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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.
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.
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
Rock samples were collected using a Van Veen style grab on a free vehicle lander.
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.
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.
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
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:
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.
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))
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.
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##'.
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.
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)
site name
collection method: CTD; RG=Rock Grabber; Lego = Leggo Lander; El = ??
taxonomic identification of isolate based on PCR
method used for growing isolates
growth medium:2216 Marine Medium (2216; BD DifcoTM); A1 Medium; or a seawater (SW) minimal medium
collection depth
sample type: seawater or sediment
incubation pressure
latitude; north is positive
longitude; east is positive
cruise identifier; R2R official code
project specific cruise identifier
station identifier
deployment or dive identifier: UW=underway - collected with ship's underway system; CTD = CTD profiler; RG = Rock Grabber; Lego = Leggo lander; EL = ??
time zone
date of deployment (yyyymmdd)
time of deployment (hhmm)
date of recovery (yyyymmdd)
date of recovery (hhmm)
latitude from deployment log; north is positive
longitude from deployment log; east is positive
target depth as measured by multibeam
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