Eastern Tropical North Pacific Research Articles

Species‐Dependent Chromium Isotope Fractionation Across the Eastern Tropical North Pacific Oxygen Minimum Zone

AbstractThe stable chromium (Cr) isotope system is an emerging paleoredox proxy. Interpretation of sedimentary and seawater δ53Cr (53Cr/52Cr relative to SRM 979) hinges on our understanding of the isotopic fractionations during Cr sequestration from seawater to sediments. Seawater δ53Cr values reported thus far are for total dissolved Cr. This study reports the δ53Cr of both dissolved Cr (III) and dissolved Cr (VI) across the oxygen minimum zone in the eastern tropical North Pacific off Manzanillo, Mexico. Dissolved Cr (III) accounts for 48% to 54% total dissolved Cr in this region. There are no correlations between O2 and Cr concentrations, or O2 concentrations and δ53Cr throughout the water column. The δ53Cr of Cr (III) is lower than that of Cr (VI) by a relatively constant offset (0.42 ± 0.15‰, 1σ, n = 5) and is also uncorrelated with dissolved O2 concentration. These observations provide part of the foundation for using δ53Cr of the authigenic Cr in organic‐rich shales to reconstruct seawater δ53Cr. A survey of growing literature Cr concentration and δ53Cr data suggests that the Cr isotope fractionation factor in the global ocean is likely more complex than previously thought. More future species‐dependent Cr isotope studies could shed new light on the biogeochemical processes controlling the oceanic Cr isotope fractionation.

Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones

Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene arrA was enriched on large particles (>30 um), similar to the forward bacterial dsrA gene of sulfate-reducing bacteria, which is involved in the cryptic cycling of sulfur in ODZs. Arsenic respiratory genes were expressed in metatranscriptomic libraries from the ETNP and the Eastern Tropical South Pacific (ETSP) ODZ, indicating arsenotrophy is a metabolic pathway actively utilized in anoxic marine water columns. Together these results suggest arsenic-based metabolisms support organic matter production and impact nitrogen biogeochemical cycling in modern oceans. In early anoxic oceans, especially during periods of high marine arsenic concentrations, they may have played a much larger role.

Centennial OMZ changes in the NW Mexican Margin from geochemical and foraminiferal sedimentary records

Oxygen minimum zones (OMZs) are predicted to expand in the near future due to continued global warming, with largest declines in oxygen occurring within the strong tropical OMZs. In this study, shifts in the position and intensity of the OMZ in the Eastern Tropical North Pacific (ETNP) were examined using three 210Pb-dated sediment cores collected along the continental shelf and slope of the NW Mexican Margin (southwest of Mazatlán). Using a suite of redox sensitive elements, bulk element and physical analyses, three main factors were identified as driving the geochemical signatures of trace elements across the NW Mexican Margin: 1) terrigenous input, 2) organic matter scavenging and 3) bottom water oxygen content. Downcore trends in benthic foraminiferal assemblages and authigenic concentrations of Mo and U suggest that dysoxic conditions were more intense and covered a larger depth range prior to the 20th century followed by a reduction in both size and strength of the OMZ over the last century.

The Carbon:234Thorium ratios of sinking particles in the California current ecosystem 1: relationships with plankton ecosystem dynamics

We investigated variability in the C:234Th ratio of sinking particles and its relationship to changing water column characteristics and plankton ecological dynamics during 29 Lagrangian experiments conducted on six cruises of the California Current Ecosystem Long-Term Ecological Research (CCE-LTER) Program. C:234Th ratios of sinking particles collected by a surface-tethered sediment trap (C:234ThST) varied from 2.3 to 20.5 μmol C dpm−1 over a depth range of 47–150 m. C:234ThST was significantly greater (by a factor of 1.8) than C:234Th ratios of suspended >51-μm particles collected in the same water parcels with in situ pumps. C:234Th ratios of large (>200-μm) sinking particles also exceeded those of smaller sinking particles. C:234ThST decreased with depth from the base of the euphotic zone through the upper twilight zone. C:234ThST was positively correlated with several indices of ecosystem productivity including particulate organic carbon (POC) and chlorophyll (Chl) concentrations, mesozooplankton biomass, and the fraction of Chl >20-μm. Principal component analysis and multiple linear regression suggested that decaying phytoplankton blooms exhibited higher C:234ThST than actively growing blooms at similar biomass levels. C:234ThST was positively correlated with indices of the fractional contribution of fecal pellets in sediment traps when the proportion of fecal pellets was low in the traps, likely because of a correlation between mesozooplankton biomass and other indices of ecosystem productivity. However, when fecal pellets were a more important component of sinking material, C:234ThST decreased with increasing fecal pellet content. C:234ThST was also positively correlated with the Si:C ratio of sinking particles. Across the dataset (and across depths) a strong correlation was found between C:234ThST and the ratio of vertically-integrated POC to vertically-integrated total water column 234Th (vC:234Thtot). A mechanistic one-layer, two-box model of thorium sorption and desorption was invoked to explain this correlation. Two empirical models (one using vC:234Thtot; one using depth and vertically-integrated Chl) were developed to predict C:234Th ratios in this coastal upwelling biome. The former regression (log10(C:234ThST) = 0.43 × log10(vC:234Thtot) + 0.53) was found to also be a reasonable predictor for C:234ThST from diverse regions including the Southern Ocean, Sargasso Sea, Subarctic North Pacific, and Eastern Tropical North Pacific.

Ocean deoxygenation and zooplankton: Very small oxygen differences matter.

Oxygen minimum zones (OMZs), large midwater regions of very low oxygen, are expected to expand as a result of climate change. While oxygen is known to be important in structuring midwater ecosystems, a precise and mechanistic understanding of the effects of oxygen on zooplankton is lacking. Zooplankton are important components of midwater food webs and biogeochemical cycles. Here, we show that, in the eastern tropical North Pacific OMZ, previously undescribed submesoscale oxygen variability has a direct effect on the distribution of many major zooplankton groups. Despite extraordinary hypoxia tolerance, many zooplankton live near their physiological limits and respond to slight (≤1%) changes in oxygen. Ocean oxygen loss (deoxygenation) may, thus, elicit major unanticipated changes to midwater ecosystem structure and function.

Intact polar lipids in the water column of the eastern tropical North Pacific: abundance and structural variety of non-phosphorus lipids

Abstract. Intact polar lipids (IPLs) are the main building blocks of cellular membranes and contain chemotaxonomic, ecophysiological and metabolic information, making them valuable biomarkers in microbial ecology and biogeochemistry. This study investigates IPLs in suspended particulate matter (SPM) in the water column of the eastern tropical North Pacific Ocean (ETNP), one of the most extensive open-ocean oxygen minimum zones (OMZs) in the world, with strong gradients of nutrients, temperature and redox conditions. A wide structural variety in polar lipid head-group composition and core structures exists along physical and geochemical gradients within the water column, from the oxygenated photic zone to the aphotic OMZ. We use this structural diversity in IPLs to evaluate the ecology and ecophysiological adaptations that affect organisms inhabiting the water column, especially the mid-depth OMZ in the context of biogeochemical cycles. Diacylglycerol phospholipids are present at all depths, but exhibit the highest relative abundance and compositional variety (including mixed acyl/ether core structures) in the upper and core OMZ where prokaryotic biomass was enriched. Surface ocean SPM is dominated by diacylglycerol glycolipids that are found in photosynthetic membranes. These and other glycolipids with varying core structures composed of ceramides and hydroxylated fatty acids are also detected with varying relative abundances in the OMZ and deep oxycline, signifying additional non-phototrophic bacterial sources for these lipids. Betaine lipids (with zero or multiple hydroxylations in the core structures) that are typically assigned to microalgae are found throughout the water column down to the deep oxycline but do not show a depth-related trend in relative abundance. Archaeal IPLs comprised of glycosidic and mixed glycosidic-phosphatidic glycerol dibiphytanyl glycerol tetraethers (GDGTs) are most abundant in the upper OMZ, where nitrate maxima point to ammonium oxidation but increase in relative abundance in the core OMZ and deep oxycline. The presence of non-phosphorus “substitute” lipids within the OMZ suggest that the indigenous microbes might be phosphorus limited (P starved) at ambient phosphate concentrations of 1 to 3.5 µM, although specific microbial sources for many of these lipids still remain unknown.

Anaerobic Ammonium Oxidation Linked to Microbial Reduction of Natural Organic Matter in Marine Sediments

Identification of microbial processes driving the loss of nitrogen from the oceans is of paramount relevance as these processes affect primary productivity in these ecosystems, which ultimately affects global biogeochemical cycles. Denitrification and anammox (anaerobic ammonium oxidation coupled to nitrite reduction) are the only identified processes so far that lead to nitrogen loss in marine environments. Here we provide stoichiometric and spectroscopic evidence, as well as tracer analysis with [15N]ammonium, revealing that anaerobic ammonium oxidation linked to the microbial reduction of natural organic matter (NOM) fuels nitrogen loss in marine sediments from the eastern tropical North Pacific coast. Tracer analysis revealed that the NOM-dependent anammox process was responsible for producing ∼1.5 μg of 15N2 (g of sediment)−1 day–1 after incubation for 27 days in sediment incubations amended with Pahokee peat, while intrinsic NOM present in the sediment promoted the production of ∼0.4 μg of 15N2 (g o...

Tracing ventilation source of tropical pacific oxygen minimum zones with an adjoint global ocean transport model

To better understand the changes in the ventilation of Oxygen Minimum Zones (OMZs) in the Eastern Tropical North Pacific (ETNP) and South Pacific (ETSP), we use an adjoint global transport model to trace the surface locations of their source waters. The transit times for surface waters to reach the OMZs are obtained for steady-state transport. For the ETNP OMZ, 26% of the water volume makes last contact with the atmosphere in the Equatorial North Pacific with mean transit time of 109 years. Mid-latitude North and South Pacific make comparable volumetric contributions (17% and 18% respectively), but have mean transit times that differ by a factor of 2 (186 and 382 years, respectively). The combined contribution of the Southern Ocean and North Atlantic accounts for 16% of the ETNP OMZ volume. The mean transit time from these remote regions is in excess of 2500 years. For the ETSP OMZ, 29% of water volume originates from the surface of the equatorial South Pacific with a mean transit time of 65 years while 36% originates from the mid-latitude South Pacific with a mean transit-time of 157 years. The relative contribution of the two regions indicates that the meridional ventilation pathway from the mid- latitudes is of equal importance as the ventilation via eastward equatorial current system. The mean transit-times computed here help clarify the timescales with which advective- diffusive processes link changes in surface ocean processes to the OMZs of the Eastern Tropical Pacific.

Accumulation of NO2 -cobalamin in nutrient-stressed ammonia-oxidizing archaea and in the oxygen deficient zone of the eastern tropical North Pacific.

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.

A gas tension device for the mesopelagic zone

Gas Tension Devices (GTDs) are used to acquire accurate and stable measurements of gas tension, or total dissolved air pressure of the gases dissolved in water. GTDs operate by measuring the barometric pressure of a small sample volume of air separated from the water by a gas-permeable membrane resting on a rigid permeable support. Existing GTDs use a compressible polydimethylsiloxane (PDMS) membrane which exhibit several undesirable features: the membrane collapses with increasing hydrostatic pressure, which reduces the permeability; a collapsed membrane increases the response; collapse and expansion generate large transient signals [McNeil et al. 2006a]. Also, reverse osmosis becomes a problem at depths greater than approximately 330 m in seawater. We present a new GTD that solves the hydrostatic pressure-generated transients and changing response times, and alleviates reverse-osmosis. These improvements allow the new GTD to be used in the mesopelagic zone. The new GTD uses a custom designed small diameter (4 cm) thin (130 µm) incompressible composite Teflon-AF 2400 membrane. It can operate to a depth of at least 1000 m with a depth-independent response time of approximately 35 min. We estimated the hydrostatic pressure dependence of Henry's Law solubilities as we characterized the new Teflon-membrane GTD using data collected in the laboratory. Field testing occurred on two APL/UW Gas-Profiling Floats deployed in the Eastern Tropical North Pacific (ETNP) for 15 days during May 2014. The floats profiled between the surface and 400 m depth, sampling gas tension within the Oxygen Deficient Zone. The gas tension-profiles from the two GTDs were validated against gas tension derived from independent N2:Ar and Ar concentrations measured by mass spectrometry, agreeing to within ± 0.6% and ± 0.4%.

Utilization of urea and cyanate in waters overlying and within the eastern tropical north Pacific oxygen deficient zone.

In marine oxygen deficient zones (ODZs), which contribute up to half of marine N loss, microbes use nitrogen (N) for assimilatory and dissimilatory processes. Here, we examine N utilization above and within the ODZ of the Eastern Tropical North Pacific Ocean, focusing on distribution, uptake and genes for the utilization of two simple organic N compounds, urea and cyanate. Ammonium, urea and cyanate concentrations generally peaked in the oxycline while uptake rates were highest in the surface. Within the ODZ, concentrations were lower, but urea N and C and cyanate C were taken up. All identified autotrophs had an N assimilation pathway that did not require external ammonium: ODZ Prochlorococcus possessed genes to assimilate nitrate, nitrite and urea; nitrite oxidizers (Nitrospina) possessed genes to assimilate nitrite, urea and cyanate; anammox bacteria (Scalindua) possessed genes to utilize cyanate; and ammonia-oxidizing Thaumarchaeota possessed genes to utilize urea. Urease genes were present in 20% of microbes, including SAR11, suggesting the urea utilization capacity was widespread. In the ODZ core, cyanate genes were largely (∼95%) associated with Scalindua, suggesting that, within this ODZ, cyanate N is primarily used for N loss via anammox (cyanammox), and that anammox does not require ammonium for N loss.

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria.

Anaerobic ammonium oxidation (anammox) contributes substantially to ocean nitrogen loss, particularly in anoxic marine zones (AMZs). Ammonium is scarce in AMZs, raising the hypothesis that organic nitrogen compounds may be ammonium sources for anammox. Biochemical measurements suggest that the organic compounds urea and cyanate can support anammox in AMZs. However, it is unclear if anammox bacteria degrade these compounds to ammonium themselves, or rely on other organisms for this process. Genes for urea degradation have not been found in anammox bacteria, and genomic evidence for cyanate use for anammox is limited to a cyanase gene recovered from the sediment bacterium Candidatus Scalindua profunda. Here, analysis of Ca. Scalindua single amplified genomes from the Eastern Tropical North Pacific AMZ revealed genes for urea degradation and transport, as well as for cyanate degradation. Urease and cyanase genes were transcribed, along with anammox genes, in the AMZ core where anammox rates peaked. Homologs of these genes were also detected in meta-omic datasets from major AMZs in the Eastern Tropical South Pacific and Arabian Sea. These results suggest that anammox bacteria from different ocean regions can directly access organic nitrogen substrates. Future studies should assess if and under what environmental conditions these substrates contribute to the ammonium budget for anammox.

Alternative Particle Formation Pathways in the Eastern Tropical North Pacific's Biological Carbon Pump

AbstractA fraction of organic carbon produced in the oceans by phytoplankton sinks storing 5–15 gigatonnes of carbon annually in the ocean interior. The accepted paradigm is that rapid aggregation of phytoplankton cells occurs, forming large, fresh particles which sink quickly; this concept is incorporated into ecosystem models used to predict the future climate. Here we demonstrate a slower, less efficient export pathway in the Eastern Tropical North Pacific. Lipid biomarkers suggest that the large, fast‐sinking particles found beneath the mixed layer are compositionally distinct from those found in the mixed layer and thus not directly and efficiently formed from phytoplankton cells. We postulate that they are formed from the in situ aggregation of smaller, slow‐sinking particles over time in the mixed layer itself. This export pathway is likely widespread where smaller phytoplankton species dominate. Its lack of representation in biogeochemical models suggests that they may be currently overestimating the ability of the oceans to store carbon if large, fast‐sinking, labile particles dominate simulated particle export.

Anaerobic ammonium oxidation linked to sulfate and ferric iron reduction fuels nitrogen loss in marine sediments.

Availability of fixed nitrogen is a pivotal driver on primary productivity in the oceans, thus the identification of key processes triggering nitrogen losses from these ecosystems is of major importance as they affect ecosystems function and consequently global biogeochemical cycles. Denitrification and anaerobic ammonium oxidation coupled to nitrite reduction (Anammox) are the only identified marine sinks for fixed nitrogen. The present study provides evidence indicating that anaerobic ammonium oxidation coupled to the reduction of sulfate, the most abundant electron acceptor present in the oceans, prevails in marine sediments. Tracer analysis with 15N-ammonium revealed that this microbial process, here introduced as Sulfammox, accounts for up to 5 μg 15N2 produced g-1 day-1 in sediments collected from the eastern tropical North Pacific coast. Raman and X-ray diffraction spectroscopies revealed that elemental sulfur and sphalerite (ZnFeS) were produced, besides free sulfide, during the course of Sulfammox. Anaerobic ammonium oxidation linked to Fe(III) reduction (Feammox) was also observed in the same marine sediments accounting for up to 2 μg 15N2 produced g-1 day-1. Taxonomic characterization, based on 16S rRNA gene sequencing, of marine sediments performing the Sulfammox and Feammox processes revealed the microbial members potentially involved. These novel nitrogen sinks may significantly fuel nitrogen loss in marine environments. These findings suggest that the interconnections among the oceanic biogeochemical cycles of N, S and Fe are much more complex than previously considered.

Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones.

Anoxic marine zones (AMZs) impact biogeochemical cycles at the global scale, particularly the nitrogen cycle. Key microbial players from AMZs have been identified, but the majority remains unrecognized or uncharacterized. Thirty-one single-cell amplified genomes (SAGs) from the eastern tropical North and South Pacific AMZs were sequenced to gain insight into the distribution, metabolic potential and contribution to the community transcriptional profile of these uncharacterized bacterial and archaeal groups. Detailed analyses focused on SAG-bins assigned to three of these groups that presented 79%-100% estimated genome completeness: the putative sulphur-oxidizing Gamaproteobacteria EOSA II clade, a Marinimicrobia member of the recently recognized PN262000N21 clade found to be abundant in AMZ anoxic cores, and a representative of the Marine Benthic Group A Thaumarchaeota. Community-based analyses revealed that these three groups are significantly more abundant and transcriptionally more active in the AMZ microbial communities than previously described phylogenetically related microbial groups. Collectively, these groups have the potential to link biogeochemically relevant processes by coupling the carbon, nitrogen and sulfur cycles. Together, these results increase our understanding of key microbial components inhabiting AMZs and other oxygen-deficient marine environments, enhancing our capacity to predict the impact of the expansion of these ecosystems due to climate change.

Glacial–interglacial changes and Holocene variations in Arabian Sea denitrification

Abstract. At present, the Arabian Sea has a permanent oxygen minimum zone (OMZ) at water depths between about 100 and 1200 m. Active denitrification in the upper part of the OMZ is recorded by enhanced δ15N values in the sediments. Sediment cores show a δ15N increase during the middle and late Holocene, which is contrary to the trend in the other two regions of water column denitrification in the eastern tropical North and South Pacific. We calculated composite sea surface temperature (SST) and δ15N ratios in time slices of 1000 years of the last 25 kyr to better understand the reasons for the establishment of the Arabian Sea OMZ and its response to changes in the Asian monsoon system. Low δ15N values of 4–7 ‰ during the last glacial maximum (LGM) and stadials (Younger Dryas and Heinrich events) suggest that denitrification was inactive or weak during Pleistocene cold phases, while warm interstadials (ISs) had elevated δ15N. Fast changes in upwelling intensities and OMZ ventilation from the Antarctic were responsible for these strong millennial-scale variations during the glacial. During the entire Holocene δ15N values > 6 ‰ indicate a relatively stable OMZ with enhanced denitrification. The OMZ develops parallel to the strengthening of the SW monsoon and monsoonal upwelling after the LGM. Despite the relatively stable climatic conditions of the Holocene, the δ15N records show regionally different trends in the Arabian Sea. In the upwelling areas in the western part of the basin, δ15N values are lower during the mid-Holocene (4.2–8.2 ka BP) compared to the late Holocene (< 4.2 ka BP) due to stronger ventilation of the OMZ during the period of the most intense southwest monsoonal upwelling. In contrast, δ15N values in the northern and eastern Arabian Sea rose during the last 8 kyr. The displacement of the core of the OMZ from the region of maximum productivity in the western Arabian Sea to its present position in the northeast was established during the middle and late Holocene. This was probably caused by (i) reduced ventilation due to a longer residence time of OMZ waters and (ii) augmented by rising oxygen consumption due to enhanced northeast-monsoon-driven biological productivity. This concurs with the results of the Kiel Climate Model, which show an increase in OMZ volume during the last 9 kyr related to the increasing age of the OMZ water mass.

