Quantification of ammonia oxidation rates and ammonia‐oxidizing archaea and bacteria at high resolution in the Gulf of California and eastern tropical North Pacific Ocean

Abstract

Ammonia-oxidizing microorganisms compete with phytoplankton for reduced nitrogen in the euphotic zone and provide oxidized nitrogen to other microbes present in the sea. We report 15 NH z 4 oxidation rate measurements made at 5-20-m resolution using an in situ array and quantification of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in corresponding samples from the upper water column and oxygen minimum zone (OMZ) of the Gulf of California (GOC) and eastern tropical North Pacific Ocean (ETNP). 15 NH z 4 oxidation rates varied substantially with depth and between stations: they were greatest at the base of the euphotic zone, and maximum rates were up to 28-fold greater than rates measured within 5-10 m. Pyrosequencing and quantitative polymerase chain reactions (QPCR) indicated that AOA were present throughout the water column at all latitudes and always outnumbered AOB. AOB constituted only 39 of 432,240 16S ribosomal ribonucleic acid gene sequences produced via pyrosequencing but were more abundant at greater depths and higher latitudes. 15 NH z 4 oxidation rates were correlated with AOA abundance at some stations and were detectable in 96% of samples, including depths where oxygen concentrations were , 5 mmol kg 21 and depths within the euphotic zone, where up to 42% of ammonia oxidation occurred. Ammonia is rapidly oxidized within discrete depth intervals in the GOC and ETNP; while pyrosequencing and QPCR demonstrate that AOB are confined to deeper portions of the water column, AOA appear to be active within the euphotic zone, where they may quickly respond to nitrogen inputs.

Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

“…Depth-integrated nitrification rates were correlated with both depth-integrated Chl a (R 2 5 0.96) and sediment trap PON export at 60 m (R 2 5 0.94), the later reported by Munson et al (2015). Previous studies in the Pacific have found positive correlations between depth-integrated primary production and nitrification (Beman et al 2012;Shiozaki et al 2016). The correlations in our data and others support a direct and quantitative connection between nitrification rates, euphotic zone biomass, and PON export (Newell et al 2011).…”

Ammonia Oxidation in the Ocean Can Be Inhibited by Nanomolar Concentrations of Hydrogen Peroxide

“…15 N-labeled ammonium ( 15 NH 4 Cl; Cambridge Isotope Laboratories) was added at a concentration of 50 nM (Santoro et al, 2010;Beman et al, 2012) to determine ammonia oxidation (AO) rates, and hydrogen peroxide (H 2 O 2 ; Fisher Scientific-Southern Ocean; J. T. Baker-GoM, GoA, Marsh Landing) was added to experimental treatments at target concentrations designated as either "low" (10-100 nM) or "high" (30-300 nM) amendments; actual H 2 O 2 additions varied by sample site ( Table 1, Supplementary Table 4). For these addition experiments, H 2 O 2 and 15 N-labeled ammonium were added directly to carboys for incubation; however, in the Southern Ocean 15 NH 4 Cl was added to duplicate, 250 mL subsamples after an initial incubation (6 h) with H 2 O 2 .…”

“…Catalase (Sigma Aldrich) was added to thawed samples (10 µL of 150 units L −1 catalase per 50 mL sample) that were incubated at room temperature for 60 min to prevent any inhibition of P. aureofaciens growth or denitrification ability by residual H 2 O 2 (no difference observed in N 2 O production with catalase addition; t-test, p = 0.43; Supplementary Table 5). AO rates were calculated from δ 15 N values as previously described (Christman et al, 2011;Beman et al, 2012); the detection limit for this measurement (0.001 nM d −1 ) was determined by using the detection limit for [NH 4 ] and [NO x ], as well as the uncertainty in stable isotope measurements with this setup (Beman et al, 2011).…”

Nitrous oxide dynamics in low oxygen regions of the Pacific: insights from the MEMENTO database

“…It is possible that some of the relatively high variability in N 2 O produced per O 2 molecule consumed observed in Fig. 5 is due to mixing of water masses (Jin and Gruber, 2003), the variable abundance of bacterial and archaeal nitrifiers (Beman et al, 2012), or composition and availability of organic matter (Nevison et al, 2003). Also note that although we proxy N 2 O production via the N 2 O xs /AOU ratio, in reality the production would ideally be described by the relationship between N 2 O production and NH + 4 and NO − 3 loss, because the N 2 O xs /AOU ratio masks changes in the relative contribution of nitrification and denitrification at a given oxygen concentration.…”

“…Archaea, for example, were only recently recognised as major contributors to nitrification (e.g., Beman et al, 2012) and marine N 2 O production (Santoro et al, 2011;Löscher et al, 2012). Information on their N 2 O production rates is still very limited.…”