http://lod.bco-dmo.org/id/dataset/897962
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
2023-06-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Lost City hydrothermal fluids sequence data from R/V Atlantis AT42-01 in the Lost City hydrothermal field from September to October 2018 (Lost City Limits to Life project)
2023-06-27
publication
2023-06-27
revision
BCO-DMO Linked Data URI
2023-06-27
creation
http://lod.bco-dmo.org/id/dataset/897962
William Brazelton
University of Utah
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: Brazelton, W. (2023) Lost City hydrothermal fluids sequence data from R/V Atlantis AT42-01 in the Lost City hydrothermal field from September to October 2018 (Lost City Limits to Life project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-06-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/897962 [access date]
Lost City hydrothermal fluids sequence data Dataset Description: <p>Amplicon sequences related to this dataset are available via NCBI BioProject&nbsp;PRJNA672129, and metagenome and metatranscriptome sequences are available via BioProject&nbsp;PRJNA779602. MAGs are associated with the same BioProject and are individually accessible via BioSamples&nbsp;SAMN23474158&nbsp;-&nbsp;SAMN23474187. In addition, GenBank accessions are listed for each MAG in Table S4. Protocols, metadata, and additional data are provided in a Zenodo-archived GitHub repository, <em>Brazelton-Lab/Brazelton-2022-Lost-City-fluids-MAGs: Final, published versions of text included</em>. Citations and links to these resources can be found within the Related Datasets section of this metadata page.</p> Methods and Sampling: <p><strong>Methods and Sampling&nbsp;</strong></p>
<p>On the seafloor, venting fluids were slowly pumped through 0.2 μm Millipore Sterivex cartridge filters or into acid-washed Kynar bags with the HOG sampler. Samples intended for RNA extractions were collected into 2 L Kynar bags containing 67 mL of a stop solution (97.5% 200 proof ethanol, 2.5% Trizol LS). Fluid temperatures were monitored in real-time during sampling with a probe embedded into the sampler intake. Immediately upon shipboard recovery of ROV Jason, all Sterivex filters were stored at -80 ºC.</p>
<p>Extraction of DNA from all Sterivex filters (including in situ-filtered fluids and fluids collected in Kynar bags and filtered shipboard) was conducted as described in the full protocol available via the Zenodo-archived GitHub repository (DOI: 10.5281/zenodo.5798015) and on protocols.io (DOI: dx.doi.org/10.17504/protocols.io.bykqpuvw). Total RNA was extracted from the Sterivex filters with a modification of the DNA extraction protocol optimized for RNA. The full protocol is available in the Zenodo-archived GitHub repository (DOI: 10.5281/zenodo.5798015) and on protocols.io (DOI: dx.doi.org/10.17504/protocols.io.bykspuwe). First-strand synthesis of cDNA was performed with SuperScript IV Reverse Transcriptase and random hexamers (Thermo Fisher).</p>
<p><br />
Sequencing of amplicons generated from 16S rRNA genes and cDNA was performed at the Genomics Core Facility at Michigan State University on an Illumina MiSeq instrument using dual-indexed Illumina fusion primers targeting the V4 region of the 16S rRNA gene. Metagenome libraries were constructed with size-selected, sonicated DNA fragments of 500-700 bp with the NEBnext Ultra DNA II library kit for Illumina (E7645S). Paired-end sequencing (2 x 125 bp) of metagenomic libraries was conducted at the University of Utah High-Throughput Genomics Core Facility at the Huntsman Cancer Institute with an Illumina HiSeq2500 platform. The two metatranscriptome libraries were constructed and sequenced by the University of Utah High-Throughput Genomics Core Facility at the Huntsman Cancer Institute. Total RNA was hybridized with NEBNext rRNA Depletion Solution Bacteria (E7850L) to substantially diminish rRNA from the samples. Stranded RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770L). Following the transfer of the flowcell to an Illumina NovaSeq 6000 instrument, a 150 cycle paired-end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312).</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1536702 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1536702
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1536405 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1536405
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1535962 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1535962
onGoing
William Brazelton
University of Utah
(801) 587-9455
Department of Biology
Salt Lake City
UT
84112
USA
william.brazelton@utah.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
accession
study
object_status
bioproject_accession
biosample_accession
sample_name
library_ID
title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
filename
filename2
filename3
filename4
assembly
fasta_file
Comment
source_file_name
HOG (hydrothermal organic geochemistry) sampler
R/V Atlantis Niskin rosette
ROV Jason
theme
None, User defined
accession number
NCBI SRA study accession (SRP)
status
NCBI BioProject accession
NCBI BioSample accession
sample identification
No BCO-DMO term
project
seq_descrip
instrument
instrument model
sampling_method
file_name
comments
featureType
BCO-DMO Standard Parameters
Hydrothermal Organic Geochemistry Sampler
Niskin bottle
ROV Jason
instrument
BCO-DMO Standard Instruments
AT42-01
service
Deployment Activity
Woods Hole, MA to San Juan, PR; Lost City hydrothermal field
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: Investigating the Lost City as an ultramafic urban center of the subseafloor, fueled by energy and carbon from the mantle
https://osprey.bco-dmo.org/project/658604
Collaborative Research: Investigating the Lost City as an ultramafic urban center of the subseafloor, fueled by energy and carbon from the mantle
<p><em>NSF Award Abstract:</em><br />
The vast majority of deep seafloor sediments are inhabited by microbial communities that survive under extreme energy limitation, with apparent generation times of centuries to millennia. Hydrothermal systems are a stark contrast to these energy-starved environments and may represent important, high-activity, 'population centers' in the oceanic subsurface. When rocks from the Earth's mantle are uplifted and exposed to water, the resulting reactions lead to acidic fluids with high concentrations of hydrogen. Under certain circumstances, small organic molecules such as methane can also form in the absence of biology. These compounds can provide energy to subseafloor microbial communities and, given the ubiquity of mantle rocks, such reactions may fuel a significant proportion of the active subsurface biosphere. The current project will characterize the microbial communities inhabiting an iconic example of this type of system, the Lost City Hydrothermal Field, using a remotely operated vehicle. The ghostly spires of Lost City are highly telegenic and have been featured in professional documentaries. The high definition underwater video footage collected during the expedition will provide the raw material for an 8 week educational training program in digital media focused on kindergarten through 12th grade high school students and undergraduate students. The resulting short documentaries will be published on YouTube and the Utah Education Network.</p>
<p>Mantle rocks comprise significant portions of the seafloor, and microbial communities hosted within them may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Upon tectonic uplift and exposure to water, the serpentinization of these materials releases potential energy in the form of hydrogen, methane, and heat, and further reaction of these products can sustain the abiogenic synthesis of small organic molecules. Recent studies have highlighted, however, the lack of alkalithermophiles that are capable of survival at the high pH (9-11) and elevated temperatures found in these systems. The almost complete lack of carbon dioxide (CO2) represents a second, and possibly more significant, limitation to growth. To better understand the extent of the serpentinite subsurface, this project will address the question: What limits biological activity in the serpentinite subsurface? Specifically, the proposed work will test the hypotheses: (1) microbial diversity spans a wider range of temperature-pH conditions than currently recognized and (2) the scarcity of CO2 is a key biological limitation to serpentinization-driven ecosystems that can be overcome by the metabolic activity of one or a few foundation species. These hypotheses will be tested during a 20 day (10 days on site) expedition to the Lost City Hydrothermal Field, focusing on fluids as windows to the subsurface biosphere. The sampling approach will capitalize on the differences in temperature, carbon availability, and microbial activity across the field. The analytical approach will integrate multidisciplinary techniques performed on replicate subsamples and feature the application of next-generation sequencing technologies to these marine serpentinizing fluids for the first time. This study will generate extensive sequence data from environmental DNA, environmental mRNA, and single-cell genomes, allowing us to identify the in situ expression of metabolic pathways and the genomics of active single cells. These efforts will be closely linked with a thorough characterization of carbon in these fluids that will focus on identifying available substrates (e.g. methane, CO2, organic acids) and on characterizing biomarkers that reflect specific metabolic pathways (e.g. lipids, amino acids).</p>
Lost City Limits to Life
largerWorkCitation
project
eng; USA
oceans
Woods Hole, MA to San Juan, PR; Lost City hydrothermal field
-42.2022
-41.9495
30.0054
30.2708
2018-09-08
2018-10-01
Lost City Hydrothermal Field
0
BCO-DMO catalogue of parameters from Lost City hydrothermal fluids sequence data from R/V Atlantis AT42-01 in the Lost City hydrothermal field from September to October 2018 (Lost City Limits to Life 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
http://lod.bco-dmo.org/id/dataset-parameter/991562.rdf
Name: accession
Units: unitless
Description: <p>NCBI Sequence Read Archive (SRA) run accession identifying a unique sequencing run.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991563.rdf
Name: study
Units: unitless
Description: <p>NCBI SRA study (project) accession grouping related sequencing runs under a single study.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991564.rdf
Name: object_status
Units: unitless
Description: <p>Status of the SRA record at the time of submission (e.g., new).</p>
http://lod.bco-dmo.org/id/dataset-parameter/991565.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject accession identifying the overarching project to which the sequencing data belong.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991566.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI BioSample accession identifying the biological sample from which sequence data were generated.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991567.rdf
Name: sample_name
Units: unitless
Description: <p>Descriptive name of the environmental or biological sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991568.rdf
Name: library_ID
Units: unitless
Description: <p>Unique identifier assigned to the sequencing library prepared from the sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991569.rdf
Name: title
Units: unitless
Description: <p>Short title or label for the sequencing library, typically matching the library identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991570.rdf
Name: library_strategy
Units: unitless
Description: <p>Sequencing strategy used to generate the data (AMPLICON indicates the sequencing of overlapping or distinct PCR or RT-PCR products; WGS indicates the random sequencing of the whole genome).</p>
http://lod.bco-dmo.org/id/dataset-parameter/991571.rdf
Name: library_source
Units: unitless
Description: <p>Source material used for library preparation (METAGENOMIC indicates the mixed material from metagenome; METATRANSCRIPTOMIC incidates transcription products from community targets).</p>
http://lod.bco-dmo.org/id/dataset-parameter/991572.rdf
Name: library_selection
Units: unitless
Description: <p>Method used to enrich or select DNA fragments for sequencing (PCR indicates source material was selected by designed primers; RANDOM indicates random selection by shearing or other method)</p>
http://lod.bco-dmo.org/id/dataset-parameter/991573.rdf
Name: library_layout
Units: unitless
Description: <p>Read configuration of the sequencing library (paired for paired-end sequencing).</p>
http://lod.bco-dmo.org/id/dataset-parameter/991574.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform used to generate the data.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991575.rdf
Name: instrument_model
Units: unitless
Description: <p>Specific sequencing instrument model used to generate the data.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991576.rdf
Name: design_description
Units: unitless
Description: <p>Description of the sequencing assay design.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991577.rdf
Name: filetype
Units: unitless
Description: <p>File format of the raw sequencing data.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991578.rdf
Name: filename
Units: unitless
Description: <p>Name of the first sequencing data file associated with the run.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991579.rdf
Name: filename2
Units: unitless
Description: <p>Name of the second sequencing data file associated with the run.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991580.rdf
Name: filename3
Units: unitless
Description: <p>Optional additional file associated with the run.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991581.rdf
Name: filename4
Units: unitless
Description: <p>Optional additional file associated with the run.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991582.rdf
Name: assembly
Units: unitless
Description: <p>Identifier for an associated genome assembly, if applicable.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991583.rdf
Name: fasta_file
Units: unitless
Description: <p>Name of an associated FASTA file contianing assembled or processed sequences, if applicable.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991584.rdf
Name: Comment
Units: unitless
Description: <p>Comment added by data manager to differentiate between metagenome and amplicon data.</p>
http://lod.bco-dmo.org/id/dataset-parameter/991585.rdf
Name: source_file_name
Units: unitless
Description: <p>Source file name added by data manger to differentiate between metagenome and amplicon data.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://osprey.bco-dmo.org/dataset/897962/data/download
download
onLine
dataset
<p><strong>Methods and Sampling&nbsp;</strong></p>
<p>On the seafloor, venting fluids were slowly pumped through 0.2 μm Millipore Sterivex cartridge filters or into acid-washed Kynar bags with the HOG sampler. Samples intended for RNA extractions were collected into 2 L Kynar bags containing 67 mL of a stop solution (97.5% 200 proof ethanol, 2.5% Trizol LS). Fluid temperatures were monitored in real-time during sampling with a probe embedded into the sampler intake. Immediately upon shipboard recovery of ROV Jason, all Sterivex filters were stored at -80 ºC.</p>
<p>Extraction of DNA from all Sterivex filters (including in situ-filtered fluids and fluids collected in Kynar bags and filtered shipboard) was conducted as described in the full protocol available via the Zenodo-archived GitHub repository (DOI: 10.5281/zenodo.5798015) and on protocols.io (DOI: dx.doi.org/10.17504/protocols.io.bykqpuvw). Total RNA was extracted from the Sterivex filters with a modification of the DNA extraction protocol optimized for RNA. The full protocol is available in the Zenodo-archived GitHub repository (DOI: 10.5281/zenodo.5798015) and on protocols.io (DOI: dx.doi.org/10.17504/protocols.io.bykspuwe). First-strand synthesis of cDNA was performed with SuperScript IV Reverse Transcriptase and random hexamers (Thermo Fisher).</p>
<p><br />
Sequencing of amplicons generated from 16S rRNA genes and cDNA was performed at the Genomics Core Facility at Michigan State University on an Illumina MiSeq instrument using dual-indexed Illumina fusion primers targeting the V4 region of the 16S rRNA gene. Metagenome libraries were constructed with size-selected, sonicated DNA fragments of 500-700 bp with the NEBnext Ultra DNA II library kit for Illumina (E7645S). Paired-end sequencing (2 x 125 bp) of metagenomic libraries was conducted at the University of Utah High-Throughput Genomics Core Facility at the Huntsman Cancer Institute with an Illumina HiSeq2500 platform. The two metatranscriptome libraries were constructed and sequenced by the University of Utah High-Throughput Genomics Core Facility at the Huntsman Cancer Institute. Total RNA was hybridized with NEBNext rRNA Depletion Solution Bacteria (E7850L) to substantially diminish rRNA from the samples. Stranded RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770L). Following the transfer of the flowcell to an Illumina NovaSeq 6000 instrument, a 150 cycle paired-end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312).</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
* This dataset was originally organized and submitted as two separate data files in different formats. These files have been merged into 897962_v1_lost_city_hydrothermal_fluids_sequence_data.csv, which is served as the primary data file of this published dataset. Columns "source_file_name" and "Comment" have been added to this data file to differentiate between the two original data sources.
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
HOG (hydrothermal organic geochemistry) sampler
HOG (hydrothermal organic geochemistry) sampler
PI Supplied Instrument Name: HOG (hydrothermal organic geochemistry) sampler PI Supplied Instrument Description:On the seafloor, venting fluids were slowly pumped through 0.2 μm Millipore Sterivex cartridge filters or into acid-washed Kynar bags with the HOG sampler. Samples intended for RNA extractions were collected into 2 L Kynar bags containing 67 mL of a stop solution (97.5% 200 proof ethanol, 2.5% Trizol LS). Fluid temperatures were monitored in real-time during sampling with a probe embedded into the sampler intake. 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.
R/V Atlantis Niskin rosette
R/V Atlantis Niskin rosette
PI Supplied Instrument Name: R/V Atlantis Niskin rosette 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:Hydrothermal fluid samples were collected from actively venting chimneys at the Lost City hydrothermal field using ROV Jason during the 2018 Lost City expedition aboard R/V Atlantis (AT42-01). This study includes 39 samples of hydrothermal fluids that were dedicated to DNA and RNA sequencing, including analyses of amplicon sequence variants (ASVs), metagenomes, and metatranscriptomes. 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/
Cruise: AT42-01
AT42-01
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT42-01
Susan Q. Lang
University of South Carolina
https://datadocs.bco-dmo.org/docs/Lost_City_Limits_to_Life/data_docs/AT42-01_Cruise%20Report_reduced.pdf
Report describing AT42-01
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel