http://lod.bco-dmo.org/id/dataset/969102
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
2025-07-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metabarcoding data from microbial diversity survey at Axial Seamount aboard the R/V Thompson cruise TN420 in Jul 2022 and Jul 2023
2025-07-29
publication
2025-07-29
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-07-29
publication
https://doi.org/10.26008/1912/bco-dmo.969102.1
Julie Huber
Woods Hole Oceanographic Institution
principalInvestigator
Sarah K. Hu
Texas A&M University
principalInvestigator
Maria G. Pachiadaki
Woods Hole Oceanographic Institution
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: Hu, S. K., Pachiadaki, M. G., Huber, J. (2025) Metabarcoding data from microbial diversity survey at Axial Seamount aboard the R/V Thompson cruise TN420 in Jul 2022 and Jul 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-07-29 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.969102.1 [access date]
Microbial diversity survey Axial Seamount 2023 Dataset Description: Methods and Sampling: <p><strong>Collection</strong></p>
<p>A subset of samples from a prior year's expedition to Axial Seamount (TN405) was also included in the analysis. During TN405 (July 2022), one ROV Jason dive collected diffuse vent fluid using the Hydrothermal Fluid and Particle Sampler (labeled "HFS" in the dataset; designed by David Butterfield) and seawater from the plume was collected via Niskin bottles during CTD casts. TN405 was interrupted and TN420 represents the majority of samples associated with this project.&nbsp;</p>
<p>Collection of diffuse vent fluid and nearby seawater (background) was conducted using the Universal Fluid Obtainer (UFO) and the SUPR sampler. The UFO was the primary device used for fluid sampling for 3 ROV dives (J2-1500 - J2-1502), while the SUPR was the primary mode of fluid collection for 4 ROV dives (J2-1503 - J2-1506). No fluid sampler was operational during the first dive (J2-1499). For the first 4 sites (J2-1499, J2-1501, J2-1502, and J2-1503), 3 Niskin bottles mounted on ROV Jason were fired a few meters above active venting fluid.&nbsp;</p>
<p>The UFO has 8 total ports for fluid collection. For each dive, 4 L bags were attached to 6 ports and sterivex filters (0.22 µm pore size) were connected to the final 2 ports. ROV Jason temperature probe would identify a suitable spot, based on consistent fluid flow and temperature (we targeted 20-80°C fluid), and then would use an intake wand connected to the UFO in the other manipulator. For sterivex filters, once they were recovered from the UFO manifold, they were preserved with RNAlater and stored at -80°C.&nbsp;</p>
<p>The SUPR sampler was typically deployed with 10 2 L bottles and 4 filter holders, where the in situ filters used were either 0.2 µm PES or 0.7 µm nominal GFF filters. The intake for the SUPR sampler includes a built in temperature probe, in order to simultaneously monitor fluid temperature while collecting vent fluid. Each filter holder used on the SUPR included a built-in reservoir for RNAlater; RNAlater would ‘weep’ onto the filter as fluid was pulled through the filter and holder.</p>
<p><strong>Sample processing</strong></p>
<p>For all samples, RNA was extracted and amplified similarly to the protocol described in Hu et al. (2018). Frozen filters were thawed and placed into sterile 15-ml falcon tubes with sterile forceps, 1-2 mL of RLT+ buffer (with β-Mercaptoethanol, Qiagen, Valencia, CA, USA) and RNase-free silica beads was added to each tube. Falcon tubes were bead-beaten by vortexing vigorously for 5 minutes. The original sample collection tubes with RNAlater were centrifuged to pellet any cellular material left in the RNAlater; the RNAlater was removed and replaced with 500-ul of RLT+ buffer (with β-Mercaptoethanol). This was vortexed and added to the 15-ml falcon tube. RNA was extracted with the RNAeasy kit (Qiagen #74104) with the in-line genomic DNA removal step (RNase-free DNase reagents, Qiagen #79254). RNA concentrations were determined using the Ribogreen protocol. Extracted RNA was reverse transcribed into cDNA using a cDNA synthesis kit (iScript Select cDNA Synthesis, BioRad, #1708896, Hercules, CA); the concentration of RNA was normalized for the cDNA synthesis reaction (input –ng of RNA). Primers targeting the V4 hypervariable region of the 18S rRNA gene (Stoeck et al. 2010; Hu et al. 2015) were used in PCR reactions, which consisted of a final concentration of 1X Q5 High Fidelity Master Mix (NEB #M0492S, Ipswich, MA), 0.5 μM each of forward and reverse primers, and 1 ng of genetic material. The PCR thermal protocol started with an initial activation step (Q5 specific) of 98°C for 2 min, followed with 10 cycles of 98°C for 10 s, 53°C for 30 s, 72°C for 30 s, and 15 cycles of 98°C for 10 s, 48°C for 30 s, and 72°C for 30 s, and a final extension of 72°C for 2 min (modified from Rodriquez Martinez et al. 2012). The original extract total RNA was also PCR amplified to ensure no genomic DNA was present in the sample. PCR products were checked by confirming the presence of an ~400 bp product on an agarose gel. In cases with no amplification, the PCR reaction was repeated with a higher concentration of cDNA (1.5-2 ng). If this did not yield the expected PCR product, the reaction was repeated with an additional 5 cycles. PCR products were sent to Georgia Genomics and Bioinformatics Core (GGBC) and sequencings using the Illumina NextSeq2000 platform.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1947776 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1947776
completed
Julie Huber
Woods Hole Oceanographic Institution
(508) 289-2556
Woods Hole Oceanographic Institution Marine Chemistry & Geochemistry, Watson Building, MS51
Woods Hole
MA
02543
USA
jhuber@whoi.edu
pointOfContact
Sarah K. Hu
Texas A&M University
skhu@tamu.edu
pointOfContact
Maria G. Pachiadaki
Woods Hole Oceanographic Institution
508 289 2943
Redfield Lab
Woods Hole
MA
02543
mpachiadaki@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Accession
Sample_Name
NCBI_Organism_Name
NCBI_Tax_ID
BioProject
dive_ctd
site_name
collection_method
sample_type
filter
processing
primer
target_population
location_name
depth_category
depth
fluid_origin
AXIAL_YEAR
lat
long
DATE
Illumina NextSeq2000
Hydrothermal Fluid and Particle Sampler
Universal Fluid Obtainer (UFO) and the SUPR sampler
Niskin bottle
ROV Jason
Vortex
theme
None, User defined
NCBI BioSample accession
sample identification
sample description
NCBI BioProject accession
dive_id
site
sampling_method
sample type
No BCO-DMO term
site description
depth
latitude
longitude
date
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Discrete water sampler
Discrete water sampler
Niskin bottle
ROV Jason
Shaker
instrument
BCO-DMO Standard Instruments
TN420
TN405
service
Deployment Activity
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.
Characterizing and quantifying the impact of phagotrophic protists at hot spots of primary production at Axial Seamount
https://osprey.bco-dmo.org/project/786461
Characterizing and quantifying the impact of phagotrophic protists at hot spots of primary production at Axial Seamount
<p>NSF Award Abstract:</p>
<p>Microorganisms are the ancestral forms of life on our planet and have been instrumental in shaping all of Earth?s environments into what they are today. In the ocean, microbial prokaryotes and eukaryotes form the foundation of marine food webs through their activity and interactions. Single-celled microbial eukaryotes (or protists) are some of the most important species on the planet, yet our understanding of how their activities influence and regulate the ocean ecosystem is poorly constrained. At deep-sea hydrothermal vents in particular, our understanding of microbial food web dynamics is incomplete without including the role of microbial eukaryotes. This project provides quantification of phagotrophic protistan grazing on the microbial communities inhabiting the highly productive diffuse vent mixing zone at hydrothermal vents, where the vent fluid-seawater interface promotes an increase in biological activity compared to the surrounding deep seawater. The results are contributing novel insights into the diversity and metabolic activities of the microbial eukaryotic community at vent fluid-seawater interfaces, establish the extent to which microbial eukaryotes impact primary production in the deep ocean by quantifying predation pressure, and estimate the amount of carbon transferred from primary producers to larger organisms. The investigators are training community college students from Cape Cod Community College by involving them in laboratory research through summer internships. The goal is to promote science, technology, engineering and math literacy among community college students through hands-on research experiences, peer-to-peer mentoring, and professional development opportunities, while also encouraging students to transfer to a four-year university, obtain a degree in a STEM subject, and continue on in a STEM field.</p>
<p>Grazing by microbial eukaryotes is a significant source of mortality for microbes in the oceans, thus influencing the composition of communities and serving as a major route for remineralization of organic material to all organisms. This project is quantifying the in situ rates of eukaryotic grazing on prokaryotic communities at hot spots of primary productivity in the deep sea and characterize the diversity of microbial eukaryotes, their abundance, and metabolic activities at the seafloor. The focus of the effort is at the underwater volcano Axial Seamount, home of the Ocean Observatories Initiative (OOI) Regional Cabled Array with well-characterized low-temperature diffusely venting fluids.</p>
<p>The two objectives of the work are to:</p>
<p>1. Quantify the rates and impact of phagotrophic microbial eukaryote grazing on prokaryotic communities at the seafloor in low-temperature diffuse fluid mixing zones.</p>
<p>2. Characterize microbial eukaryotic diversity, abundance, and metabolic gene expression at the seafloor in low-temperature diffuse fluid mixing zones.</p>
<p>The modular Microbial Sampler-Submersible Incubation Device (MS-SID) is being used for in situ seafloor tracer incubations and compared to shipboard incubations for the proposed grazing studies. This combination of technology provides detailed and quantitative assessments of protistan communities and establishes the extent to which microbial eukaryotes impact primary production in the deep ocean. Expected outcomes include the quantification of protistan grazing rates on bacterial and archaeal communities within the seafloor mixing zone, comparison of predation pressure at the vent-seawater interface and surrounding deep ocean water, as well as identification of key bacteriovores, fungi, and other protists and associated major active metabolic pathways within the hydrothermal mixing zones. The project is providing a significant advance in the understanding of the microbial loop in the deep ocean as current depictions of microbial ecology at hydrothermal vent sites do not typically include the role of microbial eukaryotes.</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>
PROT-ATAX
largerWorkCitation
project
eng; USA
biota
oceans
-130.0495
-129.979065
45.916228
45.933592
2022-07-09
2023-07-25
Axial Seamount
0
BCO-DMO catalogue of parameters from Metabarcoding data from microbial diversity survey at Axial Seamount aboard the R/V Thompson cruise TN420 in Jul 2022 and Jul 2023
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/969132.rdf
Name: Accession
Units: unitless
Description: <p>Unique identifier as cataloged in NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/969133.rdf
Name: Sample_Name
Units: unitless
Description: <p>Complete sample name, also appears as fastq file name, as well as in the SRA database</p>
http://lod.bco-dmo.org/id/dataset-parameter/969135.rdf
Name: NCBI_Organism_Name
Units: unitless
Description: <p>NCBI code for sample origin</p>
http://lod.bco-dmo.org/id/dataset-parameter/969136.rdf
Name: NCBI_Tax_ID
Units: unitless
Description: <p>NCBI taxonomy code</p>
http://lod.bco-dmo.org/id/dataset-parameter/969137.rdf
Name: BioProject
Units: unitless
Description: <p>Identifier for project submitted to NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/969138.rdf
Name: dive_ctd
Units: unitless
Description: <p>Identifier for the ROV Jason dive number or CTD cast number. "Control" and "HUBERLAB" used for control samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/969139.rdf
Name: site_name
Units: unitless
Description: <p>Name of site, abbrivated</p>
http://lod.bco-dmo.org/id/dataset-parameter/969140.rdf
Name: collection_method
Units: unitless
Description: <p>Method of fluid collection; CTD, HFS, Lab, SUPR, UFO</p>
http://lod.bco-dmo.org/id/dataset-parameter/969141.rdf
Name: sample_type
Units: unitless
Description: <p>Sample type within deep-sea vent survey</p>
http://lod.bco-dmo.org/id/dataset-parameter/969143.rdf
Name: filter
Units: unitless
Description: <p>Type of filter fluid was collected onto</p>
http://lod.bco-dmo.org/id/dataset-parameter/969144.rdf
Name: processing
Units: unitless
Description: <p>Collection in situ in the deep sea or processed on board after fluid recovery</p>
http://lod.bco-dmo.org/id/dataset-parameter/969145.rdf
Name: primer
Units: unitless
Description: <p>18S or 16S primers were used</p>
http://lod.bco-dmo.org/id/dataset-parameter/969146.rdf
Name: target_population
Units: unitless
Description: <p>Intended target for microbial diversity</p>
http://lod.bco-dmo.org/id/dataset-parameter/969147.rdf
Name: location_name
Units: unitless
Description: <p>Full site name</p>
http://lod.bco-dmo.org/id/dataset-parameter/969148.rdf
Name: depth_category
Units: unitless
Description: <p>Type of sample with respect to depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/969149.rdf
Name: depth
Units: m
Description: <p>Depth of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/969150.rdf
Name: fluid_origin
Units: unitless
Description: <p>Origin of fluid collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/969151.rdf
Name: AXIAL_YEAR
Units: unitless
Description: <p>Axial Seamount cruise year</p>
http://lod.bco-dmo.org/id/dataset-parameter/969152.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of collection, N is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/969153.rdf
Name: long
Units: decimal degrees
Description: <p>Longitude of collection, W is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/969154.rdf
Name: DATE
Units: unitless
Description: <p>Date of collection, PST</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
23277
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/2de68b2e-e28d-4949-9e80-ec269b90202c/content
download
https://doi.org/10.26008/1912/bco-dmo.969102.1
download
onLine
dataset
<p><strong>Collection</strong></p>
<p>A subset of samples from a prior year's expedition to Axial Seamount (TN405) was also included in the analysis. During TN405 (July 2022), one ROV Jason dive collected diffuse vent fluid using the Hydrothermal Fluid and Particle Sampler (labeled "HFS" in the dataset; designed by David Butterfield) and seawater from the plume was collected via Niskin bottles during CTD casts. TN405 was interrupted and TN420 represents the majority of samples associated with this project.&nbsp;</p>
<p>Collection of diffuse vent fluid and nearby seawater (background) was conducted using the Universal Fluid Obtainer (UFO) and the SUPR sampler. The UFO was the primary device used for fluid sampling for 3 ROV dives (J2-1500 - J2-1502), while the SUPR was the primary mode of fluid collection for 4 ROV dives (J2-1503 - J2-1506). No fluid sampler was operational during the first dive (J2-1499). For the first 4 sites (J2-1499, J2-1501, J2-1502, and J2-1503), 3 Niskin bottles mounted on ROV Jason were fired a few meters above active venting fluid.&nbsp;</p>
<p>The UFO has 8 total ports for fluid collection. For each dive, 4 L bags were attached to 6 ports and sterivex filters (0.22 µm pore size) were connected to the final 2 ports. ROV Jason temperature probe would identify a suitable spot, based on consistent fluid flow and temperature (we targeted 20-80°C fluid), and then would use an intake wand connected to the UFO in the other manipulator. For sterivex filters, once they were recovered from the UFO manifold, they were preserved with RNAlater and stored at -80°C.&nbsp;</p>
<p>The SUPR sampler was typically deployed with 10 2 L bottles and 4 filter holders, where the in situ filters used were either 0.2 µm PES or 0.7 µm nominal GFF filters. The intake for the SUPR sampler includes a built in temperature probe, in order to simultaneously monitor fluid temperature while collecting vent fluid. Each filter holder used on the SUPR included a built-in reservoir for RNAlater; RNAlater would ‘weep’ onto the filter as fluid was pulled through the filter and holder.</p>
<p><strong>Sample processing</strong></p>
<p>For all samples, RNA was extracted and amplified similarly to the protocol described in Hu et al. (2018). Frozen filters were thawed and placed into sterile 15-ml falcon tubes with sterile forceps, 1-2 mL of RLT+ buffer (with β-Mercaptoethanol, Qiagen, Valencia, CA, USA) and RNase-free silica beads was added to each tube. Falcon tubes were bead-beaten by vortexing vigorously for 5 minutes. The original sample collection tubes with RNAlater were centrifuged to pellet any cellular material left in the RNAlater; the RNAlater was removed and replaced with 500-ul of RLT+ buffer (with β-Mercaptoethanol). This was vortexed and added to the 15-ml falcon tube. RNA was extracted with the RNAeasy kit (Qiagen #74104) with the in-line genomic DNA removal step (RNase-free DNase reagents, Qiagen #79254). RNA concentrations were determined using the Ribogreen protocol. Extracted RNA was reverse transcribed into cDNA using a cDNA synthesis kit (iScript Select cDNA Synthesis, BioRad, #1708896, Hercules, CA); the concentration of RNA was normalized for the cDNA synthesis reaction (input –ng of RNA). Primers targeting the V4 hypervariable region of the 18S rRNA gene (Stoeck et al. 2010; Hu et al. 2015) were used in PCR reactions, which consisted of a final concentration of 1X Q5 High Fidelity Master Mix (NEB #M0492S, Ipswich, MA), 0.5 μM each of forward and reverse primers, and 1 ng of genetic material. The PCR thermal protocol started with an initial activation step (Q5 specific) of 98°C for 2 min, followed with 10 cycles of 98°C for 10 s, 53°C for 30 s, 72°C for 30 s, and 15 cycles of 98°C for 10 s, 48°C for 30 s, and 72°C for 30 s, and a final extension of 72°C for 2 min (modified from Rodriquez Martinez et al. 2012). The original extract total RNA was also PCR amplified to ensure no genomic DNA was present in the sample. PCR products were checked by confirming the presence of an ~400 bp product on an agarose gel. In cases with no amplification, the PCR reaction was repeated with a higher concentration of cDNA (1.5-2 ng). If this did not yield the expected PCR product, the reaction was repeated with an additional 5 cycles. PCR products were sent to Georgia Genomics and Bioinformatics Core (GGBC) and sequencings using the Illumina NextSeq2000 platform.&nbsp;</p>
Specified by the Principal Investigator(s)
- Imported "AxialSeamount_2023_metadata_BCO-DMO.xlsx" into the BCO-DMO system
- Converted date to ISO format YYYY-MM-DD
- Renamed fields to remove spaces and special characters
- Renamed "sample_name" to "site_name" after consulting with the submitter
- Replaced "6202024" and "7162024" values with "not applicable" in the "depth_category" parameter after consulting with submitter
- Removed "SPUID" and "sample_identifier" to reduce duplication after consulting with submitter
- Exported file as "969102_v1_microbial_diversity_axial_seamount.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
Illumina NextSeq2000
Illumina NextSeq2000
PI Supplied Instrument Name: Illumina NextSeq2000 PI Supplied Instrument Description:PCR products were sent to Georgia Genomics and Bioinformatics Core (GGBC) and sequencings using the Illumina NextSeq2000 platform. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Hydrothermal Fluid and Particle Sampler
Hydrothermal Fluid and Particle Sampler
PI Supplied Instrument Name: Hydrothermal Fluid and Particle Sampler PI Supplied Instrument Description:A subset of samples from a prior year's expedition to Axial Seamount (TN405) was also included in the analysis. During TN405 (July 2022), one ROV Jason dive collected diffuse vent fluid using the Hydrothermal Fluid and Particle Sampler (labeled "HFS" in the dataset; designed by David Butterfield) and seawater from the plume was collected via Niskin bottles during CTD casts. Instrument Name: Discrete water sampler Instrument Short Name: Instrument Description: A device that collects an in-situ discrete water sample from any depth and returns it to the surface without contamination by the waters through which it passes, such as a water bottle.
Universal Fluid Obtainer (UFO) and the SUPR sampler
Universal Fluid Obtainer (UFO) and the SUPR sampler
PI Supplied Instrument Name: Universal Fluid Obtainer (UFO) and the SUPR sampler PI Supplied Instrument Description:Collection of diffuse vent fluid and nearby seawater (background) was conducted using the Universal Fluid Obtainer (UFO) and the SUPR sampler. Instrument Name: Discrete water sampler Instrument Short Name: Instrument Description: A device that collects an in-situ discrete water sample from any depth and returns it to the surface without contamination by the waters through which it passes, such as a water bottle.
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:No fluid sampler was operational during the first dive (J2-1499). For the first 4 sites (J2-1499, J2-1501, J2-1502, and J2-1503), 3 Niskin bottles mounted on ROV Jason were fired a few meters above active venting fluid. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
ROV Jason
ROV Jason
PI Supplied Instrument Name: ROV Jason PI Supplied Instrument Description:In 2023, we completed an ROV expedition to Axial Seamount (NE Pacific), where we used ROV Jason to collect low temperature diffuse vent fluid and surrounding plume and background seawater. 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/
Vortex
Vortex
PI Supplied Instrument Name: Vortex PI Supplied Instrument Description:The original sample collection tubes with RNAlater were centrifuged to pellet any cellular material left in the RNAlater; the RNAlater was removed and replaced with 500-ul of RLT+ buffer (with β-Mercaptoethanol). This was vortexed and added to the 15-ml falcon tube. Instrument Name: Shaker Instrument Short Name: Instrument Description: A Shaker is a piece of lab equipment used to mix, blend, or to agitate substances in tube(s) or flask(s) by shaking them, which is mainly used in the fields of chemistry and biology. A shaker contains an oscillating board which is used to place the flasks, beakers, test tubes, etc.
Cruise: TN420
TN420
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN420
Julie Huber
Woods Hole Oceanographic Institution
Cruise: TN405
TN405
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN405
Julie Huber
Marine Biological Laboratory
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel