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Genomic and Physiological Analysis of Nitrogen Oxide Metabolism in Ammonia-Oxidizers Open Access

Descriptions

Other title
Subject/Keyword
nitrous oxide
Ammonia-oxidizers
nitrifier denitrification
Type of item
Thesis
Degree grantor
University of Alberta
Author or creator
Kozlowski, Jessica A.
Supervisor and department
Stein, Lisa (Biological Sciences)
Examining committee member and department
Ulrich, Ania (Environmental Engineering)
Glass, Jennifer (Georgia Institute of Technology; School of Earth and Atmospheric Sciences)
Owttrim, George (Biological Sciences)
Raivio, Tracy (Biological Sciences)
Department
Department of Biological Sciences
Specialization
Microbiology and Biotechnology
Date accepted
2016-06-03T13:44:01Z
Graduation date
2016-06:Fall 2016
Degree
Doctor of Philosophy
Degree level
Doctoral
Abstract
Ammonia oxidizers come from two different domains of life, the Archaea and Bacteria, and control a vital step in the global biogeochemical Nitrogen cycle; the conversion of ammonia to nitrite. They are abundant in a wide range of environments including marine and freshwaters, terrestrial soils, and wastewater treatment plants. This group of organisms has also been implicated in the production of the nitrous oxide, a potent greenhouse gas. Nitrous oxide has been measured from ammonia oxidizing bacteria and archaea in pure and enrichment culture but the pathways, including enzymology, intermediates, and physiological conditions for nitrous oxide production are not well understood and therefore it is not possible to accurately model contributions of this group of microorganisms to global nitrous oxide emissions. The issue has been exacerbated by lack of available and closed genomes of ammonia oxidizers, physiological analyses of nitrous oxide production on pure cultures under environmentally relevant conditions, and chemical controls to elucidate differences in biological versus abiotic contributions to nitrous oxide production. Necessary studies to fill in the gaps in knowledge hindering the field were done by utilizing various approaches to studying ammonia oxidizer physiology. Physiological experiments included growth and resting cell assays along with headspace gas measurements, and instantaneous measurements of nitric oxide and nitrous oxide production during oxidation of native energy generating substrates. All studies were complemented with a genome-inferred approach to see if genomic inventory could explain physiological results. In conclusion, the present body of work addresses the above overarching problems in the field of Nitrification by (1) determining the pathways, including enzymology, involved in nitrous oxide production by the model ammonia-oxidizing bacterium Nitrosomonas europaea ATCC 19718, (2) showing that genomic inventory and phylogeny of ammonia oxidizing bacteria do not predict contributions to nitrous oxide production, and (3) identifying key pathways and intermediates that explain differences in ammonia oxidation and nitrous oxide production between ammonia oxidizing bacteria and archaea.
Language
English
DOI
doi:10.7939/R3862BR5K
Rights
This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for the purpose of private, scholarly or scientific research. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
Citation for previous publication
Kozlowski JA, Price J, Stein LY. (2014). Revision of N2O-Producing Pathways in the Ammonia-Oxidizing Bacterium Nitrosomonas europaea ATCC 19718. Appl Environ Microbiol 80: 4930–4935.Kozlowski JA, Stieglmeier M, Schleper C, Klotz MG, Stein LY. (2016). Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota. ISME J. Epub ahead of print February 16 2016.Kozlowski JA, Kits KD, Stein LY. (2016). Genome Sequence of Nitrosomonas communis Strain Nm2, a Mesophilic Ammonia-Oxidizing Bacterium Isolated from Mediterranean Soil. Genome Announc 4: e01541–15–2.Kozlowski JA, Kits KD, Stein LY. (2016). Complete Genome Sequence of Nitrosomonas ureae Strain Nm10, an Oligotrophic Group 6a Nitrosomonad. Genome Announc 4: 1–2.

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