http://lod.bco-dmo.org/id/dataset/914399
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
2023-11-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
18S rRNA amplicon sequencing of microbial eukaryotes from the Mid-Cayman Rise acquired Jan-Feb, 2020
2023-11-06
publication
2023-11-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-11-06
publication
https://doi.org/10.26008/1912/bco-dmo.914399.1
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. (2023) 18S rRNA amplicon sequencing of microbial eukaryotes from the Mid-Cayman Rise acquired Jan-Feb, 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-11-06 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.914399.1 [access date]
18S rRNA amplicon sequencing of microbial eukaryotes Dataset Description: Methods and Sampling: <p>Samples and experiments were collected and executed during cruise AT42-22 aboard the RV Atlantis with ROV Jason in January-February 2020 at the Von Damm (2300 m; 18°23’N, 81°48’W) and Piccard (5000 m; 18°33’N, 81°43’W) hydrothermal fields located along the Mid-Cayman Rise.</p>
<p>Fluids for shipboard grazing experiments and biogeochemistry were obtained in 10L volume bags (Kynar, Keika Ventures; polyvinylidene fluoride) using the Hydrothermal Organic Geochemistry (HOG) sampler mounted on ROV Jason. Between 4-10 L of vent fluid was collected and filtered through a 47 mm polyethersulphone (PES) filter (Millipore) with a pore size of 0.2 µm and preserved with RNAlater (Ambion) at the seafloor for molecular analysis of microbial communities.&nbsp;</p>
<p>Non-vent samples were collected from within the overlying non-buoyant hydrothermal plume at each site and from background seawater via CTD-mounted Niskin bottles. Plume samples were identified using in situ CTD sensors to detect the presence of hydrothermal influence in real-time (back-scatter and temperature) above each vent field. Background seawater samples were collected outside of the influence of the hydrothermal vent at approximately the same depth as the vent sites (~2350 m and ~4950 m).</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
onGoing
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
Experiment_Accession
Experiment_Title
Organism_Name
Instrument
Study_Accession
Study_Title
Sample_Accession
Total_Size_Mb
Total_Bases
Library_Name
Library_Strategy
Library_Source
Library_Selection
Vent_field
Collection
Vent_name
DiveID
Illumina MiSeq
theme
None, User defined
accession number
sample description
instrument
NCBI SRA study accession (SRP)
NCBI SRA Sample accession (SRS)
site
dive_id
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
AT42-22
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.
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
oceans
-82
-82
18
18
2020-01-14
2020-02-05
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 18S rRNA amplicon sequencing of microbial eukaryotes from the Mid-Cayman Rise acquired Jan-Feb, 2020
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/914431.rdf
Name: Experiment_Accession
Units: unitless
Description: <p>Accession ID in SRA</p>
http://lod.bco-dmo.org/id/dataset-parameter/914432.rdf
Name: Experiment_Title
Units: unitless
Description: <p>Overall sample title</p>
http://lod.bco-dmo.org/id/dataset-parameter/914433.rdf
Name: Organism_Name
Units: unitless
Description: <p>Type of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/914434.rdf
Name: Instrument
Units: unitless
Description: <p>Sequencing platform used</p>
http://lod.bco-dmo.org/id/dataset-parameter/914435.rdf
Name: Study_Accession
Units: unitless
Description: <p>Accession ID for study in SRA</p>
http://lod.bco-dmo.org/id/dataset-parameter/914436.rdf
Name: Study_Title
Units: unitless
Description: <p>Microbial eukaryotic biodiversity (18S rRNA gene) from the Mid-Cayman Rise deep-sea hydrothermal vent field</p>
http://lod.bco-dmo.org/id/dataset-parameter/914437.rdf
Name: Sample_Accession
Units: unitless
Description: <p>Individual sample accession IDs for SRA</p>
http://lod.bco-dmo.org/id/dataset-parameter/914438.rdf
Name: Total_Size_Mb
Units: Mb
Description: <p>Size of data file</p>
http://lod.bco-dmo.org/id/dataset-parameter/914439.rdf
Name: Total_Bases
Units: bp
Description: <p>Total number of base pairs</p>
http://lod.bco-dmo.org/id/dataset-parameter/914440.rdf
Name: Library_Name
Units: unitless
Description: <p>Unique library ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/914441.rdf
Name: Library_Strategy
Units: unitless
Description: <p>Type of library preparation</p>
http://lod.bco-dmo.org/id/dataset-parameter/914442.rdf
Name: Library_Source
Units: unitless
Description: <p>Source genetic material for library preparation</p>
http://lod.bco-dmo.org/id/dataset-parameter/914443.rdf
Name: Library_Selection
Units: unitless
Description: <p>Mode of amplification or library prep</p>
http://lod.bco-dmo.org/id/dataset-parameter/914444.rdf
Name: Vent_field
Units: unitless
Description: <p>Hydrothermal vent field</p>
http://lod.bco-dmo.org/id/dataset-parameter/914445.rdf
Name: Collection
Units: unitless
Description: <p>Origin of fluid collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/914446.rdf
Name: Vent_name
Units: unitless
Description: <p>Name of vent site</p>
http://lod.bco-dmo.org/id/dataset-parameter/914447.rdf
Name: DiveID
Units: unitless
Description: <p>ID for ROV Dive or CTD cast for sample</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
8756
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a356eda7-76ad-4e46-ac2b-8fb468914dc6/content
download
https://doi.org/10.26008/1912/bco-dmo.914399.1
download
onLine
dataset
<p>Samples and experiments were collected and executed during cruise AT42-22 aboard the RV Atlantis with ROV Jason in January-February 2020 at the Von Damm (2300 m; 18°23’N, 81°48’W) and Piccard (5000 m; 18°33’N, 81°43’W) hydrothermal fields located along the Mid-Cayman Rise.</p>
<p>Fluids for shipboard grazing experiments and biogeochemistry were obtained in 10L volume bags (Kynar, Keika Ventures; polyvinylidene fluoride) using the Hydrothermal Organic Geochemistry (HOG) sampler mounted on ROV Jason. Between 4-10 L of vent fluid was collected and filtered through a 47 mm polyethersulphone (PES) filter (Millipore) with a pore size of 0.2 µm and preserved with RNAlater (Ambion) at the seafloor for molecular analysis of microbial communities.&nbsp;</p>
<p>Non-vent samples were collected from within the overlying non-buoyant hydrothermal plume at each site and from background seawater via CTD-mounted Niskin bottles. Plume samples were identified using in situ CTD sensors to detect the presence of hydrothermal influence in real-time (back-scatter and temperature) above each vent field. Background seawater samples were collected outside of the influence of the hydrothermal vent at approximately the same depth as the vent sites (~2350 m and ~4950 m).</p>
Specified by the Principal Investigator(s)
<p>Filters retrieved from ROV Jason and from the final time point of each grazing assay were processed identically. RNA was extracted from frozen filters (stored in RNAlater) as amplicon sequences originating from extracted RNA are more likely to represent metabolically active cells, rather than inactive cellular material that may have sunk from above. The filter was first separated from the RNAlater and distributed into tubes with a lysis buffer (Qiagen 1053393). The RNAlater was centrifuged for 15 minutes at 16,000 x g, and the supernatant was removed. Lysis buffer was added on top of any cellular materials collected, vortexed, and then combined with the filter. The filter and lysis buffer solution was vortexed thoroughly with RNAase-free silica beads. The lysis buffer was then separated from beads and filter material with a syringe and processed using the Qiagen RNeasy extract kit (Qiagen 74104), which included an inline RNAse-free DNase removal step (Qiagen 79256). Total RNA was reverse transcribed to cDNA and amplified with V4-specific primers. MiSeq 2 x 300 bp PE sequencing was performed at the Marine Biological Laboratory Bay Paul Centre Keck sequencing facility. Amplicon sequences were processed using QIIME2 (version 2021.4).</p>
<p>Following quality control, Amplicon Sequence Variants (or ASVs) were determined from the sequences and taxonomic assignment was done using the PR2 database (v 4.14). For this analysis, we focused primarily on the microeukaryotic population, removing sequences assigned to prokaryotes or Metazoa. ASVs were categorized as vent-only or cosmopolitan, based on their presence in only vent samples or throughout vent, plume, and background samples, respectively.</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
Illumina MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq 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.
Cruise: AT42-22
AT42-22
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT42-22
Jeffrey S. Seewald
Woods Hole Oceanographic Institution
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel