http://lod.bco-dmo.org/id/dataset/863192
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
2021-10-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI accession numbers describing nifH amplicon sequences from sediment samples collected offshore of San Francisco, Califronia, USA in March 2017 on R/V Oceanus cruise OC1703A
2021-10-13
publication
2021-10-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-08-31
publication
https://doi.org/10.26008/1912/bco-dmo.863192.1
Anne E. Dekas
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: Dekas, A. E. (2022) NCBI accession numbers describing nifH amplicon sequences from sediment samples collected offshore of San Francisco, Califronia, USA in March 2017 on R/V Oceanus cruise OC1703A. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-10-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.863192.1 [access date]
OC1703A Sediment nifH amplicon sequences Dataset Description: Methods and Sampling: <p>Sediment samples were collected using a multicorer on board the R/V Oceanus (March 2017) and sample aliquots were immediately stored at -80°C until DNA extraction. DNA was extracted in the laboratory using an RNeasy PowerSoil DNA elution kit (Qiagen, catalog no. 12867-25) after RNA was extracted using an RNeasy PowerSoil Total RNA kit. (Qiagen, catalog no. 12866-25).</p>
<p><em>nifH</em> sequences were amplified using the PCR primers described in Mehta et al., 2003 and amplicons were prepared for 2×250 bp sequencing on an Illumina MiSeq platform following the protocol described in Kapili et al., 2020.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1634297 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1634297
completed
Anne E. Dekas
Stanford University
650-736-1225
473 Via Ortega, Y2E2 Room 140
Stanford
CA
94305-4216
USA
dekas@stanford.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioProject
BioSample
SRA_study
Assay_Type
Sequencing_platform
Instrument_model
Library_layout
File_name_1
File_name_2
File_type
Sequencing_method
Library_selection
PCR_primers
Sequencing_adapters
Geographic_location
Sample_type
Sample_name
Sample_latitude
Sample_longitude
Deployment_number
Multicore_number
Seawater_depth
Sediment_depth
Illumina MiSeq platform
MC-800
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA study accession (SRP)
sampling_method
instrument
file_name
sequence
site
sample type
sample identification
latitude
longitude
deployment number
core id
depth
depth core
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Multi Corer
instrument
BCO-DMO Standard Instruments
OC1703A
service
Deployment Activity
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.
Nitrogen Fixation in Deep-Sea Sediments
https://osprey.bco-dmo.org/project/710001
Nitrogen Fixation in Deep-Sea Sediments
<p><em>NSF Award Abstract:</em><br />
Life requires nitrogen for growth. Atmospheric nitrogen (N2) is the most abundant form of nitrogen on the surface of the planet, but most organisms cannot assimilate N2 directly. Habitats can therefore be nitrogen limited, meaning the demand for "bioavailable" nitrogen exceeds the supply, and its availability controls the overall growth and productivity of the community. A small subset of microorganisms, termed diazotrophs, convert N2 to bioavailable forms of nitrogen, including ammonium and nitrogenous organic matter, in a process known as N2 fixation. Diazotrophs are the largest natural source of bioavailable nitrogen on the planet, and the rate at which they fix N2 can control the rates at which other important microbial processes occur, such as the production and consumption of greenhouse gases. Understanding diazotrophs in the environment - their identity, distribution, activity levels, and biogeochemical controls - is therefore essential to understanding overall microbial community activity and biogeochemical cycling. The goal of this project is to characterize N2 fixation in deep-sea sediments, a generally understudied but expansive habitat, covering nearly two thirds of our planet. The project will have broader impacts via educational outreach, support and training of early career scientists, and scientific impact: since rates of marine methane, carbon dioxide, and nitrous oxide cycling are affected by nitrogen availability, the results will inform our understanding of greenhouse gas cycling in the marine environment, and therefore climate stability, a topic central to global security.</p>
<p>N2 fixation is a critical and intensely studied metabolism in the marine photic zone. Much less is known about N2 fixation in deep-sea sediments, but it could be an important factor in both benthic productivity and ocean-scale elemental cycling. Several observations have suggested or directly detected N2 fixation at localized areas of enhanced productivity on the seafloor (e.g., methane seeps and hydrothermal vents), raising the possibility that deep-sea N2 fixation is widespread. However, few measurements of N2 fixation have been made outside of these anomalous areas, and thus little is known about N2 fixation in the vast majority of the deep ocean floor. Preliminary data suggest N2 fixation does occur in typical deep marine sediment, and is mediated by a diverse set of yet unidentified microorganisms. This project will combine techniques from molecular biology and geochemistry to systematically investigate N2 fixation in representative deep-sea sediments collected along a depth profile (500 to 4500 m water depth) offshore California. The project will determine the (1) rates and distribution of N2 fixation (2) abundance, diversity, and distribution of genes and transcripts associated with N2 fixation (nif) (3) phylogenetic identity of the biological mediators (diazotrophs) and (4) physiochemical controls on diazotrophic community structure and activity. For context, the activity of the non-diazotrophic bacterial community will also be characterized. The results may lead to upward revisions of the estimates of new nitrogen production in the seafloor, and therefore change our understanding of the current balance of the marine nitrogen cycle. Together, this hypothesis-driven characterization of N2 fixation in deep-sea sediments will shed light on an expansive, climatically important, and traditionally understudied habitat, and facilitate more accurate extrapolation of the rates and distribution of N2 fixation on the whole seafloor as well as the metabolic response of the seafloor community to environmental change.</p>
