Oxygen Deficient Zones (ODZs) are the largest pelagic sinks of N containing nutrients in the ocean. The offshore Eastern Tropical North Pacific (ETNP) ODZ has been shown to be limited by organic matter. We propose zooplankton/forage fish as a key source of particulate and dissolved organic matter for N 2 production that has previously been ignored. We examined data sets from four cruises (April 2012, January 2017, April 2018, October 2019) at a station in the central ETNP. Backscattering data were used to determine zooplankton vertical migration depths (250–450 m, maximum at 270–280 m). Metazoan DNA concentrations, as measured by quantitative PCR, had a reproducible maximum at 270–280 m, confirming that these signals indicate the presence of zooplankton/forage fish. Additionally, a large maximum in sinking pteropod shells was found at 270 m, indicating that pteropods were part of the migrating community. While crustacean zooplankton have been shown to reduce respiration and excretion of ammonium under anoxia, we found intermittently measurable ammonium concentrations at 270 m. Here we show signatures consistent with organic matter of zooplankton/forage fish origin in the C:N and δ 13 C of suspended and sinking organic matter at the vertical migration depth that suggest transportation to these depths by migrating zooplankton/forage fish. Also coincident with the migration maximum was a reproducible‐between‐years maximum in the biological N 2 gas, and a repeatable shoulder on the nitrite maximum, which suggest that the migrating zooplankton partially fuels N loss. Thus, zooplankton/forage fish appear to be one source of organic matter which can fuel N 2 production in ODZs.

Climate change is expected to increase the strength of ocean Oxygen Deficient Zones (ODZs), but we lack a detailed understanding of the temporal or spatial variability of these ODZs. A 50‐year time series in the Eastern Tropical North Pacific (ETNP) ODZ revealed that it has strengthened by 30% from 1994 to 2019. We subdivided the ODZ into a core and a deep layer based on potential density and revealed that different processes control the magnitude of fixed nitrogen loss between these regions. We postulate that the depth of the upper ETNP ODZ water mass, the 13°C Water, influences the organic carbon supply to the core ODZ and therefore its strength. We correlated the maximum fixed nitrogen loss in the core ODZ with a nearby sedimentary nitrogen isotope record and found that this recent increase in the magnitude of fixed nitrogen loss occurred only a few times over the last 1,200 years. Using this correlation, we derived the first confidence interval for the natural variability of the maximum fixed nitrogen loss within the ETNP ODZ, which has a range of 3.3 μmol kg −1 ( p = 0.01). While the current increase is only comparable to two previous events, it is within the confidence interval for natural variability ( p = 0.03). The deep ODZ also strengthened from 2016 to 2019 by approximately 30%, but this increase occurred more rapidly than the core ODZ, and this dramatic increase was not observed over the rest of the 40 years. Climate‐driven intensification could lead to unprecedented changes in the ETNP ODZ within the next decade.

Nitrite is a key intermediate during fixed nitrogen loss in the ocean, and it accumulates within marine Oxygen Deficient Zones (ODZ). ODZs are vast subsurface regions where nitrate is the dominant electron acceptor, and these regions host approximately 50% of the fixed nitrogen loss in the world's oceans. Nitrite accumulates in these waters, and recent research has discovered substantial reoxidation of nitrite back to nitrate, a significant process in the global nitrogen cycle. Partitioning between reduction and oxidation determines if marine fixed nitrogen is lost or recycled. Investigations into nitrite oxidation typically rely on results from incubations, which limits the spatiotemporal sampling coverage. Using basin-scale data, we analyzed the ratios of nutrient regeneration within the three water masses that feed the Eastern Tropical North Pacific (ETNP) ODZ. Deviations in the ratios of nutrient regeneration from Redfield stoichiometry indicated prolific nitrite reoxidation across this region. We estimate that 79 +/- 7% of the nitrite produced in the ODZ between the 26.2 and 26.4 kg m(-3) isopycnals is reoxidized, whereas 54 +/- 2% of the nitrite produced between the 26.7 and 26.9 kg m(-3) isopycnals is reoxidized. Our analysis also illustrates discrete "metabolic switching points" from primarily aerobic to primary anaerobic processes, which occur in each water mass. We applied water mass analysis to repeat cruises on the WOCE P18 line from Baja California to 10 degrees N, which revealed high spatiotemporal variability in nitrite reoxidation. These results confirm previous measurements of significant fixed nitrogen recycling across the ETNP; however, our analysis enables high-resolution estimates of this process.

