http://lod.bco-dmo.org/id/dataset/721437
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
2017-12-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Isolation of microbes from hadal water and sediments from Mariana and Kermadec trenches from R/V Falkor, R/V Thomas G. Thompson FK141109, TN309, FK141215, April to December 2014 (Mariana Perspectives project)
2017-12-18
publication
2017-12-18
revision
BCO-DMO Linked Data URI
2017-12-18
creation
http://lod.bco-dmo.org/id/dataset/721437
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) Isolation of microbes from hadal water and sediments from Mariana and Kermadec trenches from R/V Falkor, R/V Thomas G. Thompson FK141109, TN309, FK141215, April to December 2014 (Mariana Perspectives project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-12-18 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/721437 [access date]
Isolates from Mariana and Kermadec trenches, 2014 Dataset Description: <p>This dataset includes identifications of microbes isolated&nbsp;from hadopelagic seawater and sediment samples from the Mariana and Kermadec trenches from April, November, and December 2014.</p>
<p>NOTE: sample RG10 in this dataset is equivalent to RG09 in the event log, due to at-sea recording error. RG10-2 is equivalent to RG10 in the event log.</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, and FK141215 from Dec. 15-21, 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>Microbes were cultured at 4C on agar plates at 0.1 MPa or in transfer bulbs (Samco, Thermo Fisher Scientific) at either 0.1 MPa or high pressure. Enrichments from the Kermadec Trench were conducted using 2216 Marine Medium (2216; BD DifcoTM), A1 Medium, or a seawater minimal medium, while those from the Mariana Trench were conducted in 2216 only. For incubations at high pressure the media was inoculated, mixed with gelatin at a final concentration of 4%, transferred into bulbs, and incubated at the desired pressure (Yayanos, 2001). Kermadec Trench samples were incubated at 100 MPa while those from the Mariana Trench were incubated at in situ pressure (40-110 MPa). After ~2 months, colony forming units (CFUs) were calculated and representative isolates identified via PCR using the primers 27F and 1492R.</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
Trench
Collection_method
Taxon
Method
Medium
Depth
Type
Pressure_Mpa
Latitude
Longitude
cruise_id
cruise_name
STATION
LANDER
local_or_UTC
DATE_DEPLOYED
TIME_DEPLOYED
DATE_RECOVERED
TIME_RECOVERED
LATITUDE_log
LONGITUDE_log
MULTIBEAM_DEPTH
Rock grabber
Hadal Lander
Niskin bottle
Free vehicle coring respirometer (FVCR)
theme
None, User defined
site
sampling_method
taxon
treatment
depth
sample type
water pressure
latitude
longitude
Cruise identfier
cruise name
station
deployment number
time_zone
date_start
time_start
date end
featureType
BCO-DMO Standard Parameters
Bottom Sediment Grab Samplers
CTD - profiler
HADAL-Lander
HROV Nereus
Leggo Lander
Niskin bottle
Respirometer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
FK141109
TN309
FK141215
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
Challenger Deep, Mariana Trench
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; Challenger Deep, Mariana Trench
145
-170
-36
12.7
2014-05-01
2014-12-16
Challenger Deep, Mariana Trench
0
BCO-DMO catalogue of parameters from Isolation of microbes from hadal water and sediments from Mariana and Kermadec trenches from R/V Falkor, R/V Thomas G. Thompson FK141109, TN309, FK141215, April to December 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/721466.rdf
Name: Trench
Units: unitless
Description: <p>site name</p>
http://lod.bco-dmo.org/id/dataset-parameter/721467.rdf
Name: Collection_method
Units: unitless
Description: <p>collection method: CTD; RG=Rock Grabber; Lego = Leggo Lander; El = ??</p>
http://lod.bco-dmo.org/id/dataset-parameter/721468.rdf
Name: Taxon
Units: unitless
Description: <p>taxonomic identification of isolate based on PCR</p>
http://lod.bco-dmo.org/id/dataset-parameter/721469.rdf
Name: Method
Units: unitless
Description: <p>method used for growing isolates</p>
http://lod.bco-dmo.org/id/dataset-parameter/721470.rdf
Name: Medium
Units: unitless
Description: <p>growth medium:2216 Marine Medium (2216; BD DifcoTM); A1 Medium; or a seawater (SW) minimal medium</p>
http://lod.bco-dmo.org/id/dataset-parameter/721471.rdf
Name: Depth
Units: meters
Description: <p>collection depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/721472.rdf
Name: Type
Units: unitless
Description: <p>sample type: seawater or sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/721473.rdf
Name: Pressure_Mpa
Units: Megapascals
Description: <p>incubation pressure</p>
http://lod.bco-dmo.org/id/dataset-parameter/721474.rdf
Name: Latitude
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/721475.rdf
Name: Longitude
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/721476.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier; R2R official code</p>
http://lod.bco-dmo.org/id/dataset-parameter/721477.rdf
Name: cruise_name
Units: unitless
Description: <p>project specific cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/721478.rdf
Name: STATION
Units: unitless
Description: <p>station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/721479.rdf
Name: LANDER
Units: unitless
Description: <p>deployment or dive identifier: UW=underway - collected with ship's underway system; CTD = CTD profiler; RG = Rock Grabber; Lego = Leggo lander; EL = ??</p>
http://lod.bco-dmo.org/id/dataset-parameter/721480.rdf
Name: local_or_UTC
Units: unitless
Description: <p>time zone</p>
http://lod.bco-dmo.org/id/dataset-parameter/721481.rdf
Name: DATE_DEPLOYED
Units: unitless
Description: <p>date of deployment (yyyymmdd)</p>
http://lod.bco-dmo.org/id/dataset-parameter/721482.rdf
Name: TIME_DEPLOYED
Units: unitless
Description: <p>time of deployment (hhmm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/721483.rdf
Name: DATE_RECOVERED
Units: unitless
Description: <p>date of recovery (yyyymmdd)</p>
http://lod.bco-dmo.org/id/dataset-parameter/721484.rdf
Name: TIME_RECOVERED
Units: unitless
Description: <p>date of recovery (hhmm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/721485.rdf
Name: LATITUDE_log
Units: decimal degrees
Description: <p>latitude from deployment log; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/721486.rdf
Name: LONGITUDE_log
Units: decimal degrees
Description: <p>longitude from deployment log; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/721487.rdf
Name: MULTIBEAM_DEPTH
Units: meters
Description: <p>target depth as measured by multibeam</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
56428
https://datadocs.bco-dmo.org/file/QAAXlkJSX4kWyY/isolates.csv
isolates.csv
Primary data file for dataset ID 721437
download
https://osprey.bco-dmo.org/dataset/721437/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, and FK141215 from Dec. 15-21, 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>Microbes were cultured at 4C on agar plates at 0.1 MPa or in transfer bulbs (Samco, Thermo Fisher Scientific) at either 0.1 MPa or high pressure. Enrichments from the Kermadec Trench were conducted using 2216 Marine Medium (2216; BD DifcoTM), A1 Medium, or a seawater minimal medium, while those from the Mariana Trench were conducted in 2216 only. For incubations at high pressure the media was inoculated, mixed with gelatin at a final concentration of 4%, transferred into bulbs, and incubated at the desired pressure (Yayanos, 2001). Kermadec Trench samples were incubated at 100 MPa while those from the Mariana Trench were incubated at in situ pressure (40-110 MPa). After ~2 months, colony forming units (CFUs) were calculated and representative isolates identified via PCR using the primers 27F and 1492R.</p>
from Cruise: FK141109 <p>The subsetted data includes both FK141109 and FK141215.</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 />
- reduced Latitude and Longitude precision to 4 decimal places<br />
- replaced commas with semicolons<br />
-&nbsp;added cruise_id, cruise_name, station, date and time deployed and recovered, and local/UTC flag - from ship deployment log datasets</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
Rock grabber
Rock grabber
PI Supplied Instrument Name: Rock grabber PI Supplied Instrument Description:Rock samples were collected using a Van Veen style grab on a free vehicle lander. 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/
Hadal Lander
Hadal Lander
PI Supplied Instrument Name: Hadal Lander Instrument Name: HADAL-Lander Instrument Short Name:HADAL-Lander Instrument Description: The HADAL-Lander is a free-falling baited lander composed of two major components; the scientific payload and delivery system.
HADAL-Lander A
HADAL-Lander-B
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/
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
Cruise: FK141215
FK141215
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK141215
Douglas Bartlett
University of California-San Diego Scripps
http://dmoserv3.whoi.edu/data_docs/Mariana_Perspectives/Bartlett-final-FK141215-cruise-report.pdf
Report describing FK141215
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