http://lod.bco-dmo.org/id/dataset/636098
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
2016-01-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbial cell abundance and carbon, nitrogen, and sulfur content from venting fluids and microbial mats at Axial Seamount; from R/V Atlantis cruise AT18-08 in the Axial Seamount, Juan de Fuca Ridge in 2011
2016-01-21
publication
2016-01-21
revision
BCO-DMO Linked Data URI
2016-01-21
creation
http://lod.bco-dmo.org/id/dataset/636098
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) Microbial cell abundance and carbon, nitrogen, and sulfur content from venting fluids and microbial mats at Axial Seamount; from R/V Atlantis cruise AT18-08 in the Axial Seamount, Juan de Fuca Ridge in 2011. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 21 Jan 2016) Version Date 2016-01-21 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/636098 [access date]
Microbial cell abundance and carbon, nitrogen, and sulfur content from venting fluids and microbial mats at Axial Seamount, 2011. Dataset Description: <p>Microbial cell abundance and carbon, nitrogen, and sulfur content from venting fluids and microbial mats at Axial Seamount, 2011. Samples collected on cruise&nbsp;AT18-08.</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&nbsp;et al., 2004). White and orange flocculent materials were collected on the subsequent University of Washington Visions' 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>Subsamples of flocculent material were viewed under phase contrast, fixed and stained with DAPI for cell counting via epiflourescent microscopy, or fixed for scanning electron microscopy (SEM) with elemental detection system (EDS) on a Zeiss Supra 40VP. White and orange flocs were fixed with 2.5% glutaldehyde for both cell counts and SEM. Preserved whole fluids were also stained with DAPI for cell counts.</p>
<p>Bulk carbon and nitrogen were measured using a Thermo Scientific CN Analyzer (Model Flash 2000) from subsamples of flocculent material dried at 50–60 degrees&nbsp;C for 2 days. A standard curve for bulk carbon and nitrogen was made using aspartic acid as a standard and acetanilide and apple leaf as standard curve checks. Bulk sulfur was measured using a LECO S632 Sulfur Analyzer from subsamples of flocculent material dried in a dessicator for 4 days and supplemented with sterile sea sand (Fisher) to meet minimum volume requirements. A standard curve for bulk sulfur was made using coal with known sulfur content provided by LECO.</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: 21 Jan 2016
Unknown
cruise_id
geo_loc_name
env_feature
env_biome
organism
sample_name
lat
lon
collection_date
depth
vent_name
sample_title
env_material
cell_count
conf_level_95pcnt
pcnt_C
pcnt_N
pcnt_S
Zeiss Supra 40VP
Thermo Scientific CN Analyzer
LECO S632 Sulfur Analyzer
ROV Jason II
theme
None, User defined
Cruise identfier
No BCO-DMO term
latitude
longitude
depth
featureType
BCO-DMO Standard Parameters
Electron Microscope
Elemental Analyzer
Elemental Analyzer
ROV Jason
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
2016-01-21
NE Pacific Ocean, Juan de Fuca Ridge, Axial Seamount
0
BCO-DMO catalogue of parameters from Microbial cell abundance and carbon, nitrogen, and sulfur content from venting fluids and microbial mats at Axial Seamount; from R/V Atlantis cruise AT18-08 in 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/636103.rdf
Name: cruise_id
Units: dimensionless
Description: <p>Crusie identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636104.rdf
Name: geo_loc_name
Units: dimensionless
Description: <p>Geographic location name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636105.rdf
Name: env_feature
Units: dimensionless
Description: <p>Environmental feature.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636106.rdf
Name: env_biome
Units: dimensionless
Description: <p>Biome.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636107.rdf
Name: organism
Units: dimensionless
Description: <p>Organism.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636108.rdf
Name: sample_name
Units: dimensionless
Description: <p>Sample name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636109.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636110.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636111.rdf
Name: collection_date
Units: YYYYmmdd
Description: <p>Year, month, and day of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636112.rdf
Name: depth
Units: meters (m)
Description: <p>Depth of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636113.rdf
Name: vent_name
Units: dimensionless
Description: <p>Vent name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636114.rdf
Name: sample_title
Units: dimensionless
Description: <p>Sample title.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636115.rdf
Name: env_material
Units: dimensionless
Description: <p>Material.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636116.rdf
Name: cell_count
Units: cells/g or cells/mL
Description: <p>Cell count: Cells per gram of wet floc or cells per milliliter of fluid.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636117.rdf
Name: conf_level_95pcnt
Units: cells/g or cells/mL
Description: <p>95% confidence level for cell_count.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636118.rdf
Name: pcnt_C
Units: percentage (%)
Description: <p>Percent Carbon.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636119.rdf
Name: pcnt_N
Units: percentage (%)
Description: <p>Percent Nitrogen.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636120.rdf
Name: pcnt_S
Units: percentage (%)
Description: <p>Percent Sulfur.</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
1291
https://datadocs.bco-dmo.org/file/wnnxNPohGVqMx5/Snowblower_CellCounts.csv
Snowblower_CellCounts.csv
Primary data file for dataset ID 636098
download
https://osprey.bco-dmo.org/dataset/636098/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&nbsp;et al., 2004). White and orange flocculent materials were collected on the subsequent University of Washington Visions' 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>Subsamples of flocculent material were viewed under phase contrast, fixed and stained with DAPI for cell counting via epiflourescent microscopy, or fixed for scanning electron microscopy (SEM) with elemental detection system (EDS) on a Zeiss Supra 40VP. White and orange flocs were fixed with 2.5% glutaldehyde for both cell counts and SEM. Preserved whole fluids were also stained with DAPI for cell counts.</p>
<p>Bulk carbon and nitrogen were measured using a Thermo Scientific CN Analyzer (Model Flash 2000) from subsamples of flocculent material dried at 50–60 degrees&nbsp;C for 2 days. A standard curve for bulk carbon and nitrogen was made using aspartic acid as a standard and acetanilide and apple leaf as standard curve checks. Bulk sulfur was measured using a LECO S632 Sulfur Analyzer from subsamples of flocculent material dried in a dessicator for 4 days and supplemented with sterile sea sand (Fisher) to meet minimum volume requirements. A standard curve for bulk sulfur was made using coal with known sulfur content provided by LECO.</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>Two subsamples were analyzed for each floc sample and replicate readings were averaged for all bulk C, N, and S measurements. ± 95% confidence levels for total cell counts are reported.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- modified parameter names to conform with BCO-DMO naming conventions;<br />
- replaced "no data" with "nd";<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
Zeiss Supra 40VP
Zeiss Supra 40VP
PI Supplied Instrument Name: Zeiss Supra 40VP PI Supplied Instrument Description:Subsamples of flocculent material were viewed under phase contrast, fixed and stained with DAPI for cell counting via epiflourescent microscopy, or fixed for scanning electron microscopy (SEM) with elemental detection system (EDS) on a Zeiss Supra 40VP. Instrument Name: Electron Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of electrons behaving as waves. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB07/
Thermo Scientific CN Analyzer
Thermo Scientific CN Analyzer
PI Supplied Instrument Name: Thermo Scientific CN Analyzer PI Supplied Instrument Description:Bulk carbon and nitrogen were measured using a Thermo Scientific CN Analyzer (Model Flash 2000). Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/
LECO S632 Sulfur Analyzer
LECO S632 Sulfur Analyzer
PI Supplied Instrument Name: LECO S632 Sulfur Analyzer PI Supplied Instrument Description:Bulk sulfur was measured using a LECO S632 Sulfur Analyzer. Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/
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: AT18-08
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