1 d^-1 was detected  in the mesopelagic zone (900 to 1000 m in depth)directly below the OMZ.

AOA appear to be the dominant ammonia oxidisers in the Arabian Sea, significantly contributing to nitrite production within the primary nitrite maximum (PNM) zone above 100 m and may be responsible for 10-100% of nitrite supply required to maintain the PNM. The role of ammonia oxidising Crenarchaeota in the deep ocean remains unclear however amoA gene abundance of 10⁵ copies ml^-1 at around 1000 m indicates a large population that substantially impacts nitrogen and carbon cycling. AOA nitrification in the photic zone provides recycled nitrate for primary production and may be a significant source of nitrous oxide (a greenhouse gas) which warrants further investigation. The role of AOA in OMZs and the metabolic pathways that sustain growth in hypoxic and anoxic conditions also requires elucidation, along with microbial diversity (via 16S gene analysis) and community dynamics. Furthermore, the abundance of amoA genes in the mesopelagic zone suggests approximately 50% of microbial biomass could be autotrophic and nitrification may be the main process that utilises most of the ammonium produced from organic carbon fluxes.