Earth and Space Science Open Archive This work has been accepted for publication in Global Biogeochemical Cycles. Version of RecordESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary. Learn more about preprints. preprintOpen AccessYou are viewing an older version [v1]Go to new versionSlow particle remineralization, rather than suppressed disaggregation, drives efficient flux transfer through the Eastern Tropical North Pacific Oxygen Deficient ZoneAuthorsJacobCramiDClaraFuchsmaniDMeganDuffyiDJessicaPrettyiDRachelLekanoffJacquelynNeibaueriDShirleyLeungiDKlaus B.HuebertiDThomasWeberDanieleBianchiiDNatalyaEvansiDAllanDevoliDRichardKeiliDAndrewMcDonnelliDSee all authors Jacob CramiDCorresponding Author• Submitting AuthorHorn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, USA.iDhttps://orcid.org/0000-0001-9546-1130view email addressThe email was not providedcopy email addressClara FuchsmaniDHorn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, USA.iDhttps://orcid.org/0000-0002-9151-4984view email addressThe email was not providedcopy email addressMegan DuffyiDSchool of Oceanography, University of Washington Seattle, Seattle, WA, USA.iDhttps://orcid.org/0000-0002-3212-4927view email addressThe email was not providedcopy email addressJessica PrettyiDCollege of Fisheries and Ocean SciencesUniversity of Alaska FairbanksFairbanksAKUSA.iDhttps://orcid.org/0000-0001-6542-8540view email addressThe email was not providedcopy email addressRachel LekanoffCollege of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA.view email addressThe email was not providedcopy email addressJacquelyn NeibaueriDSchool of Oceanography, University of Washington Seattle, Seattle, WA, USA.iDhttps://orcid.org/0000-0001-9920-2558view email addressThe email was not providedcopy email addressShirley LeungiDSchool of Oceanography, University of Washington Seattle, Seattle, WA, USA.iDhttps://orcid.org/0000-0002-6659-6420view email addressThe email was not providedcopy email addressKlaus B. HuebertiDHorn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, USA.iDhttps://orcid.org/0000-0002-2432-7337view email addressThe email was not providedcopy email addressThomas WeberSchool of Arts and Sciences, University of Rochester, Rochester, NY, USA.view email addressThe email was not providedcopy email addressDaniele BianchiiDDepartment of Atmospheric and Oceanic Sciences, University of California Los Angeles, Los Angeles, CA, USA.iDhttps://orcid.org/0000-0002-6621-0858view email addressThe email was not providedcopy email addressNatalya EvansiDDepartment of Biological Sciences, University of Southern California, Los Angeles, CA, USA.iDhttps://orcid.org/0000-0002-2726-8272view email addressThe email was not providedcopy email addressAllan DevoliDSchool of OceanographyUniversity of Washington SeattleSeattleWAUSA.iDhttps://orcid.org/0000-0003-4016-9399view email addressThe email was not providedcopy email addressRichard KeiliDSchool of Oceanography, University of Washington Seattle, Seattle, WA, USA.iDhttps://orcid.org/0000-0001-7483-1606view email addressThe email was not providedcopy email addressAndrew McDonnelliDUniversity of Alaska Fairbanks, College of Fisheries and Ocean Sciences Fairbanks, AK, USA.iDhttps://orcid.org/0000-0003-1408-4869view email addressThe email was not providedcopy email address

Models and observations suggest that particle flux attenuation is lower across the mesopelagic zone of anoxic environments compared to oxic environments. Flux attenuation is controlled by microbial metabolism as well as aggregation and disaggregation by zooplankton, all of which shape the relative abundance of differently sized particles. Observing and modeling particle spectra can provide information about the contributions of these processes. We measured particle size spectrum profiles at one station in the oligotrophic Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) using an underwater vision profiler (UVP), a high‐resolution camera that counts and sizes particles. Measurements were taken at different times of day, over the course of a week. Comparing these data to particle flux measurements from sediment traps collected over the same time‐period allowed us to constrain the particle size to flux relationship, and to generate highly resolved depth and time estimates of particle flux rates. We found that particle flux attenuated very little throughout the anoxic water column, and at some time points appeared to increase. Comparing our observations to model predictions suggested that particles of all sizes remineralize more slowly in the ODZ than in oxic waters, and that large particles disaggregate into smaller particles, primarily between the base of the photic zone and 500 m. Acoustic measurements of multiple size classes of organisms suggested that many organisms migrated, during the day, to the region with high particle disaggregation. Our data suggest that diel‐migrating organisms both actively transport biomass and disaggregate particles in the ODZ core.

Oceanic oxygen deficient zones (ODZs) influence global biogeochemical cycles in a variety of ways, most notably by acting as a sink for fixed nitrogen (Codispoti et al. 2001). Optimum multiparameter analysis of data from two cruises in the Eastern Tropical North Pacific (ETNP) was implemented to develop a water mass analysis for the large ODZ in this region. This analysis reveals that the most pronounced oxygen deficient conditions are within the 13°C water (13CW) mass, which is distributed via subsurface mesoscale features such as eddies branching from the California Undercurrent. Nitrite accumulates within these eddies and slightly below the core of the 13CW. This water mass analysis also reveals that the 13CW and deeper Northern Equatorial Pacific Intermediate Water (NEPIW) act as the two Pacific Equatorial source waters to the California Current System. The Equatorial Subsurface Water and Subtropical Subsurface Water are synonymous with the 13CW and this study refers to this water mass as the 13CW based on its history. Since the 13CW has been found to dominate the most pronounced oxygen deficient conditions within the Eastern Tropical South Pacific ODZ and the Peru‐Chile Undercurrent, the 13CW and the NEPIW define boundaries for oxygen minimum conditions across the entire eastern Pacific Ocean.

The upwelling system of coastal Peru supports very high primary production, contributing to an oxygen deficient zone (ODZ) in subsurface waters and high organic matter deposition rates to underlying sediments. Although anammox and denitrification have been relatively well studied in ODZ waters, few studies have investigated these processes in the underlying sediments. We sampled seven stations over a large geographic area along the Peru margin, spanning a water depth of 100-3240 m. At two of the central shelf stations (100 m and 325 m), we observed Thioploca, with a well-developed mat at the shallowest station (100 m). We measured sediment properties and conducted shipboard N-15-incubations of homogenized sediments to determine potential rates of anammox and denitrification and potential controlling factors at each station. Diversity of anammox bacteria based on 16S rRNA and hydrazine oxidoreductase (hzo) sequences and hzo gene abundances were measured at each station. Overall, organic C content was high across the stations (3-12%), except for two of the deepest stations (similar to 1.5%). Porewater ammonium fluxes and ammonium production rates in shipboard incubations, reflecting sediment organic carbon decomposition rates, were higher at the two central shelf stations compared to the other stations. The range in average potential rates was 2.1-80.4 nmol N cm(-3)h(-1) for denitrification and 1.8-44.2 nmol N cm(-3)h(-1) for anammox. The range in relative anammox (ra) across stations was 2.6-47.4%, with an average of 34.2%. The lowest ra was found at the shallowest shelf station with Thioploca mats and highest ammonium production rates. The ra jumped up to 45.9% at the station with the next highest ammonium production rates, corresponding to the deeper shelf station (325 m). At the other stations, ra was relatively high (39.6-47.4%), except at one station (16.3%), reflecting similar ammonium production rates due to decomposition across these stations. Anammox bacteria in the Candidatus Scalindua genus were the only anammox bacteria detected in Peru margin sediments based on 16S rRNA or hzo sequences. Copy number of hzo indicated abundant populations of anammox bacteria across the stations. However, hzo copy number did not correlate with anammox rates or ra. Overall, our results suggest that anammox contributes significantly to N-2 production in Peru margin sediments, except in shelf sediments with high decomposition rates and dense Thioploca mats.

At this point ocean deoxygenation is well documented, including in oxygen minimum zones (OMZs). Within the large OMZs of the Arabian Sea and eastern Pacific are imbedded areas where oxygen concentrations are so low that they are undetectable by routine CTD sensors (oxygen deficient zones, ODZs). How do we determine if these ODZ are losing O2? Furthermore, denitrification occurs in oxygen minimum zones (OMZs) so one might hypothesize that denitrification is likewise expanding if oxygen is decreasing. This is important because the ocean's fixed nitrogen inventory limits the productivity over large marine areas. We have investigated these questions in the largest OMZ, the eastern tropical North Pacific (ETNP) through an analysis of 6 repeats of a 1000 km transect along 110o West in the heart of the ETNP ODZ between 1971-2019. We use N*, a stoichiometric parameter calculated from nitrate and phosphate, as our indicator of denitrification. The more Negative N* the more denitrification has occurred. After secondary QC the values of O2 concentration between potential density 24.75 and 1000m along with N* were integrated across the transect and over the depth of the ODZ. The results show a clear decrease in oxygen inventory along with an increase in N*, suggesting deoxygenation and intensification of denitrification over during the 50 year period. We discuss potential mechanisms for denitrification signal increase including ENSO, Pacific Decadal Oscillation, tropical hurricane intensity, and variations in thermocline depth.

Up to half of marine N losses occur in oxygen-deficient zones (ODZs). Organic matter flux from productive surface waters is considered a primary control on N 2 production. Here we investigate the offshore Eastern Tropical North Pacific (ETNP) where a secondary chlorophyll a maximum resides within the ODZ. Rates of primary production and carbon export from the mixed layer and productivity in the primary chlorophyll a maximum were consistent with oligotrophic waters. However, sediment trap carbon and nitrogen fluxes increased between 105 and 150 m, indicating organic matter production within the ODZ. Metagenomic and metaproteomic characterization indicated that the secondary chlorophyll a maximum was attributable to the cyanobacterium Prochlorococcus , and numerous photosynthesis and carbon fixation proteins were detected. The presence of chemoautotrophic ammonia-oxidizing archaea and the nitrite oxidizer Nitrospina and detection of nitrate oxidoreductase was consistent with cyanobacterial oxygen production within the ODZ. Cyanobacteria and cyanophage were also present on large (>30 μm) particles and in sediment trap material. Particle cyanophage-to-host ratio exceeded 50, suggesting that viruses help convert cyanobacteria into sinking organic matter. Nitrate reduction and anammox proteins were detected, congruent with previously reported N 2 production. We suggest that autochthonous organic matter production within the ODZ contributes to N 2 production in the offshore ETNP.

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 (NH4+)-N-15-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.

Cobalamin (vitamin B12 ) is a precious resource in natural systems that is produced by select prokaryotes and required by a broad range of organisms. In this way, the production of cobalamin reinforces numerous microbial interdependencies. Here we report the accumulation of an unusual form of cobalamin, nitrocobalamin (NO2 -cobalamin), in a marine oxygen deficient zone (ODZ), isolates of ammonia-oxidizing archaea (AOA), and an anaerobic ammonium-oxidizing (anammox) bacteria enriched bioreactor. Low oxygen waters were enriched in NO2 -cobalamin, and AOA isolates experiencing ammonia or copper stress produced more NO2 -cobalamin, though there is wide strain-to-strain and batch-to-batch variability. NO2 -cobalamin has no known biochemical role. We hypothesize that AOA and anammox bacteria are a source of marine NO2 -cobalamin in the environment via a reactive nitrogen intermediate. These findings suggest connections between cobalamin forms and nitrogen transformations, physiological stress and ocean deoxygenation.

Fingerprinting ocean acidification (OA) in US West Coast waters is extremely challenging due to the large magnitude of natural carbonate chemistry variations common to these regions. Additionally, quantifying a change requires information about the initial conditions, which is not readily available in most coastal systems. In an effort to address this issue, we have collated high-quality publicly available data to characterize the modern seasonal carbonate chemistry variability in marine surface waters of the US Pacific Northwest. Underway ship data from version 4 of the Surface Ocean CO2 Atlas, discrete observations from various sampling platforms, and sustained measurements from regional moorings were incorporated to provide ∼ 100 000 inorganic carbon observations from which modern seasonal cycles were estimated. Underway ship and discrete observations were merged and gridded to a 0.1° × 0.1° scale. Eight unique regions were identified and seasonal cycles from grid cells within each region were averaged. Data from nine surface moorings were also compiled and used to develop robust estimates of mean seasonal cycles for comparison with the eight regions. This manuscript describes our methodology and the resulting mean seasonal cycles for multiple OA metrics in an effort to provide a large-scale environmental context for ongoing research, adaptation, and management efforts throughout the US Pacific Northwest. Major findings include the identification of unique chemical characteristics across the study domain. There is a clear increase in the ratio of dissolved inorganic carbon (DIC) to total alkalinity (TA) and in the seasonal cycle amplitude of carbonate system parameters when moving from the open ocean North Pacific into the Salish Sea. Due to the logarithmic nature of the pH scale (pH = −log10[H+], where [H+] is the hydrogen ion concentration), lower annual mean pH values (associated with elevated DIC : TA ratios) coupled with larger magnitude seasonal pH cycles results in seasonal [H+] ranges that are ∼ 27 times larger in Hood Canal than in the neighboring North Pacific open ocean. Organisms living in the Salish Sea are thus exposed to much larger seasonal acidity changes than those living in nearby open ocean waters. Additionally, our findings suggest that lower buffering capacities in the Salish Sea make these waters less efficient at absorbing anthropogenic carbon than open ocean waters at the same latitude.All data used in this analysis are publically available at the following websites: Surface Ocean CO2 Atlas version 4 coastal data, https://doi.pangaea.de/10.1594/PANGAEA.866856 (Bakker et al., 2016a);National Oceanic and Atmospheric Administration (NOAA) West Coast Ocean Acidification cruise data, https://doi.org/10.3334/CDIAC/otg.CLIVAR_NACP_West_Coast_Cruise_2007 (Feely and Sabine, 2013); https://doi.org/10.7289/V5JQ0XZ1 (Feely et al., 2015b); https://data.nodc.noaa.gov/cgi-bin/iso?id=gov.noaa.nodc:0157445 (Feely et al., 2016a); https://doi.org/10.7289/V5C53HXP (Feely et al., 2015a);University of Washington (UW) and Washington Ocean Acidification Center cruise data, https://doi.org/10.5281/zenodo.1184657 (Fassbender et al., 2018);Washington State Department of Ecology seaplane data, https://doi.org/10.5281/zenodo.1184657 (Fassbender et al., 2018);NOAA Moored Autonomous pCO2 (MAPCO2) buoy data, https://doi.org/10.3334/CDIAC/OTG.TSM_LAPUSH_125W_48N (Sutton et al., 2012); https://doi.org/10.3334/CDIAC/OTG.TSM_WA_125W_47N (Sutton et al., 2013); https://doi.org/10.3334/CDIAC/OTG.TSM_DABOB_122W_478N (Sutton et al., 2014a); https://doi.org/10.3334/CDIAC/OTG.TSM_TWANOH_123W_47N (Sutton et al., 2016a);UW Oceanic Remote Chemical/Optical Analyzer buoy data, https://doi.org/10.5281/zenodo.1184657 (Fassbender et al., 2018);NOAA Pacific Coast Ocean Observing System cruise data, https://doi.org/10.5281/zenodo.1184657 (Fassbender et al., 2018).