Deep Sediment N Fix
largerWorkCitation
project
eng; USA
oceans
-124.92211
-122.544233
35.68905
37.134378
2021-10-13
California Shelf (36,-123)
0
BCO-DMO catalogue of parameters from NCBI accession numbers describing nifH amplicon sequences from sediment samples collected offshore of San Francisco, Califronia, USA in March 2017 on R/V Oceanus cruise OC1703A
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/863215.rdf
Name: BioProject
Units: unitless
Description: <p>BioProject accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/863216.rdf
Name: BioSample
Units: unitless
Description: <p>BioSample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/863217.rdf
Name: SRA_study
Units: unitless
Description: <p>SRA study accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/863218.rdf
Name: Assay_Type
Units: unitless
Description: <p>Assay type</p>
http://lod.bco-dmo.org/id/dataset-parameter/863219.rdf
Name: Sequencing_platform
Units: unitless
Description: <p>Squencing platform</p>
http://lod.bco-dmo.org/id/dataset-parameter/863220.rdf
Name: Instrument_model
Units: unitless
Description: <p>Illumina model</p>
http://lod.bco-dmo.org/id/dataset-parameter/863221.rdf
Name: Library_layout
Units: unitless
Description: <p>Library layout</p>
http://lod.bco-dmo.org/id/dataset-parameter/863222.rdf
Name: File_name_1
Units: unitless
Description: <p>File name of forward reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/863223.rdf
Name: File_name_2
Units: unitless
Description: <p>File name of reverse reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/863224.rdf
Name: File_type
Units: unitless
Description: <p>File type</p>
http://lod.bco-dmo.org/id/dataset-parameter/863225.rdf
Name: Sequencing_method
Units: unitless
Description: <p>Sequencing method</p>
http://lod.bco-dmo.org/id/dataset-parameter/863226.rdf
Name: Library_selection
Units: unitless
Description: <p>Library selection</p>
http://lod.bco-dmo.org/id/dataset-parameter/863227.rdf
Name: PCR_primers
Units: unitless
Description: <p>PCR primer sequences</p>
http://lod.bco-dmo.org/id/dataset-parameter/863228.rdf
Name: Sequencing_adapters
Units: unitless
Description: <p>Illumina adapter sequences</p>
http://lod.bco-dmo.org/id/dataset-parameter/863229.rdf
Name: Geographic_location
Units: unitless
Description: <p>Sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/863230.rdf
Name: Sample_type
Units: unitless
Description: <p>Environmental sample type</p>
http://lod.bco-dmo.org/id/dataset-parameter/863231.rdf
Name: Sample_name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/863232.rdf
Name: Sample_latitude
Units: decimal degrees North
Description: <p>Sampling latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/863233.rdf
Name: Sample_longitude
Units: decimal degrees East
Description: <p>Sampling longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/863234.rdf
Name: Deployment_number
Units: unitless
Description: <p>Deployment number</p>
http://lod.bco-dmo.org/id/dataset-parameter/863235.rdf
Name: Multicore_number
Units: unitless
Description: <p>Mulitcore number</p>
http://lod.bco-dmo.org/id/dataset-parameter/863236.rdf
Name: Seawater_depth
Units: meters below sea surface
Description: <p>Seawater depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/863237.rdf
Name: Sediment_depth
Units: centimeters below sediment surface
Description: <p>Sediment depth</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
63780
https://darchive.mblwhoilibrary.org/bitstream/1912/29305/1/dataset-863192_oc1703a-sediment-nifh-amplicon-sequences__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.863192.1
download
onLine
dataset
<p>Sediment samples were collected using a multicorer on board the R/V Oceanus (March 2017) and sample aliquots were immediately stored at -80°C until DNA extraction. DNA was extracted in the laboratory using an RNeasy PowerSoil DNA elution kit (Qiagen, catalog no. 12867-25) after RNA was extracted using an RNeasy PowerSoil Total RNA kit. (Qiagen, catalog no. 12866-25).</p>
<p><em>nifH</em> sequences were amplified using the PCR primers described in Mehta et al., 2003 and amplicons were prepared for 2×250 bp sequencing on an Illumina MiSeq platform following the protocol described in Kapili et al., 2020.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
Samples were demultiplexed at the UC Davis DNA Technologies Core facility.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- replaced "na" with "nd" (no data)</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
Illumina MiSeq platform
Illumina MiSeq platform
PI Supplied Instrument Name: Illumina MiSeq platform Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
MC-800
MC-800
PI Supplied Instrument Name: MC-800 Instrument Name: Multi Corer Instrument Short Name:Multi Corer Instrument Description: The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
Cruise: OC1703A
OC1703A
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC1703A
Anne E. Dekas
Stanford University
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel