Denitrification is a modular process that is mediated by an assemblage of microbes with varying denitrification gene combinations. The controls on these gene combinations, known as modularity, are poorly understood and marine observations are mostly limited to permanently anoxic systems. In this global metagenomic analysis representing 69 water column metagenome samples we report different modularity patterns associated with e...

Nitrification (microbial oxidation of ammonia to nitrite and nitrate) controls nitrogen speciation and is the main source of nitrous oxide (N 2 O) in the ocean. It was recently shown that the most abundant marine ammonia oxidizers, the ammonia‐oxidising archaea (AOA), are also capable of oxidising urea, providing a previously ignored source of nitrite. Here, we show that the relative magnitude of urea and ammonia oxidation rat...

Nitrogen (N) bioavailability affects phytoplankton growth and primary production in the aquatic environment. N bioavailability is partly determined by biological N cycling processes that either transform N species or remove fixed N. Reliable estimates of their kinetic parameters can help understand the distribution of N cycling processes. However, available estimates of kinetic parameters are often derived from microbial isola...

Marine oxygen‐deficient zones represent a natural source of nitrous oxide (N 2 O), a potent greenhouse gas and ozone‐depleting agent. To investigate controls on N 2 O production, the responses of ammonia oxidation (AO) to nitrite () and N 2 O with respect to oxygen (O 2 ), ammonium () and concentrations were evaluated using tracer incubations in the Eastern Tropical North Pacific. Within the oxycline, additions of and O 2 stim...

Estuaries at the global scale are significant but highly uncertain sources of atmospheric nitrous oxide (N 2 O), which is an intense greenhouse gas and ozone depletion agent. As the largest estuary in the United States, the Chesapeake Bay is suggested to be a spatially and temporally variable source and sink of N 2 O. However, limited observations of N 2 O cycling preclude us from estimating and predicting its net N 2 O flux....

Nitrous oxide (N 2 O) is a potent greenhouse gas and an ozone destroying substance. Yet, clear step-by-step protocols to measure N 2 O transformation rates in freshwater and marine environments are still lacking, challenging inter-comparability efforts. Here we present detailed protocols currently used by leading experts in the field to measure water-column N 2 O production and consumption rates in both marine and other aquati...

Recent work has suggested that the oxygen deficient zone (ODZ) and overlying surface waters of the eastern tropical South Pacific (ETSP) is a potential niche for dinitrogen (N 2 ) fixation. Rates of dinitrogen fixation were measured in the ETSP above and within the ODZ in July 2013 using a modified 15 N 2 bubble addition method, wherein a bubble was added, mixed, and then removed, and the isotopic enrichment of the dissolved N...

The three major oxygen deficient zones (ODZs) of the world oceans (eastern tropical North and South Pacific (ETNP and ETSP, respectively), and Arabian Sea (AS) host the vast majority of pelagic fixed nitrogen (N) loss and up to half of total marine N loss. The input of organic matter is an important control on the absolute and relative importance of the two main pathways of N removal (denitrification and anammox). We investiga...

Summary Ammonia‐oxidizing bacteria (AOB) and archaea (AOA) play a vital role in bridging the input of fixed nitrogen, through N‐fixation and remineralization, to its loss by denitrification and anammox. Yet the major environmental factors determining AOB and AOA population dynamics are little understood, despite both groups having a wide environmental distribution. This study examined the relative abundance of both groups of a...