Structure and Function of Ammonia-Oxidizing Archaea and Bacteria Across Physical-Chemical Gradients in the San Francisco Bay Estuary

EPA Grant Number: F07E20943
Title: Structure and Function of Ammonia-Oxidizing Archaea and Bacteria Across Physical-Chemical Gradients in the San Francisco Bay Estuary
Investigators: Mosier, Annika C.
Institution: Stanford University
EPA Project Officer: Lee, Sonja
Project Period: January 1, 2007 through January 1, 2010
RFA: STAR Graduate Fellowships (2007) RFA Text |  Recipients Lists
Research Category: Aquatic Ecology and Ecosystems , Academic Fellowships , Fellowship - Microbiology , Fellowship - Oceanography and Coastal Processes


The San Francisco Bay estuary is recognized as one of the most anthropogenically-altered estuaries in the United States. Increasing concerns about the potential for eutrophication support the need for understanding microbial nitrogen cycling within the estuary. Particularly, ammonia oxidation (the first step in nitrification) plays a quantitatively important role in the removal of external nitrogen from the system and yet little is known about the microbial communities responsible for estuarine ammonia oxidation or how eutrophication affects the microorganisms. Furthermore, while the ability to oxidize ammonia has long been assumed to be restricted to only a few groups within the domain Bacteria (ammonia-oxidizing bacteria, AOB), the recent discovery of ammonia-oxidizing archaea (AOA) necessitates a careful reevaluation of our understanding of nitrification. The proposed study will examine AOA and AOB in San Francisco Bay and elucidate the effects of nutrient loading on the microbial communities. Sediments from the estuary will be analyzed for community structure (diversity and abundance) and function (activity and rates) in natural and disturbed settings.


Ammonia oxidation within the San Francisco Bay estuary will be investigated with three complimentary approaches: 1) The relative abundance and diversity of AOA and AOB will be determined using phylogenetic analyses and quantitative-PCR; 2) Nitrification activity will be evaluated with in situ nitrification measurements, nitrification potential assays, and functional gene cDNA quantification; and 3) Sediment incubation experiments will be used to estimate AOA/AOB response to environmental disturbances linked to eutrophication.

Expected Results:

There is increasing concern about eutrophication of coastal ecosystems and yet its specific effects on microorganisms are poorly understood, despite their fundamental role in trophic interactions and geochemical cycling. The effects of eutrophication on estuarine ammonia oxidizers are inextricably linked to the health of the entire ecosystem. This study will provide critical information illuminating the molecular microbial ecology of ammonia oxidizers in San Francisco Bay, and the effects environmental factors have on their metabolism. This data should ultimately lead to informed management and policy decisions regarding nutrient loads to the estuary. These findings should be broadly applicable to estuaries around the world.

Supplemental Keywords:

nitrogen, nitrification, ammonia oxidation, ammonia-oxidizing archaea, ammonia-oxidizing bacteria, San Francisco Bay, estuary, sediments, eutrophication, environmental microbiology,

Progress and Final Reports:

  • 2007
  • 2008
  • Final