Dataset: Isolates

Name: 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)
Published: 2017-12-18
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:12.7 E:-170 S:-36 W:145

Temporal Extent: 2014-05-01 - 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

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)

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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.

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/

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.

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
- 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

Data Files

File
isolates.csv (Comma Separated Values (.csv), 55.11 KB) MD5:b7e93e04bc8fe7863f2ea907d78f5a3d Primary data file for dataset ID 721437

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.

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

HROV Nereus

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: HROV Nereus

Generic 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.

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.

Respirometer

Supplied Name: Free vehicle coring respirometer (FVCR)

Supplied 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 Type

Generic Name: Respirometer

Generic 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.

Thermal Cycler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic 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)

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Trench	site name	unitless	site
Collection_method	collection method: CTD; RG=Rock Grabber; Lego = Leggo Lander; El = ??	unitless	sampling_method
Taxon	taxonomic identification of isolate based on PCR	unitless	taxon
Method	method used for growing isolates	unitless	treatment
Medium	growth medium:2216 Marine Medium (2216; BD DifcoTM); A1 Medium; or a seawater (SW) minimal medium	unitless	treatment
Depth	collection depth	meters	depth
Type	sample type: seawater or sediment	unitless	sample_type
Pressure_Mpa	incubation pressure	Megapascals	press
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

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Dataset: Isolates