http://lod.bco-dmo.org/id/dataset/936069
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
2024-08-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metagenome and metatranscriptome sequences from deep-sea hydrothermal vent microbial communities collected on cruises AT42-22, TN405, and NA108 from May 2019 to Jun 2022
2024-12-05
publication
2024-12-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-12-05
publication
https://doi.org/10.26008/1912/bco-dmo.936069.1
Sarah K. Hu
Woods Hole Oceanographic Institution
principalInvestigator
Rika Anderson
Carleton College
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., Anderson, R., Huber, J. (2024) Metagenome and metatranscriptome sequences from deep-sea hydrothermal vent microbial communities collected on cruises AT42-22, TN405, and NA108 from May 2019 to Jun 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-12-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.936069.1 [access date]
Metagenome and metatranscriptome sequences from deep-sea hydrothermal vent microbial communities Dataset Description: Methods and Sampling: <p>All samples were collected via ROVs, where an intake valve was positioned at the location of active diffuse flow (&lt;100C) and collected into bags, bottles, or a filter directly. If collected into a bag or bottle, fluid was filtered immediately upon recovery. All filters had a pore size of 0.2µm and were composed of PES material.&nbsp;</p>
<p><!--StartFragment-->Samples collected at the Mid-Cayman Rise and the Axial Seamount locations utilized ROV Jason; at the Mid-Cayman Rise fluid was collected with the HOG sampler, the SUPR sampler was used to collected fluids at Axial Seamount. Samples collected at the Gorda Ridge used ROV Hercules with the SUPR sampler.<!--EndFragment--></p>
<p>&nbsp;</p>
<p><strong>Metatranscriptomics</strong></p>
<p>&nbsp;</p>
<p>Messenger RNA (mRNA) was subset from previously extracted RNA from all sites and grazing experiments (Qiagen RNA mini kit). Then metatranscriptome libraries were prepared from the mRNA. Library was prepped with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760S; with a Poly(A) mRNA magnetic isolation module first. For fragmentation, samples were incubated at 94C for 10 minutes. PCR cycles done until enough was isolated, range of 16-28. Mainly 20 or 22 cycles total. Input total RNA for metatranscriptome libraries was either 100 ng or 10 ng. However, with mRNA content ranging from 1-5% of the total RNA, the PCR amplification steps needed to be modified for the estimated input mRNA.</p>
<p>Libraries were sequenced with NovaSeq at the Northwest Genomics Sequence Center (Seattle, WA). Sequenced with NovaSeq S2 300 cycles. An average of 100 million sequences per sample were recovered from the metatranscriptome sequencing.</p>
<p>&nbsp;</p>
<p><strong>Metagenomics</strong></p>
<p>&nbsp;</p>
<p>Duplicate samples (other half of filter) from in situ sites at Mid-Cayman Rise were extracted for DNA (n = 12), then prepared as metagenome libraries, and sent for NovaSeq sequencing (data received January 2023). DNA extracted with MasterPure Complete DNA and RNA Purification Kit (Lucigen MC85200). Input DNA diluted to 50 ng total, or all DNA input (For low concentration samples) and sheared to target 400 bps with Covaris M220 focused-ultrasonicator, utilizing SonoLab 7.2. For 70 sections, 200 cycles (bursts) at 50 watts (Peak incident power), duty factor = 10%, and average incident power was 5 watts. Min temp: 18C, setpoint: 20C, and max: 22C.</p>
<p>Libraries were prepped with Ovation Ultralow System V2 (from Nugen). Library amplification was done at 15 cycles, and pooled. Sequencing was done with&nbsp;a NovaSeq S2 300 Cycle (UW Genomics NWGC). Over 80 million sequences per sample were recovered, to ensure sufficient sequencing depth.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2327203 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2327203
completed
Sarah K. Hu
Woods Hole Oceanographic Institution
skhu@tamu.edu
pointOfContact
Rika Anderson
Carleton College
507-222-4382
One North College Street
Northfield
MN
55057
USA
randerson@carleton.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
SAMPLE_ID
SHORT_SAMPLE_ID
SAMPLE_NAME
LAB_NUM
CRUISE_ID
FIELD_REGION
YEAR
FIELD_YEAR
VENT
LAT
LON
ORIGIN_TYPE
ORIGIN_DESCRIPTION
FRENEMIES_PROJ
LIBRARY
RUN
BIOSAMPLE
BASES
BYTES
EXPERIMENT
LIBRARY_NAME
LIBRARY_SELECTION
