Dataset: AT39-01 CathodicEET SEM
Deployment: AT39-01

Principal Investigator:

Beth N. Orcutt (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Collaborative Research: Completing North Pond Borehole Experiments to Elucidate the Hydrology of Young, Slow-Spread Crust (North Pond 2017)

Deployment Synonyms:

North Pond 2017

Data URL:

https://www.bco-dmo.org/dataset-deployment/780266/data

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Description

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.

These results were published in Jones et al. (2020).

Related datasets from the same experiment:
AT39-01 CathodicEET Chronoamperometry: https://www.bco-dmo.org/dataset/780127
AT39-01 CathodicEET CyclicVoltametry: https://www.bco-dmo.org/dataset/780248
AT39-01 CathodicEET Amplicons: https://www.bco-dmo.org/dataset/780255
AT39-01 CathodicEET Experimental Metadata:
https://www.bco-dmo.org/dataset/780225

Methods & Sampling

Dataset acquisition description

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.

Data Processing Description

Dataset Processing Description

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.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1536539	NSF Division of Ocean Sciences

Instruments

Scanning Electron Microscope

Supplied Name: Zeiss Supra25 field emission scanning microscope

Supplied Description:

Instrument Type

Generic Name: Scanning Electron Microscope

Acronym: SEM

Generic 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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
SampleID	Sample identifier (unique file names for .tif images)	unitless	sample
ExperimentID	Text description of experiment with microbial fuel cells; values of NP11, NP12, NP13, NP14 or NP15	unitless	exp_id
Treatment	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)	unitless	treatment
imagename	Scanning Electron Microscopy (SEM) photograph imagename.	unitless	file_name
FLOCSsubstrate	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	unitless	sample_descrip
FLOCSdeployDate	Date of the FLOCS deployment, in ISO 8601 format yyyy-mm-dd	unitless	date
FLOCSdepth	Approximate depth, in meters below seafloor, where the FLOCS experiment was deployed	meters below seafloor (m)	mbsf
FLOCSrecoverDate	Date of the FLOCS recovery, in ISO 8601 format yyyy-mm-dd	unitless	date
FluidcollectionCruise	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)	unitless	cruise_id
FluidcollectionDate	Date of the collection of the crustal fluids, in ISO 8601 format yyyy-mm-dd	unitless	date
Latitude	Degree decimal minutes N latitude of the FLOCS experiment	decimal degrees	lat
Longitude	Degree decimal minates W longitude of the FLOCS experiment	decimal degrees	lon
WaterDepth	water depth to seafloor of the IODP Hole	meters (m)	depth_w
imagelink	URL for SEM image	unitless	file_link

Database

Contribute Data

Dataset: AT39-01 CathodicEET SEM
Deployment: AT39-01

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: AT39-01 CathodicEET SEMDeployment: AT39-01

Dataset acquisition description

Dataset Processing Description

Dataset: AT39-01 CathodicEET SEM
Deployment: AT39-01