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  • 1
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    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2013
    Description: The stable isotopes, δ15N and δ18O, of nitrite and nitrate can be powerful tools used to interpret nitrogen cycling in the ocean. In order to interpret isotope profiles, the isotope systematics of each process involved must be known. This thesis describes numerous experiments using both cultures of nitrifying organisms as well as natural seawater samples to determine the oxygen isotope systematics of nitrification. These experiments show that the accumulation of nitrite has a large effect on the resulting δ18ONO3. Also, the δ18ONO2 was developed as a unique tracer because it undergoes abiotic equilibration with water δ18O at a predictable rate based on pH, temperature and salinity. This rate, its dependencies, and how the δ18ONO2 values can be used as not only biological source indicators but also indicators of age are described. Finally, using the isotope systematics of nitrification as well as the properties of nitrite oxygen isotope exchange described in this thesis, the final chapter interprets multi-isotope nitrate and nitrite profiles in the Costa Rica Upwelling Dome using a simple 1D model. Overall, this thesis describes new nitrogen and oxygen isotopic tracers and uses them to elucidate the complicated nitrogen biogeochemistry in oxygen deficient zones.
    Description: The work described in this thesis was funded by the National Science Foundation grants OCE 05-26277 and OCE 09-610998 to KLC, the MIT Presidential Fellowship, the WHOI Coastal Ocean Institute, the WHOI Academic Programs Office, and the MIT Houghton fund.
    Keywords: Nitrification ; Nitrogen fixation ; Melville (Ship) Cruise MV1008 ; Melville (Ship) Cruise MV1104 ; Roger Revelle (Ship) Cruise
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 2
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e78275, doi:10.1371/journal.pone.0078275.
    Description: Anaerobic ammonia oxidation (anammox) as an important nitrogen loss pathway has been reported in marine oxygen minimum zones (OMZs), but the community composition and spatial distribution of anammox bacteria in the eastern tropical North Pacific (ETNP) OMZ are poorly determined. In this study, anammox bacterial communities in the OMZ off Costa Rica (CRD-OMZ) were analyzed based on both hydrazine oxidoreductase (hzo) genes and their transcripts assigned to cluster 1 and 2. The anammox communities revealed by hzo genes and proteins in CRD-OMZ showed a low diversity. Gene quantification results showed that hzo gene abundances peaked in the upper OMZs, associated with the peaks of nitrite concentration. Nitrite and oxygen concentrations may therefore colimit the distribution of anammox bacteria in this area. Furthermore, transcriptional activity of anammox bacteria was confirmed by obtaining abundant hzo mRNA transcripts through qRT-PCR. A novel hzo cluster 2x clade was identified by the phylogenetic analysis and these novel sequences were abundant and widely distributed in this environment. Our study demonstrated that both cluster 1 and 2 anammox bacteria play an active role in the CRD-OMZ, and the cluster 1 abundance and transcriptional activity were higher than cluster 2 in both free-living and particle-attached fractions at both gene and transcriptional levels.
    Description: National Science Foundation (OCE #0961098) Hong Kong Research Grants Council (661911 and 661912) Chinese Academy of Science (SIDSSE-BR-201301).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: application/msword
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  • 3
    Publication Date: 2022-05-26
    Description: Author Posting. © Association for the Sciences of Limnology and Oceanography, 2012. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 57 (2012): 1361-1375, doi:10.4319/lo.2012.57.5.1361.
    Description: The δ18O value of nitrate produced during nitrification (δ18ONO3,nit) was measured in experiments designed to mimic oceanic conditions, involving cocultures of ammonia-oxidizing bacteria or ammonia-oxidizing archaea and nitrite-oxidizing bacteria, as well as natural marine assemblages. The estimates of ranged from −1.5‰ ± 0.1‰ to +1.3‰ ± 1.4‰ at δ18O values of water (H2O) and dissolved oxygen (O2) of 0‰ and 24.2‰ vs. Vienna Standard Mean Ocean Water, respectively. Additions of 18O-enriched H2O allowed us to evaluate the effects of oxygen (O) isotope fractionation and exchange on . Kinetic isotope effects for the incorporation of O atoms were the most important factors for setting overall values relative to the substrates (O2 and H2O). These isotope effects ranged from +10‰ to +22‰ for ammonia oxidation (O2 plus H2O incorporation) and from +1‰ to +27‰ for incorporation of H2O during nitrite oxidation. values were also affected by the amount and duration of nitrite accumulation, which permitted abiotic O atom exchange between nitrite and H2O. Coculture incubations where ammonia oxidation and nitrite oxidation were tightly coupled showed low levels of nitrite accumulation and exchange (3% ± 4%). These experiments had values of −1.5‰ to +0.7‰. Field experiments had greater accumulation of nitrite and a higher amount of exchange (22% to 100%), yielding an average value of +1.9‰ ± 3.0‰. Low levels of biologically catalyzed exchange in coculture experiments may be representative of nitrification in much of the ocean where nitrite accumulation is low. Abiotic oxygen isotope exchange may be important where nitrite does accumulate, such as oceanic primary and secondary nitrite maxima.
    Description: This research was funded by the National Science Foundation Chemical Oceanography grants 05-26277 and 09- 610998 to K.L.C.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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