http://lod.bco-dmo.org/id/dataset/780261
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
2019-10-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Scanning Electron Microscopy (SEM) photographs of biofilms on indium tin oxide electrodes from cathodic poised potential experiments with subsurface crustal samples from CORK borehole observatories at North Pond on the Mid-Atlantic Ridge during R/V A
2020-02-03
publication
2020-02-03
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-02-11
publication
https://doi.org/10.1575/1912/bco-dmo.780261.1
Beth N. Orcutt
Bigelow Laboratory for Ocean Sciences
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: Orcutt, B. (2020) Scanning Electron Microscopy (SEM) photographs of biofilms on indium tin oxide electrodes from cathodic poised potential experiments with subsurface crustal samples from CORK borehole observatories at North Pond on the Mid-Atlantic Ridge during R/V A. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-02-03 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.780261.1 [access date]
Dataset Description: <p>Scanning Electron Microscopy (SEM) photographs of biofilms on indium tin oxide electrodes from cathodic poised potential experiments with subsurface crustal samples from CORK borehole observatories at North Pond on the Mid-Atlantic Ridge during R/V Atlantis cruise AT39-01.<br />
<br />
These results were published in Jones et al. (2020).<br />
<br />
Related datasets from the same experiment:<br />
AT39-01 CathodicEET Chronoamperometry: https://www.bco-dmo.org/dataset/780127<br />
AT39-01 CathodicEET CyclicVoltametry: https://www.bco-dmo.org/dataset/780248<br />
AT39-01 CathodicEET Amplicons: https://www.bco-dmo.org/dataset/780255<br />
AT39-01 CathodicEET Experimental Metadata:<br />
https://www.bco-dmo.org/dataset/780225</p> Methods and Sampling: Microbial fuel cells (MFCs) were used to conduct cathodic poised potential experiments as described in Jones et al. (in preparation). After cyclic voltametry scanning of the indium tin oxide electrodes in the fuel cells at the end of the experiment, the ITO electrodes were carefully removed from the MFCs and split into two sections using a diamond scribe and tweezers for microscopy and DNA analysis. One piece was serially dehydrated in ethanol solutions (10 min steps each at 50:50, 60:40, 70:30, 80:20, 90:10 and 100:0 ratios of ethanol:distilled water) and hexamethyldisilizane (10 min) and air dried for 3 days in a HEPA-filtered biosafety cabinet in preparation for scanning electron microscopy (SEM), following methods available elsewhere (DAngelo and Orcutt, 2019). Dehydrated slide pieces were then mounted onto 12-mm-diameter SEM stubs with double-sided carbon tape, sputter coated with gold with a Denton Vacuum Desk IV cold sputter instrument (Denton Vacuum LLC, Moorestown, NJ), and imaged with a Zeiss Supra25 SEM at between 5-10 kV and a working distance between 3-9 mm.
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1536539 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1536539
completed
Beth N. Orcutt
Bigelow Laboratory for Ocean Sciences
207-315-2567 ext 312
60 Bigelow Drive PO Box 380
East Boothbay
Maine
04544
USA
borcutt@bigelow.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
SampleID
ExperimentID
Treatment
imagename
FLOCSsubstrate
FLOCSdeployDate
FLOCSdepth
FLOCSrecoverDate
FluidcollectionCruise
FluidcollectionDate
Latitude
Longitude
WaterDepth
imagelink
Zeiss Supra25 field emission scanning microscope
theme
None, User defined
sample identification
experiment id
treatment
file_name
sample description
date
meters below seafloor
Cruise identfier
latitude
longitude
depth_w
file_link
featureType
BCO-DMO Standard Parameters
Scanning Electron Microscope
instrument
BCO-DMO Standard Instruments
AT39-01
service
Deployment Activity
North Pond CORK Sites U1382A, U1383C
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.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Collaborative Research: Completing North Pond Borehole Experiments to Elucidate the Hydrology of Young, Slow-Spread Crust
http://www.darkenergybiosphere.org/research-activities/field-sites/
Collaborative Research: Completing North Pond Borehole Experiments to Elucidate the Hydrology of Young, Slow-Spread Crust
<p><em>NSF Award Abstract:</em><br />
Seawater circulates through the upper part of the oceanic crust much like groundwater flows through continental aquifers. However, in the ocean this seawater circulation, many times heated by buried magmatic bodies, transports and releases 25% of the Earth's heat. The rate of fluid flow through ocean crust is estimated to be equal to the amount of water delivered by rivers to the ocean. Much of what we know of this subseafloor fluid flow comes from studies in the eastern Pacific Ocean on ocean crust created by medium and fast spreading mid-ocean ridges. These studies indicate that seawater and its circulation through the seafloor significantly impact crustal evolution and biogeochemical cycles in the ocean and affect the biosphere in ways that are just now beginning to be quantified and understood. To expand this understanding, this research focuses on fluid flow of seafloor generated by slow spreading ridges, like those in the Atlantic, Indian and Arctic Oceans because it is significantly different in structure, mineralogy, and morphology than that formed at fast and intermediate spreading ridges. This research returns to North Pond, a long-term; seafloor; fluid flow monitoring site, drilled and instumented by the Ocean Drilling Program in the Atlantic Ocean. This research site was punctured by boreholes in which fluid flow and geochemical and biological samplers have been deployed for a number of years to collect data and samples. It also provides resources for shipboard and on-shore geochemical and biological analysis. Broader impacts of the work include sensor and technology development, which increases infrastructure for science and has commercial applications. It also provides training for students and the integration of education and research at three US academic institutions, one of which is an EPSCoR state (Mississippi), and supports a PI whose gender is under-represented in sciences and engineering. Public outreach will be carried out in conjunction with the Center for Dark Energy Biosphere Investigations.</p>
<p>This project completes a long-term biogeochemical and hydrologic study of ridge flank hydrothermal processes on slow-spreading, 8 million year old crust on the western flank of the Mid-Atlantic Ridge. The site, North Pond, is an isolated northeast-trending sediment pond, bounded by undersea mountains that have been studied since the 1970s. During Integrated Ocean Drilling Program Expedition 336 in 2011 and an expedition five months later (2012), sensors, samplers, and experiments were deployed in four borehole observatories drilled into the seafloor that penetrated into volcanic crust, with the purpose of monitoring changes in hydrologic properties, crustal fluid composition and mineral alteration, among other objectives. Wellhead sampling in 2012 and 2014 already revealed changes in crustal fluid compositions; and associated pressure data confirm that the boreholes are sealed and overpressured, reflecting a change in the formation as the boreholes recover from drilling disturbances. This research includes a 13-day oceanographic expedition and use of on-site robotically operated vehicles to recover downhole instrument packages at North Pond. It will allow the sampling of crustal fluids, recovering pressure data, and measuring fluid flow rates. Ship- and shore-based analyses will be used to address fundamental questions related to the hydrogeology of hydrothermal processes on slow-spread crust.</p>
North Pond 2017
largerWorkCitation
project
eng; USA
oceans
North Pond CORK Sites U1382A, U1383C
-46.0817
-46.053
22.7564
22.8023
2018-01-03
2019-01-10
North Pond, Mid-Atlantic Ridge flank CORKs
0
BCO-DMO catalogue of parameters from Scanning Electron Microscopy (SEM) photographs of biofilms on indium tin oxide electrodes from cathodic poised potential experiments with subsurface crustal samples from CORK borehole observatories at North Pond on the Mid-Atlantic Ridge during R/V A
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/789097.rdf
Name: SampleID
Units: unitless
Description: <p>Sample identifier (unique file names for .tif images)</p>
http://lod.bco-dmo.org/id/dataset-parameter/789098.rdf
Name: ExperimentID
Units: unitless
Description: <p>Text description of experiment with microbial fuel cells; values of NP11, NP12, NP13, NP14 or NP15</p>
http://lod.bco-dmo.org/id/dataset-parameter/789099.rdf
Name: Treatment
Units: unitless
Description: <p>Treatment of the microbial fuel cell; values of Offline (with sample but no voltage applied), Fluid (with filtered fluid only/no sample and with voltage applied), or Echem (with sample and voltage applied)</p>
http://lod.bco-dmo.org/id/dataset-parameter/789100.rdf
Name: imagename
Units: unitless
Description: <p>Scanning Electron Microscopy (SEM) photograph imagename.</p>
http://lod.bco-dmo.org/id/dataset-parameter/789101.rdf
Name: FLOCSsubstrate
Units: unitless
Description: <p>Description of the FLOCS sample type put into the microbial fuel cell; values of Mixed (a mixture of samples), NA (not applicable, no sample), Basalt, Glass Wool, or Pyrrhotite</p>
http://lod.bco-dmo.org/id/dataset-parameter/789102.rdf
Name: FLOCSdeployDate
Units: unitless
Description: <p>Date of the FLOCS deployment, in ISO 8601 format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/789103.rdf
Name: FLOCSdepth
Units: meters below seafloor (m)
Description: <p>Approximate depth, in meters below seafloor, where the FLOCS experiment was deployed</p>
http://lod.bco-dmo.org/id/dataset-parameter/789104.rdf
Name: FLOCSrecoverDate
Units: unitless
Description: <p>Date of the FLOCS recovery, in ISO 8601 format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/789105.rdf
Name: FluidcollectionCruise
Units: unitless
Description: <p>Name of the cruise and ROV Jason dive number when the crustal fluid was collected; values of AT39-01 (R/V Atlantis cruise AT39-01) + J2-#### (ROV Jason dive number)</p>
http://lod.bco-dmo.org/id/dataset-parameter/789106.rdf
Name: FluidcollectionDate
Units: unitless
Description: <p>Date of the collection of the crustal fluids, in ISO 8601 format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/789107.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Degree decimal minutes N latitude of the FLOCS experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/789108.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Degree decimal minates W longitude of the FLOCS experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/789109.rdf
Name: WaterDepth
Units: meters (m)
Description: <p>water depth to seafloor of the IODP Hole</p>
http://lod.bco-dmo.org/id/dataset-parameter/789110.rdf
Name: imagelink
Units: unitless
Description: <p>URL for SEM image</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
208376520
https://darchive.mblwhoilibrary.org/bitstream/1912/25358/1/SEM_images.zip
download
13989
https://darchive.mblwhoilibrary.org/bitstream/1912/25358/2/dataset-780261_at39-01-cathodiceet-sem__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.780261.1
download
onLine
dataset
Microbial fuel cells (MFCs) were used to conduct cathodic poised potential experiments as described in Jones et al. (in preparation). After cyclic voltametry scanning of the indium tin oxide electrodes in the fuel cells at the end of the experiment, the ITO electrodes were carefully removed from the MFCs and split into two sections using a diamond scribe and tweezers for microscopy and DNA analysis. One piece was serially dehydrated in ethanol solutions (10 min steps each at 50:50, 60:40, 70:30, 80:20, 90:10 and 100:0 ratios of ethanol:distilled water) and hexamethyldisilizane (10 min) and air dried for 3 days in a HEPA-filtered biosafety cabinet in preparation for scanning electron microscopy (SEM), following methods available elsewhere (DAngelo and Orcutt, 2019). Dehydrated slide pieces were then mounted onto 12-mm-diameter SEM stubs with double-sided carbon tape, sputter coated with gold with a Denton Vacuum Desk IV cold sputter instrument (Denton Vacuum LLC, Moorestown, NJ), and imaged with a Zeiss Supra25 SEM at between 5-10 kV and a working distance between 3-9 mm.
Specified by the Principal Investigator(s)
BCO-DMO Data Manager Processing Notes:
* All images zipped into SEM_images.zip
* Imagelist made of all SEM images submitted. Imagelist matched with metadata in the tabular dataset to verify each image had metadata.
* Column of direct links to download individual images added to tabular dataset.
* Sample IDs modified to match experimental metadata as discussed with data submitter.
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 Supra25 field emission scanning microscope
Zeiss Supra25 field emission scanning microscope
PI Supplied Instrument Name: Zeiss Supra25 field emission scanning microscope Instrument Name: Scanning Electron Microscope Instrument Short Name:SEM Instrument Description: A scanning electron microscope (SEM) scans a focused electron beam over a surface to create an image. The electrons in the beam interact with the sample, producing various signals that can be used to obtain information about the surface topography and composition.
Cruise: AT39-01
AT39-01
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT39-01
C. Geoffrey Wheat
University of Alaska Fairbanks
http://datadocs.bco-dmo.org/docs/Subseafloor_Microbial_Carbon_Cycling/data_docs/North_Pond_2017_Expedition%20Report_FINAL.pdf
Report describing AT39-01
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel