http://lod.bco-dmo.org/id/dataset/636566
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
2016-01-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
16S rRNA sequence data from venting fluids and microbial mats; collected on R/V Atlantis cruise AT18-08 at the Axial Seamount, Juan de Fuca Ridge in 2011
2016-01-27
publication
2016-01-27
revision
BCO-DMO Linked Data URI
2016-01-27
creation
http://lod.bco-dmo.org/id/dataset/636566
Julie Huber
Marine Biological Laboratory
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: Huber, J. (2016) 16S rRNA sequence data from venting fluids and microbial mats; collected on R/V Atlantis cruise AT18-08 at the Axial Seamount, Juan de Fuca Ridge in 2011. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 27 Jan 2016) Version Date 2016-01-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/636566 [access date]
16S rRNA sequence data from venting fluids and microbial mats at Axial Seamount, 2011. Dataset Description: <p>16S rRNA sequence data from venting fluids and microbial mats at Axial Seamount, 2011. Samples collected on the AT18-08 cruise.</p> Methods and Sampling: <p>Diffuse fluids were collected from newly discovered snowblower vents at Axial Seamount in late July 2011 with the ROV Jason II using the hydrothermal fluid and particle sampler (Butterfield et al., 2004). White and orange flocculent materials were collected on the subsequent University Of Washington Visions'&nbsp;11 cruise, in support of the Regional Scale Nodes component of the Ocean Observatories Initiative in August 2011. White flocculent material was collected from the orifice of the Subway snowblower vent on dives R1467 (White Floc 1) and R1472 (White Floc 2) and orange flocculent material was collected on the seafloor distal to Marker 33 during dive R1472 where it coated freshly deposited basalt. All of the fluid and floc samples analyzed in this study are from a small area in the south rift zone at the southeastern edge of Axial Caldera, with the exception of background seawater which was collected outside of the caldera.</p>
<p>Total genomic DNA was extracted from Sterivex filters as previously described (Sogin et al., 2006) with the minor modifications described by Akerman et al. (2013). Total genomic DNA was extracted from 20 to 30mg of wet flocculent material using a MoBio UltraClean® Soil DNA Isolation Kit. The V6 region of 16S rRNA genes were amplified in triplicate for each sample with previously reported primers designed for archaea and bacteria (Huber et al., 2007) that were modified to include indices and barcodes compatible with the Illumina HiSeq1000 platform rather than 454 Life Sciences Adapters (Eren et al., 2013). Triplicate PCR amplifications were pooled for each sample, cleaned with a Qiagen MinElute kit, and quanitified by PicoGreen assay on a Turner Biosystems spectrophotometer. Fifty nanograms of each cleaned amplicon library was then size selected with a 2% agarose PippinPrep cassette to produce a narrow range of fragment sizes from 200 to 300 bp for sequencing and cleaned again to remove agarose. All of the amplicon libraries included in this study were sequenced in the same run and on the same paired end lane, along with 60 other libraries. Equimolar amounts of pooled amplicon libraries and a metagenomic library were run in the same lane to avoid known difficulties of sequencing low complexity amplicon libraries with Illumina (Caporaso et al., 2012).</p>
<p>Related references:<br />
Meyer, J.L., Akerman, N.H., Proskurowski, G. and J.A. Huber. 2013. Microbiological characterization of post-eruption "snowblower" vents at Axial Seamount, Juan de Fuca Ridge. Frontiers in Microbiology. 4:153. doi:<a href="http://dx.doi.org/10.3389/fmicb.2013.00153" target="_blank">10.3389/fmicb.2013.00153</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0929167 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0929167
completed
Julie Huber
Marine Biological Laboratory
(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: 27 Jan 2016
Unknown
cruise_id
organism
env_biome
env_feature
geo_loc_name
sample_name
vent_name
sample_title
collection_date
depth
env_material
lat
lon
bioproject_accession
bioproject_link
biosample_number
biosample_link
Turner Biosystems spectrophotometer
theme
None, User defined
cruise_id
taxon
site description
sample identification
site
date
depth
latitude
longitude
accession number
featureType
BCO-DMO Standard Parameters
ROV Jason
Spectrophotometer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
AT18-08
service
Deployment Activity
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.
Function, activity, and adaptation of microbial communities in geochemically diverse subseafloor habitats
http://www.pmel.noaa.gov/vents/index.html
Function, activity, and adaptation of microbial communities in geochemically diverse subseafloor habitats
<p><strong>Collaborative Research: Function, activity, and adaptation of microbial communities in geochemically diverse subseafloor habitats</strong></p>
<p>
The integration of both laboratory and field-based chemical and microbiological measurements into a quantitative predictive framework is crucial to understanding the microbial ecology of marine systems. This project work will provide a quantitative assessment of the functional diversity, activity, and physiological adaptation of microbial communities in geochemically diverse subseafloor habitats. Results will guide development of models for linking biogeochemical processes with particular microbial communities at deep-sea hydrothermal vents, with implications for other marine habitats as well. The focus of the effort is at Axial Seamount, a well-studied, active, deep-sea hydrothermal seamount in the NE Pacific Ocean. Samples already collected from Axial, along with a field program in Year 2, will serve as the foundation for the three objectives, which are to:</p>
<p>1. Determine and quantify the functional diversity and activity (expression) of key subseafloor microbial lineages at Axial Seamount.</p>
<p>2. Determine physiological adaptations to the subseafloor habitat by quantifying the growth response of Axial Seamount isolates to in-situ geochemical parameters.</p>
<p>3. Develop a quantitative predictive framework for linking particular types of geochemical vent conditions with specific microbial functional groups and activities at Axial Seamount.</p>
<p>Specific outcomes of this project include the creation of a comprehensive quantitative microbiological and chemical dataset on diffuse and adjacent high-temperature vents within Axial Seamount. This database will include chemical measurements (gases, nutrients, metals, isotopes, and calculated Gibbs free energies) relevant to microbial metabolic processes that can be compared to microbiological data (abundance and activity of microbial lineages and functional genes, growth rates of subseafloor isolates at relevant environmental conditions) using statistical analysis to identify how specific microbial activity is linked to the geochemical environment. This project builds on previous studies of microbial population structure and geochemical measurements at Axial Seamount and addresses critical gaps in current knowledge and understanding that are impeding progress of modeling hydrothermal systems. Results will increase understanding of deep-sea hydrothermal ecosystems as well as provide new insights into controls on the distribution and activity of marine microbial communities throughout the world's oceans.</p>
<p>
<a href="http://data.bco-dmo.org/AXIAL/nemo10-cruise-report.pdf" target="_blank">NeMO10 TN253 Cruise Report</a></p>
AXIAL
largerWorkCitation
project
eng; USA
biota
oceans
Axial Seamount, Juan de Fuca Ridge
2016-01-27
NE Pacific Ocean, Juan de Fuca Ridge, Axial Seamount
0
BCO-DMO catalogue of parameters from 16S rRNA sequence data from venting fluids and microbial mats; collected on R/V Atlantis cruise AT18-08 at the Axial Seamount, Juan de Fuca Ridge in 2011
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/636584.rdf
Name: cruise_id
Units: dimensionless
Description: <p>Cruise identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636585.rdf
Name: organism
Units: dimensionless
Description: <p>Organism.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636586.rdf
Name: env_biome
Units: dimensionless
Description: <p>Biome.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636587.rdf
Name: env_feature
Units: dimensionless
Description: <p>Environmental feature.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636588.rdf
Name: geo_loc_name
Units: dimensionless
Description: <p>Geographic location name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636589.rdf
Name: sample_name
Units: dimensionless
Description: <p>Sample name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636590.rdf
Name: vent_name
Units: dimensionless
Description: <p>Vent name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636591.rdf
Name: sample_title
Units: dimensionless
Description: <p>Sample title.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636592.rdf
Name: collection_date
Units: YYYYmmdd
Description: <p>Year, month, and day of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636593.rdf
Name: depth
Units: meters (m)
Description: <p>Depth of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636594.rdf
Name: env_material
Units: dimensionless
Description: <p>Environmental material.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636595.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636596.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636597.rdf
Name: bioproject_accession
Units: dimensionless
Description: <p>NCBI BioProject accession number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636598.rdf
Name: bioproject_link
Units: dimensionless
Description: <p>Hyperlink to NCBI BioProject.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636599.rdf
Name: biosample_number
Units: dimensionless
Description: <p>NCBI BioSample number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636600.rdf
Name: biosample_link
Units: dimensionless
Description: <p>Hyperlink to NCBI BioSample.</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
2292
https://datadocs.bco-dmo.org/file/oAAmBENTrEmKPY/Snowblower_16SrRNA.csv
Snowblower_16SrRNA.csv
Primary data file for dataset ID 636566
download
https://osprey.bco-dmo.org/dataset/636566/data/download
download
onLine
dataset
<p>Diffuse fluids were collected from newly discovered snowblower vents at Axial Seamount in late July 2011 with the ROV Jason II using the hydrothermal fluid and particle sampler (Butterfield et al., 2004). White and orange flocculent materials were collected on the subsequent University Of Washington Visions'&nbsp;11 cruise, in support of the Regional Scale Nodes component of the Ocean Observatories Initiative in August 2011. White flocculent material was collected from the orifice of the Subway snowblower vent on dives R1467 (White Floc 1) and R1472 (White Floc 2) and orange flocculent material was collected on the seafloor distal to Marker 33 during dive R1472 where it coated freshly deposited basalt. All of the fluid and floc samples analyzed in this study are from a small area in the south rift zone at the southeastern edge of Axial Caldera, with the exception of background seawater which was collected outside of the caldera.</p>
<p>Total genomic DNA was extracted from Sterivex filters as previously described (Sogin et al., 2006) with the minor modifications described by Akerman et al. (2013). Total genomic DNA was extracted from 20 to 30mg of wet flocculent material using a MoBio UltraClean® Soil DNA Isolation Kit. The V6 region of 16S rRNA genes were amplified in triplicate for each sample with previously reported primers designed for archaea and bacteria (Huber et al., 2007) that were modified to include indices and barcodes compatible with the Illumina HiSeq1000 platform rather than 454 Life Sciences Adapters (Eren et al., 2013). Triplicate PCR amplifications were pooled for each sample, cleaned with a Qiagen MinElute kit, and quanitified by PicoGreen assay on a Turner Biosystems spectrophotometer. Fifty nanograms of each cleaned amplicon library was then size selected with a 2% agarose PippinPrep cassette to produce a narrow range of fragment sizes from 200 to 300 bp for sequencing and cleaned again to remove agarose. All of the amplicon libraries included in this study were sequenced in the same run and on the same paired end lane, along with 60 other libraries. Equimolar amounts of pooled amplicon libraries and a metagenomic library were run in the same lane to avoid known difficulties of sequencing low complexity amplicon libraries with Illumina (Caporaso et al., 2012).</p>
<p>Related references:<br />
Meyer, J.L., Akerman, N.H., Proskurowski, G. and J.A. Huber. 2013. Microbiological characterization of post-eruption "snowblower" vents at Axial Seamount, Juan de Fuca Ridge. Frontiers in Microbiology. 4:153. doi:<a href="http://dx.doi.org/10.3389/fmicb.2013.00153" target="_blank">10.3389/fmicb.2013.00153</a></p>
Specified by the Principal Investigator(s)
<p>Paired Illumina sequencing reads were quality filtered to remove any reads containing ambiguous nucleotides and only pairs with perfectly overlapping reads were used for further analysis. Quality-filtered reads are publicly available through the VAMPS database, <a href="http://vamps.mbl.edu" target="_blank">http://vamps.mbl.edu</a>,under the project name JAH_AXV_Bv6 and JAH_AXV_Av6, where orange floc is listed as "eruption mat",&nbsp;white floc 1 is listed as "snow_R1467",&nbsp;and white floc 2 is listed as "snow_R1472".&nbsp;Sequences were clustered at 97% similarity with a minimum word length of 30, using usearch (Edgar, 2010). Taxonomy was assigned by global alignment for sequence taxonomy (GAST; Huse et al., 2008) with the SILVA 111 database (Quast et al., 2012). Operational taxonomic units (OTUs) were then analyzed with Qiime 1.5 (Caporaso et al., 2010). Even sequencing depth per sample was established by multiple rarefactions to roughly 75% of the smallest sequencing depth, using a total of 195,000 bacterial reads and 145,000 archaeal reads per sample. To compare bacterial communities in snowblower fluids and flocculent samples to background seawater by dendrogram, we retrieved bacterial V6 454 reads from background seawater collected outside the Axial Caldera from the VAMPS database under the project name KCK_SMT_Bv6, fluid sample FS501. To compensate for the fewer number of reads in the background seawater sample, a second set of multiple rarefactions was performed with 7112 reads per sample. Distance matrices were calculated for 10 rarefactions using the Morisita-Horn index (Horn, 1966) and the resulting tree topographies were clustered using UPGMA to create a final jackknifed tree.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- modified parameter names to conform with BCO-DMO naming conventions;<br />
- removed "m" (meters) in depth column;<br />
- changed format of date to YYYYmmdd;<br />
- replaced commas with semi-colons;<br />
- Added cruise_id field.</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
PI Supplied Instrument Name: 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/
Turner Biosystems spectrophotometer
Turner Biosystems spectrophotometer
PI Supplied Instrument Name: Turner Biosystems spectrophotometer Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
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: AT18-08
AT18-08
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT18-08
William Chadwick
National Oceanic and Atmospheric Administration
http://dmoserv3.whoi.edu/data_docs/C-DEBI/cruise_reports/AT18-08_nemo11-cruise-report.pdf
Report describing AT18-08
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel