http://lod.bco-dmo.org/id/dataset/940537
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2024-10-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
V3-V4 16S sequence accessions from samples of whole Gigantidas childressi as well as seafloor water samples collected on R/V Thompson cruise TN391 in Mississippi Canyon 853 in the Gulf of Mexico during May 2021
2024-10-15
publication
2024-10-15
revision
BCO-DMO Linked Data URI
2024-10-15
creation
http://lod.bco-dmo.org/id/dataset/940537
Shawn M. Arellano
Western Washington University - Shannon Point Marine Center
principalInvestigator
David B. Eggleston
North Carolina State University - Center for Marine Science and Technology
principalInvestigator
Craig M. Young
University of Oregon
principalInvestigator
Ruoying He
North Carolina State University - Marine, Earth and Atmospheric Sciences
principalInvestigator
Ahna Van Gaest
Western Washington University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Beaver, T. F., Arellano, S. M., Young, C. M., He, R., Eggleston, D. B., Van Gaest, A. (2024) V3-V4 16S sequence accessions from samples of whole Gigantidas childressi as well as seafloor water samples collected on R/V Thompson cruise TN391 in Mississippi Canyon 853 in the Gulf of Mexico during May 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-10-15 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/940537 [access date]
V3-V4 16S rRNA sequence accessions from whole larvae and juveniles of Gigantidas childressi and co-located water samples Dataset Description: Methods and Sampling: <p>Veligers, pediveligers, juveniles, and adult mussels of <em>Gigantidas childressi</em> 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). Adult <em>Gigantidas childressi</em> are morphologically distinguishable. <em>Gigantidas childressi </em>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 <em>G. childressi</em> 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). A paired 2-liter (L) water sample was also taken at an altitude of 1.5 meters above the bottom at the time of fauna collection with two 4L Niskin bottles equipped on ROV Jason.</p>
<p>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 <em>G. childressi</em> 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. Snips of gill tissue from adult mussels were dissected aseptically on the ship and stored at -80°C in 2 mL cryovials. Background water samples were collected into sterilized plastic canisters, stored at ambient seafloor temperature (8°C), and processed immediately after recovery. Each sample was vacuum filtered onto a 0.2 um polycarbonate filter. Filters were placed into sterile 2-mL centrifuge tubes and stored at -80 °C until further processing.</p>
<p>All sample processing for DNA sequencing was conducted at Shannon Point Marine Center in Anacortes, Washington. DNA was extracted from individual larvae, juveniles, and samples of adult gill tissue (2.5 milligrams) using the Nucleospin Tissue XS kit (Machery-Nagel) following the manufacturer's instructions. DNA was extracted from filters using the Fast DNA Spin Kit for Soil (MP Bio) according to the manufacturer's instructions. The concentration of extracted DNA was quantified using a Qubit fluorometer (2.0).</p>
<p>For microbiome community composition, amplification, library preparation, and sequencing of the V3-V4 regions of the 16S rRNA gene was conducted by Exact Scientific (Ferndale, WA). Library preparation was performed following the Illumina 16S Metagenomic Sequencing Library Preparation protocol (15044223B). DNA was amplified using the following bacterial-specific primers: Forward: 5’ TACGGGNGGCWGCAG, Reverse: 5’ GACTACHVGGGTATCTAATCC (S-DBact-0341-b-S-17/S-D-Bact-0785-a-A-2; Klindworth et al. 2013). PCR conditions for 16S rRNA amplicons were 95 °C for 3 minutes, with 25 cycles at 95°C for 30 seconds, 55°C for 30 seconds, and 72°C for 30 seconds, followed by 72°C for 5 minutes and a holding temperature of 4°C. Multiplexing indices and Illumina overhang adapters were attached with a second limited-cycle PCR step using the NEXTERA® XT Index Kit. Resulting PCR products were purified after each step with Ampure XP Beads™, 80% EtOH, and 10 mM Tris pH 8.5. Libraries were then normalized, pooled, and sequenced on an Illumina MiSeq platform using 600 cycle v3 chemistry.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851383 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851383
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851286 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851286
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851421 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851421
onGoing
Shawn M. Arellano
Western Washington University - Shannon Point Marine Center
360-650-3634
Western Washington University 1900 Shannon Point Road
Anacortes
WA
98221
USA
arellas@wwu.edu
pointOfContact
David B. Eggleston
North Carolina State University - Center for Marine Science and Technology
919-515-7840
32800 Faucette Drive PO Box 8208
Raleigh
NC
27695
USA
eggleston@ncsu.edu
pointOfContact
Craig M. Young
University of Oregon
541-346-7274
Oregon Institute of Marine Biology P.O. Box 5389
Charleston
Oregon
97420
USA
cmyoung@uoregon.edu
pointOfContact
Ruoying He
North Carolina State University - Marine, Earth and Atmospheric Sciences
919-513-0249
Jordan Hall - Rm 4149
Raleigh
NC
27695-8208
USA
rhe@ncsu.edu
pointOfContact
Ahna Van Gaest
Western Washington University
vangaea@wwu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Site
Latitude
Longitude
Collection_Date
Depth
Dive_Collected
Collection_Method
Sample_ID
Sample_Group
Sequence_File_ID
SRA_Accession
Raw_Reads
Final_Reads
Chimeric_Reads
Pcnt_Reads_Retained
Number_of_ASVs
automated underwater vehicle (AUV) Sentry
SyPRID plankton sampler
Qubit fluorometer (2.0)
remotely-operated vehicle (ROV) Jason II
PCR amplification
theme
None, User defined
Cruise identfier
site
latitude
longitude
date
depth
dive_id
sampling_method
sample identification
stage
sequence
NCBI SRA Sample accession (SRS)
count
ratio
number
featureType
BCO-DMO Standard Parameters
AUV Sentry
AUV Sentry Precision Robotic Impeller Driven Sampler
Qubit fluorometer
ROV Jason
Thermal Cycler
instrument
BCO-DMO Standard Instruments
TN391
service
Deployment Activity
Woods Hole, Massachusetts to Gulfport, Mississippi
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: dispersal depth and the transport of deep-sea, methane-seep larvae around a biogeographic barrier
https://wp.wwu.edu/arellanolab/category/salt/
Collaborative Research: dispersal depth and the transport of deep-sea, methane-seep larvae around a biogeographic barrier
<p><em>NSF Award Abstract:</em><br />
Ever since hydrothermal vents and methane seeps were first discovered in the deep ocean more than 40 years ago, scientists have wondered how these isolated communities, fully dependent on underwater "islands" of toxic chemicals, are first colonized by organisms, and how the populations of these specialized animals are exchanged and maintained. These fundamental processes depend on the transport of babies (larvae) by the ocean currents, yet because the larvae are microscopic and diluted in the vastness of the ocean, it is very difficult to determine where and how they drift. This project uses an autonomous underwater vehicle to collect larvae from precise regions of the water column. Larval traps on the bottom and chemical analyses of larval shells will also be used to determine the depths where larvae swim. These findings will provide realistic estimates for mathematical models that show how biology interacts with ocean currents to predict which methane seeps will be colonized by larvae originating at different depths. A detailed knowledge of larval dispersal is needed for conservation and management of the deep sea. Without such information, we cannot know the best placement of marine protected areas, nor can we facilitate the reestablishment of communities impacted by deep-sea mining, drilling, or other human activities. This project will provide hands-on at-sea training for college students to learn the rapidly vanishing skills needed for studies of larvae and embryos in their natural habitats. Learning opportunities will also be available to individuals of all ages through new, interactive exhibits on deep-sea biology and larval ecology produced for small museums and aquaria on the coasts of Oregon, Washington and North Carolina.</p>
<p>Reliable estimates of connectivity among metapopulations are increasingly important in marine conservation biology, ecology and phylogeography, yet biological parameters for biophysical models in the deep sea remain largely unavailable. The movements of deep-sea vent and seep larvae among islands of habitat suitable for chemosynthesis have been inferred from current patterns using numerical modeling, but virtually all such models have used untested assumptions about biological parameters that should have large impacts on the predictions. This project seeks to fill in the missing biological parameters while developing better models for predicting the dispersal patterns of methane seep animals living in the Gulf of Mexico and on the Western Atlantic Margin. Despite the existence of similar seeps at similar depths on two sides of the Florida peninsula, the Western Atlantic seeps support only a subset of the species found in the Gulf of Mexico. It is hypothesized that the ability of larvae to disperse through the relatively shallow waters of the Florida Straits depends on an interaction between the adult spawning depth and the dispersal depth of the larvae. Dispersal depth, in turn, will be influenced by larval flotation rates, swimming behaviors, feeding requirements, and ontogenetic migration patterns during the planktonic period. The recently developed SyPRID sampler deployed on AUV Sentry will be used to collect larvae from precise depth strata in the water column, including layers very near the ocean floor. Larval traps deployed on the bottom at three depths in each region will be used in conjunction with the plankton collections to determine what proportion of larvae are demersal. Comparisons of stable oxygen isotopes between larval and juvenile mollusk shells will provide information on the temperatures (and therefore depths) that larvae develop, and geochemical analyses of larval and juvenile shells will determine whether larval cohorts mix among depth strata. Ocean circulation and particle transport modeling incorporating realistic biological parameters will be used to predict the movements of larvae around the Florida Peninsula for various spawning depths and seasons.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
SALT
largerWorkCitation
project
eng; USA
oceans
Woods Hole, Massachusetts to Gulfport, Mississippi
-89.140333
-89.140333
28.122833
28.122833
2021-06-16
2021-08-31
Methane seeps on the shelf and slope of Louisiana, Mississippi, Florida, North Carolina, Virginia and Maryland
0
BCO-DMO catalogue of parameters from V3-V4 16S sequence accessions from samples of whole Gigantidas childressi as well as seafloor water samples collected on R/V Thompson cruise TN391 in Mississippi Canyon 853 in the Gulf of Mexico during May 2021
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/940559.rdf
Name: Cruise
Units: unitless
Description: <p>Number identifier for UNOLS research vessel cruise</p>
http://lod.bco-dmo.org/id/dataset-parameter/940560.rdf
Name: Site
Units: unitless
Description: <p>Site name where samples were taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/940561.rdf
Name: Latitude
Units: unitless
Description: <p>Latitude of collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/940562.rdf
Name: Longitude
Units: unitless
Description: <p>Longitude of collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/940563.rdf
Name: Collection_Date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/940564.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/940565.rdf
Name: Dive_Collected
Units: unitless
Description: <p>ROV Jason (J2-) or AUV Sentry (S-) dive numbers on which the samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/940566.rdf
Name: Collection_Method
Units: unitless
Description: <p>Mussel scoopers and slurps were taken by Jason, SyPRID samples were take by Sentry</p>
http://lod.bco-dmo.org/id/dataset-parameter/940567.rdf
Name: Sample_ID
Units: unitless
Description: <p>Unique ID for each sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940568.rdf
Name: Sample_Group
Units: unitless
Description: <p>Developmental stage, tissue type, or type for each sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/940569.rdf
Name: Sequence_File_ID
Units: unitless
Description: <p>unique ID for each sequence file</p>
http://lod.bco-dmo.org/id/dataset-parameter/940570.rdf
Name: SRA_Accession
Units: unitless
Description: <p>SRA Accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/940571.rdf
Name: Raw_Reads
Units: counts
Description: <p>total unprocessed read count</p>
http://lod.bco-dmo.org/id/dataset-parameter/940572.rdf
Name: Final_Reads
Units: counts
Description: <p>number of reads after quality score filtering</p>
http://lod.bco-dmo.org/id/dataset-parameter/940573.rdf
Name: Chimeric_Reads
Units: counts
Description: <p>number of chimeric reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/940574.rdf
Name: Pcnt_Reads_Retained
Units: proportion
Description: <p>Proportion of raw reads retained in the dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/940575.rdf
Name: Number_of_ASVs
Units: counts
Description: <p>total number of ASVs</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://osprey.bco-dmo.org/dataset/940537/data/download
download
onLine
dataset
<p>Veligers, pediveligers, juveniles, and adult mussels of <em>Gigantidas childressi</em> 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). Adult <em>Gigantidas childressi</em> are morphologically distinguishable. <em>Gigantidas childressi </em>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 <em>G. childressi</em> 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). A paired 2-liter (L) water sample was also taken at an altitude of 1.5 meters above the bottom at the time of fauna collection with two 4L Niskin bottles equipped on ROV Jason.</p>
<p>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 <em>G. childressi</em> 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. Snips of gill tissue from adult mussels were dissected aseptically on the ship and stored at -80°C in 2 mL cryovials. Background water samples were collected into sterilized plastic canisters, stored at ambient seafloor temperature (8°C), and processed immediately after recovery. Each sample was vacuum filtered onto a 0.2 um polycarbonate filter. Filters were placed into sterile 2-mL centrifuge tubes and stored at -80 °C until further processing.</p>
<p>All sample processing for DNA sequencing was conducted at Shannon Point Marine Center in Anacortes, Washington. DNA was extracted from individual larvae, juveniles, and samples of adult gill tissue (2.5 milligrams) using the Nucleospin Tissue XS kit (Machery-Nagel) following the manufacturer's instructions. DNA was extracted from filters using the Fast DNA Spin Kit for Soil (MP Bio) according to the manufacturer's instructions. The concentration of extracted DNA was quantified using a Qubit fluorometer (2.0).</p>
<p>For microbiome community composition, amplification, library preparation, and sequencing of the V3-V4 regions of the 16S rRNA gene was conducted by Exact Scientific (Ferndale, WA). Library preparation was performed following the Illumina 16S Metagenomic Sequencing Library Preparation protocol (15044223B). DNA was amplified using the following bacterial-specific primers: Forward: 5’ TACGGGNGGCWGCAG, Reverse: 5’ GACTACHVGGGTATCTAATCC (S-DBact-0341-b-S-17/S-D-Bact-0785-a-A-2; Klindworth et al. 2013). PCR conditions for 16S rRNA amplicons were 95 °C for 3 minutes, with 25 cycles at 95°C for 30 seconds, 55°C for 30 seconds, and 72°C for 30 seconds, followed by 72°C for 5 minutes and a holding temperature of 4°C. Multiplexing indices and Illumina overhang adapters were attached with a second limited-cycle PCR step using the NEXTERA® XT Index Kit. Resulting PCR products were purified after each step with Ampure XP Beads™, 80% EtOH, and 10 mM Tris pH 8.5. Libraries were then normalized, pooled, and sequenced on an Illumina MiSeq platform using 600 cycle v3 chemistry.</p>
Specified by the Principal Investigator(s)
<p>Processing and analysis of Illumina sequences followed the QIIME2 computational pipeline for the V3/V4 region of the 16S rRNA gene as in Carrier et al. (2021). Illumina reads with quality information were processed using QIIME 2 (ver. 2021.8; Bolyen et al., 2019). Adapters and primers were removed and forward and reverse reads were paired with VSEARCH (Rognes et al. 2016). Paired sequences were filtered by a minimum quality score of 25 and denoised with Deblur (Amir et al. 2017). Features were analyzed as amplicon sequence variants (ASVs) and were assigned taxonomy using the latest version of the SILVA (ver. 138.1) bacterial database.</p>
Specified by the Principal Investigator(s)
- Imported original file "BeaverAndArellano2024_SRA.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 "940537_v1_v3-v4_16s_rrna_sequences_g_childressi.csv"
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
automated underwater vehicle (AUV) Sentry
automated underwater vehicle (AUV) Sentry
PI Supplied Instrument Name: automated underwater vehicle (AUV) Sentry Instrument Name: AUV Sentry Instrument Short Name:AUV Sentry Instrument 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: https://ndsf.whoi.edu/sentry/
SyPRID plankton sampler
SyPRID plankton sampler
PI Supplied Instrument Name: SyPRID plankton sampler Instrument Name: AUV Sentry Precision Robotic Impeller Driven Sampler Instrument Short Name:SyPRID Sampler Instrument 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
Qubit fluorometer (2.0)
Qubit fluorometer (2.0)
PI Supplied Instrument Name: Qubit fluorometer (2.0) Instrument Name: Qubit fluorometer Instrument Short Name: Instrument 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.)
remotely-operated vehicle (ROV) Jason II
remotely-operated vehicle (ROV) Jason II
PI Supplied Instrument Name: remotely-operated vehicle (ROV) Jason II Instrument Name: ROV Jason Instrument Short Name:ROV Jason Instrument 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. https://ndsf.whoi.edu/jason/
PCR amplification
PCR amplification
PI Supplied Instrument Name: PCR amplification Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument 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)
Cruise: TN391
TN391
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN391
Craig M. Young
University of Oregon
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel