Microbial biogeochemistry of ammonia oxidation in coastal environments

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The processes responsible for the fixation and removal of nitrogen (N) from the ocean are ultimately linked by nitrification, the sequential oxidation of ammonia (NH3) to nitrite (NO2 ) and then nitrate (NO3-). It is estimated that almost all of the approximately 4x1011 kg of N that cycles through the ocean annually is nitrified at least one time. The degree to which nitrification occurs within a given environment alters the distribution of inorganic nitrogen available to support the growth of phytoplankton in surface waters of the ocean. In coastal environments, the process plays another critical part in N cycling, by linking the decomposition of organic matter to N loss via denitrification. It has been nearly a decade since the discovery of the ammonia oxidizing archaea expanded our perspective of N cycling in terrestrial and marine environments. Initial reports of their widespread abundance in all major biomes called for a reexamination of nitrification, and the role the archaea (and the ammonia oxidizing bacteria, AOB) play in the global N cycle. At present there is insurmountable support for nitrification being a largely archaeal-mediated process both on land and at sea. Estuaries remain a grey zone, where either the AOA or the AOB may be the primary organisms responsible for ammonia oxidation. This dissertation focuses on microbial N transformations through field studies of the distribution and activity of ammonia oxidizing microorganisms in sediments and water columns of the coastal environment, using an approach that includes molecular biology, microbial ecology and biogeochemistry.The broad objective of my thesis research was to investigate the roles of the AOA and AOB in the cycling of inorganic N, and how specific environmental conditions select for their activity in two important parts of the coastal environment: the upper ocean, where N plays a key role in supporting phytoplankton growth, and intertidal sediments, responsible for removing vast amounts of anthropogenic N pollution from coastal waters.


Type of resource text
Form electronic; electronic resource; remote
Extent 1 online resource.
Publication date 2013
Issuance monographic
Language English


Associated with Smith, Jason Michel
Associated with Stanford University, Department of Environmental Earth System Science.
Primary advisor Francis, Christopher
Thesis advisor Francis, Christopher
Thesis advisor Casciotti, Karen Lynn, 1974-
Thesis advisor Welander, Paula
Advisor Casciotti, Karen Lynn, 1974-
Advisor Welander, Paula


Genre Theses

Bibliographic information

Statement of responsibility Jason Michel Smith.
Note Submitted to the Department of Environmental Earth System Science.
Thesis Thesis (Ph.D.)--Stanford University, 2013.
Location electronic resource

Access conditions

© 2013 by Jason Michel Smith
This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).

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