Oxygen deficient zones host up to 50% of marine N-2 production and the Eastern Tropical North Pacific (ETNP) is the largest marine oxygen deficient zone. We measured delta N-55-NO3-, delta N-55-NO2-, and delta N-55-N-2 at 7 stations along a transect normal to the coast in the heart of the ETNP oxygen deficient zone in 2012. The delta N-55-N-2 minimum was 0.34 parts per thousand at 300 m, which corresponded with the N-2:Ar maximum. When the atmospheric N-2 background was removed, the biological delta N-55-N2 for the ODZ ranged from -7 parts per thousand to -22 parts per thousand. In the ODZ, delta N-55-NO3- ranged from 15 to 24 parts per thousand while delta N-55-NO2- was generally between -11 and -18 parts per thousand, generating differences up to 40 parts per thousand between delta N-55-NO3- and delta N-55-NO2-. The isotopic separation between nitrite and nitrogen gas (Delta N-15 (NO2-N2)) changed sign from similar to 5 parts per thousand at the top of the oxygen deficient zone to similar to-10 parts per thousand at 300 m, indicating an important shift in nitrogen cycling with depth. We calculated the closed system Rayleigh isotope effect (epsilon) for N-2 production from both the delta N-55-DIN (epsilon(DIN) = 26 parts per thousand +/- 11 parts per thousand) and delta N-55-N-2 (epsilon(N2) = 27 +/- 6 parts per thousand) data. When examined individually by depth, both epsilon(DIN), and epsilon(N2) matched closely and both epsilon depth profiles showed maximal fractionation at 300 m. Additionally, closed system isotope effects were calculated for one offshore station from the Arabian Sea in 2007 using delta N-55-N-2 (epsilon(N2) = 24 +/- 4 parts per thousand) and delta N-55-DIN (epsilon(DIN) = 26 +/- 3 parts per thousand). The relatively large isotope effects for N-2 production appear to be found in both major offshore oxygen deficient zones, which implies a large denitrification term in the marine N budget.

Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to half of marine N loss through conversion of nutrients to N2O and N2. This N loss is accomplished by a consortium of diverse microbes, many of which remain uncultured. Here, we characterize genes for all steps in the anoxic N cycle in metagenomes from the water column and >30 μm particles from the Eastern Tropical North Pacific (ETNP) ODZ. We use an approach that allows for both phylogenetic identification and semi-quantitative assessment of gene abundances from individual organisms, and place these results in context of chemical measurements and rate data from the same location. Denitrification genes were enriched in >30 μm particles, even in the oxycline, while anammox bacteria were not abundant on particles. Many steps in denitrification were encoded by multiple phylotypes with different distributions. Notably three N2O reductases (nosZ), each with no cultured relative, inhabited distinct niches; one was free-living, one dominant on particles and one had a C terminal extension found in autotrophic S-oxidizing bacteria. At some depths >30% of the community possessed nitrite reductase nirK. A nirK OTU linked to SAR11 explained much of this abundance. The only bacterial gene found for NO reduction to N2O in the ODZ was a form of qnorB related to the previously postulated "nitric oxide dismutase," hypothesized to produce N2 directly while oxidizing methane. However, similar qnorB-like genes are also found in the published genomes of many bacteria that do not oxidize methane, and here the qnorB-like genes did not correlate with the presence of methane oxidation genes. Correlations with N2O concentrations indicate that these qnorB-like genes likely facilitate NO reduction to N2O in the ODZ. In the oxycline, qnorB-like genes were not detected in the water column, and estimated N2O production rates from ammonia oxidation were insufficient to support the observed oxycline N2O maximum. However, both qnorB-like and nosZ genes were present within particles in the oxycline, suggesting a particulate source of N2O and N2. Together, our analyses provide a holistic view of the diverse players in the low oxygen nitrogen cycle.

Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1T, HCA1T, HCE1T and PS0T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15-0.26 µm in diameter and 0.50-1.59 µm in length. Motility was not observed, although strain PS0T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1T, HCE1T, and PS0T. Strain PS0T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B1 (thiamine), B2 (riboflavin), B6 (pyridoxine), and B12 (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0-34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1T (=ATCC TSD-97T =NCIMB 15022T), HCA1T (=ATCC TSD-96T), HCE1T (=ATCC TSD-98T), and PS0T (=ATCC TSD-99T) are type strains of the species Nitrosopumilusmaritimus sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria.

In the Bering Sea, the nitrogen cycle near Nunivak Island is complicated due to limited nutrient replenishment across this broad shelf, and substantial nitrogen loss through sedimentary processes. While diffusion at the inner front may periodically support new production, the inner shelf in this region is generally described as a regenerative system. This study combines hydrographic surveys with measurements of nitrogen assimilation and benthic fluxes to examine nitrogen cycling on the inner shelf, and connectivity between the middle and inner shelves of the southern and central Bering Sea. Results establish the inner shelf as primarily a regenerative system even in spring, although new production can occur at the inner front. Results also identify key processes that influence nutrient supply to the inner shelf and reveal coupling between the middle shelf nutrient pool and production on the inner shelf.

High representation by ammonia-oxidizing archaea (AOA) in marine systems is consistent with their high affinity for ammonia, efficient carbon fixation, and copper (Cu)-centric respiratory system. However, little is known about their response to nutrient stress. We therefore used global transcriptional and proteomic analyses to characterize the response of a model AOA, Nitrosopumilus maritimus SCM1, to ammonia starvation, Cu limitation and Cu excess. Most predicted protein-coding genes were transcribed in exponentially growing cells, and of ~74% detected in the proteome, ~6% were modified by N-terminal acetylation. The general response to ammonia starvation and Cu stress was downregulation of genes for energy generation and biosynthesis. Cells rapidly depleted transcripts for the A and B subunits of ammonia monooxygenase (AMO) in response to ammonia starvation, yet retained relatively high levels of transcripts for the C subunit. Thus, similar to ammonia-oxidizing bacteria, selective retention of amoC transcripts during starvation appears important for subsequent recovery, and also suggests that AMO subunit transcript ratios could be used to assess the physiological status of marine populations. Unexpectedly, cobalamin biosynthesis was upregulated in response to both ammonia starvation and Cu stress, indicating the importance of this cofactor in retaining functional integrity during times of stress.

Recent studies point to the importance of oxygen (O2 ) in controlling the distribution and activity of marine ammonia-oxidizing archaea (AOA), one of the most abundant prokaryotes in the ocean. The AOA are associated with regions of low O2 tension in oceanic oxygen minimum zones (OMZs), and O2 availability is suggested to influence their production of the ozone-depleting greenhouse gas nitrous oxide (N2 O). We show that marine AOA available in pure culture sustain high ammonia oxidation activity at low μM O2 concentrations, characteristic of suboxic regions of OMZs (<10 µM O2 ), and that atmospheric concentrations of O2 may inhibit the growth of some environmental populations. We quantify the increasing N2 O production by marine AOA with decreasing O2 tensions, consistent with the plausibility of an AOA contribution to the accumulation of N2 O at the oxic-anoxic redox boundaries of OMZs. Variable sensitivity to peroxide also suggests that endogenous or exogenous reactive oxygen species are of importance in determining the environmental distribution of some populations.