http://lod.bco-dmo.org/id/dataset/862731
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
2021-10-07
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
19 Metagenomes and 7 metatranscriptomes from sediment samples collected offshore of San Francisco, Califronia, USA
2021-10-11
publication
2021-10-11
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-05-08
publication
https://doi.org/10.26008/1912/bco-dmo.862731.1
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
documentDigital
Cite this dataset as: Dekas, A. E. (2023) 19 Metagenomes and 7 metatranscriptomes from sediment samples collected offshore of San Francisco, Califronia, USA. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-10-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.862731.1 [access date]
OC1703A Sediment MG-MT Dataset Description: Methods and Sampling: <p>Sediment was collected with an MC-800 multicorer aborad the R/V Oceanus (expedition 1703A) approximately 0-300 km off the coast of San Francisco, CA, USA. Cores were stored at 4C until extrusion and sectioning within 24h of collection. Cores were sectioned into 2.5-5cm vertical horizons, and approximately 2g of sediment were sampled from each horizon with a cut-off syringe, flash frozen in liquid nitrogen, and stored at -80C until extraction of nucleic acids. DNA was extracted with an RNeasy PowerSoil DNA elution kit (Qiagen, cat. no 12867-25) in combination with an RNeasy PowerSoil Total RNA kit (Qiagen, cat. no 12866-25). The manufacturer's protocol was modified to include a bead-beating step of 5.5 m/s for 2x45s with a FastPrep-24 instrument. DNA and RNA were eluted in 100 microliters of DNAse and RNAse-free water or 1xTE and stored at -80C. Total RNA was treated with DNAse (Thermo Fisher Scientific,cat. no AM1907). Three DNA samples were additionally processed for long-read sequencing by size-selection with the BluePippin instrument targeting the size range of 10-50kb and a library was prepared for sequencing with the 10x Genomics Chromium system according to manufacturer's protocol and described in Bishara et al. (2018, <a href="https://doi.org/10.1038/nbt.4266" target="_blank">https://doi.org/10.1038/nbt.4266</a>). Chromium libraries were sequenced with 2 x 151bp sequencing on an HiSeq 4000 instrument (Illumina). All other samples were processed by the Joint Genome Institute (Department of Energy). DNA was sheared to approximately 300bp using a Covaris LE220 ultrasonicator and size selected with SPRI beads and libraries prepared and barcoded using Kapa Biosystems library preparation kit. Total RNA was treated with Ribo-Zero rRNA removal kit (Illumina) and cDNA libraries generated using the Illumina Truseq Stranded mRNA Library Prep kit. The rRNA depleted RNA was fragmented and reversed transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with end-pair, A-tailing, adapter ligation, and 10 cycles of PCR. DNA and cDNA were sequenced with 2 x 151bp sequencing on a Nova Seq S4 (Illumina) instrument.</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
Funding provided by US Department of Energy - Joint Genome Institute (DOE-JGI) Award Number: 504079
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_run_ID
SRA_run_link
SRA_study_ID
SRA_title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
elevation
depth
latitude
longitude
collection_date
Illumina NovaSeq 6000
Illumina HiSeq 4000
Sea-Bird Scientific CTD
MC-800
BluePippin
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA run accession (SRR)
NCBI SRA study accession (SRP)
sampling_method
instrument
depth
altitude
latitude
longitude
date
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
CTD Sea-Bird
Multi Corer
Sage Science BluePippin DNA size selection device
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
-123.08
-121.03
35.69
37.13
2017-03-14
2017-03-21
California Shelf (36,-123)
0
BCO-DMO catalogue of parameters from 19 Metagenomes and 7 metatranscriptomes from sediment samples collected offshore of San Francisco, Califronia, USA
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/862957.rdf
Name: BioProject
Units: unitless
Description: <p>BioProject accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/862958.rdf
Name: BioSample
Units: unitless
Description: <p>BioSample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/862959.rdf
Name: SRA_run_ID
Units: unitless
Description: <p>SRA run accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/862960.rdf
Name: SRA_run_link
Units: unitless
Description: <p>Hyperlink to SRA run</p>
http://lod.bco-dmo.org/id/dataset-parameter/862961.rdf
Name: SRA_study_ID
Units: unitless
Description: <p>SRA study accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/862962.rdf
Name: SRA_title
Units: unitless
Description: <p>SRA title</p>
http://lod.bco-dmo.org/id/dataset-parameter/862963.rdf
Name: library_strategy
Units: unitless
Description: <p>Sequence library type</p>
http://lod.bco-dmo.org/id/dataset-parameter/862964.rdf
Name: library_source
Units: unitless
Description: <p>Source of nucleic acids</p>
http://lod.bco-dmo.org/id/dataset-parameter/862965.rdf
Name: library_selection
Units: unitless
Description: <p>Library selection</p>
http://lod.bco-dmo.org/id/dataset-parameter/862966.rdf
Name: library_layout
Units: unitless
Description: <p>Library layout</p>