geo_loc_name_country
geo_loc_name_country_continent
geo_loc_name
Illumina NovaSeq 6000
ROV Jason, HOG sampler
Covaris M220 focused-ultrasonicator
theme
None, User defined
sample identification
Cruise identfier
site
date
site description
latitude
longitude
sample description
project
NCBI SRA run accession (SRR)
NCBI BioSample accession
genetic material concentration
file_size
NCBI SRA experiment accession (SRX)
sampling_method
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Hydrothermal Organic Geochemistry Sampler
ultrasonic cell disrupter (sonicator)
instrument
BCO-DMO Standard Instruments
AT42-22
TN405
NA108
FK010
TN300
service
Deployment Activity
Gorda Ridges, Pacific Ocean
Axial Seamount, Juan de Fuca Ridge
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: Microbes need frenemies: unveiling microbial relationships with protists and viruses that support deep-sea hydrothermal vent food webs
https://osprey.bco-dmo.org/project/875053
Collaborative Research: Microbes need frenemies: unveiling microbial relationships with protists and viruses that support deep-sea hydrothermal vent food webs
<p><em>Non-technical abstract:</em><br />
Ecological interactions among microbes (bacteria and archaea), viruses, and eukaryotic microorganisms are critical junctions in marine food webs. These interactions range from mutually beneficial relationships to sources of microbial mortality. Interactions between viruses-microbes and eukaryotes-microbes at deep-sea hydrothermal vents impact local carbon cycling. This project aims to identify these microbial interactions, specifically those related to cell death by protistan grazing or viral lysis, and explore how they vary across different hydrothermal vent habitats. By providing a better understanding of the composition and nature of these relationships, the investigators aim to build a better food web model of deep-sea hydrothermal vents and improve our understanding of how climate change and other human activities impact the ecosystem. Outcomes from this project include the generation of new microbiology, oceanography, and computer science curricula targeted at community college students. In addition, it involves research with undergraduate students at all stages of the research process and provides opportunities for professional development and peer-to-peer mentoring.</p>
<p><em>Technical abstract:</em><br />
This project examines trophic interactions among microbial eukaryotes, viruses, bacteria, and archaea at deep-sea hydrothermal vents using metagenomics and metatranscriptomics and characterizes these ecologically-significant interactions, such as mutualism, predator-prey, or virus-host. The investigators are sequencing samples collected to target archaea/bacteria, viruses, and eukaryotic grazers during a 2020 expedition to the Mid-Cayman Rise hydrothermal vent field to accomplish these goals. Specific aims of this project are to 1) Investigate the microbial, viral, and protistan assemblages and determine how lifestyle, community composition, and metabolism vary across venting fluids of the Mid-Cayman Rise; and 2) Identify ecologically-significant interactions among protists, viruses, bacteria, and archaea and incorporate these interactions into a model for turnover and exchange of carbon in the vent-associated food web. By modeling how trophic interactions influence microbial mortality, the proposed project substantially contributes to our understanding of the fate of carbon in one of the most productive ecosystems of the deep sea.</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>
frenemies
largerWorkCitation
project
eng; USA
biota
oceans
Gorda Ridges, Pacific Ocean; Axial Seamount, Juan de Fuca Ridge
-126.7
-81.7
18.13
45.9
2013-09-01
2022-07-12
0
BCO-DMO catalogue of parameters from Metagenome and metatranscriptome sequences from deep-sea hydrothermal vent microbial communities collected on cruises AT42-22, TN405, and NA108 from May 2019 to Jun 2022
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/940054.rdf
Name: SAMPLE_ID
Units: unitless
Description: <p>Complete sample ID associated with fastq files</p>
http://lod.bco-dmo.org/id/dataset-parameter/940055.rdf
Name: SHORT_SAMPLE_ID
Units: unitless
Description: <p>Short name sample identifier associated with cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/940056.rdf
Name: SAMPLE_NAME
Units: unitless
Description: <p>Related sample name associated with vent site</p>
http://lod.bco-dmo.org/id/dataset-parameter/940057.rdf
Name: LAB_NUM
Units: unitless
Description: <p>Internal number for sample inventory</p>
http://lod.bco-dmo.org/id/dataset-parameter/940058.rdf
Name: CRUISE_ID
Units: unitless
Description: <p>Identifer of cruise during which sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/940059.rdf
Name: FIELD_REGION
Units: unitless
Description: <p>Region of hydrothermal vent field</p>
http://lod.bco-dmo.org/id/dataset-parameter/940060.rdf
Name: YEAR
Units: unitless
Description: <p>Year of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/940061.rdf
Name: FIELD_YEAR
Units: unitless
Description: <p>Hydrothermal vent field with year of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/940062.rdf
Name: VENT
Units: unitless
Description: <p>Name of individual vent site or sample origin</p>
http://lod.bco-dmo.org/id/dataset-parameter/940063.rdf
Name: LAT
Units: Decimal Degrees
Description: <p>Latitude of site where samples were collected. Negative values indicate South.</p>
http://lod.bco-dmo.org/id/dataset-parameter/940064.rdf
Name: LON
Units: Decimal Degrees
Description: <p>Longitude of site where samples were collected. Negative values indicate West.</p>
http://lod.bco-dmo.org/id/dataset-parameter/940065.rdf
Name: ORIGIN_TYPE
Units: unitless
Description: <p>Origin of the sample, either in situ or grazing experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/940066.rdf
Name: ORIGIN_DESCRIPTION
Units: unitless
Description: <p>Collection method description</p>
http://lod.bco-dmo.org/id/dataset-parameter/940067.rdf
Name: FRENEMIES_PROJ
Units: unitless
Description: <p>Associated project</p>
http://lod.bco-dmo.org/id/dataset-parameter/940068.rdf
Name: LIBRARY
Units: unitless
Description: <p>Type of fastq sequence file</p>
http://lod.bco-dmo.org/id/dataset-parameter/940069.rdf
Name: RUN
Units: unitless
Description: <p>SRR number in NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/940070.rdf
Name: BIOSAMPLE
Units: unitless
Description: <p>Biosample ID number in NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/940071.rdf
Name: BASES
Units: Giga base pairs (Gb)
Description: <p>Total number of bps in giga base pairs (Gb)</p>
http://lod.bco-dmo.org/id/dataset-parameter/940072.rdf
Name: BYTES
Units: Gigabytes
Description: <p>Total size of the sequence file in Gigabytes (GB)</p>
http://lod.bco-dmo.org/id/dataset-parameter/940073.rdf
Name: EXPERIMENT
Units: unitless
Description: <p>Experiment ID for locating sequences in NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/940074.rdf
Name: LIBRARY_NAME
Units: unitless
Description: <p>Sample identifer for fastq files</p>
http://lod.bco-dmo.org/id/dataset-parameter/940075.rdf
Name: LIBRARY_SELECTION
Units: unitless
Description: <p>Amplication used in library prep</p>
http://lod.bco-dmo.org/id/dataset-parameter/940076.rdf
Name: geo_loc_name_country
Units: unitless
Description: <p>Geo location name for SRA metadata</p>
http://lod.bco-dmo.org/id/dataset-parameter/940077.rdf
Name: geo_loc_name_country_continent
Units: unitless
Description: <p>Geo location associated with continent</p>
http://lod.bco-dmo.org/id/dataset-parameter/940078.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Geo location name for site of vent field</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
19703
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/8d53fe49-b1cc-4a64-8cef-31fe05ac05b2/content
download
https://doi.org/10.26008/1912/bco-dmo.936069.1
download
onLine
dataset
<p>All samples were collected via ROVs, where an intake valve was positioned at the location of active diffuse flow (&lt;100C) and collected into bags, bottles, or a filter directly. If collected into a bag or bottle, fluid was filtered immediately upon recovery. All filters had a pore size of 0.2µm and were composed of PES material.&nbsp;</p>
<p><!--StartFragment-->Samples collected at the Mid-Cayman Rise and the Axial Seamount locations utilized ROV Jason; at the Mid-Cayman Rise fluid was collected with the HOG sampler, the SUPR sampler was used to collected fluids at Axial Seamount. Samples collected at the Gorda Ridge used ROV Hercules with the SUPR sampler.<!--EndFragment--></p>
<p>&nbsp;</p>
<p><strong>Metatranscriptomics</strong></p>
<p>&nbsp;</p>
<p>Messenger RNA (mRNA) was subset from previously extracted RNA from all sites and grazing experiments (Qiagen RNA mini kit). Then metatranscriptome libraries were prepared from the mRNA. Library was prepped with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760S; with a Poly(A) mRNA magnetic isolation module first. For fragmentation, samples were incubated at 94C for 10 minutes. PCR cycles done until enough was isolated, range of 16-28. Mainly 20 or 22 cycles total. Input total RNA for metatranscriptome libraries was either 100 ng or 10 ng. However, with mRNA content ranging from 1-5% of the total RNA, the PCR amplification steps needed to be modified for the estimated input mRNA.</p>
<p>Libraries were sequenced with NovaSeq at the Northwest Genomics Sequence Center (Seattle, WA). Sequenced with NovaSeq S2 300 cycles. An average of 100 million sequences per sample were recovered from the metatranscriptome sequencing.</p>
<p>&nbsp;</p>
<p><strong>Metagenomics</strong></p>
<p>&nbsp;</p>
<p>Duplicate samples (other half of filter) from in situ sites at Mid-Cayman Rise were extracted for DNA (n = 12), then prepared as metagenome libraries, and sent for NovaSeq sequencing (data received January 2023). DNA extracted with MasterPure Complete DNA and RNA Purification Kit (Lucigen MC85200). Input DNA diluted to 50 ng total, or all DNA input (For low concentration samples) and sheared to target 400 bps with Covaris M220 focused-ultrasonicator, utilizing SonoLab 7.2. For 70 sections, 200 cycles (bursts) at 50 watts (Peak incident power), duty factor = 10%, and average incident power was 5 watts. Min temp: 18C, setpoint: 20C, and max: 22C.</p>
<p>Libraries were prepped with Ovation Ultralow System V2 (from Nugen). Library amplification was done at 15 cycles, and pooled. Sequencing was done with&nbsp;a NovaSeq S2 300 Cycle (UW Genomics NWGC). Over 80 million sequences per sample were recovered, to ensure sufficient sequencing depth.</p>
Specified by the Principal Investigator(s)
- Imported submitted file "bco-dmo_Frenemies.csv" into the BCO-DMO system
- Split lat_lon field into separate fields
- Converted lon to lon W, (West is negative)
- Created YEAR field in format YYYY by pulling the year from FIELDYR
- Added a CRUISE_ID field with corresponding cruise IDs given in submission by year
- Added cruise id for 2013 item
- Exported dataset as 936069_v1_frenemies_accession_metadata.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 NovaSeq 6000
Illumina NovaSeq 6000
PI Supplied Instrument Name: Illumina NovaSeq 6000 PI Supplied Instrument Description:Libraries were sequenced with NovaSeq at the Northwest Genomics Sequence Center (Seattle, WA). 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.
ROV Jason, HOG sampler
ROV Jason, HOG sampler
PI Supplied Instrument Name: ROV Jason, HOG sampler PI Supplied Instrument Description:All samples were collected via ROVs, where an intake valve was positioned at the location of active diffuse flow ( Instrument Name: Hydrothermal Organic Geochemistry Sampler Instrument Short Name:HOG sampler Instrument Description: The Hydrothermal Organic Geochemistry (HOG) sampler is designed to collect large volume (2–9 L) fluid samples with minimal introduction of organic or microbial contamination, and to be powered and deployed in real time from a submersible. Additional design constraints include utilizing materials appropriate for sampling fluids with elevated temperatures, fitting the sampler into the space available on the submersible, and minimizing the time needed to remove samples and prepare the sampler for re-deployment between dives.
Covaris M220 focused-ultrasonicator
Covaris M220 focused-ultrasonicator
PI Supplied Instrument Name: Covaris M220 focused-ultrasonicator PI Supplied Instrument Description:Input DNA diluted to 50 ng total, or all DNA input (For low concentration samples) and sheared to target 400 bps with Covaris M220 focused-ultrasonicator Instrument Name: ultrasonic cell disrupter (sonicator) Instrument Short Name: Instrument Description: Instrument that applies sound energy to agitate particles in a sample.
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
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
Cruise: NA108
NA108
E/V Nautilus
E/V Nautilus
vessel
NA108
Darlene Lim
National Aeronautics and Space Administration
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
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
E/V Nautilus
E/V Nautilus
vessel
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel