Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

Nitrous oxide (N2O)[N subscript 2 O] is a trace gas that contributes to the greenhouse effect and stratospheric ozone depletion. The N2O [N subscript 2 O] yield from nitrification (moles N2O-N [N subscript 2 O - N] produced per mole ammonium-N consumed) has been used to estimate marine N2O [N subscript 2 O] production rates from measured nitrification rates and global estimates of oceanic export production. However, the N2O [N subscript 2 O] yield from nitrification is not constant. Previous culture-based measurements indicate that N2O [N subscript 2 O] yield increases as oxygen (O2) [O subscript 2] concentration decreases and as nitrite (NO2−) [NO subscript 2 overscore] concentration increases. Here, we have measured yields of N2O [N subscript 2 O] from cultures of the marine β-proteobacterium [beta-proteobacterium] Nitrosomonas marina C-113a as they grew on low-ammonium (50 μM)[50 mu M] media. These yields, which were typically between 4 × 10−4 [10 superscript -4] and 7 × 10−4 [10 superscript -4] for cultures with cell densities between 2 × 102 [10 super script 2] and 2.1 × 104 [10 superscript 4] cells ml−1 [ml superscript -1], were lower than previous reports for ammonia-oxidizing bacteria. The observed impact of O2 [O subscript 2] concentration on yield was also smaller than previously reported under all conditions except at high starting cell densities (1.5 × 106 cells ml−1) [1.5 x 10 superscript 6 cells ml superscript -1], where 160-fold higher yields were observed at 0.5% O2 [O subscript 2](5.1 μM [mu M] dissolved O2 [O subscript 2]) compared with 20% O2 [O subscript 2] (203 μM [mu M] dissolved O2 O subscript 2]). At lower cell densities (2 × 102 [10 superscript 2] and 2.1 × 104 [10 superscript 4] cells ml−1 [ml superscript -1]), cultures grown under 0.5% O2 [O subscript 2] had yields that were only 1.25- to 1.73-fold higher than cultures grown under 20% O2 [O subscript 2]. Thus, previously reported many-fold increases in N2O [N subscript 2 O] yield with dropping O2 [O subscript 2] could be reproduced only at cell densities that far exceeded those of ammonia oxidizers in the ocean. The presence of excess NO2− [NO subscript 2 overscore] (up to 1 mM) in the growth medium also increased N2O [N subscript 2 O] yields by an average of 70% to 87% depending on O2 [O subscript 2] concentration. We made stable isotopic measurements on N2O [N subscript 2 O] from these cultures to identify the biochemical mechanisms behind variations in N2O [N subscript 2 O] yield. Based on measurements of δ15Nbulk [delta superscript 15 N superscript bulk], site preference (SP = δ15Nα−δ15Nβ [delta superscript 15 N superscript alpha - delta superscript 15 N superscript beta]), and δ18O [delta superscript 18 O] of N2O [N subscript 2 O] (δ18O-N2O [delta superscript 18 O - N subscript 2 O]), we estimate that nitrifier-denitrification produced between 11% and 26% of N2O [N subscript 2 O] from cultures grown under 20% O2 [O subscript 2] and 43% to 87% under 0.5% O2 [O subscript 2]. We also demonstrate that a positive correlation between SP and δ18O-N2O [delta superscript 18 O - N subscript 2 O] is expected when nitrifying bacteria produce N2O [N subscript 2 O]. A positive relationship between SP and δ18O-N2O [delta superscript 18 O - N subscript 2 O] has been observed in environmental N2O [N subscript 2 O] datasets, but until now, explanations for the observation invoked only denitrification. Such interpretations may overestimate the role of heterotrophic denitrification and underestimate the role of ammonia oxidation in environmental N2O [N subscript 2 O] production

Testing the influence of light on nitrite cycling in the eastern tropical North Pacific

Light is considered a strong controlling factor of nitrification rates in the surface ocean. Previous work has shown that ammonia oxidation and nitrite oxidation may be inhibited by high light levels, yet active nitrification has been measured in the sunlit surface ocean. While it is known that photosynthetically active radiation (PAR) influences microbial nitrite production and consumption, the level of inhibition of nitrification is variable across datasets. Additionally, phytoplankton have light-dependent mechanisms for nitrite production and consumption that co-occur with nitrification around the depths of the primary nitrite maximum (PNM). In this work, we experimentally determined the direct influence of light level on net nitrite production, including all major nitrite cycling processes (ammonia oxidation, nitrite oxidation, nitrate reduction and nitrite uptake) in microbial communities collected from the base of the euphotic zone. We found that although ammonia oxidation was inhibited at the depth of the PNM and was further inhibited by increasing light at all stations, it remained the dominant nitrite production process at most stations and treatments, even up to 25 % surface PAR. Nitrate addition did not enhance ammonia oxidation in our experiments but may have increased nitrate and nitrite uptake at a coastal station. In contrast to ammonia oxidation, nitrite oxidation was not clearly inhibited by light and sometimes even increased at higher light levels. Thus, accumulation of nitrite at the PNM may be modulated by changes in light, but light perturbations did not exclude nitrification from the surface ocean. Nitrite uptake and nitrate reduction were both enhanced in high-light treatments relative to low light and in some cases showed high rates in the dark. Overall, net nitrite production rates of PNM communities were highest in the dark treatments.</p

Modeling oceanic nitrate and nitrite concentrations and isotopes using a 3-D inverse N cycle model

Nitrite (NO2-) is a key intermediate in the marine nitrogen (N) cycle and a substrate in nitrification, which produces nitrate (NO3-), as well as water column N loss processes denitrification and anammox. In models of the marine N cycle, NO2- is often not considered as a separate state variable, since NO3- occurs in much higher concentrations in the ocean. In oxygen deficient zones (ODZs), however, NO2- represents a substantial fraction of the bioavailable N, and modeling its production and consumption is important to understand the N cycle processes occurring there, especially those where bioavailable N is lost from or retained within the water column. Improving N cycle models by including NO2- is important in order to better quantify N cycling rates in ODZs, particularly N loss rates. Here we present the expansion of a global 3-D inverse N cycle model to include NO2- as a reactive intermediate as well as the processes that produce and consume NO2- in marine ODZs. NO2- accumulation in ODZs is accurately represented by the model involving NO3- reduction, NO2- reduction, NO2- oxidation, and anammox. We model both 14N and 15N and use a compilation of oceanographic measurements of NO3- and NO2- concentrations and isotopes to place a better constraint on the N cycle processes occurring. The model is optimized using a range of isotope effects for denitrification and NO2- oxidation, and we find that the larger (more negative) inverse isotope effects for NO2- oxidation, along with relatively high rates of NO2-, oxidation give a better simulation of NO3- and NO2- concentrations and isotopes in marine ODZs.</p

Carbon sequestration in the deep Atlantic enhanced by Saharan dust

sinking rates of particulate organicmatter. Here we present a two-year time series of sediment trap observations of particulate organic carbon flux to 3,000m depth, measured directly in two locations: the dust-rich central North Atlantic gyre and the dust-poor South Atlantic gyre. We find that carbon fluxes are twice as high and a higher proportion of primary production is exported to depth in the dust-rich North Atlantic gyre. Low stable nitrogen isotope ratios suggest that high fluxes result from the stimulation of nitrogen fixation and productivity following the deposition of dust-borne nutrients. Sediment traps in the northern gyre also collected intact colonies of nitrogen-fixing Trichodesmium species. Whereas ballast in Enhanced atmospheric input of dust-borne nutrients and minerals to the remote surface ocean can potentially increase carbon uptake and sequestration at depth. Nutrients can enhance primary productivity, and mineral particles act as ballast, increasing the southern gyre is predominantly biogenic, dust-derived mineral particles constitute the dominant ballast element during the enhanced carbon fluxes in the northern gyre. We conclude that dust deposition increases carbon sequestration in the North Atlantic gyre through the fertilization of the nitrogen-fixing community in surface waters and mineral ballasting of sinking particles

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean : phylogeny, physiology and stable isotope fractionation

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 5 (2011): 1796–1808, doi:10.1038/ismej.2011.58.Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the north Pacific Ocean that have been maintained in laboratory culture for over three years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S rRNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98-99% identity) to those recovered in DNA and cDNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonium (NH4 +) to nitrite (NO2 -). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (15εNH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15εNH3 ranged from 13- 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15εNH3 is similar.This work was supported by a Woods Hole Oceanographic Institution (WHOI) Postdoctoral Scholar fellowship to AES and the WHOI Ocean Life Institute

Dual isotope analyses indicate efficient processing of atmospheric nitrate by forested watersheds in the northeastern U.S.

Author Posting. © Springer, 2008. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Biogeochemistry 90 (2008): 15-27, doi:10.1007/s10533-008-9227-2.Nitrogen from atmospheric deposition serves as the dominant source of new nitrogen to forested ecosystems in the northeastern U.S.. By combining isotopic data obtained using the denitrifier method, with chemistry and hydrology measurements we determined the relative importance of sources and control mechanisms on nitrate (NO3-) export from five forested watersheds in the Connecticut River watershed. Microbially produced NO3- was the dominant source (82-100%) of NO3- to the sampled streams as indicated by the δ15N and δ18O of NO3-. Seasonal variations in the δ18O-NO3- in streamwater are controlled by shifting hydrology and temperature affects on biotic processing, resulting in a relative increase in unprocessed NO3- export during winter months. Mass balance estimates find that the unprocessed atmospherically derived NO3- stream flux represents less than 3% of the atmospherically delivered wet NO3- flux to the region. This suggests that despite chronically elevated nitrogen deposition these forests are not nitrogen saturated and are retaining, removing, and reprocessing the vast majority of NO3- delivered to them throughout the year. These results confirm previous work within Northeastern U.S. forests and extend observations to watersheds not dominated by a snow-melt driven hydrology. In contrast to previous work, unprocessed atmospherically derived NO3- export is associated with the period of high recharge and low biotic activity as opposed to spring snowmelt and other large runoff events.This work was funded by an EPA STAR Fellowship (FP-91637501-1) and a grant from QLF/The Sound Conservancy to RTB

An intermediate-depth source of hydrothermal 3He and dissolved iron in the North Pacific

We observed large water column anomalies in helium isotopes and trace metal concentrations above the Loihi Seamount. The 3He/4He of the added helium was 27.3 times the atmospheric ratio, clearly marking its origin to a primitive mantle plume. The dissolved iron to 3He ratio (dFe:3He) exported to surrounding waters was 9.3 ± 0.3 × 106. We observed the Loihi 3He and dFe “signal” at a depth of 1100 m at several stations within ∼100 – 1000 km of Loihi, which exhibited a distal dFe:3He ratio of ∼4 × 106, about half the proximal ratio. These ratios were remarkably similar to those observed over and near the Southern East Pacific Rise (SEPR) despite greatly contrasting geochemical and volcanictectonic origins. In contrast, the proximal and distal dMn:3He ratios were both ∼ 1 × 106, less than half of that observed at the SEPR. Dissolved methane was minimally enriched in waters above Loihi Seamount and was distally absent. Using an idealized regional-scale model we replicated the historically observed regional 3He distribution, requiring a hydrothermal 3He source from Loihi of 10.4 ± 4.2 mola−1, ∼2% of the global abyssal hydrothermal 3He flux. From this we compute a corresponding dFe flux of ∼40 Mmola−1. Global circulation model simulations suggest that the Loihi-influenced waters eventually upwell along the west coast of North America, also extending into the shallow northwest Pacific, making it a possibly important determinant of marine primary production in the subpolar North Pacific

Nitrate stable isotopes and major ions in snow and ice samples from four Svalbard sites

Increasing reactive nitrogen (N-r) deposition in the Arctic may adversely impact N-limited ecosystems. To investigate atmospheric transport of N-r to Svalbard, Norwegian Arctic, snow and firn samples were collected from glaciers and analysed to define spatial and temporal variations (1 10 years) in major ion concentrations and the stable isotope composition (delta N-15 and delta O-18) of nitrate (NO3-) across the archipelago. The delta N-15(NO3-) and delta O-18(NO3-) averaged -4 parts per thousand and 67 parts per thousand in seasonal snow (2010-11) and -9 parts per thousand and 74 parts per thousand in firn accumulated over the decade 2001-2011. East-west zonal gradients were observed across the archipelago for some major ions (non-sea salt sulphate and magnesium) and also for delta N-15(NO3-) and delta O-18(NO3-) in snow, which suggests a different origin for air masses arriving in different sectors of Svalbard. We propose that snowfall associated with long-distance air mass transport over the Arctic Ocean inherits relatively low delta N-15(NO3-) due to in-transport N isotope fractionation. In contrast, faster air mass transport from the north-west Atlantic or northern Europe results in snowfall with higher delta N-15(NO3-) because in-transport fractionation of N is then time-limited

Measurements of nitrite production in and around the primary nitrite maximum in the central California Current

Nitrite (NO2&minus;) is a substrate for both oxidative and reductive microbial metabolism. NO2&minus; accumulates at the base of the euphotic zone in oxygenated, stratified open-ocean water columns, forming a feature known as the primary nitrite maximum (PNM). Potential pathways of NO2&minus; production include the oxidation of ammonia (NH3) by ammonia-oxidizing bacteria and archaea as well as assimilatory nitrate (NO3&minus;) reduction by phytoplankton and heterotrophic bacteria. Measurements of NH3 oxidation and NO3&minus; reduction to NO2&minus; were conducted at two stations in the central California Current in the eastern North Pacific to determine the relative contributions of these processes to NO2&minus; production in the PNM. Sensitive (Synechococcus, and Prochlorococcus) were present at the depth of the PNM. Rates of NO2&minus; production from NO3&minus; were highest within the upper mixed layer (4.6 nmol L-1 d-1) but were either below detection limits or 10 times lower than NH3 oxidation rates around the PNM. One-dimensional modeling of water column NO2&minus; production agreed with production determined from 15N bottle incubations within the PNM, but a modeled net biological sink for NO2&minus; just below the PNM was not captured in the incubations. Residence time estimates of NO2&minus; within the PNM ranged from 18 to 470 days at the mesotrophic station and was 40 days at the oligotrophic station. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation. © 2013 Author(s)

Initiation of the spring phytoplankton increase in the Antarctic Polar Front Zone at 170°W

During austral summer 1997, satellite imagery revealed enhanced chlorophyll associated with the Antarctic Polar Front at 170°W. Phytoplankton growth conditions during the early stages of the spring increase were investigated on the Antarctic Environment and Southern Ocean Process Study Survey I cruise using flow cytometry (FCM) and microscopy to characterize community biomass, composition and biological stratification and dilution experiments to estimate growth and grazing rates. Physical and biological measures showed a general shoaling of mixed layer depth from ~200 to 20 μm) cells, greater contributions if diatoms and ciliate, and a twofold higher ratio of protistan grazers to photoautotrophs. Phytoplankton community growth rates from incubations at 10 and 23% of surface incident light showed good agreement between high-performance liquid chromatography estimated of chlorophyll a (Chl a) (0.20 d¯¹) and FCM cell-based (0.21 d¯¹) results. Fucoxanthin-based estimates for diatoms were 0.24 d¯¹. Mean estimates of microzooplankton grazing from the three phytoplankton measures were 0.16, 0.12, and 0.11 d¯¹, respectively. Heterotrophs typically consumed 40-100% of their carbon per day and this presumably grew at rates similar to phytoplankton. The low net rates of Chl a increase in shipboard bottle incubations (0.04 d¯¹) were consistent with the slow downstream accumulation of phytoplankton biomass (0.03 d¯¹) as measured with instrumented Lagrangian drifters through the month of November. Both were slightly less than the net rate estimates from SeaSoar surveys (0.05 d¯¹) because of the effects of pigment photoadaption (bleaching) during this time of increasing light level and water column stratification.Copyrighted by American Geophysical Union