http://lod.bco-dmo.org/id/dataset/664306
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)
NH4Cl effect on growth, yield, and methane production of thermophyles, Table 3 from Topcuoglu et al (2016)
2016-11-08
publication
2016-11-08
revision
BCO-DMO Linked Data URI
2016-11-08
creation
http://lod.bco-dmo.org/id/dataset/664306
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) NH4Cl effect on growth, yield, and methane production of thermophyles, Table 3 from Topcuoglu et al (2016). 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/664306 [access date]
NH4Cl effect on growth, yield, production of thermophyles, Table 3 from Topcuoglu et al (2016) Dataset Description: <p>This dataset includes growth rate, cell yield based on methane production and cell-specific CH4 production rate for <em>Methanocaldococcus </em><em>jannaschii</em><em>, Methanothermococcus </em><em>thermolithotrophicus</em><em>, Methanocaldococcus </em><em>bathoardescens</em> (from Ver Eecke et al., 2013) grown with varying concentrations of NH4Cl in otherwise nitrogen-free medium</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/664280">Thermophile abundance - MPN</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 (dives J820-J826) 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>For each sample site, 25 ml of hydrothermal fluid or background seawater was added without exposure to air to each of 16 sealed 60 ml serum bottles that had been pre-flushed with either H<sub>2</sub>:CO<sub>2</sub> (80%:20%) or N<sub>2</sub>:CO<sub>2</sub> (80%:20%), depending on the headspace composition used for incubation (see table in <a href="http://dmoserv3.bco-dmo.org/data_docs/NeMO2015/NeMO2015_methods.pdf" target="_blank">full methods</a> pdf). The bottles were divided into four sets of four bottles with a pair of bottles from each set incubated at 55°C and 80°C for up to a week or until visibly turbid. Three of the four sets of microcosms (sets A-C) were incubated each of the four study years. Set A was flushed and filled with 200 kPa of H<sub>2</sub>:CO<sub>2</sub> yielding an estimated aqueous H<sub>2</sub> concentration of 1.2 mM at their incubation temperatures based on calculations using the geochemical prediction software Geochemist’s Workbench. Sets B and C were flushed and filled with 200 kPa of N<sub>2</sub>:CO<sub>2</sub>, and half of these bottles (set B) were given 1 ml of H<sub>2</sub>:CO<sub>2</sub> in exchange for 1 ml of N<sub>2</sub>:CO<sub>2</sub> to produce an estimated aqueous H<sub>2</sub> concentration of 20 mM at their incubation temperatures. In 2012 and 2013, the remaining four serum bottles (set D) were amended with 4.7 mM NH<sub>4</sub>Cl (2012 only) or 47 mM NH<sub>4</sub>Cl (2013 only) and flushed and filled with 200 kPa of H<sub>2</sub>:CO<sub>2</sub> to test for growth stimulation by ammonium. The NH<sub>4</sub>Cl concentration was based on that added to our defined methanogen growth medium (see below). In 2014 and 2015, the remaining four serum bottles (set E) were amended with 0.5% (wt vol<sup>-1</sup>) tryptone plus 0.01% (wt vol<sup>-1</sup>) yeast extract and flushed and filled with 200 kPa of N<sub>2</sub>:CO<sub>2</sub> to test for H<sub>2</sub> syntrophy. All samples were reduced with 0.025% (wt vol<sup>-1</sup>) each of cysteine-HCl and Na<sub>2</sub>S•9H<sub>2</sub>O. Growth of methanogens was determined by analyzing for CH<sub>4</sub> in the headspace using gas chromatography once the cells in the bottle had reached stationary growth phase. In 2015, an aliquot of the 80°C and 55°C tryptone/no H<sub>2</sub> samples (set E) that showed CH<sub>4</sub> production were filtered onto 0.2-µm pore size nucleopore filters prestained with Irgalan black (Sterlitech, Kent, WA, USA), stained with acridine orange, and examined using epifluorescence microscopy. In 2015, the 80°C and 55°C tryptone/no H<sub>2</sub> samples from the Marker 113 vent site were also separately filtered through Sterivex GP 0.22 µm sterile filter units (Millipore, Billerica, MA, USA) and frozen at -80°C until analyzed. In2015, 10 ml of hydrothermal fluid was added to sealed Balch tubes without exposure to air, amended separately with 0.1% (wt vol<sup>-1</sup>) sodium formate and 0.5% (wt vol<sup>-1</sup>) sodium acetate, flushed and filled with 200 kPa N<sub>2</sub>:CO<sub>2</sub>, and incubated in duplicate at 80°C and55°C for up to seven days to determine if these substrates can support methanogenesis at high temperatures.</p>
<p>Total cell counts in the original hydrothermal fluids were done by preserving in duplicate 18 ml of hydrothermal fluid with 1.8 ml of 37% formaldehyde. Samples were stored at 4°C for less than a month prior to counting by epifluorescence microscopy as described above.</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
species
NH4Cl
growth_rate
growth_rate_err
yield
yield_err
CH4_prod_rate
CH4_prod_rate_err
phase-contrast light microscope
theme
None, User defined
species scientific name (binomial)
treatment
growth
standard error
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Microscope - Optical
instrument
BCO-DMO Standard Instruments
TN327
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.
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
biota
oceans
Axial Seamount, Juan de Fuca Ridge
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 NH4Cl effect on growth, yield, and methane production of thermophyles, Table 3 from Topcuoglu et al (2016)
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/664316.rdf
Name: species
Units: unitless
Description: <p>experimental species</p>
http://lod.bco-dmo.org/id/dataset-parameter/664317.rdf
Name: NH4Cl
Units: micromoles or millimoles
Description: <p>concentration of ammonium chloride used in experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/664318.rdf
Name: growth_rate
Units: (k) (h-1)
Description: <p>growth rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/664319.rdf
Name: growth_rate_err
Units: (k) (h-1)
Description: <p>growth rate error: 95% confidence interval (alpha = 0.05)</p>
http://lod.bco-dmo.org/id/dataset-parameter/664320.rdf
Name: yield
Units: 10^12 cells mol-1 CH4
Description: <p>yield</p>
http://lod.bco-dmo.org/id/dataset-parameter/664321.rdf
Name: yield_err
Units: 10^12 cells mol-1 CH4
Description: <p>yield error: 95% confidence interval (alpha = 0.05)</p>
http://lod.bco-dmo.org/id/dataset-parameter/664322.rdf
Name: CH4_prod_rate
Units: picomoles methane/cell/hr (pmol CH4 cell-1 h-1)
Description: <p>methane production rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/664323.rdf
Name: CH4_prod_rate_err
Units: picomoles methane/cell/hr (pmol CH4 cell-1 h-1)
Description: <p>methane production rate error: 95% confidence interval (alpha = 0.05)</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
1114
https://datadocs.bco-dmo.org/file/oAAmo2RhDNjr8Y/thermophile_growth.csv
thermophile_growth.csv
Primary data file for dataset ID 664306
download
https://osprey.bco-dmo.org/dataset/664306/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 (dives J820-J826) 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>For each sample site, 25 ml of hydrothermal fluid or background seawater was added without exposure to air to each of 16 sealed 60 ml serum bottles that had been pre-flushed with either H<sub>2</sub>:CO<sub>2</sub> (80%:20%) or N<sub>2</sub>:CO<sub>2</sub> (80%:20%), depending on the headspace composition used for incubation (see table in <a href="http://dmoserv3.bco-dmo.org/data_docs/NeMO2015/NeMO2015_methods.pdf" target="_blank">full methods</a> pdf). The bottles were divided into four sets of four bottles with a pair of bottles from each set incubated at 55°C and 80°C for up to a week or until visibly turbid. Three of the four sets of microcosms (sets A-C) were incubated each of the four study years. Set A was flushed and filled with 200 kPa of H<sub>2</sub>:CO<sub>2</sub> yielding an estimated aqueous H<sub>2</sub> concentration of 1.2 mM at their incubation temperatures based on calculations using the geochemical prediction software Geochemist’s Workbench. Sets B and C were flushed and filled with 200 kPa of N<sub>2</sub>:CO<sub>2</sub>, and half of these bottles (set B) were given 1 ml of H<sub>2</sub>:CO<sub>2</sub> in exchange for 1 ml of N<sub>2</sub>:CO<sub>2</sub> to produce an estimated aqueous H<sub>2</sub> concentration of 20 mM at their incubation temperatures. In 2012 and 2013, the remaining four serum bottles (set D) were amended with 4.7 mM NH<sub>4</sub>Cl (2012 only) or 47 mM NH<sub>4</sub>Cl (2013 only) and flushed and filled with 200 kPa of H<sub>2</sub>:CO<sub>2</sub> to test for growth stimulation by ammonium. The NH<sub>4</sub>Cl concentration was based on that added to our defined methanogen growth medium (see below). In 2014 and 2015, the remaining four serum bottles (set E) were amended with 0.5% (wt vol<sup>-1</sup>) tryptone plus 0.01% (wt vol<sup>-1</sup>) yeast extract and flushed and filled with 200 kPa of N<sub>2</sub>:CO<sub>2</sub> to test for H<sub>2</sub> syntrophy. All samples were reduced with 0.025% (wt vol<sup>-1</sup>) each of cysteine-HCl and Na<sub>2</sub>S•9H<sub>2</sub>O. Growth of methanogens was determined by analyzing for CH<sub>4</sub> in the headspace using gas chromatography once the cells in the bottle had reached stationary growth phase. In 2015, an aliquot of the 80°C and 55°C tryptone/no H<sub>2</sub> samples (set E) that showed CH<sub>4</sub> production were filtered onto 0.2-µm pore size nucleopore filters prestained with Irgalan black (Sterlitech, Kent, WA, USA), stained with acridine orange, and examined using epifluorescence microscopy. In 2015, the 80°C and 55°C tryptone/no H<sub>2</sub> samples from the Marker 113 vent site were also separately filtered through Sterivex GP 0.22 µm sterile filter units (Millipore, Billerica, MA, USA) and frozen at -80°C until analyzed. In2015, 10 ml of hydrothermal fluid was added to sealed Balch tubes without exposure to air, amended separately with 0.1% (wt vol<sup>-1</sup>) sodium formate and 0.5% (wt vol<sup>-1</sup>) sodium acetate, flushed and filled with 200 kPa N<sub>2</sub>:CO<sub>2</sub>, and incubated in duplicate at 80°C and55°C for up to seven days to determine if these substrates can support methanogenesis at high temperatures.</p>
<p>Total cell counts in the original hydrothermal fluids were done by preserving in duplicate 18 ml of hydrothermal fluid with 1.8 ml of 37% formaldehyde. Samples were stored at 4°C for less than a month prior to counting by epifluorescence microscopy as described above.</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 blank cells with NA (not applicable)<br />
- split +/- error into two columns</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
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel