README
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Dataset title:
Subcellular Thiol Distribution in Geobacter sulfurreducens Revealed by Hg LIII-Edge EXAFS: Research Data

Creators:
Yu Song

Contact for Data:
Yu Song (yu.song@slu.se)

Keywords
mercury (Hg), thiols, subcellular fractions, Geobacter sulfurreducens, EXAFS, XANES, microbial uptake, environmental geochemistry

Description:
This dataset contains research data for the manuscript “Subcellular Thiol Functional Group Distribution in Geobacter sulfurreducens Determined by Hg LIII-Edge EXAFS”, submitted to Geochimica et Cosmochimica Acta. 

- File Format
All data are provided in tab-delimited text and TSV files, suitable for direct reuse in R, Python, or spreadsheet software. 

- License
Creative Commons Public Domain Dedication (CC0 1.0)


- Material and analytical methods: 

The dataset includes 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 Geobacter sulfurreducens PCA (G. sulfurreducens, 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 methodological details will be available in the published article, which will be attached once the manuscript is accepted.


Details of Data Files: 

- F2_Data_for_Figure_2 _mass_TOC_TS_RSH.tsv: mass, TOC, TS, and RSH distributions across subcellular compartments in G. sulfurreducens.
Column 1: sample type "(a)" represents distribution within whole cells, excluding extracellular fractions; "(b)" represents distribution in the bacterial culture, including both whole-cell and extracellular fractions.
Column 2: subcellular compartments, including cytoplasm, periplasm, inner membrane, outer membrane, and debris.
Column 3: names of the analytical indicators, including mass, total organic carbon (TOC), total sulfur (TS), and thiol functional group (RSH). 
Columns 4 and 5: distribution values (%) and standard deviations (SD) of the different analytical indicators. 

- F3a_Data_for_Figure_3a_S_xanes_data_and_fitting.tsv: Sulfur XANES data and fitting of G. sulfurreducens 
Column 1: subcellular compartments, including extracellular, cytoplasm, periplasm, and whole-cell.
Column 2: energy (eV)
Column 3: "variable" indicates different S XANES datasets or components, including data (raw data); fit (linear combination fitting, LCF); individual S species (RSSR, RSH, RSR, Sulfoxide, Sulfonate, SO4).
Column 4: absorption value

- F3b_Data_for_Figure_3b_S_speciation.tsv: S xanes data and fitting.tsv: sulfur speciation in subcellular fractions of G. sulfurreducens.
Column 1: subcellular compartments, including extracellular, cytoplasm, periplasm, and whole-cell.
Column 2: S speciation, including RSSR, RSH, RSR, Sulfoxide, Sulfonate, and SO4. 
Column 3: S species contribution.
Column 4: S species percentage (%).

- F4_Data_for_Figure_4_EXAFS_data_and_fitting.tsv: Hg EXAFS data and fitting for cytoplasmic, periplasmic, extracellular, and whole-cell samples of G. sulfurreducens.

Column 1: space includes k_space_data and r_space_data, indicating EXAFS spectra in k-space, and Fourier-transformed (FT) spectra (not phase corrected) in R-space.
Column 2: energy in k space (Å−1).
Column 3: weighted EXAFS oscillation function, χ(k)k3 (Å-3) in k space and |χ(k)k3| (Å-4) in R space.
Column 4: "variable" includes Data and Fit, representing the raw and fitting data, respectively.
Column 5: subcellular compartments, including extracellular, cytoplasm, periplasm, and whole-cell.
Column 6: "stage" refers to the mid- or late-exponential growth phase.
Column 7: "Std" = Standard growth medium, "HC" = High-carbon medium (3× fumarate), "HS"= High-sulfur medium (10× sulfate), "Di"= Cell disruptor treatment.
Column 8:  final Hg concentration (µmol g−1).

- F5_Data_for_Figure_5_first_derivative_Hg_XANES.tsv: First-derivative Hg XANES for cytoplasmic, periplasmic, extracellular, and whole-cell samples of G. sulfurreducens.
Column 1: energy (eV).
Column 2: first derivative absorption.
Column 3: subcellular compartments, including extracellular, cytoplasm, periplasm, and whole-cell.
Column 4: OD600 refers to the optical density measured at 600nm.
Column 5: "stage" refers to the mid- or late-exponential growth phase.
Column 6: "Std" = Standard growth medium, "HC" = High-carbon medium (3× fumarate), "HS"= High-sulfur medium (10× sulfate), "Di"= Cell disruptor treatment.
Column 7: final Hg concentration in µmol g−1.

- F6_Data_for_Figure_6_Hg_loss.tsv: associated between Hg losses and the Hg-to-RSH ratio in extracellular and cytoplasmic fractions of G. sulfurreducens.
Column 1: Hg_add indicates the initial Hg(II) concentration added , 
Columns 2 and 3: Hg_final represents the final total Hg concentration determined after EXAFS experiments, and standard deviation (SD), respectively. 
Unit of Columns 1-3: (µmol g−1).
Columns 4 and 5: Hg loss and SD. Units for both are %.
Columns 6 and 7: Hg to thiol ratio and SD.
Column 8: "phase" refers to the mid- or late-exponential growth phase.
Columns 9 and 10: thiol (RSH) concentrations and SD. Units for both are µmol g−1.
Column 11: subcellular compartments, including extracellular and cytoplasm.
Column 12: "General" = Standard growth medium, "carbon" = High-carbon medium (3× fumarate), "sulfur"= High-sulfur medium (10× sulfate).

- FS1a_Data_for_Figure_S1a_cell_growth_curve.tsv: cell growth curve of G. sulfurreducens.
Column 1: time (day).
Columns 2 and 3: OD600 refers to the optical density measured at 600nm, and SD.

- FS1b_Data_for_Figure_S1b_cell_density.tsv: cell density of G. sulfurreducens.
Columns 1 and 2: OD600 refers to the optical density measured at 600nm, and SD.
Columns 3 and 4 represent the cell density (×1011 cell L-1) and standard deviation (SD), respectively.

- FS1c_Data_for_Figure_S1c_OD600_OD660_relationship.tsv: the relationship between OD600 and OD660  of G. sulfurreducens.
Columns 1 and 2: OD600 refers to the optical density measured at 600nm.
Columns 3 and 4: OD660 refers to the optical density measured at 660nm.

- FS2_Data_for_Figure_S2_correlation_matrix.tsv: the correlation matrix among dry mass, TOC, TS, and RSH of G. sulfurreducens.
Column 1: subcellular compartments, including cytoplasm, periplasm, inner membrane, outer membrane, and debris.
Column 2: "variable" lists the analytical indicators, including mass, total organic carbon (TOC), total sulfur (TS), and thiol functional group (RSH). 
Columns 3 and 4: concentrations of analytical indicators listed in column 2.
The corresponding units are shown in column 5.

- T1_Data_for_Table_1_mass_TOC_TS_RSH.tsv: mass, TOC, TS, and thiols (RSH) concentrations and distributions across subcellular compartments in G. sulfurreducens.
Column 1: subcellular compartments, including cytoplasm, periplasm, inner membrane, outer membrane, and debris.
Column 2: names of the analytical indicators, including mass, total organic carbon (TOC), total sulfur (TS), and thiol functional group (RSH). 
Columns 3 and 4: concentrations of mass, TS, and RSH, with units of (g cell-1), (μmol cell-1), and (μmol cell-1), respectively.

- T2_Data_for_Table_2_S speciation.tsv: sulfur speciation in subcellular fractions of G. sulfurreducens determined by Sulfur K-edge XANES.
Column 1: subcellular compartments, including cytoplasm, periplasm, extracellular, and whole-cell.
Column 2: S speciation, including RSSR, RSH, RSR, Sulfoxide, Sulfonate, and SO4. 
Column 3: S species contribution.
Column 4: S species percentage (%).

- T3_Data_for_Table_3_first_shell_fits_Hg_EXAFS.tsv: first coordination shell model fits to full k-space Hg LIII-edge EXAFS data in subcellular fractions of G. sulfurreducens.
Column 1: sample name follows the format "Subcellular - Growth Phase - Treatment", where: subcellular includes cytoplasm, periplasm, extracellular, and whole-cell. "Mid" refers to the middle-exponential phase, and "Late" refers to the late-exponential phase. "General" = Standard growth medium, "High carbon"= High-carbon medium (3× fumarate), "High sulfur" = High-sulfur medium (10× sulfate). 
Columns 2 and 3: final Hg concentrations and SD (µmol g−1).
Columns 4 and 5: RSH concentration and SD (µmol g−1).
Column 6: RSH concentration (×10-12 μmol cell-1)
Column 7: RSH concentration_SD (μmol cell-1)
Column 8: dletaE0 refers to Edge Energy Shift (eV).
Column 9: Merit-of-Fit (%), corresponding to "Rp" in the manuscript.
Columns 10-12:  Hg-Hg at Hg(RS)2, in the format "Hg-S_".
Columns 13-15:  Hg-O/N at Hg(RO/N)2, in the format "Hg-O_".
Columns 16-18:  Hg-Hg at Hg0, in the format "Hg-Hg_".
Columns 19-21:  Hg-S at HgS, in the format "Hg-S_".
CN refers to Coordination Number.
R refers to Bond Distance (Å).
sigma2 refers to the Debye-Waller factor (Å).

- TS1_Data_for_Table_S1_Hg_loss.tsv: Hg losses percentages in subcellular fractions of G. sulfurreducens during titration experiments.
Column 1: subcellular compartments, including cytoplasm, periplasm, extracellular, and whole-cell.
Column 2: sample name follows the format "Treatment - Growth Phase - OD", where: "General" = Standard growth medium, "High carbon"= High-carbon medium (3× fumarate), "High sulfur" = High-sulfur medium (10× sulfate). "Mid" refers to the middle-exponential phase, and "Late" refers to the late-exponential phase.
Column 3: Hg_add indicates the initial Hg(II) concentration added (µmol g−1).
Columns 4 and 5: Hg_final represents the final total Hg concentration determined after EXAFS experiments, and SD, respectively. 
Columns 6 and 7: Hg losses and SD.

- TS2_Data_for_Table_S2_mass.tsv: dry mass and distributions across subcellular compartments in G. sulfurreducens.
Column 1: subcellular compartments, including cytoplasm, periplasm, extracellular, membranes, inner membrane. outer membrane, and whole-cell. "Membranes" indicates pooled values when inner and outer membranes are not separated. Recovery (%) calculated as: (cytoplasm + periplasm + inner membrane + outer membrane + debris) / whole-cell × 100%.
Columns 2 and 3: subcellular dry mass values obtained using "Protocol 1" subcellular isolation method.
Columns 4 and 5: subcellular dry mass values obtained using "Protocol 2" subcellular isolation method.
Columns 6 and 7: averaged or final results from Protocols 1 and 2.
unit of Columns 2-7: (×10-12 g cell-1).
Columns 8 and 9: percentage of each subcellular fraction relative to the total whole-cell mass (excluding extracellular fractions).
Columns 10 and 11: percentage of each fraction relative to total biomass in the entire culture (including both whole-cell and extracellular fractions).
unit of Columns 8-11: (%).

- TS3_Data_for_Table_S3_TOC.tsv: TOC concentrations and distributions across subcellular compartments in G. sulfurreducens.
Column 1: subcellular compartments, including cytoplasm, periplasm, extracellular, membranes, inner membrane. outer membrane, and whole-cell. "Membranes" indicates pooled values when inner and outer membranes are not separated. Recovery (%) calculated as: (cytoplasm + periplasm + inner membrane + outer membrane + debris) / whole-cell × 100%.
Columns 2 and 3: subcellular TOC values obtained using "Protocol 1" subcellular isolation method.
Columns 4 and 5: subcellular TOC values obtained using "Protocol 2" subcellular isolation method.
Columns 6 and 7: averaged or final results from Protocols 1 and 2.
unit of Columns 2-7: (×10-13 g cell-1).
Columns 8 and 9: percentage of TOC relative to the whole-cell (excluding extracellular content).
Columns 10 and 11: percentage of TOC in each fraction relative to cell culture (including both whole-cell and extracellular TOC).
Columns 12 and 13: percentage of TOC relative to the dry mass of each individual subcellular compartment.
unit of Columns 8-13: (%).

- TS4_Data_for_Table S4_TS.tsv: TS concentrations and distributions across subcellular compartments in G. sulfurreducens.
Column 1: subcellular compartments, including cytoplasm, periplasm, extracellular, membranes, inner membrane. outer membrane, and whole-cell. "Membranes" indicates pooled values when inner and outer membranes are not separated. Recovery (%) calculated as: (cytoplasm + periplasm + inner membrane + outer membrane + debris) / whole-cell × 100%.
Columns 2 and 3: subcellular TS values obtained using "Protocol 1" subcellular isolation method.
Columns 4 and 5: subcellular TS values obtained using "Protocol 2" subcellular isolation method.
Columns 6 and 7: averaged or final results from Protocols 1 and 2.
unit of Columns 2-7: (×10-10 μmol cell-1).
Columns 8 and 9: percentage of TS in the whole-cell (excluding the extracellular component).
Columns 10 and 11: percentage of TS relative to the dry mass of each individual subcellular compartment.
unit of Columns 8-11: (%).


- TS5_Data_for_Table_S5_1st_and_2nd_shell_fits_Hg_EXAFS .tsv: 1st and 2nd shell mode fitting data in subcellular fractions of G. sulfurreducens by Hg LIII-edge EXAFS.
Column 1: sample name follows the format " Subcellular - Growth Phase - Treatment", where: "Subcellular" includes cytoplasm, periplasm, extracellular, and whole cell. "mid" refers to the middle-exponential phase, and "late" refers to the late-exponential phase. "Standard" = Standard growth medium, "High carbon"= High-carbon medium (3× fumarate), "High sulfur" = High-sulfur medium (10× sulfate), "disruptor" = cell disruptor treatment.
Column 2: OD600 refers to the optical density measured at 600nm.
Columns 3 and 4: final Hg represents the final total Hg concentration (µmol g−1) determined after EXAFS experiments.
Column 5: dletaE0 refers to Edge Energy Shift (eV).
Column 6: Merit-of-Fit (%), corresponding to "Rp" in the manuscript.
Columns 7-9: 1st S coordination shell fitting at Hg(RS)2, in the format "Hg-S_"; Columns 10-12: 2nd C (-RS) coordination shell fitting at Hg(RS)2, in the format "Hg-C_"; Columns 13-15: MS (S-Hg-S) fitting at Hg(RS)2, in the format "MS_"; Columns 16-18: 2nd RSSR coordination fitting at Hg(RS)2, in the format "RSSR_".
Columns 19-21: 1st O coordination shell fitting at Hg(RO/N)2, in the format "Hg-O_".
Columns 22-24:  Hg-Hg1 fitting at Hg0, in the format "Hg-Hg1_"; Columns 25-27:  Hg-Hg2 fitting at Hg0, in the format "Hg-Hg2_"; Columns 28-30:  Hg-Hg3 fitting at Hg0, in the format "Hg-Hg3_"; Columns 31-33:  Hg-Hg4 fitting at Hg0, in the format "Hg-Hg4_".
Columns 34-36:  1st S coordination shell fitting at HgS, in the format "1st S shell_"; Columns 37-39:  2nd Hg coordination shell fitting at HgS, in the format "2nd Hg shell_"; Columns 40-42:  2nd S coordination shell fitting at HgS, in the format "2nd S shell_".
CN refers to Coordination Number.
R refers to Bond Distance (Å).
sigma2 refers to the Debye-Waller factor (Å).

File dependencies and relationships:
F3b and T2 share the same dataset.
F6 and TS1 contain partially overlapping data.
F2, FS2, TS2, TS3, and TS4 are interrelated and dependent on each other.
TS5 includes the data from T3.

Notes on data representation
n.a. = not available
n.d. = not determined
“/ " and space = no data
Scientific notation (e.g., 1.2E-03) represents values in the form ×10ⁿ (here, 1.2×10⁻³)