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ABSTRACT: Nitrification is a globally important biogeochemical process, helping to remove excess nitrogen from the biosphere. Thaumarchaeota are important contributors to ammonium oxidation, the first step in nitrification, especially in the ocean. A phylogenetic distinction between clades of marine Thaumarchaeota from shallow versus mesopelagic habitats emerged from the earliest analyses of sequence databases, yet the environmental factors driving these distributions, and their biogeochemical significance, are still debated. Steady-state ammonium concentrations are important determinants; however, environmental concentrations may fluctuate on short time scales, depending on localized coupling between production and consumption. Substrate pulses have been shown to inhibit the activity of Thaumarchaeota cultures via the accumulation of toxic intermediates. Evidence from experiments performed with samples from the Southern Ocean off the West Antarctic Peninsula show that ammonia oxidation can be strongly inhibited by ammonium amendments. We found greater inhibition with mesopelagic samples than with those from shallower water. Pulses of urea also inhibited the oxidation of urea-N, but to a lesser extent than ammonium pulses affected ammonia oxidation. The inhibition also affects carbon fixation, which may thus be greater in the dark ocean than currently believed. The differential response of meso- versus epipelagic Thaumarchaeota populations to pulses of ammonium potentially explains the evolutionary divergence of marine Thaumarchaeota into deep- and shallow-water clades. Measurements of ammonium oxidation rates needed for biogeochemical models are typically made with substrate amendments that may yield artificially low rates, to 25% of the uninhibited rate, in mesopelagic samples. 

NOTE: THIS MS IS TO BE SUBMITTED FOLLOWING OUTCOME OF NATURE COMMUNICATIONS REVIEW OF A COMPANION MS. ABSTRACT (246 words, 1,457 characters including spaces) We measured the oxidation rates of N supplied as urea (UO) and ammonium (AO) in continental shelf and slope waters of the Southern Ocean west of the Antarctic Peninsula during the austral summer of 2018. The response of rates to substrate concentration varied by water mass. Rates increased moderately (up to 200%) with 440 vs 6 nM substrate amendments to samples from the Winter Water (WW, sampled at 35-100 m), but decreased (down to 7%) in samples from the Circumpolar Deep Water (CDW, 175-1000 m). AO rates decreased more than UO rates. This response suggests that CDW Thaumarchaeota are not well adapted to short-term variation in substrate concentrations and that even low amendments (we used 44 or 47 nM) may inhibit oxidation. Rates of AO and UO were not correlated; nor were they correlated with the abundance, or ratios of abundance, of marker genes; or with [NH4+]; or [urea]. UO and AO were distributed uniformly across the study area within a water mass; however, they displayed strong vertical gradients. Rates in most samples from Antarctic Surface Water (ASW, 10-15 m) were below the limit of detection. Highest rates of both processes were in samples from the WW (21.2 and 1.6 nmol L-1 d-1 for AO vs UO, respectively) and CDW (7.9 and 2.5 nmol L-1 d-1), comparable to rates from the study area reported previously. The contribution of UO to nitrite production was ~24% of that from AO alone, comparable to ratios measured at lower latitudes. 

We performed assays of chemoautotrophic carbon fixation and compared measured rates to rates predicted from oxidation of ammonia (AO), urea (UO) and nitrite (NO) N. Water samples used in this study were taken from aerobic shelf waters at stations on the continental shelf and slope west of the Antarctic Peninsula during January and February of 2018 (LMG1801). Chemoautotrophic carbon fixation rates averaged 1.8 and 1.7 nmol C L-1 d-1 in Winter Water (WW, 35-100 m) and Circumpolar Deep Water (CDW, 175-1000 m) water masses, respectively. Integrated over 1 year and a 440 m water column (excluding the Antarctic Surface Water mass, 0-34 m), chemoautotrophic production accounted for ~7 gC m2 yr-1, compared to an estimated mean annual photoautotrophic production of 180 gC m2 y-1. Chemoautotrophy in WW samples supported by AO, UO or NO was the equivalent of 0.91, 0.06, 0.13 nmol C L-1 d-1, while it was the equivalent of 0.37, 0.21 and 0.08 nmol C L-1 d-1 in samples from the CDW water mass. Chemoautotrophy coupled to AO+UO accounted for ~124% and ~55% of measured C fixation rates in these water masses, while chemoautotrophy coupled to complete nitrification (AO+UO+NO) accounted for ~128 and ~60% of measured C fixation rates. The mean turnover times for nitrite pools base on NO were 138 ± 35 d and 15 ± 3 d in WW and CDW samples, respectively. The rate of nitrite production from AO+UO in WW and CDW samples was 503 ± 233 and 24 ± 7 nmol L-1 d-1, respectively. The replacement time for the nitrite pool in the WW water mass by AO+UO calculated from these averages is 33 d while it is 9 d in the CDW. These calculations suggest the possibility of an additional sink for nitrite in the WW. 

NOTE: THIS MS IS STILL IN REVIEW: 8 OCTOBER, 2023.   SUMMARY STATEMENT: Nitrification is a globally important biogeochemical process, helping to remove excess nitrogen from the biosphere. Thaumarchaeota are important contributors to ammonium oxidation, the first step in nitrification, especially in the ocean. A phylogenetic distinction between clades of marine Thaumarchaeota from shallow versus mesopelagic habitats emerged from the earliest analyses of sequence databases, yet the environmental factors driving these distributions, and their biogeochemical significance, are still debated. Steady-state ammonium concentrations are important determinants; however, environmental concentrations may fluctuate on short time scales, depending on localized coupling between production and consumption. Substrate pulses have been shown to inhibit the activity of Thaumarchaeota cultures via the accumulation of toxic intermediates. Here we provide field evidence that ammonia oxidation can be inhibited by ammonium amendments. We found greater inhibition with mesopelagic samples than with those from shallower water, potentially explaining the evolutionary divergence of marine Thaumarchaeota into deep- and shallow-water clades. Further, measurements of ammonium oxidation rates needed for biogeochemical models are typically made with substrate amendments that may yield artificially low rates, to 25% of the uninhibited rate, in mesopelagic samples. The inhibition also affects carbon fixation, which may thus be greater in the dark ocean than currently believed.   ABSTRACT: Oxidation rates of N supplied as ammonium (AO) or urea (UO) by Thaumarchaeota-dominated nitrifying communities in samples of aerobic waters from continental shelf and slope waters of the Southern Ocean west of the Antarctic Peninsula were inhibited by substrate amendments in the low nM range. We found that the response varied consistently by water mass. Rates increased moderately (up to 2-fold) with 44 or 440 vs 6 nM NH4+ amendments to samples from the Winter Water (sampled at 70-80 m), but decreased (down to 7%) in samples from the Circumpolar Deep Water (400-600 m). AO rates decreased more than UO rates. Cell-specific AO rates were lower in CDW samples than in WW samples and chemoautotrophic carbon fixation was also inhibited by NH4+ amendments. We identified similar responses to substrate amendments in data collected elsewhere by others, indicating that inhibition of AO, and to a lesser extent UO, by substrate pulses may be a general phenomenon. Current estimates of nitrification in the epipelagic zone may be ~2-fold greater than in situ, while estimates for the mesopelagic may be ~25% of in situ. Our data suggest that differential adaptation to fluctuating resources may be the basis for the divergence of epipelagic and mesopelagic Thaumarchaeota ecotypes. 

Midwater zooplankton are major agents of biogeochemical transformation in the open ocean; however their characteristics and activity remain poorly known. Here we evaluate midwater zooplankton biomass, amino acid (AA)-specific stable isotope composition (δ15N values) using compound-specific isotope analysis of amino acids (CSIA-AA), trophic position, and elemental composition in the North Pacific Subtropical Gyre (NPSG). We focus on zooplankton collected in the winter, spring, and summer to evaluate midwater trophic dynamics over a seasonal cycle. For the first time we find that midwater zooplankton respond strongly to seasonal changes in production and export in the NPSG. In summer, when export from the euphotic zone is elevated and this ‘summer pulse’ material is transported rapidly to depth, CSIA-AA indicates that large particles (> 53 μm) dominate the food web base for zooplankton throughout the midwaters, and to a large extent even into the upper bathypelagic zone. In winter, when export is low, zooplankton in the mid-mesopelagic zone continue to rely on large particle basal resources, but resident zooplankton in the lower mesopelagic and upper bathypelagic zones switch to include smaller particles (0.7–53 μm) in their food web base, or even a subset of the small particle pool. Midwater zooplankton migration patterns also vary with season, with migrants distributed more evenly at night through the euphotic zone in summer as compared to being more compressed in the upper mixed layer in winter. Deeper zooplankton migration within the mesopelagic zone is also reduced in late summer, likely due to the increased magnitude of large particle material available at depth during this season. Our observed seasonal change in activity and trophic dynamics drives modestly greater biomass in summer than winter through the mesopelagic zone. In contrast midwater zooplankton carbon (C), nitrogen (N), and phosphorus (P) composition does not change with season. Instead we find increasing C:N, C:P, and N:P ratios with greater depths, likely due to decreases in proteinaceous structures and organic P compounds and increases in storage lipids with depth. Our study highlights the importance and diversity of feeding strategies for small zooplankton in NPSG midwaters. Many small zooplankton, such as oncaeid and oithonid copepods, are able to access small particle resources at depth and may be an important trophic link between the microbial loop and deep dwelling micronekton species that also rely on small particle-based food webs. Our observed midwater zooplankton trophic response to export-driven variation in the particle field at depth has important implications for midwater metabolism and the export of C to the deep sea.