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This dataset includes cell counts from hadopelagic seawater 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/
For cell counts, seawater was fixed with 1% paraformaldehyde and stored at -80C. Samples were later thawed, stained with SYBR Green (Thermo Fisher Scientific, Waltham, MA), and cells enumerated using flow cytometry (Attune Acoustic Focusing Flow Cytometer, Applied Biosystems, Foster City, CA).
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 - reduced cell count precision to whole values - 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.
Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. (from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)
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
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.
sample identifier
site name
cell concentration
cellection depth
sample type: seawater or sediment
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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