http://lod.bco-dmo.org/id/dataset-parameter/862967.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform</p>
http://lod.bco-dmo.org/id/dataset-parameter/862968.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencer model</p>
http://lod.bco-dmo.org/id/dataset-parameter/862969.rdf
Name: design_description
Units: unitless
Description: <p>Sampling design</p>
http://lod.bco-dmo.org/id/dataset-parameter/862970.rdf
Name: elevation
Units: meters (m)
Description: <p>Depth from sea level surface</p>
http://lod.bco-dmo.org/id/dataset-parameter/862971.rdf
Name: depth
Units: centimeters (cm)
Description: <p>Depth from seafloor</p>
http://lod.bco-dmo.org/id/dataset-parameter/862972.rdf
Name: latitude
Units: decimal degrees North
Description: <p>Sampling latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/862973.rdf
Name: longitude
Units: decimal degrees East
Description: <p>Sampling longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/862974.rdf
Name: collection_date
Units: unitless
Description: <p>Date sample collected; format: YYYY-MM-DD</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
11072
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/43989309-5538-4b48-a6f6-773d7b1c47e0/content
download
https://doi.org/10.26008/1912/bco-dmo.862731.1
download
onLine
dataset
<p>Sediment was collected with an MC-800 multicorer aborad the R/V Oceanus (expedition 1703A) approximately 0-300 km off the coast of San Francisco, CA, USA. Cores were stored at 4C until extrusion and sectioning within 24h of collection. Cores were sectioned into 2.5-5cm vertical horizons, and approximately 2g of sediment were sampled from each horizon with a cut-off syringe, flash frozen in liquid nitrogen, and stored at -80C until extraction of nucleic acids. DNA was extracted with an RNeasy PowerSoil DNA elution kit (Qiagen, cat. no 12867-25) in combination with an RNeasy PowerSoil Total RNA kit (Qiagen, cat. no 12866-25). The manufacturer's protocol was modified to include a bead-beating step of 5.5 m/s for 2x45s with a FastPrep-24 instrument. DNA and RNA were eluted in 100 microliters of DNAse and RNAse-free water or 1xTE and stored at -80C. Total RNA was treated with DNAse (Thermo Fisher Scientific,cat. no AM1907). Three DNA samples were additionally processed for long-read sequencing by size-selection with the BluePippin instrument targeting the size range of 10-50kb and a library was prepared for sequencing with the 10x Genomics Chromium system according to manufacturer's protocol and described in Bishara et al. (2018, <a href="https://doi.org/10.1038/nbt.4266" target="_blank">https://doi.org/10.1038/nbt.4266</a>). Chromium libraries were sequenced with 2 x 151bp sequencing on an HiSeq 4000 instrument (Illumina). All other samples were processed by the Joint Genome Institute (Department of Energy). DNA was sheared to approximately 300bp using a Covaris LE220 ultrasonicator and size selected with SPRI beads and libraries prepared and barcoded using Kapa Biosystems library preparation kit. Total RNA was treated with Ribo-Zero rRNA removal kit (Illumina) and cDNA libraries generated using the Illumina Truseq Stranded mRNA Library Prep kit. The rRNA depleted RNA was fragmented and reversed transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with end-pair, A-tailing, adapter ligation, and 10 cycles of PCR. DNA and cDNA were sequenced with 2 x 151bp sequencing on a Nova Seq S4 (Illumina) instrument.</p>
Specified by the Principal Investigator(s)
<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 NovaSeq 6000
Illumina NovaSeq 6000
PI Supplied Instrument Name: Illumina NovaSeq 6000 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.
Illumina HiSeq 4000
Illumina HiSeq 4000
PI Supplied Instrument Name: Illumina HiSeq 4000 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.
Sea-Bird Scientific CTD
Sea-Bird Scientific CTD
PI Supplied Instrument Name: Sea-Bird Scientific CTD PI Supplied Instrument Description:provided real-time collection of depth, temperature, salinity Instrument Name: CTD Sea-Bird Instrument Short Name:CTD Sea-Bird Instrument Description: A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
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/
BluePippin
BluePippin
PI Supplied Instrument Name: BluePippin Instrument Name: Sage Science BluePippin DNA size selection device Instrument Short Name:BluePippin Instrument Description: An automated DNA size selection instrument, with pulsed-field electrophoresis for resolving and collecting high molecular weight DNA. The instrument is used to automatically extract DNA fragments of a user selected size for downstream technologies such as miRNA isolation, DNA sequencing, RNA-seq, genotyping, DNA sequencing, ChIP-seq, and Long-read sequencing. The instrument uses electrophoresis along with laser detection or other imaging technology to determine when to start collecting DNA based on size ranges entered by the user. Once the DNA is no longer in the desired size range, collection ceases. The instrument has electrophoresis voltage options: 25V, 100V or 150V constant, or 100V pulsed field. The optical detection wavelength is 470 nm excitation, and 525 nm emission. The instrument can run up to 5 samples/gel cassettes at a time, with no possibility of cross contamination.
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