http://lod.bco-dmo.org/id/dataset/684211
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-03-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Ammonia-Oxidizing Arachae (AOA) whole genome sequence accessions from samples collected during the 2006 R/V Endeavor RMP Sediment Cruise in San Francisco Bay August 2-9, 2006 (N-Cycling Microbial Communities project)
2017-07-03
publication
2017-07-03
revision
BCO-DMO Linked Data URI
2017-07-03
creation
http://lod.bco-dmo.org/id/dataset/684211
Christopher Francis
Stanford University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Francis, C. (2017) Ammonia-Oxidizing Arachae (AOA) whole genome sequence accessions from samples collected during the 2006 R/V Endeavor RMP Sediment Cruise in San Francisco Bay August 2-9, 2006 (N-Cycling Microbial Communities project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-07-03 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/684211 [access date]
Whole genome sequence accessions from Ammonia-Oxidizing Arachae (AOA) Dataset Description: <p>This dataset contains Ammonia-Oxidizing Archaea (AOA) sequence accession information&nbsp;National Center for Biotechnology Information (<a href="https://www.ncbi.nlm.nih.gov" target="_blank">NCBI</a>). &nbsp;Samples were collected during the R/V Endeavor RMP Sediment Cruise in San Francisco Bay August 2-9, 2006.</p>
<p><strong>For related datasets, click on the project link at the top of the page.</strong></p> Methods and Sampling: <p>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 <a href="http://jb.asm.org/external-ref?link_type=GEN&amp;access_num=AEXL00000000">AEXL00000000</a>. The raw sequence reads are available in the NCBI SRA database under accession number <a href="http://jb.asm.org/external-ref?link_type=GEN&amp;access_num=PRJNA50075">PRJNA50075</a>.</p>
<p>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 <a href="http://jb.asm.org/external-ref?link_type=GEN&amp;access_num=AHJG00000000">AHJG00000000</a>. The raw sequence reads are available in the NCBI SRA database under accession number <a href="http://jb.asm.org/external-ref?link">PRJNA50027</a>.</p>
<p>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<a href="http://jb.asm.org/external-ref?link_type=GEN&amp;access_num=AEGP00000000" target="_blank"> AEGP00000000</a>. The version described in the paper is the first version, AEGP01000000.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0847266 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0847266
completed
Christopher Francis
Stanford University
650-724-0301
Environmental Earth System Science 473 Via Ortega, Y2E2 Bldg
Stanford
CA
94305-4216
USA
caf@stanford.edu
pointOfContact
asNeeded
Unknown
Station
Latitude
Longitude
Salinity
Depth
Organism
Draft_Genome_Accession
SRA_Accession
theme
None, User defined
station
latitude
longitude
salinity
depth
sample description
accession number
featureType
BCO-DMO Standard Parameters
RMP_2006_Sediment
service
Deployment Activity
San Francisco Bay
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Spatial and Temporal Dynamics of Nitrogen-Cycling Microbial Communities Across Physicochemical Gradients in the San Francisco Bay Estuary
https://osprey.bco-dmo.org/project/546278
Spatial and Temporal Dynamics of Nitrogen-Cycling Microbial Communities Across Physicochemical Gradients in the San Francisco Bay Estuary
<p><em>Description from the NSF award abstract:</em></p>
<p>This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).</p>
<p>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.</p>
<p>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.</p>
N-Cycling Microbial Communities
largerWorkCitation
project
eng; USA
oceans
San Francisco Bay
-122.363
-121.815
38.024
38.099
2017-07-03
San Francisco Bay
0
BCO-DMO catalogue of parameters from Ammonia-Oxidizing Arachae (AOA) whole genome sequence accessions from samples collected during the 2006 R/V Endeavor RMP Sediment Cruise in San Francisco Bay August 2-9, 2006 (N-Cycling Microbial Communities project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/708194.rdf
Name: Station
Units: unitless
Description: <p>Station sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/708195.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/708196.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sample; west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/708197.rdf
Name: Salinity
Units: Practical Salinity Units (PSU)
Description: <p>Saility of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/708198.rdf
Name: Depth
Units: meters
Description: <p>Depth of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/708199.rdf
Name: Organism
Units: unitless
Description: <p>Organism name (enriched and isolated from sediments)</p>
http://lod.bco-dmo.org/id/dataset-parameter/708200.rdf
Name: Draft_Genome_Accession
Units: unitless
Description: <p>Link to accession at NCBI for the draft genome</p>
http://lod.bco-dmo.org/id/dataset-parameter/708201.rdf
Name: SRA_Accession
Units: unitless
Description: <p>Link to accession at NCBI for SRA</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
742
https://datadocs.bco-dmo.org/file/R88XmgqcGNm8Aq/AOA.csv
AOA.csv
Primary data file for dataset ID 684211
download
https://osprey.bco-dmo.org/dataset/684211/data/download
download
onLine
dataset
<p>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 <a href="http://jb.asm.org/external-ref?link_type=GEN&amp;access_num=AEXL00000000">AEXL00000000</a>. The raw sequence reads are available in the NCBI SRA database under accession number <a href="http://jb.asm.org/external-ref?link_type=GEN&amp;access_num=PRJNA50075">PRJNA50075</a>.</p>
<p>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 <a href="http://jb.asm.org/external-ref?link_type=GEN&amp;access_num=AHJG00000000">AHJG00000000</a>. The raw sequence reads are available in the NCBI SRA database under accession number <a href="http://jb.asm.org/external-ref?link">PRJNA50027</a>.</p>
<p>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<a href="http://jb.asm.org/external-ref?link_type=GEN&amp;access_num=AEGP00000000" target="_blank"> AEGP00000000</a>. The version described in the paper is the first version, AEGP01000000.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Data Manager Processing Notes:<br />
* added a conventional header with dataset name, PI name, version date<br />
* blank values replaced with no data value 'nd'</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Cruise: RMP_2006_Sediment
RMP_2006_Sediment
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
RMP_2006_Sediment
http://dmoserv3.bco-dmo.org/data_docs/N_Cycling_Microbial_Communities/cruise_reports/2006-08-02-Sediment.pdf
Report describing RMP_2006_Sediment
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel