http://lod.bco-dmo.org/id/dataset/720916
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
2017-12-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
515F-926R 16S rRNA gene sequencing accessions from seawater and sediment samples from R/V Falkor FK141109 and R/V Thompson TN309 from the Mariana and Kermadec trenches, 2014 (Mariana Perspectives project)
2017-12-13
publication
2017-12-13
revision
BCO-DMO Linked Data URI
2017-12-13
creation
http://lod.bco-dmo.org/id/dataset/720916
Douglas Bartlett
University of California-San Diego Scripps
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: Bartlett, D. (2017) 515F-926R 16S rRNA gene sequencing accessions from seawater and sediment samples from R/V Falkor FK141109 and R/V Thompson TN309 from the Mariana and Kermadec trenches, 2014 (Mariana Perspectives project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-12-13 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/720916 [access date]
515F-926R 16S rRNA accessions, Mariana and Kermadec trenches, 2014 Dataset Description: <p>This dataset includes links to 515F-926R 16S rRNA gene sequencing accessions archived at NCBI and associated collection data from seawater and sediment samples from the Mariana and Kermadec trenches from April and November 2014.</p>
<p>For those accessions with a status of 'not yet available' at NCBI, they will be made available once the paper has been published, likely by mid-2018. Please check back for them then or contact the PI.</p> Methods and Sampling: <p>This data set is associated with PI Douglas Bartlett (NSF OCE-1536776) and R/V Thomas G. Thompson from Apr. 10 - May 20 to the Kermadec Trench adjacent to New Zealand and Schmidt Ocean Institute R/V Falkor cruise FK141109 from Nov. 9 - Dec. 9, 2014, to the Mariana Trench. During the cruises, sediment and water samples were collected. Additional details can be found at: <a href="https://schmidtocean.org/cruise/expanding-mariana-trench-perspectives/" target="_blank">https://schmidtocean.org/cruise/expanding-mariana-trench-perspectives/</a> and <a href="https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-deep-cruise-2014/" target="_blank">https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-deep-cruise-2014/</a></p>
<p>Seawater (40-120 L per sample) was serially filtered through 3.0 (47 mm diameter), 0.2 (47 mm or Sterivex), and 0.1 µm (142 mm) polycarbonate filters using a peristaltic pump. Filters were then placed into a sucrose buffer (Rusch et al., 2007) and frozen at -80°C. DNA was extracted from whole filters using a protocol previously described (Fuhrman et al., 1988; Tarn et al., 2016). Negative controls using blank filters were extracted in concomitance with every extraction performed.</p>
<p>DNA from sediment (5 g wet-weight) samples was extracted using a modified version of Lysis Protocol II described by Lever et al. (2015). 2.5 V of lysis solution (30 mM EDTA, 30 mM Tris-HCl, 800 mM guanidine hydrochloride, 0.5% Triton X-100, final pH 10) and 500 µmol pyrophosphate was added to each sample and the mixture briefly vortexed. Samples were then subjected to two 15 minute freeze-thaw cycles at -80°C, followed by incubation at 50°C with shaking at 150 rpm&nbsp; for one hour. Samples were centrifuged and the supernatant was treated twice with 1 V chloroform isoamyl alcohol. DNA was precipitated using 5 M NaCl and ethanol for two hours at room temperature and resuspended in nuclease-free water. Extracted DNA was cleaned again using a Quick-gDNA MiniPrep kit (Zymo Research, Irvine, CA). Negative control blanks, consisting of all reagents but no sediment material, were performed in concomitance with every extraction.</p>
<p>The V4-V5 16S rRNA gene region between 515f-926R was amplified (Parada et al., 2015) and tagged with Illumina barcodes using a secondary PCR procedure. Samples were pooled at equimolar concentrations and sent for sequencing on an Illumina Miseq at the Institute for Genomic Medicine Genomics Center (University of California, San Diego, La Jolla, CA).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1536776 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1536776
completed
Douglas Bartlett
University of California-San Diego Scripps
858-534-5233
9500 Gilman Dr., MC 0210
La Jolla
CA
92093
USA
dbartlett@ucsd.edu
pointOfContact
asNeeded
Unknown
Sample_name
Sample_title
Collection_date
Depth
Type
Location
lat
lon
filter_size
status
Bioproject_link
Biosample_link
sediment_depth
Illumina Miseq
Rock grabber
Niskin bottle
UW
Free vehicle coring respirometer (FVCR)
theme
None, User defined
sample identification
date
depth
sample type
site
latitude
longitude
filter_size
status
accession number
depth_interval
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Bottom Sediment Grab Samplers
CTD - profiler
HROV Nereus
Leggo Lander
Niskin bottle
Pump - Surface Underway Ship Intake
Respirometer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
FK141109
TN309
service
Deployment Activity
Mariana Trench adjacent to Guam: approximately 12 45 N and 144 50 E to 11 25 N and 144 25 E
Kermadec Trench adjacent to New Zealand: approximately 37 12.75 S and 178 51.43 E to 31 51.29 S and 176 49.07 W
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.
Patterns of Microbial Community Structure Within and Between Hadal Environments
https://osprey.bco-dmo.org/project/675560
Patterns of Microbial Community Structure Within and Between Hadal Environments
<p><em>Award Abstract from NSF:</em><br />
The deepest portion of the ocean is present in ocean trenches, whose steep walls descend from approximately 4 miles down to depths that in some cases are close to 7 miles below the seawater surface. At these locations Earth's crust is recycled. Perhaps not surprisingly given their remoteness, deep ocean trenches are the least understood habitats in the ocean. The researchers participating in this project are working to characterize the microbes present in two of the deepest trenches present on Earth, both in the Pacific Ocean, the Kermadec Trench located north of New Zealand, and the Mariana Trench, located east and south of the island of Guam. Most of the Mariana Trench is located within the United States Mariana Trench Marine National Monument. Relatively little is known about the diversity and adaptations of the microorganisms in deep ocean trenches. An unknown fraction of the microbes present have descended from shallow waters above and are unlikely to participate in any nutrient cycles in the deep sea. Others are adapted to near freezing temperatures and up to pressures greater than 10e7 kilograms per square meter (16,000 pounds per square inch). These latter microbes perform important roles recycling organic matter. But who are they? This project is contributing to the training of diverse undergraduate and graduate students participating in research, additional undergraduate students learning about microbes inhabiting extreme environments in a web-based class, and additional graduate students and postdoctoral scientists participating in an advanced training course being offered in Antarctica.</p>
<p>Experiments being performed include direct counts of prokaryotes and viruses in seawater and sediments, analyses of the abundance and phylogenetic breadth of culturable heterotrophic bacteria at a range of pressures, measurements of bacterial community species diversity and richness both within and across seawater and sediment samples, as well as within and across the two trench systems, measurements of microbial activity as a function of pressure and the identification of high pressure-active cells. The data generated from these analyses are being integrated into the results of additional chemical, geological and biological measurements performed by others as a part of the National Science Foundation funded Hadal Ecosystems Studies Project. Two of the working hypotheses are that prokaryote numbers and diversity are generally positively correlated with surface productivity and proximity to the trench axis and that bacterial taxa exist which are endemic to specific trenches, present in multiple trenches and more widely distributed in deep-sea environments.</p>
Mariana Perspectives
largerWorkCitation
project
eng; USA
biota
oceans
Mariana Trench adjacent to Guam: approximately 12 45 N and 144 50 E to 11 25 N and 144 25 E; Kermadec Trench adjacent to New Zealand: approximately 37 12.75 S and 178 51.43 E to 31 51.29 S and 176 49.07 W
145
-170
-37.7337
12.7306
2014-04-10
2014-12-09
Challenger Deep, Mariana Trench
0
BCO-DMO catalogue of parameters from 515F-926R 16S rRNA gene sequencing accessions from seawater and sediment samples from R/V Falkor FK141109 and R/V Thompson TN309 from the Mariana and Kermadec trenches, 2014 (Mariana Perspectives 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/720939.rdf
Name: Sample_name
Units: unitless
Description: <p>sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/720940.rdf
Name: Sample_title
Units: unitless
Description: <p>NCBI sample title</p>
http://lod.bco-dmo.org/id/dataset-parameter/720941.rdf
Name: Collection_date
Units: unitless
Description: <p>sample collection date</p>
http://lod.bco-dmo.org/id/dataset-parameter/720942.rdf
Name: Depth
Units: meters
Description: <p>sample deplth</p>
http://lod.bco-dmo.org/id/dataset-parameter/720943.rdf
Name: Type
Units: unitless
Description: <p>sample type: seawater or sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/720944.rdf
Name: Location
Units: unitless
Description: <p>collection location: ocean and trench name</p>
http://lod.bco-dmo.org/id/dataset-parameter/720945.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/720946.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/720947.rdf
Name: filter_size
Units: microns
Description: <p>filter size fractions</p>
http://lod.bco-dmo.org/id/dataset-parameter/720948.rdf
Name: status
Units: unitless
Description: <p>whether access to NCBI pages are public or not</p>
http://lod.bco-dmo.org/id/dataset-parameter/720949.rdf
Name: Bioproject_link
Units: unitless
Description: <p>NCBI BioProject accession number and link to associated NCBI web page</p>
http://lod.bco-dmo.org/id/dataset-parameter/720950.rdf
Name: Biosample_link
Units: unitless
Description: <p>NCBI BioSample accession number and link to associated NCBI web page</p>
http://lod.bco-dmo.org/id/dataset-parameter/723276.rdf
Name: sediment_depth
Units: centimeters
Description: <p>sediment core depth of the sample</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
56871
https://datadocs.bco-dmo.org/file/R88XmO4sYLBAL/accessions.csv
accessions.csv
Primary data file for dataset ID 720916
download
https://osprey.bco-dmo.org/dataset/720916/data/download
download
onLine
dataset
<p>This data set is associated with PI Douglas Bartlett (NSF OCE-1536776) and R/V Thomas G. Thompson from Apr. 10 - May 20 to the Kermadec Trench adjacent to New Zealand and Schmidt Ocean Institute R/V Falkor cruise FK141109 from Nov. 9 - Dec. 9, 2014, to the Mariana Trench. During the cruises, sediment and water samples were collected. Additional details can be found at: <a href="https://schmidtocean.org/cruise/expanding-mariana-trench-perspectives/" target="_blank">https://schmidtocean.org/cruise/expanding-mariana-trench-perspectives/</a> and <a href="https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-deep-cruise-2014/" target="_blank">https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-deep-cruise-2014/</a></p>
<p>Seawater (40-120 L per sample) was serially filtered through 3.0 (47 mm diameter), 0.2 (47 mm or Sterivex), and 0.1 µm (142 mm) polycarbonate filters using a peristaltic pump. Filters were then placed into a sucrose buffer (Rusch et al., 2007) and frozen at -80°C. DNA was extracted from whole filters using a protocol previously described (Fuhrman et al., 1988; Tarn et al., 2016). Negative controls using blank filters were extracted in concomitance with every extraction performed.</p>
<p>DNA from sediment (5 g wet-weight) samples was extracted using a modified version of Lysis Protocol II described by Lever et al. (2015). 2.5 V of lysis solution (30 mM EDTA, 30 mM Tris-HCl, 800 mM guanidine hydrochloride, 0.5% Triton X-100, final pH 10) and 500 µmol pyrophosphate was added to each sample and the mixture briefly vortexed. Samples were then subjected to two 15 minute freeze-thaw cycles at -80°C, followed by incubation at 50°C with shaking at 150 rpm&nbsp; for one hour. Samples were centrifuged and the supernatant was treated twice with 1 V chloroform isoamyl alcohol. DNA was precipitated using 5 M NaCl and ethanol for two hours at room temperature and resuspended in nuclease-free water. Extracted DNA was cleaned again using a Quick-gDNA MiniPrep kit (Zymo Research, Irvine, CA). Negative control blanks, consisting of all reagents but no sediment material, were performed in concomitance with every extraction.</p>
<p>The V4-V5 16S rRNA gene region between 515f-926R was amplified (Parada et al., 2015) and tagged with Illumina barcodes using a secondary PCR procedure. Samples were pooled at equimolar concentrations and sent for sequencing on an Illumina Miseq at the Institute for Genomic Medicine Genomics Center (University of California, San Diego, La Jolla, CA).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- split lat and lon into separate columns and rounded to 4 decimal places<br />
- removed blank spaces in 3 sample names.</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
Illumina Miseq
PI Supplied Instrument Name: Illumina Miseq PI Supplied Instrument Description:Sequencing was performed at the Institute for Genomic Medicine Genomics Center (University of California, San Diego, La Jolla, CA). 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.
Rock grabber
Rock grabber
PI Supplied Instrument Name: Rock grabber Instrument Name: Bottom Sediment Grab Samplers Instrument Short Name:BSGS 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/50/
PI Supplied Instrument Name: Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
PI Supplied Instrument Name: Instrument Name: HROV Nereus Instrument Short Name:HROV Nereus Instrument Description: Nereus is an efficient, multi-purpose “hybrid” vehicle that can explore and operate in the crushing pressures of the greatest ocean depths. An unmanned vehicle, Nereus operates in two complementary modes. It can swim freely as an autonomous underwater vehicle (AUV) to survey large areas of the depths, map the seafloor, and give scientists a broad overview. When Nereus locates something interesting, the vehicle’s support team can bring the vehicle back on board the ship and transforms it into a remotely operated vehicle (ROV) tethered to the ship via a micro-thin, fiber-optic cable. Through this tether, Nereus can transmit high-quality, real-time video images and receive commands from skilled pilots on the ship to collect samples or conduct experiments with a manipulator arm.
Technical specifications:
Weight on land: 2,800 kg
Payload capacity: 25 kg
Maximum speed: 3 knots
Batteries: rechargable lithium ion, 15 kilowatt hours in two pressure housings
Thrusters: 2 fore and aft, 2 vertical, 1 lateral (ROV mode) 2 fore and aft, 1 vertical (AUV mode)
Lights: variable output LED array, strobes
Manipulator arm: Kraft TeleRobotics 7-function hydraulic manipulator
Sonar: scanning sonar, forward look and profile, 675 KHz
Sensors: magnetometer, CTD (to measure conductivity, temperature, and depth)
Nereus supports a variety of science operations: Push coring, measuring heat flow, geotechnical and geochemical sensing, rock sampling and drilling, biological sampling, water sampling, high resolution acoustic bathymetry, and optical still and video imagery.
More information is available from the operator site at URL.
PI Supplied Instrument Name: Instrument Name: Leggo Lander Instrument Short Name: Instrument Description: The "Leggo Lander" is a lander system that primarily relies on syntactic foam for buoyancy and uses iridium GPS, radio signal, strobe light and flag for surface recovery, and acoustics for underwater monitoring and instrument control. The lander has a timer with 5 control settings for various operations. It routinely measures pressure (depth) throughout its dive and temperature on the seafloor. The lander payloads include a pressure-retaining seawater sampler plus 2 liter Niskin bottle, and a camera/battery/light system that also includes a 30 liter Niskin bottle and a sea cucumber trap. With the camera payload it travels down or up the water column at about 39 meters per minute (~ 4.5 hours for a descent to the Challenger Deep at ~10,920 m).
(Description obtained from the R/V Falkor FK141215 post-cruise report (PDF))
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
UW
UW
PI Supplied Instrument Name: UW PI Supplied Instrument Description:The underway system used to collect samples aboard the Falkor. Instrument Name: Pump - Surface Underway Ship Intake Instrument Short Name:Pump-Ship Intake Instrument Description: The 'Pump-underway ship intake' system indicates that samples are from the ship's clean water intake pump. This is essentially a surface water sample from a source of uncontaminated near-surface (commonly 3 to 7 m) seawater that can be pumped continuously to shipboard laboratories on research vessels. There is typically a temperature sensor near the intake (known as the hull temperature) to provide measurements that are as close as possible to the ambient water temperature. The flow from the supply is typically directed through continuously logged sensors such as a thermosalinograph and a fluorometer. Water samples are often collected from the underway supply that may also be referred to as the non-toxic supply. Ideally the data contributor has specified the depth in the ship's hull at which the pump is mounted. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/31/
Free vehicle coring respirometer (FVCR)
Free vehicle coring respirometer (FVCR)
PI Supplied Instrument Name: Free vehicle coring respirometer (FVCR) PI Supplied Instrument Description:The Free Vehicle Coring Respirometer (FVCR) is deployed from the ship and sinks slowly to the seafloor. After landing on a targeted soft bottom it slowly inserts four megacore tubes into the mud and retracts them using a drive motor, which closes the lids and seals the core. Each tube is equipped with an oxygen optode and water mixing pump to measure sediment community oxygen consumption in each core. Each core is trapped by a standard megacore core catching device and returned to the surface with the lander. The instrument also includes an oxygen sensor to measure the ambient bottom water. Data and a video of the coring operation are stored inside the titanium pressure housing. Samples from this instrument are designated with 'CR##'. Instrument Name: Respirometer Instrument Short Name: Instrument Description: A device that measures the rate of respiration by a living organism or organic system by measuring its rate of exchange of oxygen and/or carbon dioxide.
PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. 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. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Cruise: FK141109
FK141109
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK141109
Jeffrey C. Drazen
University of Hawaiʻi at Mānoa
https://datadocs.bco-dmo.org/d3/data_docs/Mariana_Perspectives/FK141109_Cruise_Report_JDC_2015-01-12.pdf
Report describing FK141109
Cruise: TN309
TN309
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN309
Timothy M. Shank
Woods Hole Oceanographic Institution
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel