http://lod.bco-dmo.org/id/dataset/828345
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
2020-11-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
High throughput tag-sequencing accessions (18S rRNA gene region) and environmental metadata from Axial Seamount, 2013-2015
2020-11-05
publication
2020-11-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-01-06
publication
https://doi.org/10.26008/1912/bco-dmo.828345.1
Sarah K. Hu
Woods Hole Oceanographic Institution
principalInvestigator
Julie Huber
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., Huber, J. (2021) High throughput tag-sequencing accessions (18S rRNA gene region) and environmental metadata from Axial Seamount, 2013-2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-11-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.828345.1 [access date]
Axial seamount SRA Dataset Description: <p>See SRA BioProject accession: PRJNA641911 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA641911)&nbsp;and BioSample accession IDs: SAMN15376334-SAMN15376347.&nbsp;Sequences are available via SRA (NCBI).</p> Methods and Sampling: <p><strong>Sample collection from Axial Seamount:</strong></p>
<p>From Fortunato et al (2018)</p>
<p>Sample collection from Axial Seamount took place in September 2013, August 2014, and August 2015. ROVs ROPOS and JASON were used to collect diffuse hydrothermal venting fluid. At each site, 3-L of diffuse venting fluid was pumped (100-150-ml per minute) onto a 0.22-um 47mm GWSP filter (Millipore). This fluid was collected using the Hydrothermal Fluid and Particle Sampler (HFPS; Butterfield et al. 2004), which was mounted on an ROV. The fluid intake for the HFPS has a temperature sensor to ensure a constant temperature during fluid collection. Filters were preserved in situ with RNALater. Background seawater was collected from a depth of 1500-m using a CTD mounted with 10-L Niskin bottles.</p>
<p><strong>Extraction and sequencing for 18S tag-sequencing:</strong></p>
<p>For all samples, RNA was extracted and amplified similarly to the protocol described in Hu et al. 2018 (https://dx.doi.org/10.17504/protocols.io.hk3b4yn). 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. Three shipboard blanks (MilliQ water) and one extraction blank were also extracted and PCR amplified; while no PCR product was observed in these control samples they were processed similarly to all true samples and sequenced. All PCR products were cleaned using the AMPure bead clean up (Beckman Coulter #A63881, Brea, CA). Samples were multiplexed, pooled at equimolar concentrations and sequenced using the MiSeq 300 x 300 bp PE sequencing at Marine Biological Laboratory Bay Paul Center sequencing facility.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
completed
Sarah K. Hu
Woods Hole Oceanographic Institution
skhu@tamu.edu
pointOfContact
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
asNeeded
Dataset Version: 1
Unknown
biosample_accession
library_ID
title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
description
filetype
filename
filename2
sample_title
bioproject_accession
organism
isolation_source
year
collection_date
geo_loc_name
lat
lon
source_material_id
Vent_site
related_Axial_Seamount_projects
MiSeq 300 x 300 bp PE
Beckman Coulter #A63881, Brea, CA
Hydrothermal Fluid and Particle Sampler (HFPS)
Niskin bottle
theme
None, User defined
sample identification
sample description
instrument
No BCO-DMO term
file_name
accession number
year
date
region
latitude
longitude
sampling_method
site description
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Coulter Counter
HOV Alvin Slurp Samplers
Niskin bottle
Thermal Cycler
instrument
BCO-DMO Standard Instruments
FK010
TN300
RB1403
TN327
service
Deployment Activity
Axial Seamount, Juan de Fuca Ridge
Axial Seamount, Juan de Fuca Ridge, Northeast Pacific
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.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Probing subseafloor microbial interactions via hydrothermal vent fluids: A focus on protists
https://www.darkenergybiosphere.org/award/probing-subseafloor-microbial-interactions-via-hydrothermal-vent-fluids-a-focus-on-protists/
Probing subseafloor microbial interactions via hydrothermal vent fluids: A focus on protists
<p>Adjusted C-DEBI Award Description:</p>
<p>Highly reduced and thermally charged venting fluids from the subseafloor mix with surrounding seawater, creating a sharp geochemical gradient which promotes a hub of biological diversity at hydrothermal vent ecosystems. While studies of prokaryotic diversity at hydrothermal vent sites have highlighted the important roles microorganisms play in deep sea carbon cycling and offered a unique window into subseafloor microbial communities, depictions of deep-sea marine ecology and food webs are incomplete without characterization of single-celled microbial eukaryotes (protists). I propose to use culture-independent techniques (tag-sequencing and metatranscriptomics) to provide a thorough understanding of protistan biogeography in and near venting fluids, focusing on the vent fluid-seawater interface. Additionally, these qualitative analyses will be paired with quantitative experiments that measure protistan grazing pressure. Understanding trophic interactions within the protistan community is incredibly important, as these processes form the foundation of deep-sea marine food webs and mediate a significant amount of carbon transferred to higher trophic levels.</p>
<p>C-DEBI project link: <a href="https://www.darkenergybiosphere.org/award/probing-subseafloor-microbial-interactions-via-hydrothermal-vent-fluids-a-focus-on-protists/">https://www.darkenergybiosphere.org/award/probing-subseafloor-microbial-interactions-via-hydrothermal-vent-fluids-a-focus-on-protists/ </a></p>
Microbial eukaryotes at hydrothermal vents
largerWorkCitation
project
eng; USA
biota
oceans
Axial Seamount, Juan de Fuca Ridge; Axial Seamount, Juan de Fuca Ridge, Northeast Pacific
-130.0137
-129.7955
45.8799
46.2739
2013-09-01
2015-08-31
Axial Seamount Juan de Fuca Ridge NE Pacific 46 N 130 W, Gorda Ridge NE Pacific 41 N 127 W, Mid-Cayman Rise Caribbean Sea 18 N 82 W
0
BCO-DMO catalogue of parameters from High throughput tag-sequencing accessions (18S rRNA gene region) and environmental metadata from Axial Seamount, 2013-2015
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/828558.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/828559.rdf
Name: library_ID
Units: unitless
Description: <p>Short unique identifier for the sequencing library.</p>
http://lod.bco-dmo.org/id/dataset-parameter/828560.rdf
Name: title
Units: unitless
Description: <p>Short description that will identify the dataset on public pages.</p>
http://lod.bco-dmo.org/id/dataset-parameter/828561.rdf
Name: library_strategy
Units: unitless
Description: <p>Amplicon = Sequencing of overlapping or distinct PCR or RT-PCR products</p>
http://lod.bco-dmo.org/id/dataset-parameter/828562.rdf
Name: library_source
Units: unitless
Description: <p>Metagenomic = Mixed material from metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/828563.rdf
Name: library_selection
Units: unitless
Description: <p>PCR = Source material was selected by designed primers</p>
http://lod.bco-dmo.org/id/dataset-parameter/828564.rdf
Name: library_layout
Units: unitless
Description: <p>Paired-end or Single</p>
http://lod.bco-dmo.org/id/dataset-parameter/828565.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platforms [Illumina]</p>
http://lod.bco-dmo.org/id/dataset-parameter/828566.rdf
Name: instrument_model
Units: unitless
Description: <p>Illumina instrument and model used for sequencing</p>
http://lod.bco-dmo.org/id/dataset-parameter/828567.rdf
Name: design_description
Units: unitless
Description: <p>Free-form description of the methods used to create the sequencing library; a brief materials and methods section.</p>
http://lod.bco-dmo.org/id/dataset-parameter/828568.rdf
Name: description
Units: unitless
Description: <p>Description of the project</p>
http://lod.bco-dmo.org/id/dataset-parameter/828569.rdf
Name: filetype
Units: unitless
Description: <p>file type: fastq</p>
http://lod.bco-dmo.org/id/dataset-parameter/828570.rdf
Name: filename
Units: unitless
Description: <p>NCBI R1 filename</p>
http://lod.bco-dmo.org/id/dataset-parameter/828571.rdf
Name: filename2
Units: unitless
Description: <p>NCBI R2 filename</p>
http://lod.bco-dmo.org/id/dataset-parameter/828572.rdf
Name: sample_title
Units: unitless
Description: <p>NCBI sample title</p>
http://lod.bco-dmo.org/id/dataset-parameter/828573.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/828574.rdf
Name: organism
Units: unitless
Description: <p>Description of sample organism(s)</p>
http://lod.bco-dmo.org/id/dataset-parameter/828575.rdf
Name: isolation_source
Units: unitless
Description: <p>Type of source: environmental</p>
http://lod.bco-dmo.org/id/dataset-parameter/828576.rdf
Name: year
Units: unitless
Description: <p>year of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/828577.rdf
Name: collection_date
Units: unitless
Description: <p>Collection date(s)</p>
http://lod.bco-dmo.org/id/dataset-parameter/828578.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Geographic location of sample source</p>
http://lod.bco-dmo.org/id/dataset-parameter/828579.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/828580.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/828581.rdf
Name: source_material_id
Units: unitless
Description: <p>Description of methodology</p>
http://lod.bco-dmo.org/id/dataset-parameter/828582.rdf
Name: Vent_site
Units: unitless
Description: <p>Description of sample site</p>
http://lod.bco-dmo.org/id/dataset-parameter/828583.rdf
Name: related_Axial_Seamount_projects
Units: unitless
Description: <p>List of related BioProjects focused on the Axial Seamount</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
11156
https://darchive.mblwhoilibrary.org/bitstream/1912/26535/1/dataset-828345_microbial-eukaryotic-diversity-axial-seamount-sra__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.828345.1
download
onLine
dataset
<p><strong>Sample collection from Axial Seamount:</strong></p>
<p>From Fortunato et al (2018)</p>
<p>Sample collection from Axial Seamount took place in September 2013, August 2014, and August 2015. ROVs ROPOS and JASON were used to collect diffuse hydrothermal venting fluid. At each site, 3-L of diffuse venting fluid was pumped (100-150-ml per minute) onto a 0.22-um 47mm GWSP filter (Millipore). This fluid was collected using the Hydrothermal Fluid and Particle Sampler (HFPS; Butterfield et al. 2004), which was mounted on an ROV. The fluid intake for the HFPS has a temperature sensor to ensure a constant temperature during fluid collection. Filters were preserved in situ with RNALater. Background seawater was collected from a depth of 1500-m using a CTD mounted with 10-L Niskin bottles.</p>
<p><strong>Extraction and sequencing for 18S tag-sequencing:</strong></p>
<p>For all samples, RNA was extracted and amplified similarly to the protocol described in Hu et al. 2018 (https://dx.doi.org/10.17504/protocols.io.hk3b4yn). 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. Three shipboard blanks (MilliQ water) and one extraction blank were also extracted and PCR amplified; while no PCR product was observed in these control samples they were processed similarly to all true samples and sequenced. All PCR products were cleaned using the AMPure bead clean up (Beckman Coulter #A63881, Brea, CA). Samples were multiplexed, pooled at equimolar concentrations and sequenced using the MiSeq 300 x 300 bp PE sequencing at Marine Biological Laboratory Bay Paul Center sequencing facility.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes: </strong><br />
- data submitted in Excel files "Axial-Metagenome.environmental.1.0_JH.xlsx" sheet "tmp" and file "Axial-SRA_metadata_acc.xlsx" sheet "SRA_data"&nbsp;and extracted to csv<br />
- added conventional header with dataset name, PI name, version date<br />
- renamed columns to conform with BCO-DMO naming conventions (removed spaces)<br />
- combined environmental and SRA tables into one table; joined on sample_name and library_ID<br />
- removed unpopulated columns (ref_biomaterial, rel_to_oxygen, samp_collect_device, samp_mat_process, samp_size, host)<br />
- split lat_lon into lat and lon columns; changed sign of lon to negative&nbsp;to signify degrees west; reduced precision from variable to 4 decimal places<br />
- replaced commas with semi-colons</p>
Specified by the Principal Investigator(s)
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
MiSeq 300 x 300 bp PE
MiSeq 300 x 300 bp PE
PI Supplied Instrument Name: MiSeq 300 x 300 bp PE 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.
Beckman Coulter #A63881, Brea, CA
Beckman Coulter #A63881, Brea, CA
PI Supplied Instrument Name: Beckman Coulter #A63881, Brea, CA PI Supplied Instrument Description:Used to clean PCR products. Instrument Name: Coulter Counter Instrument Short Name: Instrument Description: An apparatus for counting and sizing particles suspended in electrolytes. It is used for cells, bacteria, prokaryotic cells and virus particles. A typical Coulter counter has one or more microchannels that separate two chambers containing electrolyte solutions.
from https://en.wikipedia.org/wiki/Coulter_counter
Hydrothermal Fluid and Particle Sampler (HFPS)
Hydrothermal Fluid and Particle Sampler (HFPS)
PI Supplied Instrument Name: Hydrothermal Fluid and Particle Sampler (HFPS) PI Supplied Instrument Description:The HFPS pumps vent fluid through a titanium intake nozzle and measures the temperature of the fluid just inside the nozzle and at a second point inside the titanium/Teflon fluid line near the sample containers. Sample containers are either collapsible plastic bags (with valves) within rigid housings, or PVC piston samplers with Teflon spring seals. Teflon check valves prevent the samples from leaking out or being drawn out of the containers. The HFPS was configured to collect 14 discrete fluid samples of up to 800 ml volume each, with the option of filtering eight of those samples. In addition, nine separate filters can concentrate particles from fluids of known temperature by in situ filtration, allowing us to collect and analyze minerals or microbes by a number of techniques. Two additional titanium gas-tight samplers are connected to the HFPS fluid line to collect samples of known temperature. Instrument Name: HOV Alvin Slurp Samplers Instrument Short Name: Instrument Description: Small and large capacity vacuum pump samplers. May have single or multiple chambers.
Slurp Samplers (from https://ndsf.whoi.edu/alvin/systems/)
The slurp samplers consist of a collection chamber and a hydraulically powered water pump. A nozzle with a tube connected to it is held and moved by a manipulator while water is pulled into the nozzle by the pump. The water travels down the tube into the collection chamber, and then goes through a mesh screen before going through the pump itself. Biological samples are sucked into the nozzle and deposited in the collection chamber. They are kept from going into the pump by the mesh screen. The screen can be changed for coarser or finer mesh as needed. Two styles of collection chamber are available; single chamber and 5-chamber.
Single chamber: a large cylindrical single collection chamber into which all samples will be deposited. Water weight 2 lbs, 27 lbs full of water.
5-chamber: five separate cylindrical collection chambers of 4.5 inch ID x 11.5 inch height. One chamber is used at a time and the chambers are rotated by a hydraulic actuator mounted to the bottom of the 5-chamber assembly. Water weight 10 lbs, 140 lbs full of water.
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:Used to collect background seawater sample. 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/
PI Supplied Instrument Name: 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: FK010
FK010
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK010
Julie Huber
Marine Biological Laboratory
https://datadocs.bco-dmo.org/d3/data_docs/Subseafloor_Life/FK010_CruiseReport_Huber_Final.pdf
Report describing FK010
Cruise: TN300
TN300
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN300
William Chadwick
National Oceanic and Atmospheric Administration
Cruise: RB1403
RB1403
Community Standard Description
International Council for the Exploration of the Sea
NOAA Ship Ronald H. Brown
vessel
RB1403
David A. Butterfield
National Oceanic and Atmospheric Administration
Cruise: TN327
TN327
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN327
William Chadwick
National Oceanic and Atmospheric Administration
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
Community Standard Description
International Council for the Exploration of the Sea
NOAA Ship Ronald H. Brown
vessel