Dataset: Mitochondrial COI barcode sequencing data for Gigantidas childressi veligers, pediveligers, and juveniles

Name: Mitochondrial COI barcode sequencing data for Gigantidas childressi veligers, pediveligers, and juveniles from samples collected on R/V Thompson cruise TN391 in Mississippi Canyon 853 in the Gulf of Mexico during May 2021
Published: 2024-10-15
Keywords: microbiome, methane seep, Symbiosis, chemosymbiosis, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:28.122833 E:-89.140333 S:28.122833 W:-89.140333

Mississippi Canyon 853, Gulf of Mexico

Temporal Extent: 2021-06 - 2021-08

Project:

Collaborative Research: dispersal depth and the transport of deep-sea, methane-seep larvae around a biogeographic barrier (SALT)

Principal Investigator:

Shawn M. Arellano (Western Washington University - Shannon Point Marine Center, SPMC)

David B. Eggleston (North Carolina State University - Center for Marine Science and Technology, NCSU CMAST)

Craig M. Young (University of Oregon, OIMB)

Co-Principal Investigator:

Ruoying He (North Carolina State University - Marine, Earth and Atmospheric Sciences, NCSU MEAS)

Scientist:

Ahna Van Gaest (Western Washington University, WWU)

Student:

Tessa Francisca Beaver (Western Washington University, WWU)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-10-15

Restricted:

Validated:

Current State:

Data not available

Mitochondrial COI barcode sequencing data for Gigantidas childressi veligers, pediveligers, and juveniles from samples collected on R/V Thompson cruise TN391 in Mississippi Canyon 853 in the Gulf of Mexico during May 2021

Abstract:

This dataset includes mitochondrial COI barcode sequence accessions from samples of whole Gigantidas childressi larvae and juveniles collected from Mississippi Canyon 853 in the Gulf of Mexico during May 2021 and sequenced in August 2021, with links to the NCBI GenBank accession pages. Samples were collected on SALT cruise TN391 with AUV Sentry and ROV Jason and later sequenced to examine the microbiome of G. childressi across early developmental stages, compared with the water samples. Researchers interested in chemosymbiotic organisms and the acquisition of beneficial symbionts during early development may find these data useful. The collection of animals was carried out by the group of scientists aboard the R/V Thompson during the TN391 SALT cruise. The party responsible for the collection and interpretation of samples and sequences were Tessa Beaver, M.S., and Dr. Shawn Arellano (both of Western Washington University).

Expand/Collapse All

Methods & Sampling

Veligers, pediveligers, juveniles, and adult mussels of Gigantidas childressi were collected using the remotely-operated vehicle (ROV) Jason II and automated underwater vehicle (AUV) Sentry (National Deep Submergence Facility, Woods Hole Oceanographic Institution) onboard the R/V Thomas G. Thompson (University of Washington) during cruise TN391. Samples were collected from Mississippi Canyon 853 (28° 7.37’ N, 89° 8.42’ W) in the Gulf of Mexico at a depth of 1070 meters on June 16th, 2021 (Jason dive J2-1337 and Sentry dive S595P). Gigantidas childressi adults were sampled with ROV Jason and recovered to the surface in insulated bioboxes. Pediveligers (swimming larvae with a developed foot that are competent to undergo metamorphosis) and juveniles (metamorphosed) of G. childressi were collected from the interstices of mussel beds with the ROV Jason suction sampler and within samples of adults. Veligers (pre-competent swimming larvae without a developed foot) were collected in the water column at an altitude of 5 meters above bottom with AUV Sentry fitted with the SyPRID plankton sampler with 150-micron mesh nets (Billings et al. 2016).

Plankton samples recovered by the AUV Sentry SyPRID sampler were immediately rinsed from the collectors with cold 0.3-micrometer (um) filtered seawater (FSW) into canisters of chilled FSW. Larvae and juveniles recovered from ROV Jason suction and scoop samples were retained on a 253 um mesh sieve and resuspended in cold FSW. All live plankton and juveniles were maintained below 8 degrees Celsius (°C) (ambient temperature) during subsequent processing. Live G. childressi larvae were immediately sorted from the samples under a dissecting microscope, imaged on a compound light microscope, then preserved individually in 0.5 milliliters (mL) centrifuge tubes with 95% molecular grade ethanol. Adult G. childressi are morphologically identifiable, so gill samples were not sequenced.

All sample processing for DNA sequencing was conducted at Shannon Point Marine Center in Anacortes, Washington. DNA was extracted from individual larvae and juveniles using the Nucleospin Tissue XS kit (Machery-Nagel) following the manufacturer's instructions. The concentration of extracted DNA was quantified using a Qubit fluorometer (2.0). To confirm the identity of the veligers, pediveligers, and juveniles, PCR amplification of the mitochondrial COI (mtCOI) barcode region using bathymodiolin-specific primers (BATH-COI F/R, van der Heijden et al. 2012) was carried out and followed by bidirectional Sanger sequencing (Sequetech, Mountain View, CA). PCR conditions were as follows: 15 minutes at 95°C with 35 cycles of 35 seconds (s) at 94°C, 35s at 48°C, and 70s at 72°C, followed by 7 minutes at 72°C and a final holding temperature of 10°C. PCR products were purified prior to Sanger sequencing using the ExoSAP-IT PCR product clean-up reagent. Mitochondrial COI barcode sequences were processed in Geneious 10.1 (Dotmatic) and compared to those in GenBank using the BLAST search and alignment tool.

BCO-DMO Processing

- Imported original file "BeaverAndArellano2024_COI.csv" into the BCO-DMO system.
- Added columns for collection latitude, longitude, date, and depth.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved final file as "940497_v1_mitochondrial_coi_barcodes_g_childressi.csv".

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851286
NSF Division of Ocean Sciences	OCE-1851383
NSF Division of Ocean Sciences	OCE-1851421

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
TN391	SALT summer 2021 cruise	2021-05-25	R/V Thomas G. Thompson	Craig M. Young (Chief Scientist)	data info

Instruments

AUV Sentry

Supplied Name: automated underwater vehicle (AUV) Sentry

Supplied Description:

Instrument Type

Generic Name: AUV Sentry

Generic Description:

The autonomous underwater vehicle (AUV) Sentry is a fully autonomous underwater vehicle capable of exploring the ocean down to 6,000 meters (19,685 feet) depth. Sentry builds on the success of its predecessor the ABE, with improved speed, range, and maneuverability.

Sentry's hydrodynamic shape also allows faster ascents and descents. Sentry carries a superior science sensor suite and an increased science payload enabling it to be used for both mid-water and near-seabed oceanographic investigations. Sentry produces bathymetric, sidescan, subbottom, and magnetic maps of the seafloor and is capable of taking digital bottom photographs in a variety of deep-sea terrains such as mid-ocean ridges, deep-sea vents, and cold seeps at ocean margins. Sentry is uniquely able to operate in extreme terrain, including volcano caldera and scarps. Sentry's navigation system uses a doppler velocity log and inertial navigation system, aided by acoustic navigation systems (USBL or LBL). The USBL system also provides acoustic communications, which can be used to obtain the vehicle state and sensor status as well as to retask the vehicle while on the bottom. In addition its standard sensors, Sentry has carried a variety of science-supplied sensors, including the Nakamura redox potential probe, ACFR 3-D imaging system, and the Tethys in-situ mass spectrometer.

Sentry can be used to locate and quantify hydrothermal fluxes. Sentry is also capable of a much wider range of oceanographic applications due to its superior sensing suite, increased speed and endurance, improved navigation, and acoustic communications. Sentry can be used as a stand alone vehicle or in tandem with Alvin or an ROV to increase the efficiency of deep-submergence investigations.

More information is available from the operator site at URL: http://www.whoi.edu/main/sentry

Qubit fluorometer

Supplied Name: Qubit fluorometer (2.0)

Supplied Description:

Instrument Type

Generic Name: Qubit fluorometer

Generic Description:

Benchtop fluorometer. The Invitrogen Qubit Fluorometer accurately and quickly measures the concentration of DNA, RNA, or protein in a single sample. It can also be used to assess RNA integrity and quality.

Manufactured by Invitrogen, Carlsbad, CA, USA (Invitrogen is one of several brands under the Thermo Fisher Scientific corporation.)

ROV Jason

Supplied Name: remotely-operated vehicle (ROV) Jason II

Supplied Description:

Instrument Type

Generic Name: ROV Jason

Generic Description:

The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL.

Sentry Precision Robotic Impeller Driven Sampler

Supplied Name: SyPRID plankton sampler

Supplied Description:

Instrument Type

Generic Name: Sentry Precision Robotic Impeller Driven Sampler

Acronym: SyPRID Sampler

Generic Description:

The SyPRID (Sentry Precision Robotic Impeller Driven) sampler is an innovative deep-rated (6000 m) plankton sampler that partners with the Sentry Autonomous Underwater Vehicle (AUV) to obtain paired, large-volume plankton samples at specified depths and survey lines to within 1.5 m of the seabed and with simultaneous collection of sensor data.

SyPRID uses a perforated Ultra-High-Molecular-Weight (UHMW) plastic tube to support a fine mesh net within an outer carbon composite tube (tube-within-a-tube design), with an axial flow pump located aft of the capture filter. The pump facilitates flow through the system and minimizes the bow wave at the mouth opening. The cod end, a hollow truncated cone, is also made of UHMW plastic and is designed to 'soften' the landing of zooplankton on the capture surface. SyPRID attaches as a saddle-pack to the Sentry vehicle.

Sentry itself is configured with a flight control system that enables autonomous survey paths to altitudes as low as 1.5 m. In its inaugural deployment at the Blake Ridge Seep (2160 m) on the US Atlantic Margin, SyPRID was operated for 6 h at an altitude of 5 m. It recovered plankton samples from that stratum in excellent condition and with greater larval numbers than recovered in a typical 'near-bottom' MOCNESS sample from comparable habitats and depths. The prototype SyPRID and its next generations will enable studies of plankton or other particulate distributions associated with patchy habitats, localized physico-chemical strata (e.g., above and below the thermocline), or discrete water masses at an unprecedented spatial resolution for a large volume system [1].

More information is available by contacting:
Carl Kaiser
Program Manager
Applied Ocean Physics & Engineering
NDSF AUV Operations Manager
Office Phone: +1 508 289 3269
ckaiser@whoi.edu

[1] Billings, A., Kaiser, C., Young, C. M., Hiebert, L. S., Cole, E., Wagner, J. K. S., & Van Dover, C. L. (2017). SyPRID sampler: A large-volume, high-resolution, autonomous, deep-ocean precision plankton sampling system. In Deep Sea Research Part II: Topical Studies in Oceanography (Vol. 137, pp. 297–306). Elsevier BV. https://doi.org/10.1016/j.dsr2.2016.05.007

Thermal Cycler

Supplied Name: PCR amplification

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
Site	Site name where samples were taken	unitless	site
Latitude	Latitude of collection site	decimal degrees North	lat
Longitude	Longitude of collection site	decimal degrees East	lon
Collection_Date	Date of sample collection Format: %Y-%m-%d	unitless	date
Depth	Depth of sample collection	meters (m)	depth
Dive_Collected	ROV Jason (J2-) or AUV Sentry (S-) dive numbers on which the samples were collected	unitless	dive_id
Collection_Method	Mussel scoopers and slurps were taken by Jason, SyPRID samples were take by Sentry	unitless	sampling_method
Sample_ID	Unique ID for each sample	unitless	sample
Sample_Stage	Developmental stage or sample tissue type for each sample	unitless	stage
Accession_Number	GenBank Accession number for COI sequences	unitless	Genbank_accession

Status message

Database

Contribute Data

Dataset: Mitochondrial COI barcode sequencing data for Gigantidas childressi veligers, pediveligers, and juveniles