An N isotopic mass balance of the Eastern Tropical North Pacific oxygen deficient zone

Oxygen deficient zones host up to 50% of marine N2 production and the Eastern Tropical North Pacific (ETNP) is the largest marine oxygen deficient zone. We measured δ15N-NO3-, δ15N-NO2-, and δ15N-N2 at 7 stations along a transect normal to the coast in the heart of the ETNP oxygen deficient zone in 2012. The δ15N-N2 minimum was 0.34‰ at 300 m, which corresponded with the N2:Ar maximum. When the atmospheric N2 background was removed, the biological δ15N-N2 for the ODZ ranged from −7‰ to −22‰. In the ODZ, δ15N-NO3- ranged from 15 to 24‰ while δ15N-NO2- was generally between − 11 and −18‰, generating differences up to 40‰ between δ15N-NO3- and δ15N-NO2-. The isotopic separation between nitrite and nitrogen gas (Δ15N NO2-N2) changed sign from ~5‰ at the top of the oxygen deficient zone to ~−10‰ at 300 m, indicating an important shift in nitrogen cycling with depth. We calculated the closed system Rayleigh isotope effect (ε) for N2 production from both the δ15N-DIN (εDIN = 26 ± 11‰) and δ15N-N2 (εN2 = 27 ± 6‰) data. When examined individually by depth, both εDIN and εN2 matched closely and both ε 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 δ15N-N2 ( εN2 = 24 ± 4‰) and δ15N-DIN (εDIN = 26 ± 3‰). The relatively large isotope effects for N2 production appear to be found in both major offshore oxygen deficient zones, which implies a large denitrification term in the marine N budget.

Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone.

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.

Dependence of nitrite oxidation on nitrite and oxygen in low‐oxygen seawater

AbstractNitrite oxidation is an essential step in transformations of fixed nitrogen. The physiology of nitrite oxidizing bacteria (NOB) implies that the rates of nitrite oxidation should be controlled by concentration of their substrate, nitrite, and the terminal electron acceptor, oxygen. The sensitivities of nitrite oxidation to oxygen and nitrite concentrations were investigated using 15N tracer incubations in the Eastern Tropical North Pacific. Nitrite stimulated nitrite oxidation under low in situ nitrite conditions, following Michaelis‐Menten kinetics, indicating that nitrite was the limiting substrate. The nitrite half‐saturation constant (Ks = 0.254 ± 0.161 μM) was 1–3 orders of magnitude lower than in cultivated NOB, indicating higher affinity of marine NOB for nitrite. The highest rates of nitrite oxidation were measured in the oxygen depleted zone (ODZ), and were partially inhibited by additions of oxygen. This oxygen sensitivity suggests that ODZ specialist NOB, adapted to low‐oxygen conditions, are responsible for apparently anaerobic nitrite oxidation.

Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean.

Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nM day-1) occurred in coastal surface waters and lowest detectable rates (~0.2 nM day-1) were found in the anoxic region of offshore stations. BNF was not detectable in most samples from oxygen-depleted waters. The composition of the N2-fixing assemblage was investigated by sequencing of nifH genes. The diazotrophic assemblage in surface waters contained mainly Proteobacterial sequences (Cluster I nifH), while both Proteobacterial sequences and sequences with high identities to those of anaerobic microbes characterized as Clusters III and IV type nifH sequences were found in the anoxic waters. Our results indicate modest input of N through BNF in oxygen-depleted zones mainly due to the activity of proteobacterial diazotrophs.