Dataset: 515F-926R 16S rRNA accessions

Name: 515F-926R 16S rRNA gene sequencing accessions from seawater and sediment samples from R/V Falkor FK141109 and R/V Thompson TN309 from the Mariana and Kermadec trenches, 2014 (Mariana Perspectives project)
Published: 2017-12-13
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:12.7306 E:-170 S:-37.7337 W:145

Temporal Extent: 2014-04-10 - 2014-12-09

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:

2017-12-13

Restricted:

Validated:

Yes

Current State:

Final no updates expected

515F-926R 16S rRNA gene sequencing accessions from seawater and sediment samples from R/V Falkor FK141109 and R/V Thompson TN309 from the Mariana and Kermadec trenches, 2014 (Mariana Perspectives project)

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Description

This dataset includes links to 515F-926R 16S rRNA gene sequencing accessions archived at NCBI and associated collection data from seawater and sediment samples from the Mariana and Kermadec trenches from April and November 2014.

For those accessions with a status of 'not yet available' at NCBI, they will be made available once the paper has been published, likely by mid-2018. Please check back for them then or contact the PI.

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, 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/

Seawater (40-120 L per sample) was serially filtered through 3.0 (47 mm diameter), 0.2 (47 mm or Sterivex), and 0.1 µm (142 mm) polycarbonate filters using a peristaltic pump. Filters were then placed into a sucrose buffer (Rusch et al., 2007) and frozen at -80°C. DNA was extracted from whole filters using a protocol previously described (Fuhrman et al., 1988; Tarn et al., 2016). Negative controls using blank filters were extracted in concomitance with every extraction performed.

DNA from sediment (5 g wet-weight) samples was extracted using a modified version of Lysis Protocol II described by Lever et al. (2015). 2.5 V of lysis solution (30 mM EDTA, 30 mM Tris-HCl, 800 mM guanidine hydrochloride, 0.5% Triton X-100, final pH 10) and 500 µmol pyrophosphate was added to each sample and the mixture briefly vortexed. Samples were then subjected to two 15 minute freeze-thaw cycles at -80°C, followed by incubation at 50°C with shaking at 150 rpm for one hour. Samples were centrifuged and the supernatant was treated twice with 1 V chloroform isoamyl alcohol. DNA was precipitated using 5 M NaCl and ethanol for two hours at room temperature and resuspended in nuclease-free water. Extracted DNA was cleaned again using a Quick-gDNA MiniPrep kit (Zymo Research, Irvine, CA). Negative control blanks, consisting of all reagents but no sediment material, were performed in concomitance with every extraction.

The V4-V5 16S rRNA gene region between 515f-926R was amplified (Parada et al., 2015) and tagged with Illumina barcodes using a secondary PCR procedure. Samples were pooled at equimolar concentrations and sent for sequencing on an Illumina Miseq at the Institute for Genomic Medicine Genomics Center (University of California, San Diego, La Jolla, 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
- split lat and lon into separate columns and rounded to 4 decimal places
- removed blank spaces in 3 sample names.

Data Files

File
accessions.csv (Comma Separated Values (.csv), 55.54 KB) MD5:005ac80dc77e7a594d52c107a8b9681e Primary data file for dataset ID 720916

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
TN309	HADES-K HADESK	2014-04-10	R/V Thomas G. Thompson	Timothy M. Shank (Chief Scientist)	data info
FK141109	HADES-M HADESM	2014-11-09	R/V Falkor	Jeffrey C. Drazen (Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina Miseq

Supplied Description:

Sequencing was performed at the Institute for Genomic Medicine Genomics Center (University of California, San Diego, La Jolla, CA).

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Bottom Sediment Grab Samplers

Supplied Name: Rock grabber

Supplied Description:

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.

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.

Pump - Surface Underway Ship Intake

Supplied Name: UW

Supplied Description:

The underway system used to collect samples aboard the Falkor.

Instrument Type

Generic Name: Pump - Surface Underway Ship Intake

Acronym: Pump-Ship Intake

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/31/

Generic Description:

The 'Pump-underway ship intake' system indicates that samples are from the ship's clean water intake pump. This is essentially a surface water sample from a source of uncontaminated near-surface (commonly 3 to 7 m) seawater that can be pumped continuously to shipboard laboratories on research vessels. There is typically a temperature sensor near the intake (known as the hull temperature) to provide measurements that are as close as possible to the ambient water temperature. The flow from the supply is typically directed through continuously logged sensors such as a thermosalinograph and a fluorometer. Water samples are often collected from the underway supply that may also be referred to as the non-toxic supply. Ideally the data contributor has specified the depth in the ship's hull at which the pump is mounted.

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
Sample_name	sample identifier	unitless	sample
Sample_title	NCBI sample title	unitless	sample
Collection_date	sample collection date	unitless	date
Depth	sample deplth	meters	depth
Type	sample type: seawater or sediment	unitless	sample_type
Location	collection location: ocean and trench name	unitless	site
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
filter_size	filter size fractions	microns	filter_size
status	whether access to NCBI pages are public or not	unitless	status
Bioproject_link	NCBI BioProject accession number and link to associated NCBI web page	unitless	accession_number
Biosample_link	NCBI BioSample accession number and link to associated NCBI web page	unitless	accession_number
sediment_depth	sediment core depth of the sample	centimeters	depth_interval

Database

Contribute Data

Dataset: 515F-926R 16S rRNA accessions