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Subcellular Thiol Functional Group Distribution in Geobacter sulfurreducens Determined by Hg LIII-Edge EXAFS: Research Data

https://doi.org/10.5878/r92f-7869
This dataset contains the research data underlying the article “Subcellular Thiol Functional Group Distribution in Geobacter sulfurreducens Determined by Hg LIII-Edge EXAFS,” published in Frontiers in Microbiology (https://doi.org/10.3389/fmicb.2025.1728775Opens in a new tab). The dataset comprises measurements of subcellular biomass, total organic carbon (TOC), total sulfur (TS), thiol groups (RSH), and spectroscopic data (EXAFS and XANES) collected to characterize subcellular compartments of G. sulfurreducens PCA (Caccavo et al., 1994), including extracellular, periplasmic, cytoplasmic, and membrane fractions. TOC and TS were quantified using an elemental analyzer (Vario MACRO cube) with a relative standard deviation (RSD) of 0.5%. Total mercury concentrations were determined by combustion atomic absorption spectrometry with a direct mercury analyzer (DMA-80, Milestone; detection limit = 0.01 ng; RSD = 6%). Sulfur K-edge XANES spectra were collected at the 4B7A Medium Energy X-ray Beamline of the Beijing Synchrotron Radiation Facility. Data processing, including normalization and linear combination fitting (LCF), was performed using the Larch software package. Hg LIII-edge EXAFS spectra were acquired at Diamond Light Source (Beamline I20-scanning). Data analysis and fitting were carried out using WinXAS in combination with FEFF-7. Further details are provided in the accompanying README.txt file.
Download data and documentation (20 files / 2.22 MiB)

Data files

  • F2a_Data_for_Figure_2a_S_xanes_data_and_fitting.tsv
    111.35 KiB
  • F2b_Data_for_Figure_2b_S_speciation.tsv
    731 Bytes
  • F3_Data_for_Figure_3_EXAFS_data_and_fitting.tsv
    1.49 MiB
  • F4_Data_for_Figure_4_first_derivative_Hg_XANES.tsv
    595.34 KiB
  • F5_Data_for_Figure_5 _RSH_concentration_density.tsv
    396 Bytes
  • F6_Data_for_Figure_6_Hg_loss.tsv
    4.49 KiB
  • FS1a_Data_for_Figure_S1a_cell_growth_curve.tsv
    181 Bytes
  • FS1b_Data_for_Figure_S1b_cell_density.tsv
    184 Bytes
  • FS1c_Data_for_Figure_S1c_OD600_OD660_relationship.tsv
    251 Bytes
  • FS2_Data_for_Figure_S2_correlation_matrix.tsv
    1.49 KiB
  • T1_Data_for_Table_1_mass_TOC_TS_RSH_concentration.tsv
    1.2 KiB
  • T2_Data_for_Table_2 _mass_TOC_TS_RSH_distribution.tsv
    1.14 KiB
  • T3_Data_for_Table_3_S speciation.tsv
    731 Bytes
  • T4_Data_for_Table_4_first_shell_fits_Hg_EXAFS.tsv
    2.54 KiB
  • TS1_Data_for_Table_S1_Hg_loss.tsv
    3.26 KiB
  • TS2_Data_for_Table_S2_mass.tsv
    870 Bytes
  • TS3_Data_for_Table_S3_TOC.tsv
    982 Bytes
  • TS4_Data_for_Table S4_TS.tsv
    802 Bytes
  • TS5_Data_for_Table_S5_1st_and_2nd_shell_fits_Hg_EXAFS .tsv
    4.08 KiB

Documentation files

  • README.txt
    16.44 KiB

Citation and access

Data access level:

Creator/​Principal investigator(s):

Research principal:

Principal's reference number:

  • SLU.seksko.2025.4.2-76

Data contains personal data:

No

Citation:

License:

Language:

Method and outcome

Time period(s) investigated:

Data format/​data structure:

Species and taxons:

Data collection Laboratory experiment

Mode of collection:

Laboratory experiment

Description of the mode of collection:

Hg LIII-edge EXAFS spectra were acquired at Diamond Light Source (Beamline I20-scanning). Data analysis and fitting were carried out using WinXAS in combination with FEFF-7.

Time period(s) for data collection:

2022-05-01 - 2025-04-30

Data collector:

Source of the data:

  • Processes
  • Biological samples

Instrument

Name:

Synchrotron X-ray facility

Type:

Technical instrument(s)

Description of the instrument:

Synchrotron X-ray Beamline I20-scanning at Synchrotron X-ray facility, Diamond Light Source, UK

Data collection Laboratory experiment

Mode of collection:

Laboratory experiment

Description of the mode of collection:

Total organic carbon and total sulfur content were quantified using an elemental analyzer (Vario MACRO cube) with a relative standard deviation (RSD) of 0.5%. Total mercury concentrations were determined by combustion atomic absorption spectrometry with a direct mercury analyzer (DMA-80, Milestone; detection limit = 0.01 ng; RSD = 6%).

Time period(s) for data collection:

2022-06-01 - 2024-10-31

Data collector:

Instrument

Name:

Elemental analyzer (Vario MACRO cube)

Type:

Technical instrument(s)

Name:

Direct mercury analyzer (DMA-80, Milestone)

Type:

Technical instrument(s)

Data collection Laboratory experiment

Mode of collection:

Laboratory experiment

Description of the mode of collection:

Sulfur K-edge XANES spectra were collected at the 4B7A Medium Energy X-ray Beamline of the Beijing Synchrotron Radiation Facility. Data processing, including normalization and linear combination fitting, was performed using the Larch software package.

Time period(s) for data collection:

2022-06-01 - 2024-12-31

Data collector:

Source of the data:

  • Processes
  • Biological samples

Instrument

Name:

Synchrotron X-ray facility

Type:

Technical instrument(s)

Description of the instrument:

Synchrotron X-ray at 4B7A Medium Energy X-ray Beamline of the Beijing Synchrotron Radiation Facility

Administrative information

Responsible department/​unit:

Department of Forest Ecology and Management

Funding

Funding agency:

Award number:

2021-00551_Formas

Award URI:

https://www.vr.se/english/swecris.html#/project/2021-00551_FormasOpens in a new tab

Award title:

Mechanisms of Cellular Mercury (II) Uptake by Mercury Methylating Bacteria

Topic and keywords

Standard för svensk indelning av forskningsämnen 2025:

Keywords:

Publications

Citation:

Meng F., Skyllberg U., Li Y., Hayama S., Björn E. and Song Y. (2026). Subcellular thiol functional group distribution in Geobacter sulfurreducens determined by Hg LIII-edge EXAFS. Frontiers in Microbiology, 16, 1728775. https://doi.org/10.3389/fmicb.2025.1728775Opens in a new tab

Contact

Yu Songyu.song@slu.seOpens in a new tab

Metadata

Versions

Version:

2

DOI:

https://doi.org/10.5878/r92f-7869Opens in a new tab

  • Metadata added:

    The README file was updated with information about a new data file and with a link to the published article.

  • Data added:

    An additional data file, “T2_Data_for_Table_2_mass_TOC_TS_RSH_distribution.tsv”, was added, reporting the percentage distribution of dry mass, total organic carbon (TOC), total sulfur (TS), and thiol groups (RSH) across extracellular and subcellular fractions of G. sulfurreducens.

Published:

Version:

1

DOI:

https://doi.org/10.5878/qpef-2205Opens in a new tab

Published:

doris
slu
Published: