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Data server object:  nitrogen_reductase

    Nitrite reductase genes sequence accessions from the 2004 R/V Endeavor RMP Sediment Cruise in San Francisco Bay (N-Cycling Microbial Communities project)

Nitrite reductase genes sequence accessions from the 2004 R/V Endeavor RMP Sediment Cruise in San Francisco Bay (N-Cycling Microbial Communities project)

Website: https://www.bco-dmo.org/dataset/683969
Data Type: Cruise Results
Version Date: 2017-07-03

» Spatial and Temporal Dynamics of Nitrogen-Cycling Microbial Communities Across Physicochemical Gradients in the San Francisco Bay Estuary (N-Cycling Microbial Communities)
Francis, ChristopherStanford UniversityLead Principal Investigator, Contact
York, Amber D.Woods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Dataset Description

 09 Mar 2017 NOTE: The data were submitted to BCO-DMO and are in the process of being served

This dataset contains accession numbers and associated metdata for nitrite reductase genes sequences collected during the R/V Endeavor, 2004 Regional Monitoring Program (RMP) Sediment Cruise in San Francisco Bay (July 27-August 3, 2004). Sediment DNA extracts were PCR amplified with primers targeting nirK (copper-containing nitrite reductase ) and nirS (cytochrome-cd1 nitrite reductase).

Related Manuscript:

Mosier, A. C., and C. A. Francis. 2010. Denitrifier abundance and activity across the San Francisco Bay estuary. Environmental Microbiology Reports 2:667-676. doi: 10.1111/j.1758-2229.2010.00156.x

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

Acquisition Description

Sediment samples (upper 5-cm) were collected in conjunction with the Regional Monitoring Program (RMP) managed by the San Francisco Estuary Institute (http://www.sfei.org/). Surface sediment was retrieved using a modified Van Veen grab, and cores were taken from each grab sample using sterile, cut-off 5 mL syringes and immediately placed on dry ice prior to storage at –80C. DNA was extracted from approximately 250–300 mg of sediment from the upper 5 mm of the cores using the FastDNA SPIN kit for soil (MP Biomedicals) with a 30 s bead beating time at speed 5.5. Duplicate DNA extractions were performed for each sediment core. Sediment DNA extracts were PCR amplified with primers targeting nirK and nirS: nirK583FdegCF(5′-TCATGGTGCTGCCGCGYGANGG; Santoro et al., 2006) and nirK5R (Braker et al., 1998); nirS1F and nirS6R (Braker et al., 1998). Clone libraries of nirK and nirS gene fragments were constructed using the TOPO TA cloning(R) kit (Invitrogen) and 28–45 clones from each library were sequenced (ABI 3100 Capillary Sequencer). Sequences reported in this study have been deposited in GenBank under Accession No. GQ454031 to GQ454413 for nirK and GQ453671 to GQ454030 for nirS.

Processing Description

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'
* replaced unsupported characters in parameter names +-/()
* converted degrees decimal minutes to decimal degrees
* collection dates added from cruise report

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stationstation where sample was taken unitless
latlatitude decimal degrees
lonlongitude decimal degrees
organismorganism analyzed unitless
genegene analyzed unitless
accession_rangeRange of Genbank accession numbers unitless
accession_idGenbank accession number
accession_linkLink to the accession at NCBI Genbank; HTML formatted link
dateDate of sample collection in format yyyy-mm-dd. unitless

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Dataset-specific Instrument Name
Van Veen grab
Generic Instrument Name
Bottom Sediment Grab Samplers
Generic Instrument Description
These samplers are designed to collect an accurate representative sample of the sediment bottom. The bite of the sampler should be deep enough so all depths are sampled equally. The closing mechanism is required to completely close and hold the sample as well as prevent wash-out during retrieval. Likewise, during descent the sampler should be designed to minimize disturbance of the topmost sediment by the pressure wave as it is lowered to the bottom.

Dataset-specific Instrument Name
StepOnePlus Real-Time PCR System
Generic Instrument Name
PCR Thermal Cycler
Dataset-specific Description
Genes quantified using gene-specific SYBR qPCR assays
Generic Instrument Description
General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

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R/V Endeavor
Start Date
End Date
2004 Regional Monitoring Program (RMP) Sediment Cruise

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Project Information

Spatial and Temporal Dynamics of Nitrogen-Cycling Microbial Communities Across Physicochemical Gradients in the San Francisco Bay Estuary (N-Cycling Microbial Communities)

Coverage: San Francisco Bay

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.

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Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database.    2021-04-10  15:24:04