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

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 15NH z4 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). 15NH z4 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. 15NH z4 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 kg21 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. Nitrification is a central process in the oceanic nitrogen (N) cycle that acts as a biogeochemical bridge between N inputs from the atmosphere via N2 fixation and N losses via the anaerobic processes of denitrification and anaerobic ammonium oxidation (anammox) (Francis et al. 2007; Canfield et al. 2010a). Because N is a required nutrient for all organisms and limits primary production across large areas of the ocean (Mills et al. 2004), determining how nitrification may affect N availability is of critical importance. However, two emerging lines of research indicate that our understanding of oceanic nitrification is incomplete: nitrification is now thought to occur at higher rates and over greater depth ranges than previously appreciated (Yool et al. 2007; Church et al. 2010; Santoro et al. 2010), and marine Thaumarchaeota (BrochierArmanet et al. 2008) play a substantial but poorly constrained role in nitrification (Agogue et al. 2008; Beman et al. 2008; Santoro et al. 2010). Because the cultivated marine thaumarchaeon Nitrosopumilus maritimus (Könneke et al. 2005) has a remarkable affinity for ammonia (NH3) that would allow organisms with similar physiology to directly and successfully compete with phytoplankton for N (Martens-Habbena et al. 2009), placing quantitative constraints on nitrification rates and nitrifier distributions in the sea is essential to our understanding of oceanic N cycling. The two sequential steps of nitrification are catalyzed by different groups of microorganisms: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) oxidize ammonia (NH3) to nitrite (NO { 2 ), and nitriteoxidizing bacteria (NOB) subsequently oxidize NO 2 to nitrate (NO 3 ); our focus in this study is the first and ratelimiting step of the process: ammonia oxidation. Coupled ammonia and nitrite oxidation consequently convert the most reduced form of N in the ocean (NH3) to the most oxidized form (NO 3 ) such that the energy gained by AOA, AOB, and NOB must ultimately be expended by other organisms when they assimilate NO 2 or NO { 3 (Raven 2009)—phytoplankton, for instance, must reduce NO 2 or NO 3 when these oxidized forms of N are incorporated for biosynthesis. Light is thought to inhibit nitrification, with ammonia oxidizers being less sensitive than NOB (reviewed by Lomas and Lipschultz 2006). However, nitrification can be detected in the euphotic zone (Wankel et al. 2007; Church et al. 2010; Santoro et al. 2010), indicating that nitrification occurs in the light. This also suggests that nitrifiers directly compete with phytoplankton for reduced N. In fact, Yool et al. (2007) combined published open ocean nitrification rate measurements (mostly using 15Nlabeled NH z4 ) with an intensive measurement program in the North Atlantic Ocean and found that specific nitrification rates (normalized to [NH z4 ] and expressed as day21) were high in surface waters and showed little seasonality or variation with latitude. The major implication of this work was that estimates of the f-ratio (Eppley and Peterson 1979)—and hence carbon export—were significantly lower when accounting for near-surface nitrification. Yool and colleagues calculated that 25–30% * Corresponding author: [email protected] Limnol. Oceanogr., 57(3), 2012, 711–726 E 2012, by the Association for the Sciences of Limnology and Oceanography, Inc. doi:10.4319/lo.2012.57.3.0711