http://lod.bco-dmo.org/id/dataset/933609
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
2024-07-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Single-cell amplified genomes (SAGs) of uncultivated Aminicenantia bacteria from the subseafloor of Juan de Fuca Ridge (JdFR) from deployments of R/V Atlantis AT18-07 and AT42-11 from 2011 and 2019
2024-12-27
publication
2024-12-27
revision
BCO-DMO Linked Data URI
2024-12-27
creation
http://lod.bco-dmo.org/id/dataset/933609
Beth N. Orcutt
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Anne Booker
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Timothy D'Angelo
Bigelow Laboratory for Ocean Sciences
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: Orcutt, B. N., D'Angelo, T., Booker, A. (2024) Single-cell amplified genomes (SAGs) of uncultivated Aminicenantia bacteria from the subseafloor of Juan de Fuca Ridge (JdFR) from deployments of R/V Atlantis AT18-07 and AT42-11 from 2011 and 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-12-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/933609 [access date]
Methods and Sampling: <p><strong>Sample collection:</strong><em> </em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">Borehole observatories accessing subseafloor crustal fluids were installed on the eastern flank of the JdFR in 2004 and 2010 during IODP Expeditions 301 and 327, respectively (Fisher et al. 2011; Fisher et al. 2005). These observatories penetrate ~ 240 m of sediment and ~110-290 m of underlying basement to enable crustal fluid collection from 8-190 m below the sediment-basement interface. Crustal fluids in this region are consistently 62-64°C, anoxic, and sulfate-replete (~18 mmol sulfate per kg water; Wheat et al. 2013). New crustal fluid sampling occurred in May 2019 during expedition AT42-11 on R/V </span><em>Atlantis</em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt"> with ROV </span><em>Jason II, </em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">both operated by Woods Hole Oceanographic Institution. Single cell genomic data was generated from cells collected from borehole observatory U1362B using established syringe sampling approaches (Carr et al. 2019; Wheat et al. 2011). Briefly, the top plug on the wellhead of U1362B was removed to freely vent crustal fluid from the top of the observatory (Fisher et al. 2011). After the borehole dead volume had been flushed, crustal fluid was collected using a sterilized syringe (Wheat et al. 2011). Once recovered, the fluid was distributed in a nitrogen-flushed glove bag into cryovials, amended with 5% glycerol and 1X-Tris-EDTA buffer (final concentrations), and immediately flash-frozen with liquid nitrogen before long term storage at -70°C . In addition to the new sample, we examined existing single cell genomic and metagenomic data generated from samples collected from borehole observatories in International Ocean Discovery Program (IODP) Holes U1301A, U1362A, and U1362B in 2011 (AT18-07) using methods described elsewhere (Carr et al. 2019; Jungbluth et al. 2016; Fisher et al. 2012; Jungbluth et al. 2017).</span><br />
&nbsp;</p>
<p dir="ltr"><strong>Genomic sequencing, assembly, and phylogenomic analysis:</strong><em> </em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">Nineteen JdFR </span><em>Aminicenantia</em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt"> metagenome assembled genomes (MAGs) and single-cell amplified genomes (SAGs) were identified across three independent sampling expeditions that occurred over a nine-year period. Two new metagenome assembled genomes (MAGs 3300037598_45, 3300037558_26) were sequenced, assembled, and binned from 2010 and 2011 metagenomes by the Joint Genome Institute (Jungbluth et al. 2013; Clum et al. 2021). Four MAGs from 2011 sampling were produced previously (Jungbluth et al. 2016; Jungbluth et al. 2017). Single cell amplified genomes (SAGs) from 2011 sampling were created as previously described from Holes U1362A and U1362B (Jungbluth et al. 2016; Carr et al. 2019). </span><span style="background-color:transparent; color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">This study </span><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">examines ten of these 2011 SAGs from U1362B (IDs with AC-334- and AC-335-) and two SAGs from U1362A (AC-708-). One new SAG was generated from the 2019 Hole U1362B fluid sampling (AH-873) following the same cell sorting, lysis, amplification, sequencing, and assembly approach as described elsewhere (Carr et al. 2019), and based on the standard workflow of the Single Cell Genomics Center at Bigelow Laboratory for Ocean Sciences (East Boothbay, Maine, USA; Stepanauskas et al. 2017). Nine SAGs within the </span><em>Aminicenantia</em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt"> order JdFR-78 are nearly identical (average pairwise nucleotide identity, ANI, &gt;99%), prompting the generation of a nearly complete composite genome assembly from these SAGs named JDF1.</span></p>
<p dir="ltr">&nbsp;</p>
<p dir="ltr"><strong>Genome annotation and assessment of viral interactions:</strong><em> </em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">JdFR </span><em>Aminicenantia </em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">SAGs and MAGs were annotated with KOFAMSCAN using KEGG Orthology Hidden Markov Model (KO HMM) version 4.3, -mapper option using default settings (Kanehisa and Sato, 2020). Single KEGG Orthology IDs were reported for each open reading frame (ORF) that met default thresholds (Aramaki et al. 2020). Annotations were input into KEGGDecoder and KEGG Mapper - Reconstruct Pathway visualization tools (Kanehisa and Sato; Graham et al., 2018).</span></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737017 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1737017
onGoing
Beth N. Orcutt
Bigelow Laboratory for Ocean Sciences
207-315-2567 ext 312
60 Bigelow Drive PO Box 380
East Boothbay
Maine
04544
USA
borcutt@bigelow.org
pointOfContact
Anne Booker
Bigelow Laboratory for Ocean Sciences
abooker@bigelow.org
pointOfContact
Timothy D'Angelo
Bigelow Laboratory for Ocean Sciences
207-315-2567
60 Bigelow Drive
East Boothbay
ME
04544
USA
tdangelo@bigelow.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioProject
BioSample
Sample_name
Taxonomy_ID
Cruise
Location
IODP_borehole
Collection_date
Latitude
Longitude
Depth_bsf
Sample_type
Assembly_Accession
Assembly_Name
Assembly_Stats_Total_Sequence_Length
Assembly_Level
WGS_project_accession
ROV Jason II
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
sample identification
taxon
Cruise identfier
site
Site_ID
date
latitude
longitude
depth below seafloor
sample type
NCBI Genbank nucleotide accession
No BCO-DMO term
genetic material concentration
accession number
featureType
BCO-DMO Standard Parameters
ROV Jason
instrument
BCO-DMO Standard Instruments
AT18-07
AT42-11
service
Deployment Activity
Pacific North-West
Juan de Fuca Ridge flank CORKs, 47N/127W
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.
Microbial activity in the crustal deep biosphere
https://osprey.bco-dmo.org/project/700324
Microbial activity in the crustal deep biosphere
<p><em>NSF Award Abstract:</em><br />
The marine deep biosphere is the habitat for life existing under the sea floor. The zone has remarkably low energy sources creating a paradox of how life can persist there. Resolving this energy paradox is a grand challenge in deep biosphere research. The Juan de Fuca Ridge flank off the coast of Washington, USA, is an accessible, low energy environment making it an attractive location for addressing this challenge. A series of experiments will be conducted on the seafloor at the Juan de Fuca Ridge flank, using established subseafloor observatories that access the crustal deep biosphere, to provide the first direct in situ measurement of microbial activity in the crustal subsurface. This project will provide essential information about the ability of life to survive under conditions that we are not able to replicate in the laboratory, but that are increasingly important for understanding microbial community interaction in the environment. This information can then be used in models of global microbial activity for estimating the impact of this biosphere on elemental cycling, transforming our understanding of microbial processes within this vast subseafloor habitat. To communicate these discoveries to the public, the project will include a ship-to-shore outreach program during the cruise. In addition public lectures will be presented, and an interactive display of deep-sea video footage will be set up for the annual public Open House at the Bigelow Laboratory for Ocean Sciences in Maine. Diverse undergraduate students and a postdoctoral researcher will be recruited to participate in the research and public outreach activities.</p>
<p>This project proposes to leverage existing subsurface infrastructure on the eastern flank of the Juan de Fuca Ridge with advances in single-cell based molecular and geochemical approaches to make fundamental new discoveries about the activity of life in the deep crustal biosphere. During a two-week research cruise, the research team will incubate crustal fluids in situ and in the laboratory with labeled substrates for tracking single-cell activity, coupled with radioisotope tracer activity and potentiostat measurements, with the objective of determining in situ and potential rates of activity and cellular physiology. The research will also identify which metabolisms active microorganisms utilize under in situ and laboratory conditions, the rates of these processes, and the microorganisms involved. The results are expected to provide explicit hypothesis testing of microbial activity and in situ microbial growth rates from the crustal deep biosphere to transform understanding of microbial activity in the crustal deep biosphere and generate critical information about the ability of life to survive under low energy conditions.</p>
Slow Life in Crust
largerWorkCitation
project
eng; USA
oceans
Pacific North-West; Juan de Fuca Ridge flank CORKs, 47N/127W
2024-12-27
Juan de Fuca Ridge flank CORKs, 47N/127W
0
BCO-DMO catalogue of parameters from Single-cell amplified genomes (SAGs) of uncultivated Aminicenantia bacteria from the subseafloor of Juan de Fuca Ridge (JdFR) from deployments of R/V Atlantis AT18-07 and AT42-11 from 2011 and 2019
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/947207.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI (National Center for Biotechnology Information) BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/947208.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI (National Center for Biotechnology Information) BioSample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/947209.rdf
Name: Sample_name
Units: unitless
Description: <p>Name of genome sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/947210.rdf
Name: Taxonomy_ID
Units: unitless
Description: <p>Candidate taxonomic name assignment of genome data used by NCBI (National Center for Biotechnology Information)</p>
http://lod.bco-dmo.org/id/dataset-parameter/947211.rdf
Name: Cruise
Units: unitless
Description: <p>Name of research cruise</p>
http://lod.bco-dmo.org/id/dataset-parameter/947212.rdf
Name: Location
Units: unitless
Description: <p>Name of sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/947213.rdf
Name: IODP_borehole
Units: unitless
Description: <p>Name of IODP borehole</p>
http://lod.bco-dmo.org/id/dataset-parameter/947214.rdf
Name: Collection_date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/947215.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sample collection, South is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/947216.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sample collection, West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/947217.rdf
Name: Depth_bsf
Units: meters (m)
Description: <p>Depth below seafloor</p>
http://lod.bco-dmo.org/id/dataset-parameter/947218.rdf
Name: Sample_type
Units: unitless
Description: <p>Type of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/947219.rdf
Name: Assembly_Accession
Units: unitless
Description: <p>NCBI (National Center for Biotechnology Information) GenBank Assembly Accession Number</p>
http://lod.bco-dmo.org/id/dataset-parameter/947220.rdf
Name: Assembly_Name
Units: unitless
Description: <p>NCBI (National Center for Biotechnology Information) Assembly Accession Name</p>
http://lod.bco-dmo.org/id/dataset-parameter/947221.rdf
Name: Assembly_Stats_Total_Sequence_Length
Units: basepairs
Description: <p>DNA basepair length of assembly</p>
http://lod.bco-dmo.org/id/dataset-parameter/947222.rdf
Name: Assembly_Level
Units: unitless
Description: <p>NCBI (National Center for Biotechnology Information) assembly type</p>
http://lod.bco-dmo.org/id/dataset-parameter/947223.rdf
Name: WGS_project_accession
Units: unitless
Description: <p>NCBI (National Center for Biotechnology Information) WGS project accession number</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/933609/data/download
download
onLine
dataset
<p><strong>Sample collection:</strong><em> </em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">Borehole observatories accessing subseafloor crustal fluids were installed on the eastern flank of the JdFR in 2004 and 2010 during IODP Expeditions 301 and 327, respectively (Fisher et al. 2011; Fisher et al. 2005). These observatories penetrate ~ 240 m of sediment and ~110-290 m of underlying basement to enable crustal fluid collection from 8-190 m below the sediment-basement interface. Crustal fluids in this region are consistently 62-64°C, anoxic, and sulfate-replete (~18 mmol sulfate per kg water; Wheat et al. 2013). New crustal fluid sampling occurred in May 2019 during expedition AT42-11 on R/V </span><em>Atlantis</em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt"> with ROV </span><em>Jason II, </em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">both operated by Woods Hole Oceanographic Institution. Single cell genomic data was generated from cells collected from borehole observatory U1362B using established syringe sampling approaches (Carr et al. 2019; Wheat et al. 2011). Briefly, the top plug on the wellhead of U1362B was removed to freely vent crustal fluid from the top of the observatory (Fisher et al. 2011). After the borehole dead volume had been flushed, crustal fluid was collected using a sterilized syringe (Wheat et al. 2011). Once recovered, the fluid was distributed in a nitrogen-flushed glove bag into cryovials, amended with 5% glycerol and 1X-Tris-EDTA buffer (final concentrations), and immediately flash-frozen with liquid nitrogen before long term storage at -70°C . In addition to the new sample, we examined existing single cell genomic and metagenomic data generated from samples collected from borehole observatories in International Ocean Discovery Program (IODP) Holes U1301A, U1362A, and U1362B in 2011 (AT18-07) using methods described elsewhere (Carr et al. 2019; Jungbluth et al. 2016; Fisher et al. 2012; Jungbluth et al. 2017).</span><br />
&nbsp;</p>
<p dir="ltr"><strong>Genomic sequencing, assembly, and phylogenomic analysis:</strong><em> </em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">Nineteen JdFR </span><em>Aminicenantia</em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt"> metagenome assembled genomes (MAGs) and single-cell amplified genomes (SAGs) were identified across three independent sampling expeditions that occurred over a nine-year period. Two new metagenome assembled genomes (MAGs 3300037598_45, 3300037558_26) were sequenced, assembled, and binned from 2010 and 2011 metagenomes by the Joint Genome Institute (Jungbluth et al. 2013; Clum et al. 2021). Four MAGs from 2011 sampling were produced previously (Jungbluth et al. 2016; Jungbluth et al. 2017). Single cell amplified genomes (SAGs) from 2011 sampling were created as previously described from Holes U1362A and U1362B (Jungbluth et al. 2016; Carr et al. 2019). </span><span style="background-color:transparent; color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">This study </span><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">examines ten of these 2011 SAGs from U1362B (IDs with AC-334- and AC-335-) and two SAGs from U1362A (AC-708-). One new SAG was generated from the 2019 Hole U1362B fluid sampling (AH-873) following the same cell sorting, lysis, amplification, sequencing, and assembly approach as described elsewhere (Carr et al. 2019), and based on the standard workflow of the Single Cell Genomics Center at Bigelow Laboratory for Ocean Sciences (East Boothbay, Maine, USA; Stepanauskas et al. 2017). Nine SAGs within the </span><em>Aminicenantia</em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt"> order JdFR-78 are nearly identical (average pairwise nucleotide identity, ANI, &gt;99%), prompting the generation of a nearly complete composite genome assembly from these SAGs named JDF1.</span></p>
<p dir="ltr">&nbsp;</p>
<p dir="ltr"><strong>Genome annotation and assessment of viral interactions:</strong><em> </em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">JdFR </span><em>Aminicenantia </em><span style="color:rgb(0, 0, 0); font-family:arial,sans-serif; font-size:11pt">SAGs and MAGs were annotated with KOFAMSCAN using KEGG Orthology Hidden Markov Model (KO HMM) version 4.3, -mapper option using default settings (Kanehisa and Sato, 2020). Single KEGG Orthology IDs were reported for each open reading frame (ORF) that met default thresholds (Aramaki et al. 2020). Annotations were input into KEGGDecoder and KEGG Mapper - Reconstruct Pathway visualization tools (Kanehisa and Sato; Graham et al., 2018).</span></p>
Specified by the Principal Investigator(s)
<p><em>Genome annotation and assessment of viral interactions: </em>JdFR <em>Aminicenantia </em>SAGs and MAGs were annotated with KOFAMSCAN using KEGG Orthology Hidden Markov Model (KO HMM) version 4.3, -mapper option using default settings. Single KEGG Orthology IDs were reported for each open reading frame (ORF) that met default thresholds. Annotations were input into&nbsp;KEGGDecoder and KEGG Mapper - Reconstruct Pathway visualization tools.</p>
<p>&nbsp;</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
ROV Jason II
ROV Jason II
PI Supplied Instrument Name: ROV Jason II 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: AT18-07
AT18-07
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT18-07
Andrew Fisher
University of California-Santa Cruz
Cruise: AT42-11
AT42-11
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT42-11
Beth N. Orcutt
Bigelow Laboratory for Ocean Sciences
https://datadocs.bco-dmo.org/docs/302/Slow_Life_in_Crust/data_docs/AT42-11_CruiseReport_v3.pdf
Report describing AT42-11
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel