Electron microprobe wavelength dispersive spectroscopy from seafloor sulfide deposits in the East Pacific Rise 9-10 North from R/V Atlantis and R/V Roger Revelle, AT42-09, AT42-21, RR2102 from October 2020 (Hot2cold Vents project)

Website: https://www.bco-dmo.org/dataset/988651
Data Type: Cruise Results
Version: 1
Version Date: 2025-11-11

Project
» Collaborative Research: From hot to cold in the dark - shifts in seafloor massive sulfide microbial communities as physical and geochemical conditions change after venting ceases (Hot2cold Vents)
ContributorsAffiliationRole
Toner, Brandy MarieUniversity of Minnesota Twin Cities (UMTC)Principal Investigator
Jones, RoseUniversity of Minnesota (UMN)Scientist
Newman, SawyerWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
Electron microprobe wavelength dispersive spectroscopy (WDS) data were collected for seafloor sulfide deposits. Seafloor sulfide mineral samples were collected from hydrothermally active chimneys and inactive off-axis massive sulfide deposits at East Pacific Rise (EPR) 9.50°N during 2019–2021 on cruises AT42-09, AT42-21, and RR2102. Samples were collected using the HOV Alvin or ROV Jason II. Samples were placed in a positive-pressure glove bag flushed with N₂(g), sparged with N₂, heat-sealed into Mylar bags containing AnaeroPaks, and stored at −20 °C. Epoxy-embedded petrographic thin sections were prepared from these samples. Subsamples were dried for 24 hours under N₂(g), vacuum-embedded in epoxy resin (Struers EpoFix Resin, 1 L kit; Part #40200030) following the manufacturer’s guidelines, and cured under N₂(g) for 24 hours. Each epoxy-embedded sample was pre-cut using a wafering saw and then sent to Spectrum Petrographics, Inc. (Washington, USA) for preparation as 30 µm thick, double-polished thin sections mounted on quartz slides, using methods designed to limit sample exposure to water and ambient air. When not in use, thin sections were stored under N₂(g) to limit oxidation. Thin sections were analyzed by electron microprobe WDS using a JEOL JXA-8530FPlus Electron Probe Microanalyzer at the Electron Microprobe Laboratory, Earth and Environmental Sciences, Twin Cities, University of Minnesota.


Coverage

Location: East Pacific Rise (EPR) 9.50°N
Spatial Extent: N:9.89478369 E:-104.1749216 S:9.495434 W:-104.2935759
Temporal Extent: 2020-10-09

Methods & Sampling

Electron microprobe wavelength dispersive spectroscopy data were collected from hydrothermally active chimneys and inactive off-axis massive sulfide deposits at East Pacific Rise (EPR) 9.50°N during 2019–2021 on cruises AT42-09, AT42-21, and RR2102. Samples were collected using the HOV Alvin or ROV Jason II. Samples were placed in a positive-pressure glove bag flushed with N₂(g), sparged with N₂, heat-sealed into Mylar bags containing AnaeroPaks, and stored at −20 °C. Epoxy-embedded petrographic thin sections were prepared from these samples. Subsamples were dried for 24 hours under N₂(g), vacuum-embedded in epoxy resin (Struers EpoFix Resin, 1 L kit; Part #40200030) following the manufacturer’s guidelines, and cured under N₂(g) for 24 hours. Each epoxy-embedded sample was pre-cut using a wafering saw and then sent to Spectrum Petrographics, Inc. (Washington, USA) for preparation as 30 µm thick, double-polished thin sections mounted on quartz slides, using methods designed to limit sample exposure to water and ambient air. When not in use, thin sections were stored under N₂(g) to limit oxidation.


Data Processing Description

Data was analyzed using probe software (https://www.probesoftware.com/).


BCO-DMO Processing Description

- Loaded data from WDS_combined.xlsx (sheet 1) with headers on row 1, treating empty strings as missing values
- Renamed 7 columns: Acc.Voltage_kV to Acc_Voltage_kV, BG-_mm to BG_lower_wavelength_mm, BG+_mm to BG_higher_wavelength_mm, Bg-_cps to Bg_lower_wavelength_cps, Bg+_cps to Bg_higher_wavelength_cps, K-raw_percent to K_raw_percent, Curr._A to Curr_A
- Combined date (format %m-%d-%y) and time (format %H:%M) columns into new ISO_DateTime_UTC column formatted as %Y-%m-%d %H:%M:%S in UTC
- Deleted original date and time columns
- Reordered columns to: name, ISO_DateTime_UTC, comment, stage_x, stage_y, stage_z, Acc_Voltage_kV, Probe_Dia_um, Scan, Mag, Curr_A, Element, Crystal, Peak_mm, BG_lower_wavelength_mm, BG_higher_wavelength_mm, Net_cps, Bg_lower_wavelength_cps, Bg_higher_wavelength_cps, ZAF_type, K_raw_percent, Mass_percent, Atom_percent, Cation_percent, K_percent, ZAF
- Set types for all columns: ISO_DateTime_UTC as datetime (%Y-%m-%dT%H:%M:%S), Acc_Voltage_kV and Mag and Probe_Dia_um as integer, stage_x/y/z, Curr_A, Peak_mm, BG_lower/higher_wavelength_mm, Net_cps, Bg_lower/higher_wavelength_cps, K_raw_percent, Mass_percent, Atom_percent, Cation_percent, K_percent, ZAF as number, and name/comment/Scan/Element/Crystal/ZAF_type as string
- Output to 988651_v1_EPR_9-10_North_Electron_Microprobe_Wavelength_Spectroscopy.csv, which is the Primary data file for this dataset


[ table of contents | back to top ]

Data Files

File
988651_v1_EPR_9-10_North_Electron_Microprobe_Wavelength_Spectroscopy.csv
(Comma Separated Values (.csv), 24.66 KB)
MD5:164b9cc9108c48cf93425952d690b12d
Primary data file for dataset ID 988651, version 1

[ table of contents | back to top ]

Supplemental Files

File
988651_v1_2020-10-09_WDS_scans_documentation.pdf
(Portable Document Format (.pdf), 357.46 KB)
MD5:4e9d10335fc8c06512bb9f46ade18508
File (a slide presentation file converted to pdf format) showing locations of WDS scan points on thin section images.
988651_v1_Element_percentage.zip
(ZIP Archive (ZIP), 25.99 KB)
MD5:59509cc1bb7d1d9db33894572af970aa
Zip folder containing the raw spot text files, which have been combined and represented in tabular format within the primary data files of this dataset (988651_v1_EPR_9-10_North_Electron_Microprobe_Wavelength_Spectroscopy.csv).
988651_v1_Plotted_peaks.zip
(ZIP Archive (ZIP), 370.67 KB)
MD5:ce6445b486634548c7d0d223f577a850
Zipped folder containing plotted peak graph png files associated with this dataset.
988651_v1_WDS_Metadata.csv
(Comma Separated Values (.csv), 2.46 KB)
MD5:7bb4030875ce5f060ad3c5ef56454f58
File containing collection metadata of thin-sections including original collection of samples.

File parameters (i.e., column header names) include: File name, Spot name, Elements, Spectrogram_filename, Sample name, Latitude_dd, Longitude_dd, Depth_mbs, Heading_deg, Date_collected_MMDDYYYY, Time_collected
Acquisition parameters associated with the map images
filename: 988651_v1_WDS_Element_Data.csv
(Comma Separated Values (.csv), 18.10 KB)
MD5:c35b95307a1bb8428f5cb011365e68fd
Standard settings that the sensing machine used to evaluate elements.

File parameters (i.e., column header names) include: Identification, At.No., Acq.Flag, Peak(keV), Bkg1(keV), Bkg2(kev), Time(s) Bkg Cnts, Possible, Present, Rule, Low keV, High keV, Step eV, Dwell Sec, Bias V, Baseline V, Window V, Gain, Stnd Order, Stnd(keV), Stnd Bkg1(keV), Stnd Bkg2(keV), Stnd Min.Time(s), Stnd Max.Time(s), Stnd Stat.%, Stnd Pk. Srch., Stnd Avg.Calib., Stnd.Compositon, Stnd Date, Quant(keV), Quant Bkg1(keV), Quant Bkg2(keV), Quant Min.Time(s), Quant Max.Time(s), Quant Stat.%, Count Stnd.

[ table of contents | back to top ]

Related Datasets

IsRelatedTo
Brandy Marie Toner, Rose Jones (2025) Synchrotron micro-probe X-ray diffraction data from seafloor sulfide deposits collected during cruise AT42-09 on the East Pacific Rise (EPR) in April 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2025-11-25 doi:10.26008/1912/bco-dmo.937020.2 [view at BCO-DMO]

[ table of contents | back to top ]

Parameters

ParameterDescriptionUnits
name

Filename of original raw spot TXT file.

unitless
ISO_DateTime_UTC

Datetime of sample collection, derived from the original date and time columns of this datafile.

unitless
comment

Additional comments documented in the original raw spot txt file.

unitless
stage_x

X position of stage at time of collection.

micrometer (um)
stage_y

Y position of stage at time of collection.

micrometer (um)
stage_z

Z position of stage at time of collection.

micrometer (um)
Acc_Voltage_kV

Voltage of electron beam current.

kilovolt (kV)
Probe_Dia_um

Beam spot size.

micrometer (um)
Scan

WDS scan active.

unitless
Mag

Magnification at time of collection.

unknown
Curr_A

Amperage of electron beam current.

amperage (A)
Element

Element detected.

unitless
Crystal

Analysis crystal type.

unitless
Peak_mm

Characteristic peak position.

millimeter (mm)
BG_lower_wavelength_mm

Background lower peak position.

millimeter (mm)
BG_higher_wavelength_mm

Background upper peak position.

millimeter (mm)
Net_cps

Net electron counts per second.

counts per second
Bg_lower_wavelength_cps

Background lower peak counts per second.

counts per second
Bg_higher_wavelength_cps

Background upper peak counts per second.

counts per second
ZAF_type

Indicates whether elemental concentrations are reported as atomic elements (for metals) or as oxide forms (for oxide-based materials).

unitless
K_raw_percent

Uncorrected k-ratio expressed as percent, calculated as the background-corrected characteristic X-ray intensity of an element in the sample divided by that of a reference standard analyzed under identical EPMA/WDS conditions (I_sample / I_standard _ 100), prior to application of ZAF matrix corrections.

percent (%)
Mass_percent

Elemental concentration expressed as weight percent (wt%), calculated from ZAF-corrected k-ratios obtained by electron microprobe wavelength dispersive spectroscopy (EPMA-WDS).

percent (%)
Atom_percent

Elemental concentration expressed as atomic percent (at%), calculated from ZAF-corrected weight percent data and normalized to the total number of atoms in the analyzed phase.

percent (%)
Cation_percent

Cation proportion expressed as percent of total cations, calculated from ZAF-corrected compositional data and normalized to a defined stoichiometric basis appropriate for the analyzed mineral phase.

percent (%)
K_percent

ZAF-corrected k-ratio expressed as percent, representing the matrix-corrected ratio of sample to standard characteristic X-ray intensity.

percent (%)
ZAF

Composite matrix correction factor applied during quantitative EPMA analysis to account for atomic number (Z), X-ray absorption (A), and fluorescence (F) effects in the analyzed material.

unitless


[ table of contents | back to top ]

Instruments

Dataset-specific Instrument Name
JEOL JXA-8530FPlus Electron Probe Microanalyzer
Generic Instrument Name
Electron Microprobe
Dataset-specific Description
Wavelength dispersive spectroscopy (WDS) measurements were collected from carbon-coated thin sections using a JEOL JXA-8530FPlus Electron Probe Microanalyzer operated at an accelerating voltage of 20.0 kV, a dwell time of 100 ms, and a probe diameter of 5 µm.
Generic Instrument Description
Instruments that chemically analyse a small area of a sample by bombarding it with electrons and spectroscopically assaying the resulting X-Ray emissions.


[ table of contents | back to top ]

Deployments

AT42-09

Website
Platform
R/V Atlantis
Start Date
2019-03-25
End Date
2019-04-23

AT42-21

Website
Platform
R/V Atlantis
Start Date
2019-12-17
End Date
2020-01-07

RR2102

Website
Platform
R/V Roger Revelle
Start Date
2021-03-24
End Date
2021-04-25


[ table of contents | back to top ]

Project Information

Collaborative Research: From hot to cold in the dark - shifts in seafloor massive sulfide microbial communities as physical and geochemical conditions change after venting ceases (Hot2cold Vents)

Coverage: East Pacific Rise


NSF Award Abstract:
Hydrothermal vents, which deposit seafloor massive sulfides (SMS), occur along the 89,000 km of mid-ocean ridges, submarine volcanoes, and backarc basins that occur at tectonic plate boundaries in the ocean. Active hydrothermal vent sulfide chimneys are hotspots of biodiversity and productivity in the deep ocean, as well as potential resources for metals. While significant effort has focused on understanding the diversity of biological communities and geochemistry associated with actively venting SMS, relatively little is known about the biological communities associated with SMS once venting ceases. Furthermore, little is known about the microbiological and geochemical changes that occur during the transition period from active to inactive, during which an important succession occurs in the microbial community and geochemistry of fluids within the chimney. This interdisciplinary project will create and sample this transition period by collecting multiple active SMS samples from individual vents at 9 degrees N East Pacific Rise and allowing them to transition to inactive on the seafloor, mimicking the end of venting while allowing for the exact time when venting ceased to be known, something not possible when sampling naturally formed inactive SMS. Microbial community diversity and metabolism will be analyzed in parallel with bulk and fine-scale geological measurements for active, transitioning, and inactive sulfides. This seafloor experimental and analytical approach will provide knowledge of how microbial communities, rates of biogeochemical transformations, and geological conditions change as SMS transition from hot and actively venting to cold and inactive. Students in grades 6-8 will be entrained into the project through research cruise "ship-to-shore" interactions and communications, post-cruise workshops for educators working with students typically underrepresented in STEM fields, and a collaboration with the Science, Engineering, Art and Design Gallery (SEAD), a community and economic development project in Bryan, TX.

Hydrothermal vents are quantitatively important to the biology and chemistry of the deep ocean, but the vast majority of current knowledge focuses on actively venting deposits. However, after venting ceases, sulfides can persist on the seafloor for tens of thousands of years, making them long-lived, globally-abundant microbial substrates. In recent years, studies of inactive SMS found drastically different microbial communities than those on active deposits, indicating a succession of the microbial community, and thus a potentially different impact on deep ocean biodiversity and biogeochemistry than actively venting deposits. However, ages of the inactive structures are often not known, so it is impossible to estimate how quickly these changes occur, and how quickly co-occurring changes in sulfide mineralogy and microbiological communities occur. This project will provide the first insight into what happens at the microbial and mineralogical level as SMS initially transition from active to inactive. Active SMS will be sampled and analyzed for microbial community composition, functional capacity, gene expression and metabolic rates. Co-located subsamples will be analyzed for porosity and bulk and fine-scale mineralogy. Subsamples of those active SMS samples will be left on the seafloor to incubate and be collected weeks and a year or more later, with the same analyses conducted upon collection. This will allow for determination of microbiological and mineralogical changes that occur during that initial transition and for comparison with older inactive SMS from the same vent fields. Together, the data collected will be integrated to generate a conceptual model of succession of biology, mineralogy, porosity and pore distribution as vent deposits transition from active to inactive. This project will fill a knowledge gap about hydrothermal ecosystems and has the potential to transform the current understanding of diversity and rates of change in these important seafloor biomes.



[ table of contents | back to top ]

Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)
NSF Division of Ocean Sciences (NSF OCE)
NSF Division of Ocean Sciences (NSF OCE)

[ table of contents | back to top ]