Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Parameters
• Deployments
• Project Information
• Funding

This dataset contains Ammonia-Oxidizing Archaea (AOA) sequence accession information National Center for Biotechnology Information (NCBI).  Samples were collected during the R/V Endeavor RMP Sediment Cruise in San Francisco Bay August 2-9, 2006.

For related datasets, click on the project link at the top of the page.

The draft genome sequence of “Ca. Nitrosopumilus salaria” BD31 was obtained as described in Mosier et al. (2012a) and is available in the NCBI GenBank database under accession number AEXL00000000. The raw sequence reads are available in the NCBI SRA database under accession number PRJNA50075.

The draft genome sequence of “Ca. Nitrosoarchaeum limnia” BG20 was obtained as described in Mosier et al. (2012b) and is available in the NCBI GenBank database under accession number AHJG00000000. The raw sequence reads are available in the NCBI SRA database under accession number PRJNA50027.

The draft genome sequence of “Ca. Nitrosoarchaeum limnia” SFB1 was obtained as described in Blainey et al. (2011) and is available in the NCBI GenBank database under accession number AEGP00000000. The version described in the paper is the first version, AEGP01000000. 

BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* blank values replaced with no data value 'nd'

Description from the NSF award abstract:

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

Although nitrogen (N) acts as a limiting nutrient in many marine ecosystems, from estuaries to the open ocean, N in excess can be extremely detrimental. Eutrophication is of particular concern in estuaries, with over half of the estuaries in the United States experiencing its effects. Harmful levels of N in estuaries can be diminished through tightly coupled processes in the microbial nitrogen cycle, including nitrification (chemoautotrophic oxidation of ammonia to nitrite and nitrate) and denitrification (the dissimilatory reduction of nitrate to N2 gas). In fact, coupled nitrification-denitrification can remove up to 50% of external dissolved inorganic nitrogen inputs to estuaries, thereby reducing the risk of eutrophication. Despite the biogeochemical importance of both nitrification and denitrification in estuarine systems, surprisingly little is known regarding the underlying microbial communities responsible for these processes, or how they are influenced by key physical/chemical factors.

The investigators will work in San Francisco Bay - the largest estuary on the west coast of the United States - using molecular, biogeochemical and cultivation approaches to explore how the distribution, diversity, abundance, and activities of key N-cycling communities are influenced by environmental gradients over temporal and spatial scales. Denitrifying communities will be studied using functional genes (nirK and nirS) encoding the key denitrification enzyme nitrite reductase, while genes encoding ammonia monooxygenase subunit A (amoA) will be used to study both ammonia-oxidizing bacteria (AOB) and the recently-discovered ammonia-oxidizing archaea (AOA)- members of one of the most ubiquitous and abundant prokaryotic groups on the planet, the mesophilic Crenarchaeota. Analyzing sediments from sites spanning a range of physical and chemical conditions in the Bay, seasonally over the course of several years, will represent an unprecedented opportunity to examine spatial, physical/chemical, and temporal effects on both denitrifier and ammonia-oxidizer communities in this large, urban estuary. Concurrently, an intensive cultivation effort will also be undertaken, in order to compile a novel culture collection of estuarine denitrifiers and ammonia-oxidizers, for which virtually nothing is currently known. Taken together, these complimentary approaches will help reveal how complex physical/chemical gradients influence the diversity and functioning of key estuarine N-cycling communities over time and space.