http://lod.bco-dmo.org/id/dataset/664280
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
2016-11-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Most probable number of various thermophiles, and total CH4 produced in microcosms from hydrothermal sampling sites from 5 cruises to the Axial Seamount, Juan de Fuca Ridge from 2012 to 2015 (NeMO2015 project)
2016-11-08
publication
2016-11-08
revision
BCO-DMO Linked Data URI
2016-11-08
creation
http://lod.bco-dmo.org/id/dataset/664280
James Holden
University of Massachusetts Amherst
principalInvestigator
David A. Butterfield
National Oceanic and Atmospheric Administration
principalInvestigator
William Chadwick
Oregon State University
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: Holden, J., Chadwick, W., Butterfield, D. A. (2016) Most probable number of various thermophiles, and total CH4 produced in microcosms from hydrothermal sampling sites from 5 cruises to the Axial Seamount, Juan de Fuca Ridge from 2012 to 2015 (NeMO2015 project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-11-08 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/664280 [access date]
Abundances of various thermophiles, and total CH4 produced in microcosms Dataset Description: <p>This dataset includes Most-Probable Number (MPN, L-1) estimates of heterotrophs, H2-producing heterotrophs, methanogens, and non-methanogenic hydrogenotrophs that grow at 55 C and 80 C.</p>
<p><strong>Relevant Reference:</strong> Topcuoglu, BD, Stewart LC, Morrison HG, Butterfield DA, Huber JA and Holden JF (2016) Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents. Front. Microbiol. 7:1240. doi: <a href="http://journal.frontiersin.org/article/10.3389/fmicb.2016.01240/full" target="_blank">10.3389/fmicb.2016.01240</a></p>
<p><strong>Related Datasets:</strong><br />
<a href="http://www.bco-dmo.org/dataset/664201">Axial Seamount hydrothermal sampling sites</a><br />
<a href="http://www.bco-dmo.org/dataset/664306">Thermophile growth</a></p> Methods and Sampling: <p>In August 2012, September and October 2013, August 2014, and August 2015, 7-40°C diffuse hydrothermal fluids were collected from 10 vent sites at 1515-1716 m depths from Axial Seamount on the Juan de Fuca Ridge. The fluid samples were drawn into 650 ml Tedlar plastic bags with polyethylene valves within rigid housings using the NOAA Hydrothermal Fluid and Particle Sampler. The sampler pumped vent fluid through a titanium nozzle and recorded the temperature of the fluid within the intake nozzle once every second during pumping. Samples were collected using the research submarines Jason II and ROPOS. Background seawater was collected by shipboard hydrocasts at 1500 m depth directly over the caldera (25 m above the bottom) and 3 km west of the summit with 10 L Niskin bottles. The hydrothermal fluid and background seawater samples were divided for cultivation-dependent Most Probable Number (MPN) concentration estimates of thermophiles and hyperthermophiles (100 ml), microcosm incubations (400 ml), and total cell counts (40 ml). All operations at sea occurred on the research vessels Marcus G. Langseth, Thomas G. Thompson, Falkor, and Ronald H. Brown.</p>
<p><strong>Most Probable Number (MPN) Cell Estimates:</strong>&nbsp;Three-tube MPN analyses were used by adding 3.3, 0.33, and 0.03 ml of the hydrothermal fluid samples in triplicate to the methanogen, autotrophic sulfur reducer, and heterotroph media. After inoculation, the tubes were incubated at 80°C and 55°C for up to 7 days. Growth in the tubes was confirmed using phase-contrast light microscopy. Growth of methanogens and H2-producing heterotrophs was verified by analyzing all of the tubes for CH4 and H2, respectively, in the headspace using gas chromatography. Total and H2-producing heterotroph cell concentration estimates were scored and reported separately based on tubes that had cells versus those with H2. In order to estimate the concentration of non-methanogenic autotrophs in the autotrophic sulfur medium, the estimated number of methanogens in the autotrophic sulfur medium MPN tubes was subtracted from the estimated concentration of total cells.</p>
<p><a href="http://dmoserv3.bco-dmo.org/data_docs/NeMO2015/NeMO2015_methods.pdf" target="_blank">Full methodology</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1547004 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1547004
completed
James Holden
University of Massachusetts Amherst
413-577-1742
Department of Microbiology 639 N. Pleasant St.
Amherst
MA
010039242
USA
jholden@microbio.umass.edu
pointOfContact
David A. Butterfield
National Oceanic and Atmospheric Administration
206-526-6722
1045 PMEL, Bldg 3 7600 Sand Point Way NE
Seattle
WA
98115
USA
david.a.butterfield@noaa.gov
pointOfContact
William Chadwick
Oregon State University
(541) 867-0179
Hatfield Marine Science Center 2115 S.E. OSU Dr.
Newport
OR
97365
USA
pointOfContact
asNeeded
Unknown
temp
year
site
organism
MPN_L
lat
lon
phase-contrast light microscope
theme
None, User defined
water temperature at measurement depth
year
site
taxon
cell_concentration
latitude
longitude
featureType
BCO-DMO Standard Parameters
Microscope - Optical
instrument
BCO-DMO Standard Instruments
TN327
TN300
FK010
MGL1216
RB1403
service
Deployment Activity
Axial Seamount, Juan de Fuca Ridge
Axial Seamount, Juan de Fuca Ridge, Northeast 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.
Ocean Observatories Initiative
http://oceanobservatories.org/
Ocean Observatories Initiative
The Ocean Observatories Initiative (OOI) is a science-driven ocean observing network that delivers real-time data to address critical science questions regarding the world's oceans. Funded by the National Science Foundation to encourage scientific investigation, OOI data are freely available online to anyone with an Internet connection. OOI was designed as a long-term project to collect ocean data for up to 30 years. This longevity makes it possible to measure and directly observe both short-lived episodic events and longer-term changes occurring in the ocean. Such data make it possible to better understand ocean processes and how the ocean is changing.
The OOI has five active research arrays that comprise the three major observatory elements linked together by instrument, infrastructure, and information management systems. Global Ocean Arrays consist of moored arrays and autonomous vehicles that provide time-series observations and mesoscale spatial sampling at sparsely sampled, high-latitude regions critical to our understanding of climate, the carbon cycle, and ocean circulation. The Regional Cabled Array consists of fiber-optic cables off the Oregon coast that provide unprecedented power, bandwidth, and communication to seafloor instrumentation and profiler moorings, enabling monitoring of volcanic and hydrothermal activity, methane seeps, earthquakes, and myriad ocean processes in coastal and blue water environments. Coastal Arrays consist of cross-shelf moored arrays and autonomous vehicles that observe the dynamic coastal environment, enabling examination of upwelling, shelf break fronts, and cross-shelf exchanges.
These marine arrays are outfitted with more than 900 instruments — of 45 different types — measuring more than 200 different parameters. These instruments gather physical, chemical, geological, and biological data – from the air-sea interface to the seafloor. The data collected are transmitted through a cyberinfrastructure, an information management system that allows users to access real- to near real-time data from suites of sensors. The OOI provides annotations and automated quality control for data streams and is working to meet the IOOS Quality Assurance of Real Time Ocean Data (QARTOD) standards.
OOI
largerWorkCitation
program
Event response to an eruption at Axial Seamount
http://axial2015.blogspot.com
Event response to an eruption at Axial Seamount
<p>On 24 April 2015, the NSF-funded Ocean Observatories Initiative's (OOI) Cabled Array detected the onset of a probable eruption at Axial Seamount, heralded by a swarm of >8000 small earthquakes and a rapid subsidence of the seafloor by >2.4 meters at the center of the caldera. Evidence that lava was erupted in or near the summit caldera includes a dramatic temperature rise recorded by instruments on the OOI Cabled Array-- up to 0.6-0.7°C above ambient sustained for weeks after the event. This eruption is likely to have significantly perturbed the hydrothermal and biological systems in and around the summit caldera, and provides the rare opportunity to address time-critical scientific questions that can only be investigated with the near-term seafloor investigations. A currently scheduled NSF and NOAA funded cruise to Axial Seamount on R/V Thompson with ROV Jason and AUV Sentry in August 2015 provides an excellent opportunity for such a response. This study adds 3 days onto this cruise to facilitate time-critical event response science.</p>
<p>Detailed seafloor mapping with shipboard multi-beam sonar and near-bottom Sentry surveys will cover areas of the caldera and adjacent rift zones that are expected eruption site(s). Fresh rock, if located, will be sampled and dated using the 210Po-210Pb technique. Hydrothermal plumes will be discerned with CTD casts and sensor tows. A mooring will be deployed with Miniature Autonomous Plume Recorders to measure temperature, light attenuation, and redox potential. The at-sea team plans to make samples and data available to the broader science community for targeted research on seafloor processes.</p>
NeMO2015
largerWorkCitation
project
eng; USA
oceans
Axial Seamount, Juan de Fuca Ridge; Axial Seamount, Juan de Fuca Ridge, Northeast Pacific
2016-11-08
Axial Seamount, Juan de Fuca Ridge, northeastern Pacific Ocean (46.06°N 130.00°W)
0
BCO-DMO catalogue of parameters from Most probable number of various thermophiles, and total CH4 produced in microcosms from hydrothermal sampling sites from 5 cruises to the Axial Seamount, Juan de Fuca Ridge from 2012 to 2015 (NeMO2015 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/664297.rdf
Name: temp
Units: degrees Celsius
Description: <p>experimental incubation temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/664298.rdf
Name: year
Units: year
Description: <p>sampling year</p>
http://lod.bco-dmo.org/id/dataset-parameter/664299.rdf
Name: site
Units: unitless
Description: <p>location where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/664300.rdf
Name: organism
Units: unitless
Description: <p>type of organism in sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/664301.rdf
Name: MPN_L
Units: cells/liter
Description: <p>Most-probable number of microbes in sample after incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/664302.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/664303.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</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
31414
https://datadocs.bco-dmo.org/file/jAABjRQh3kX327/thermophile_abund.csv
thermophile_abund.csv
Primary data file for dataset ID 664280
download
https://osprey.bco-dmo.org/dataset/664280/data/download
download
onLine
dataset
<p>In August 2012, September and October 2013, August 2014, and August 2015, 7-40°C diffuse hydrothermal fluids were collected from 10 vent sites at 1515-1716 m depths from Axial Seamount on the Juan de Fuca Ridge. The fluid samples were drawn into 650 ml Tedlar plastic bags with polyethylene valves within rigid housings using the NOAA Hydrothermal Fluid and Particle Sampler. The sampler pumped vent fluid through a titanium nozzle and recorded the temperature of the fluid within the intake nozzle once every second during pumping. Samples were collected using the research submarines Jason II and ROPOS. Background seawater was collected by shipboard hydrocasts at 1500 m depth directly over the caldera (25 m above the bottom) and 3 km west of the summit with 10 L Niskin bottles. The hydrothermal fluid and background seawater samples were divided for cultivation-dependent Most Probable Number (MPN) concentration estimates of thermophiles and hyperthermophiles (100 ml), microcosm incubations (400 ml), and total cell counts (40 ml). All operations at sea occurred on the research vessels Marcus G. Langseth, Thomas G. Thompson, Falkor, and Ronald H. Brown.</p>
<p><strong>Most Probable Number (MPN) Cell Estimates:</strong>&nbsp;Three-tube MPN analyses were used by adding 3.3, 0.33, and 0.03 ml of the hydrothermal fluid samples in triplicate to the methanogen, autotrophic sulfur reducer, and heterotroph media. After inoculation, the tubes were incubated at 80°C and 55°C for up to 7 days. Growth in the tubes was confirmed using phase-contrast light microscopy. Growth of methanogens and H2-producing heterotrophs was verified by analyzing all of the tubes for CH4 and H2, respectively, in the headspace using gas chromatography. Total and H2-producing heterotroph cell concentration estimates were scored and reported separately based on tubes that had cells versus those with H2. In order to estimate the concentration of non-methanogenic autotrophs in the autotrophic sulfur medium, the estimated number of methanogens in the autotrophic sulfur medium MPN tubes was subtracted from the estimated concentration of total cells.</p>
<p><a href="http://dmoserv3.bco-dmo.org/data_docs/NeMO2015/NeMO2015_methods.pdf" target="_blank">Full methodology</a></p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- replaced 'ND' with 'not_detected'<br />
- replaced '-' with nd (no data)<br />
- replaced blank cells with NA (not applicable)<br />
- removed special characters '(' and ')' from site names<br />
- reformatted table into a flat file<br />
- added latitudes and longitudes</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
phase-contrast light microscope
phase-contrast light microscope
PI Supplied Instrument Name: phase-contrast light microscope PI Supplied Instrument Description:Used to confirm growth of cultures Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Cruise: TN327
TN327
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN327
William Chadwick
National Oceanic and Atmospheric Administration
Cruise: TN300
TN300
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN300
William Chadwick
National Oceanic and Atmospheric Administration
Cruise: FK010
FK010
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK010
Julie Huber
Marine Biological Laboratory
https://datadocs.bco-dmo.org/d3/data_docs/Subseafloor_Life/FK010_CruiseReport_Huber_Final.pdf
Report describing FK010
Cruise: MGL1216
MGL1216
R/V Marcus G. Langseth
Community Standard Description
International Council for the Exploration of the Sea
R/V Marcus G. Langseth
vessel
MGL1216
David A. Butterfield
National Oceanic and Atmospheric Administration
Cruise: RB1403
RB1403
Community Standard Description
International Council for the Exploration of the Sea
NOAA Ship Ronald H. Brown
vessel
RB1403
David A. Butterfield
National Oceanic and Atmospheric Administration
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
R/V Marcus G. Langseth
Community Standard Description
International Council for the Exploration of the Sea
R/V Marcus G. Langseth
vessel
Community Standard Description
International Council for the Exploration of the Sea
NOAA Ship Ronald H. Brown
vessel