http://lod.bco-dmo.org/id/dataset/626572
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
2015-11-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Station data and nutrient profiles for analysis of microbial communities from R/V Thomas G. Thompson TN268 in the North Pacific from August to September 2011 (Sulfur Oxidizers project)
2015-11-17
publication
2015-11-17
revision
BCO-DMO Linked Data URI
2015-11-17
creation
http://lod.bco-dmo.org/id/dataset/626572
Robert Morris
University of Washington
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: Morris, R. (2015) Station data and nutrient profiles for analysis of microbial communities from R/V Thomas G. Thompson TN268 in the North Pacific from August to September 2011 (Sulfur Oxidizers project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version working) Version Date 2015-11-17 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/626572 [access date]
sample station data for analysis of microbial communities Dataset Description: <p>Coordinates of sample locations, depths and analyses conducted during the biogeochemical hot spot study.</p>
<p>These data are reported and discussed in <a href="http://dmoserv3.bco-dmo.org/data_docs/SulfurOxidizers/Mattes_2013_PlumeProt.pdf" target="_blank">Mattes et al., 2013</a>.</p> Methods and Sampling: <p>All samples were collected onboard the R/V Thomas G. Thompson during a University of Washington led research cruise in support of the National Science Foundation’s Ocean Observatory Initiative-Regional Scale Nodes cruise (August 19 – September 1, 2011) from Seattle, WA to Hydrate Ridge and Axial Seamount (Figure 1). Water samples for microbial and chemical analyses were collected using a Conductivity, Temperature, and Depth (CTD) rosette profiler equipped with 12 L Niskin bottles. Samples were collected from 5 different stations (CTD7 Cascadia Basin (lat: 45.8602/lon:-127.9353), CTD8 base of Axial Seamount (lat:45.8202/lon:-129.7567), CTD11 ASHES vent field (lat:45.9339/lon:-130.0136), CTD13 Coquille vent (lat:45.9264/lon:-129.9803), and CTD 17 ASHES vent field (lat: 45.9340/lon:-130.0138)).</p>
<p>Contextual data and site description</p>
<p>Partial and full water column profile measurements were conducted using a rosette-mounted instrument package that included a Seabird 9plus CTD with dual temperature and conductivity sensors, a Seabird 43 oxygen sensor (calibrated to onboard Winkler titrations), and a WET Labs C-Star transmissometer. Using the down-cast profile measurements, the position and extent of the hydrothermal plume was identified by large negative deflections in beam transmission (corresponding to the high particulate load generated from precipitating metal sulfides in the hydrothermal fluid), and subtle positive anomalies in temperature (corresponding to the heat input from high-temperature fluids), following well established plume identification practices (Baker et al 1993). At the summit of Axial seamount, hydrothermal plumes were 30-100 meters thick, with the neutrally buoyant plume having a typical rise height of 75-200 meters above the seafloor.</p>
<p>During the profile up-cast, 12 L Niskin water sampling bottles (General Oceanics) were triggered at depths determined to be within the hydrothermal plume, and at regular intervals in the water column above the plume. Water samples were analyzed for methane (CH4) and hydrogen (H2) concentrations using shipboard gas chromatography. Samples were headspace extracted and inlet into a gas chromatograph (SRI Instruments) configured with a helium carrier, a 30 meter 5Å mol sieve column, a 50°C isothermal temperature program, and flame ionization (FID) and pulse discharge (PDD) detectors. This method provided the sensitivity to measure the low gas concentrations of background seawater (CH4 0.5-1 nM, H2 0.1-0.5 nM). Hydrothermal fluids are enriched in both CH4 and H2 (Lilley et al 1982, Proskurowski et al 2008).</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1232840 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1232840
completed
Robert Morris
University of Washington
206-221-7228
School of Oceanography Box 357940
Seattle
WA
98195-7940
USA
morrisrm@uw.edu
pointOfContact
asNeeded
Dataset Version: working
Unknown
ctd_station
site
lat
lon
depth
sample_no
PO4
SiOH_4
NO3
NO2
NH4
DON
DOC
T_RFLP
clone_library
proteomics
CTD Seabird 911+
Seabird 43 Oxygen Sensor
Wet Labs C-Star transmissometer
theme
None, User defined
station
site
latitude
longitude
depth
sample identification
reactive phosphorus (PO4)
Silicate, Si(OH)4, silicic acid
Nitrate
Nitrite
Ammonium
Dissolved Organic Nitrogen
dissolved organic Carbon
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird 911
Sea-Bird SBE 43 Dissolved Oxygen Sensor
WET Labs {Sea-Bird WETLabs} C-Star transmissometer
instrument
BCO-DMO Standard Instruments
TN268
service
Deployment Activity
North Pacific
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.
Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade
http://morrislab.ocean.washington.edu/
Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade
<p><em>Description from NSF award abstract:</em><br />
The ocean serves an immense reservoir of carbon, nitrogen, phosphorus, sulfur, and other elements required for all life. The active and diverse microbial populations that inhabit the oceans are responsible for mediating nutrient transformations that maintain the chemistry of seawater. A recent study identified a ubiquitous group of marine bacteria from the Arctic96BD-19 gamma-proteobacterial sulfur oxidizer (GSO) lineage that is closely related to known sulfur oxidizing species that fix inorganic carbon and oxidize sulfide in low-oxygen waters. The potential for GSOs to use reduced forms of sulfur in oxygenated waters suggests that they are a keystone species that link the marine carbon and sulfur cycles. The only known isolates from the Arctic96BD-19 lineage of GSOs are now in culture, allowing fundamental questions about their roles in carbon and sulfur cycling to be investigated. Preliminary data suggest that they use energy from the oxidation of sulfur to assimilate carbon. This project seek to address the overarching hypothesis that sulfur transformations provide the Arctic96BD- 19 lineage of GSOs with energy for organic and inorganic carbon cycling throughout the water column.</p>
<p>Three specific hypotheses will be tested.<br />
1. Arctic96BD-19 cells assimilate either organic carbon or fixes inorganic carbon, depending on environmental conditions.<br />
2. Arctic96BD-19 cells oxidize thiosulfate via formation of a tetrathionate intermediate, or using the branched thiosulfate oxidation pathway.<br />
3. Arctic96BD-19 cells are ubiquitous sulfur oxidizers that assimilate organic and inorganic carbon through the Pacific Northwest.</p>
<p>A combination of laboratory growth studies of the investigator's pure cultures and comparative genomic analyses will be used. The genomic data will be used to determine whether the Arctic96BD-19 cultures possess the genetic potential to oxidize reduced sulfur to sulfate (based on possession of known core and ancillary sulfur oxidation genes), which potential oxidation pathways are used, and whether they can fix inorganic carbon. These data will help guide the physiology studies by determining the most likely forms of inorganic and organic compounds that can be utilized.</p>
<p>Marine bacteria are critical players in global nutrient cycles, but many of their individual and community functions in the ecosystem are not well understood. Future oceanographers will need to use cultivation-dependent and cultivation-independent methods to identify metabolic process that shape microbial communities and impact biogeochemical cycles. Student education, scientific advancement, and public awareness are all important components of this project.</p>
Sulfur Oxidizers
largerWorkCitation
project
eng; USA
biota
oceans
North Pacific
2015-11-17
North Pacific Ocean
0
BCO-DMO catalogue of parameters from Station data and nutrient profiles for analysis of microbial communities from R/V Thomas G. Thompson TN268 in the North Pacific from August to September 2011 (Sulfur Oxidizers 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/628925.rdf
Name: ctd_station
Units: number
Description: <p>station number where CTD was deployed</p>
http://lod.bco-dmo.org/id/dataset-parameter/628926.rdf
Name: site
Units: text
Description: <p>descriptive term of sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/628927.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/628928.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude; West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/628929.rdf
Name: depth
Units: meters
Description: <p>Sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/628930.rdf
Name: sample_no
Units: number
Description: <p>sequential sampling identification number</p>
http://lod.bco-dmo.org/id/dataset-parameter/628931.rdf
Name: PO4
Units: micromoles per kilogram
Description: <p>nutrient phosphate</p>
http://lod.bco-dmo.org/id/dataset-parameter/628932.rdf
Name: SiOH_4
Units: micromoles per kilogram
Description: <p>silicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/628933.rdf
Name: NO3
Units: micromoles per kilogram
Description: <p>nitrate</p>
http://lod.bco-dmo.org/id/dataset-parameter/628934.rdf
Name: NO2
Units: micromoles per kilogram
Description: <p>nitrite</p>
http://lod.bco-dmo.org/id/dataset-parameter/628935.rdf
Name: NH4
Units: micromoles per kilogram
Description: <p>ammonium</p>
http://lod.bco-dmo.org/id/dataset-parameter/628936.rdf
Name: DON
Units: micromoles per kilogram
Description: <p>Dissolved Organic Nitrogen; here the difference between Total Dissolved Nitrogen (TDN) and Dissolved Inorganic Nitrogen (DIN)</p>
http://lod.bco-dmo.org/id/dataset-parameter/628937.rdf
Name: DOC
Units: micromoles C per kilogram
Description: <p>Dissolved Organic Carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/628938.rdf
Name: T_RFLP
Units: text
Description: <p>terminal restriction fragment length polymorphism assessment done if 'X' is present</p>
http://lod.bco-dmo.org/id/dataset-parameter/628939.rdf
Name: clone_library
Units: text
Description: <p>16S rRNA gene clone library assessment done if 'X' is present</p>
http://lod.bco-dmo.org/id/dataset-parameter/628940.rdf
Name: proteomics
Units: text
Description: <p>an 'X' indicated that samples were used for proteomics work</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
4763
https://datadocs.bco-dmo.org/file/VJJWD12hPKm9ZP/nutrients.csv
nutrients.csv
Primary data file for dataset ID 626572
download
https://osprey.bco-dmo.org/dataset/626572/data/download
download
onLine
dataset
<p>All samples were collected onboard the R/V Thomas G. Thompson during a University of Washington led research cruise in support of the National Science Foundation’s Ocean Observatory Initiative-Regional Scale Nodes cruise (August 19 – September 1, 2011) from Seattle, WA to Hydrate Ridge and Axial Seamount (Figure 1). Water samples for microbial and chemical analyses were collected using a Conductivity, Temperature, and Depth (CTD) rosette profiler equipped with 12 L Niskin bottles. Samples were collected from 5 different stations (CTD7 Cascadia Basin (lat: 45.8602/lon:-127.9353), CTD8 base of Axial Seamount (lat:45.8202/lon:-129.7567), CTD11 ASHES vent field (lat:45.9339/lon:-130.0136), CTD13 Coquille vent (lat:45.9264/lon:-129.9803), and CTD 17 ASHES vent field (lat: 45.9340/lon:-130.0138)).</p>
<p>Contextual data and site description</p>
<p>Partial and full water column profile measurements were conducted using a rosette-mounted instrument package that included a Seabird 9plus CTD with dual temperature and conductivity sensors, a Seabird 43 oxygen sensor (calibrated to onboard Winkler titrations), and a WET Labs C-Star transmissometer. Using the down-cast profile measurements, the position and extent of the hydrothermal plume was identified by large negative deflections in beam transmission (corresponding to the high particulate load generated from precipitating metal sulfides in the hydrothermal fluid), and subtle positive anomalies in temperature (corresponding to the heat input from high-temperature fluids), following well established plume identification practices (Baker et al 1993). At the summit of Axial seamount, hydrothermal plumes were 30-100 meters thick, with the neutrally buoyant plume having a typical rise height of 75-200 meters above the seafloor.</p>
<p>During the profile up-cast, 12 L Niskin water sampling bottles (General Oceanics) were triggered at depths determined to be within the hydrothermal plume, and at regular intervals in the water column above the plume. Water samples were analyzed for methane (CH4) and hydrogen (H2) concentrations using shipboard gas chromatography. Samples were headspace extracted and inlet into a gas chromatograph (SRI Instruments) configured with a helium carrier, a 30 meter 5Å mol sieve column, a 50°C isothermal temperature program, and flame ionization (FID) and pulse discharge (PDD) detectors. This method provided the sensitivity to measure the low gas concentrations of background seawater (CH4 0.5-1 nM, H2 0.1-0.5 nM). Hydrothermal fluids are enriched in both CH4 and H2 (Lilley et al 1982, Proskurowski et al 2008).</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Samples for nutrients, DOC and TDN analyses were stored frozen in 60 mL HDPE bottles until analysis within 2 months of the completion of the cruise. Nutrient concentrations were assessed by follow the protocols of the WOCE Hydrographic Program using a Technicon AAII system at the University of Washington. DOC and TDN concentrations were assessed by high temperature combustion using a Shimadzu TOC-csh with auto injection (Dickson et al 2007). Four point standard curves using KHP and KNO3 were run daily to calibrate the response of the high temperature combustion system. Measurements were quality controlled using Consensus Reference Materials (CRM’s) distributed to the international community by the Hansell laboratory (Hansell 2005). The CRMs were analyzed at regular intervals during each analytical day. Low C reference water was employed to determine system blanks. DON was determined as the difference in concentrations of TDN and DIN. (See <a href="http://dmoserv3.bco-dmo.org/data_docs/SulfurOxidizers/SupplementalFigureOneMorris.pdf" target="_blank">Supplementary Figure One (pdf)</a>)</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
CTD Seabird 911+
CTD Seabird 911+
PI Supplied Instrument Name: CTD Seabird 911+ PI Supplied Instrument Description:Partial and full water column profile measurements were conducted using a rosette-mounted instrument package that included a Seabird 9plus CTD with dual temperature and conductivity sensors Instrument Name: CTD Sea-Bird 911 Instrument Short Name:CTD SBE 911 Instrument Description: The Sea-Bird SBE 911 is a type of CTD instrument package. The SBE 911 includes the SBE 9 Underwater Unit and the SBE 11 Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). More information from Sea-Bird Electronics. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0035/
Seabird 43 Oxygen Sensor
Seabird 43 Oxygen Sensor
PI Supplied Instrument Name: Seabird 43 Oxygen Sensor PI Supplied Instrument Description:Seabird 43 oxygen sensor (calibrated to onboard Winkler titrations) Instrument Name: Sea-Bird SBE 43 Dissolved Oxygen Sensor Instrument Short Name:SBE-43 DO Instrument Description: The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0036/
Wet Labs C-Star transmissometer
Wet Labs C-Star transmissometer
PI Supplied Instrument Name: Wet Labs C-Star transmissometer Instrument Name: WET Labs {Sea-Bird WETLabs} C-Star transmissometer Instrument Short Name:WL CSTAR Trans Instrument Description: The C-Star transmissometer has a novel monolithic housing with a highly intgrated opto-electronic design to provide a low cost, compact solution for underwater measurements of beam transmittance. The C-Star is capable of free space measurements or flow-through sampling when used with a pump and optical flow tubes. The sensor can be used in profiling, moored, or underway applications. Available with a 6000 m depth rating.
More information on Sea-Bird website: https://www.seabird.com/c-star-transmissometer/product?id=60762467717 Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0160/
Cruise: TN268
TN268
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN268
Dr John R. Delaney
University of Washington
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel