Long-distance electron transfer along redox gradients in the subsurface
Cite this dataset
Zhang, Yanting et al. (2024). Long-distance electron transfer along redox gradients in the subsurface [Dataset]. Dryad. https://doi.org/10.5061/dryad.xd2547dq8
Abstract
Electron transfer (ET) is the fundamental process of life and element cycling. In the subsurface, the distance of ET determines its influencing area, normally as short as nanometers or micrometers. Here we provide direct evidence from column experiments that ET can last over 10 cm along the redox gradient in sediment columns, through a long-distance ET chain constituted by a series of short-distance electron hopping reactions involving with microbes and redox-active species like iron ions (and/or minerals) and natural organic matters. Microbial processes contribute largely under biologically active conditions, while chemical processes are important under extremely acidic/alkaline and cold conditions. Microbial and chemical processes synergistically mediate the long-distance ET process, with an estimated electron flux of 6.73 μmol e-/cm2 per day. This long-distance ET represents an overlooked but important background process influencing subsurface biogeochemical processes and remediation activities.
README: Long-distance electron transfer along redox gradients in the subsurface
https://doi.org/10.5061/dryad.xd2547dq8
This dataset corresponds to the experimental source data associated with the research paper titled "Long-distance electron transfer along redox gradients in the subsurface." The data, obtained through experimental testing, include comprehensive insights into empirical foundations and results presented in the paper. The dataset is structured within a compressed archive containing 2 folders and 6 Excel tables.
Description of the data and file structure
FOLDER & FILE OVERVIEW
1. Folder List:
A) Sediment_EDCandFeII
Including the following six lists:
a) Initial_EDCandFeII.xlsx
b) DifferentTextures_EDC.xlsx
c) DifferentTextures_Fe(II).xlsx
d) DifferentSterilized_EDC.xlsx
e) DifferentSterilized_FeII.xlsx
f) DifferentPerturbated_EDC.xlsx
B) SedimentPoreWater_DissolvedSpecies
Including the following three lists:
a) Sterilized_Pertuated_DissolvedSpecies.xlsx
b) SedimentPoreWater_EDCandEAC.xlsx
c) Gamma_DissolvedSpecies.xlsx
2. Individual File List:
A) XRD.xlsx
B) EDC_Feasibility.xlsx
C) RNA_based_16S rRNA_genes.xlsx
D) AmpliconSequenceAnalysis_MicrobialCommunity.xlsx
E) PerturbatedColumns_pH.xlsx
F) ETflux_CalculationData.xlsx
3. Relationship between files, if important: None
4. Additional related data collected that was not included in the current data package: None
5. Are there multiple versions of the dataset? No
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DATA-SPECIFIC INFORMATION FOR: Initial_EDCandFeII.xlsx
1. Number of data titles: 20
2. Number of sheets: 2
3. Experimental systems：
* sand column (treated by HgCl2 + NaN3): the sand loams in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* silt column (treated by HgCl2 + NaN3): the silt loams in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* clay loam-1 column (treated by HgCl2 + NaN3): the clay loam-1 sediments in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* clay loam-1 column (inclusion of sand): the clay loam-1 column (treated by HgCl2 + NaN3) was filled with inclusion of sand at the interface.
* clay loam-1 column (inclusion of 1-cm sterilized): the clay loam-1 column (treated by HgCl2 + NaN3) was with inclusion of a 1-cm thick clay loam-1 interlayer treated by concentrated HgCl2 + NaN3 above or below the interface
* untreated clay loam-1 columns: the clay loam-1 column with no treatment.
* autoclaved clay loam-1 columns: the clay loam-1 sediments in the column were autoclaved prior to filling.
* O2-perturbated clay loam-1 columns: the clay loam-1 column was treated by O2-perturbation.
* high initial △Eh of clay loam-2 + clay loam-1 columns (treated by HgCl2 + NaN3): this column refers to the bottom half filled with reduced clay loam-1 and the upper half filled with oxidized clay loam-2. Both clay loam-1 and clay loam-2 sediments in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* untreated clay loam-2 columns: the clay loam-2 column with no treatment.
*“Low temperature” clay loam-2 columns: the clay loam-2 column was treated by low temperature.
*“Acid perturbation” clay loam-2 columns: the initial pH of clay loam-2 sediments in the column was acidified to ~4.
*“Base perturbation” clay loam-2 columns: the initial pH of clay loam-2 sediments in the column was alkalized to ~12.
*“Gamma-rays” clay loam-3 columns: the clay loam-3 column was treated by gamma radiation.
4. Reaction time point：0 d
5. Variables description:
* EDC: refers to electron donating capacity.
* Fe(II): refers to iron(II).
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: DifferentTextures_EDC.xlsx
1. Number of data titles: 11
2. Number of sheets: 4
3. Experimental systems：
* sand column (treated by HgCl2 + NaN3): the sand loams in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* silt column (treated by HgCl2 + NaN3): the silt loams in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* clay loam-1 column (treated by HgCl2 + NaN3): the clay loam-1 sediments in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* clay loam-1 column (inclusion of sand): the clay loam-1 column (treated by HgCl2 + NaN3) was filled with inclusion of sand at the interface.
4. Reaction time point：0 d, 8 d, 14 d, 24 d
5. Variables description:
* EDC: refers to electron donating capacity.
* DEDC: refers to variation of electron donating capacity (EDC).
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: DifferentTextures_Fe(II).xlsx
1. Number of data titles: 6
2. Number of sheets: 3
3. Experimental systems：
* silt column (treated by HgCl2 + NaN3): the silt loams in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* clay loam-1 column (treated by HgCl2 + NaN3): the clay loam-1 sediments in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* clay loam-1 column (inclusion of sand): the clay loam-1 column (treated by HgCl2 + NaN3) was filled with inclusion of sand at the interface.
4. Reaction time point：0 d, 8 d, 14 d, 24 d
5. Variables description:
* Fe(II): refers to iron(II).
* DFe(II): refers to variation of iron(II).
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: DifferentSterilized_EDC.xlsx
1. Number of data titles: 10
2. Number of sheets: 4
3. Experimental systems：
* untreated clay loam-1 columns: the clay loam-1 column with no treatment.
* autoclaved clay loam-1 columns: the clay loam-1 sediments in the column were autoclaved prior to filling.
*“Gamma-rays” clay loam-3 columns: the clay loam-3 column was treated by gamma radiation.
* clay loam-1 column (inclusion of 1-cm sterilized): the clay loam-1 column (treated by HgCl2 + NaN3) was with inclusion of a 1-cm thick clay loam-1 interlayer treated by concentrated HgCl2 + NaN3 above or below the interface
4. Reaction time point：0 d, 8 d, 14 d, 24 d
5. Variables description:
* EDC: refers to electron donating capacity.
* DEDC: refers to variation of electron donating capacity (EDC).
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: DifferentSterilized_FeII.xlsx
1. Number of data titles: 8
2. Number of sheets: 4
3. Experimental systems：
* untreated clay loam-1 columns: the clay loam-1 column with no treatment.
* autoclaved clay loam-1 columns: the clay loam-1 sediments in the column were autoclaved prior to filling.
*“Gamma-rays” clay loam-3 columns: the clay loam-3 column was treated by gamma radiation.
* clay loam-1 column (inclusion of 1-cm sterilized): the clay loam-1 column (treated by HgCl2 + NaN3) was with inclusion of a 1-cm thick clay loam-1 interlayer treated by concentrated HgCl2 + NaN3 above or below the interface
4. Reaction time point：0 d, 8 d, 14 d, 24 d
5. Variables description:
* Fe(II): refers to iron(II).
* DFe(II): refers to variation of iron(II).
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: DifferentPerturbated_EDC.xlsx
1. Number of data titles: 11
2. Number of sheets: 5
3. Experimental systems：
* untreated clay loam-2 columns: the clay loam-2 column with no treatment.
* O2-perturbated clay loam-1 columns: the clay loam-1 column was treated by O2-perturbation.
*“Low temperature” clay loam-2 columns: the clay loam-2 column was treated by low temperature.
*“Acid perturbation” clay loam-2 columns: the initial pH of clay loam-2 sediments in the column was acidified to ~4.
*“Base perturbation” clay loam-2 columns: the initial pH of clay loam-2 sediments in the column was alkalized to ~12.
4. Reaction time point：0 d, 8 d, 14 d, 24 d
5. Variables description:
* EDC: refers to electron donating capacity.
* DEDC: refers to variation of electron donating capacity (EDC).
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DATA-SPECIFIC INFORMATION FOR: Sterilized_Pertuated_DissolvedSpecies.xlsx
1. Number of data titles: 3
2. Number of sheets: 3
3. Experimental systems：
* oxidized clay loam-2 suspensions (Untreated): 500 g/L of oxidized clay loam-2 suspensions with no treatment.
* oxidized clay loam-2 suspensions (“HgCl2 + NaN3”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by 250 mg/L HgCl2 and 500 mg/L NaN3.
* oxidized clay loam-2 suspensions (“Concentrated HgCl2 + NaN3”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by concentrated HgCl2 (1 g/L) and NaN3 (9.75 g/L).
* oxidized clay loam-2 suspensions (“Autoclaved”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by autoclavation.
* oxidized clay loam-2 suspensions (“Gamma-rays”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by gamma radiation.
* oxidized clay loam-2 suspensions (“Acid perturbation”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by dilute H2SO4.
* oxidized clay loam-2 suspensions (“Base perturbation”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by dilute NaOH.
* oxidized clay loam-2 suspensions (“Low temperature”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by gamma radiation.
4. Reaction time point：0 d, 8 d, 14 d, 24 d
5. Variables description:
* DOC: refers to dissolved organic matter.
* dissolved total Fe: refers to total Fe in the aqueous phase of suspension.
* dissolved Fe(II): refers to Fe(II) in the aqueous phase of suspension.
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: SedimentPoreWater_EDCandEAC.xlsx
1. Number of data titles: 12
2. Number of sheets: 2
3. Experimental systems：
* sand column (treated by HgCl2 + NaN3): the sand loams in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* silt column (treated by HgCl2 + NaN3): the silt loams in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* clay loam-1 column (treated by HgCl2 + NaN3): the clay loam-1 sediments in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
4. Reaction time point：0 d
5. Variables description:
* water-extracted EDC value: the sediment samples in the column were mixed with water and then separated the water. The dissolved EDC value was measured as water-extracted EDC value.
* estimated EDC value: refers to the EDC value in the sediment pore which was calculated by converting the water-extracted EDC value based on the dilution factor and water content of sample.
* water-extracted EAC value: the sediment samples in the column were mixed with water and then separated the water. The dissolved EAC value was measured as water-extracted EDC value.
* estimated EAC value: refers to the EAC value in the sediment pore which was calculated by converting the water-extracted EAC value based on the dilution factor and water content of sample.
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: Gamma_DissolvedSpecies.xlsx
1. Number of data titles: 8
2. Number of sheets: 4
3. Experimental systems：
*“Gamma-rays” clay loam-3 columns: the clay loam-3 column was treated by gamma radiation.
4. Reaction time point：0 d, 24 d
5. Variables description:
* water-extracted DOC: the sediment samples in the column were mixed with water and then separated the water. The DOC value was measured as water-extracted DOC value.
* estimated DOC: refers to the DOC concentration in the sediment pore which was calculated by converting the water-extracted DOC concentration based on the dilution factor and water content of sample.
* water-extracted dissolved total Fe: the sediment samples in the column were mixed with water and then separated the water. The dissolved total Fe concentration was measured as water-extracted dissolved total Fe concentration.
* estimated dissolved total Fe: refers to the dissolved total Fe concentration in the sediment pore which was calculated by converting the water-extracted dissolved total Fe concentration based on the dilution factor and water content of sample.
* water-extracted dissolved Fe(II): the sediment samples in the column were mixed with water and then separated the water. The dissolved Fe(II) concentration was measured as water-extracted dissolved Fe(II) concentration.
* estimated dissolved Fe(II): refers to the dissolved Fe(II) concentration in the sediment pore which was calculated by converting the water-extracted dissolved Fe(II) concentration based on the dilution factor and water content of sample.
* water-extracted EDC value: the sediment samples in the column were mixed with water and then separated the water. The dissolved EDC value was measured as water-extracted EDC value.
* estimated EDC value: refers to the EDC value in the sediment pore which was calculated by converting the water-extracted EDC value based on the dilution factor and water content of sample.
* water-extracted EAC value: the sediment samples in the column were mixed with water and then separated the water. The dissolved EAC value was measured as water-extracted EDC value.
* estimated EAC value: refers to the EAC value in the sediment pore which was calculated by converting the water-extracted EAC value based on the dilution factor and water content of sample.
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: XRD.xlsx
1. Number of data titles: 2
2. Number of sheets: 2
3. Samples：
* pristine reduced clay loam
* pristine reduced silt loam
* pristine reduced sand loam
* clay loam-1 samples near the oxidized/reduced interface (locations at 1.3 and -1.3 cm) in the clay loam-1 column treated by 250 mg/L HgCl2 and 500 mg/L NaN3.
4. Reaction time point：0 d
5. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: EDC_Feasibility.xlsx
1. Number of data titles: 10
2. Number of sheets: 4
3. Experimental systems：
* oxidized clay loam-1 suspension: the oxidized clay loam-1 suspensions at the dosage of 200, 400 and 600 g/L.
* reduced clay loam-1 suspension: the reduced clay loam-1 suspensions at the dosage of 200, 400 and 600 g/L.
* mixed clay loam-1 suspension: The mixture of oxidized and reduced clay loam-1 at the dosage of 200 g/L.
* oxidized clay loam-2 suspension: the oxidized clay loam-2 suspensions at the dosage of 200 g/L.
* high initial △Eh of clay loam-2 + clay loam-1 columns (treated by HgCl2 + NaN3): this column refers to the bottom half filled with reduced clay loam-1 and the upper half filled with oxidized clay loam-2. Both clay loam-1 and clay loam-2 sediments in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* clay loam-2 + clay loam-1 columns with inclusion of quartz sand: this column refers to the bottom half filled with reduced clay loam-1 and the upper half filled with oxidized clay loam-2, with inclusion of 1-cm thick of quartz sand in the interface. Both clay loam-1 and clay loam-2 sediments in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
4. Reaction time point：0 d, 4 d, 8 d, 14 d, 24 d
5. Variables description:
* EDC: refers to electron donating capacity.
* DEDC: refers to variation of electron donating capacity (EDC).
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: RNA_based_16S rRNA_genes.xlsx
1. Number of data titles: 1
2. Number of sheets: 1
3. Experimental systems：
* oxidized clay loam-2 suspensions (Untreated): 500 g/L of oxidized clay loam-2 suspensions with no treatment.
* oxidized clay loam-2 suspensions (“HgCl2 + NaN3”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by 250 mg/L HgCl2 and 500 mg/L NaN3.
* oxidized clay loam-2 suspensions (“Concentrated HgCl2 + NaN3”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by concentrated HgCl2 (1 g/L) and NaN3 (9.75 g/L).
* oxidized clay loam-2 suspensions (“Autoclaved”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by autoclavation.
* oxidized clay loam-2 suspensions (“Gamma-rays”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by gamma radiation.
* oxidized clay loam-2 suspensions (“Acid perturbation”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by dilute H2SO4.
* oxidized clay loam-2 suspensions (“Base perturbation”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by dilute NaOH.
* oxidized clay loam-2 suspensions (“Low temperature”): the oxidized clay loam-2 sediments in the 500 g/L of suspension were treated by gamma radiation.
4. Reaction time point：0 d
5. Variables description:
* EDC: refers to electron donating capacity.
* Fe(II): refers to iron(II).
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: AmpliconSequenceAnalysis_MicrobialCommunity.xlsx
1. Number of data titles: 1
2. Number of sheets: 1
3. Experimental systems：
* clay loam-1 column (treated by HgCl2 + NaN3): the clay loam-1 sediments in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* clay loam-1 column (inclusion of 1-cm sterilized): the clay loam-1 column (treated by HgCl2 + NaN3) was with inclusion of a 1-cm thick clay loam-1 interlayer treated by concentrated HgCl2 + NaN3 above or below the interface
4. Reaction time point：0 d, 8 d, 24 d
5. Variables description:
* distribution of microbial community at genus-level.
6. Specialized statement: Sequence data are available in NCBI (BioProject PRJNA949398).
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DATA-SPECIFIC INFORMATION FOR: ETflux_CalculationData.xlsx
1. Number of data titles: 7
2. Number of sheets: 6
3. Experimental systems：
* clay loam-1 column (treated by HgCl2 + NaN3): the clay loam-1 sediments in the column were immersed in 250 mg/L HgCl2 and 500 mg/L NaN3 prior to filling.
* untreated clay loam-1 columns: the clay loam-1 column with no treatment.
* autoclaved clay loam-1 columns: the clay loam-1 sediments in the column were autoclaved prior to filling.
* O2-perturbated clay loam-1 columns: the clay loam-1 column was treated by O2-perturbation.
* untreated clay loam-2 columns: the clay loam-2 column with no treatment.
*“Low temperature” clay loam-2 columns: the clay loam-2 column was treated by low temperature.
*“Acid perturbation” clay loam-2 columns: the initial pH of clay loam-2 sediments in the column was acidified to ~4.
*“Base perturbation” clay loam-2 columns: the initial pH of clay loam-2 sediments in the column was alkalized to ~12.
*“Gamma-rays” clay loam-3 columns: the clay loam-3 column was treated by gamma radiation.
4. Reaction time point：0 d, 8 d, 14 d, 24 d
5. Variables description:
* ET flux: refers to the sum of DEDC in the whole reduced half or oxidized half.
6. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: PerturbatedColumns_pH.xlsx
1. Number of data titles: 1
2. Number of sheets: 1
3. Experimental systems：
*“Acid perturbation” clay loam-2 columns: the initial pH of clay loam-2 sediments in the column was acidified to ~4.
*“Base perturbation” clay loam-2 columns: the initial pH of clay loam-2 sediments in the column was alkalized to ~12.
4. Reaction time point：0 d, 8 d, 14 d, 24 d
5. Variables description:
* pH: refers to pH of sediment samples in the column.
6. Specialized formats or other abbreviations used: None
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Detailed Descriptions:
For a comprehensive understanding of the experimental setup and procedures, refer to the associated research paper. Proper citation and acknowledgment details are available in the original paper.
Methods
The data in this dataset were obtained through experimental testing, and the calculations and processing are documented within the dataset. For detailed information about the dataset, please refer to the "README" file.
Funding
National Natural Science Foundation of China, Award: 42025703
National Natural Science Foundation of China, Award: 42277072
National Key Technology Research and Development Program of China, Award: 2022YFC3701403