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    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)
    
  
  
    
    

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)

Website: https://www.bco-dmo.org/dataset/721437
Data Type: Other Field Results
Version:
Version Date: 2017-12-18

Project
» Patterns of Microbial Community Structure Within and Between Hadal Environments (Mariana Perspectives)
ContributorsAffiliationRole
Bartlett, DouglasUniversity of California-San Diego (UCSD-SIO)Principal Investigator
Copley, NancyWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Coverage

Spatial Extent: N:12.7 E:-170 S:-36 W:145
Temporal Extent: 2014-05-01 - 2014-12-16

Dataset Description

This dataset includes identifications of microbes isolated from hadopelagic seawater and sediment samples from the Mariana and Kermadec trenches from April, November, and December 2014.

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.


Acquisition Description

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: https://schmidtocean.org/cruise/expanding-mariana-trench-perspectives/ and https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-deep-cruise-2014/

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.


Processing Description

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- reduced Latitude and Longitude precision to 4 decimal places
- replaced commas with semicolons
- added cruise_id, cruise_name, station, date and time deployed and recovered, and local/UTC flag - from ship deployment log datasets


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Related Publications

Yayanos, A. Aristides (2001). Deep-sea piezophilic bacteria. Marine Microbiology, 615–637. doi:10.1016/s0580-9517(01)30065-x https://doi.org/10.1016/S0580-9517(01)30065-X
Methods

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Parameters

ParameterDescriptionUnits
Trenchsite name unitless
Collection_methodcollection method: CTD; RG=Rock Grabber; Lego = Leggo Lander; El = ?? unitless
Taxontaxonomic identification of isolate based on PCR unitless
Methodmethod used for growing isolates unitless
Mediumgrowth medium:2216 Marine Medium (2216; BD DifcoTM); A1 Medium; or a seawater (SW) minimal medium unitless
Depthcollection depth meters
Typesample type: seawater or sediment unitless
Pressure_Mpaincubation pressure Megapascals
Latitudelatitude; north is positive decimal degrees
Longitudelongitude; east is positive decimal degrees
cruise_idcruise identifier; R2R official code unitless
cruise_nameproject specific cruise identifier unitless
STATIONstation identifier unitless
LANDERdeployment or dive identifier: UW=underway - collected with ship's underway system; CTD = CTD profiler; RG = Rock Grabber; Lego = Leggo lander; EL = ?? unitless
local_or_UTCtime zone unitless
DATE_DEPLOYEDdate of deployment (yyyymmdd) unitless
TIME_DEPLOYEDtime of deployment (hhmm) unitless
DATE_RECOVEREDdate of recovery (yyyymmdd) unitless
TIME_RECOVEREDdate of recovery (hhmm) unitless
LATITUDE_loglatitude from deployment log; north is positive decimal degrees
LONGITUDE_loglongitude from deployment log; east is positive decimal degrees
MULTIBEAM_DEPTHtarget depth as measured by multibeam meters


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Instruments

Dataset-specific Instrument Name
Niskin bottle
Generic Instrument Name
Niskin bottle
Generic 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.

Dataset-specific Instrument Name
Generic Instrument Name
CTD profiler
Generic 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 and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the 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 instrument designation is used when specific make and model are not known.

Dataset-specific Instrument Name
Rock grabber
Generic Instrument Name
Bottom Sediment Grab Samplers
Dataset-specific Description
Rock samples were collected using a Van Veen style grab on a free vehicle lander.
Generic 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.

Dataset-specific Instrument Name
Generic Instrument Name
HROV Nereus
Generic 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.

Dataset-specific Instrument Name
Generic Instrument Name
PCR Thermal Cycler
Generic Instrument Description
General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). 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. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Dataset-specific Instrument Name
Hadal Lander
Generic Instrument Name
HADAL-Lander
Generic 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

Dataset-specific Instrument Name
Generic Instrument Name
Leggo Lander
Generic 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))

Dataset-specific Instrument Name
Free vehicle coring respirometer (FVCR)
Generic Instrument Name
Respirometer
Dataset-specific 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##'.
Generic 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.


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Deployments

FK141109

Website
Platform
R/V Falkor
Report
Start Date
2014-11-09
End Date
2014-12-09
Description
The very deepest reaches of the sea are one of the planet’s last true frontiers. That’s mostly because a lack of support for needed technological advancements and vehicles has severely limited access to depths beyond 7,000 meters. But the situation is finally beginning to change, and SOI is helping push the process forward. In November, the institute collaborated with a group of biologists and geologists working aboard R/V Falkor to conduct a new study of one of the deepest places in the world. The team deployed SOI's new full-ocean-depth landers—frames equipped with cameras, sensors and sample collection devices that return to the surface automatically after a set time on the seafloor—as well as three other landers, in the Mariana Trench's Sirena Deep, near Guam. The work, at depths down to almost 11,000 meters, will help answer enduring questions about the biology of such alien zones, including who lives there and how they survive the massive pressure. The research should also improve understanding of the processes that control earthquake and tsunami formation, among others geological goals. Original cruise data are available from the NSF R2R data catalog (Cruise DOI: 10.7284/900733)

Acquisition Description
The subsetted data includes both FK141109 and FK141215.

TN309

Website
Platform
R/V Thomas G. Thompson
Start Date
2014-04-10
End Date
2014-05-20
Description
Original data are available from the NSF R2R data catalog

FK141215

Website
Platform
R/V Falkor
Report
Start Date
2014-12-15
End Date
2014-12-21
Description
During this cruise the Leggo lander was deployed multiple times and drops 1 and 3 recovered seawater samples that were analyzed. Additional details can be found at: https://schmidtocean.org/cruise/expanding-mariana-trench-perspectives/ and https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-deep-cruise-2.... More information is available in the post-cruise and final expedition reports (PDF). Original cruise data are available from the NSF R2R data catalog


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Project Information

Patterns of Microbial Community Structure Within and Between Hadal Environments (Mariana Perspectives)

Coverage: Challenger Deep, Mariana Trench


Award Abstract from NSF:
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.

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.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database.    2022-05-17  09:48:52