Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes a-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis-Menten kinetics curve for ammonia oxidation by the natural community and found that the measured K m of 98 ± 14 nmol l À 1 was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 1C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a K m for the natural community to better constrain ammonia oxidation rates determined with the commonly used 15 NH 4 þ dilution technique.

Nitrification is a critical process for the balance of reduced and oxidized nitrogen pools in nature, linking mineralization to the nitrogen loss processes of denitrification and anammox. Recent studies indicate a significant contribution of ammonia-oxidizing archaea (AOA) to nitrification. However, quantification of the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to in situ ammonia oxidation remains challenging. We show here the production of nitric oxide (NO) by Nitrosopumilus maritimus SCM1. Activity of SCM1 was always associated with the release of NO with quasi-steady state concentrations between 0.05 and 0.08 μM. NO production and metabolic activity were inhibited by the nitrogen free radical scavenger 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl-3-oxide (PTIO). Comparison of marine and terrestrial AOB strains with SCM1 and the recently isolated marine AOA strain HCA1 demonstrated a differential sensitivity of AOB and AOA to PTIO and allylthiourea (ATU). Similar to the investigated AOA strains, bulk water column nitrification at coastal and open ocean sites with sub-micromolar ammonia/ammonium concentrations was inhibited by PTIO and insensitive to ATU. These experiments support predictions from kinetic, molecular and biogeochemical studies, indicating that marine nitrification at low ammonia/ammonium concentrations is largely driven by archaea and suggest an important role of NO in the archaeal metabolism.

The eastern tropical North Pacific (ETNP) is a large region of anoxic water that hosts widespread water column N loss (denitrification). There is some disagreement about the long‐term trends of denitrification and anoxia and long‐term studies of water column denitrification within the anoxic zone are lacking. In this study, we compared ETNP water column nitrite, N*, and O2 data along the same transect for four studies ranging from 1972 to 2012. Anoxic water volume increased, and low‐oxygen conditions expanded into shallower isopycnals from 1972 to 2012. A geochemical marker for cumulative N loss indicates that denitrification was highest in 2012 and the upper oxygen‐deficient zone (ODZ) experienced the most change. Oxygen and N loss changes in the world's largest ODZ for 2012 could not be explained by the Pacific Decadal Oscillation, and decreased O2 in supply currents and increased wind‐driven upwelling are likely mechanisms contributing to increased N loss and anoxia.

Thaumarchaeota are implicated as the major ammonia oxidizers in the ocean. However, the influence of various abiotic factors in determining their distribution and activity in the upper ocean remain largely unclear. Here, we examined the influence of light, hydrogen peroxide (H2O2), and temperature on ammonia oxidation rates for communities dominated by Thaumarchaeota at the nitrite maximum across two North Pacific transects. In situ ammonia oxidation was almost exclusively driven by Thaumarchaeota, as inferred from ammonia monooxygenase subunit A (amoA) genes, amoA transcripts, and inhibitor studies. A major shift in population structure near the eastern North Pacific Subtropical Front was revealed by sequence variation of amoA genes, showing different Thaumarchaeota community structure in oligotrophic gyre and temperate regions. While the most dominant OTUs were closely related, we found significant differences in physiological responses to light and temperature of incubation. At four stations in different biogeochemical regimes, the impact of sunlight intensity and temperature on activity was evaluated using 15 NH4+‐spiked whole seawater collected from the nitrite maximum and incubated at different depths on a free floating in situ array. Ammonia oxidation was usually completely inhibited by PAR at the surface and 21–45% inhibited at 1% surface PAR, whereas a temperature effect on ammonia oxidation was observed at only two of four stations. While inhibition due to H2O2 cannot be ruled out in surface waters, our findings show that below the mixed layer, photoinhibition, and not H2O2 toxicity, had a greater influence on ammonia oxidation.