Dataset: Cell counts - water

Name: Cell counts from hadopelagic samples in the Mariana and Kermadec trenches, collected on R/V Falkor FK141109, FK141215, and R/V Thompson TN309, 2014 (Mariana Perspectives project)
Published: 2017-12-18
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:12.7 E:-170 S:-38 W:145

Temporal Extent: 2014-04-03 - 2014-12-16

Project:

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

Principal Investigator:

Douglas Bartlett (University of California-San Diego, UCSD-SIO)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2017-12-18

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Cell counts from hadopelagic samples in the Mariana and Kermadec trenches, collected on R/V Falkor FK141109, FK141215, and R/V Thompson TN309, 2014 (Mariana Perspectives project)

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Description

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.

Methods & Sampling

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).

Data 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
- 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

Data Files

File
cellcounts_water.csv (Comma Separated Values (.csv), 4.05 KB) MD5:5b4ba572d0183fc9e0b1303823d7e63a Primary data file for dataset ID 721385

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1536776

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
FK141109	HADES-M HADESM	2014-11-09	R/V Falkor	Jeffrey C. Drazen (Chief Scientist)	data info
FK141215		2014-12-15	R/V Falkor	Douglas Bartlett (Chief Scientist)	data info
TN309	HADES-K HADESK	2014-04-10	R/V Thomas G. Thompson	Timothy M. Shank (Chief Scientist)	data info

Instruments

Bottom Sediment Grab Samplers

Supplied Name: Rock grabber

Supplied Description:

Rock samples were collected using a Van Veen style grab on a free vehicle lander.

Instrument Type

Generic Name: Bottom Sediment Grab Samplers

Acronym: BSGS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/50/

Generic 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.

CTD - profiler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic 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.

Flow Cytometer

Supplied Name: Attune Acoustic Focusing Flow Cytometer, Applied Biosystems, Foster City, CA

Supplied Description:

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

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)

HADAL-Lander

Supplied Name: Hadal Lander

Supplied Description:

Instrument Type

Generic Name: HADAL-Lander

Generic 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

Leggo Lander

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Leggo Lander

Generic 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

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_ID	sample identifier	unitless	sample
Trench	site name	unitless	site
Cell_counts_mL	cell concentration	cells/millliliter	cell_concentration
Depth	cellection depth	meters	depth
Type	sample type: seawater or sediment	unitless	sample_type
Latitude	latitude; north is positive	decimal degrees	lat
Longitude	longitude; east is positive	decimal degrees	lon
cruise_id	cruise identifier; R2R official code	unitless	cruise_id
cruise_name	project specific cruise identifier	unitless	cruise_name
STATION	station identifier	unitless	station
LANDER	deployment or dive identifier: UW=underway - collected with ship's underway system; CTD = CTD profiler; RG = Rock Grabber; Lego = Leggo lander; EL = ??	unitless	deployno
local_or_UTC	time zone	unitless	time_zone
DATE_DEPLOYED	date of deployment (yyyymmdd)	unitless	date_start
TIME_DEPLOYED	time of deployment (hhmm)	unitless	time_start
DATE_RECOVERED	date of recovery (yyyymmdd)	unitless	date_end
TIME_RECOVERED	date of recovery (hhmm)	unitless	date_end
LATITUDE_log	latitude from deployment log; north is positive	decimal degrees	lat
LONGITUDE_log	longitude from deployment log; east is positive	decimal degrees	lon
MULTIBEAM_DEPTH	target depth as measured by multibeam	meters	depth

Database

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Dataset: Cell counts - water