Probing the fate of structurally distinct Siderophores with reactive soil components
Data files
May 01, 2026 version files 115.44 KB
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Evers_2025_GCA_Data.zip
112.42 KB
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README.md
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Abstract
Siderophores, iron (Fe) chelating agents produced by fungi, bacteria, and grassy plants, play critical roles in the acquisition of Fe and other trace metals in terrestrial systems. Siderophores are essential to proper plant nutrition as well as the maintenance of soil quality and the suppression of plant diseases. The ability of siderophores to solubilize metals from minerals and the details of cellular uptake systems have been well-explored. However, limited studies have investigated mineral surface disruption of siderophore-promoted nutrient uptake processes, or the variable fate of structurally distinct siderophores and their metal complexes. Here, we examine the bacterial trishydroxamate siderophore desferrioxamine B (DFOB), the bacterial triscatecholamide siderophore protochelin, and the synthetic carboxylate phytosiderophore analog proline-2’-deoxymugeneic acid (PDMA), with soil aluminosilicates and metal (oxyhydr)oxides, including montmorillonite, kaolinite, goethite, ferrihydrite, and δ-MnO2. Apo- and metal-siderophore complex sorption was studied using adsorption isotherm experiments, and the fate of complexes on the mineral surfaces was studied using gallium X-ray absorption spectroscopy. In general, siderophore–mineral interactions were governed by complex charge, molecular structure, and mineral surface reactivity. DFOB and PDMA complexes exhibited similar overall trends, with swelling clays acting as major sinks through intercalation of DFOB complexes and inner-sphere adsorption of PDMA complexes. Both showed limited retention on Fe (oxyhydr)oxides, with evidence for complex dissociation on ferrihydrite and inner-sphere complexation on goethite. In contrast, apo-PDMA showed negligible adsorption across all minerals, highlighting the importance of metal complexation in controlling phytosiderophore reactivity. Protochelin exhibited distinct behavior, with its anionic, hydrophobic complexes showing limited sorption, extensive dissociation, and susceptibility to degradation, particularly in reactions with montmorillonite and δ-MnO2. Across all siderophores, Mn oxides promoted reductive dissolution with concomitant ligand degradation, indicating that mineral-driven transformation processes can be as important as sorption in controlling siderophore fate. Understanding these differences in siderophore fate will provide a new angle for managing agricultural systems so that nutrient deficiencies and crop disease susceptibility are minimized.
Dataset DOI: 10.5061/dryad.4b8gthtsq
Description of the data and file structure
File: Evers_2025_GCA_Data.zip
Figures 2-7
Figure 2-7 contain adsorption isotherm data for the siderophores/Fe-siderophore complexes of DFOB, PDMA, or protochelin, onto the minerals, montmorillonite, kaolinite, goethite, ferrihydrite, and birnessite where:
- measured C (micromolar siderophore)= equilibrium concentration of siderophore/Fe-siderophore in the supernatant
- measured S (micromolar siderophore/g soil)= amount of siderophore/Fe-siderophore adsorbed to the mineral
- modeled S (micromolar siderophore/ g soil)= Langmuir/freundlich isotherm fits of the data
Example for Figures 2-7: For Figure 4, the figure is composed of 4 individual isotherms. Figure 4 contains isotherm data for Fe-PDMA birnessite, Fe-PDMA ferrihydrite, Fe-PDMA montmorillonite, and Fe-PDMA goethite. The file "FePDMA goethite"; contains isotherm data for Fe-PDMA complex adsorbing onto the iron oxide goethite as well as a fit for that data; measured C (x axis), measured S (y axis) , and Modeled S (y axis). Modeled S is a fitting tool, and is represented as a dashed line in the figures. For isotherms were no adsorption occurred, there is no individual file associated with that mineral.
Figures 8-10
Figure 8-10 are EXAFS chi spectra of Ga-siderophore adsorbed to mineral surfaces
x axis=k(Å^-1) ^
y axis=χ(k)*(k^3)
Example file: "Figure 8"; this file contains data for the entire figure (Ga-DFOB (aq), GaDFOB goethite, Ga-DFOB montmorillonite, Ga-DFOB kaolinite, Ga-DFOB birnessite, Ga-DFOB ferrihydrite) Each set of data (For example Ga-DFOB montmorillonite) contains 4 columns; where the first column represents the x axis, and the second column is the y (this x and y is raw data), the third column is the x axis again, and the fourth column is the least square fit for the second column (also y axis).
SI Figures 1-2
SI Figures 1-2 represent Manganese (Mn) dissolution data from isotherms, where; x axis is in micromolar siderophore present in solution, and the y axis is micromolar Mn dissolved into solution.
SI Figures 3
SI Figure 3: a) Aqueous Ga(III)-PDMA and Ga(III)-protochelin Ga K-edge EXAFS spectra
x axis=k(Å^-1)
y axis=χ(k)*(k^3)
b) FT magnitude plots of Ga(III)-PDMA and Ga(III)-protochelin.
x axis= R+deltaR y axis=FT magnitude (unitless)
SI Figures 4
SI Figure 4: a) Ga(III)-mineral Ga K-edge EXAFS spectra
x axis=k(Å^-1)
y axis=χ(k)*(k^3)
b) FT magnitude plots of Ga(III)-mineral samples.
x axis= R+deltaR y axis=FT magnitude (unitless)
Sorption Isotherms (Figures 2-7). Sorption experiments were performed with apo-siderophores, and with Fe(III)- and Ga(III)-siderophore complexes. DFOB, PDMA, and protochelin isotherms were conducted with a solid to solution ratio of 2 g/L, 10 mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer, and 0.02 M KCl background electrolyte, at pH 6. Initial concentrations included 0, 10, 50, 100, 150, 200, 250, 300, 400, and 500 µM siderophore or siderophore complex. Sorption (q) was calculated as amount lost from solution per gram solid, and equilibrium concentration refers to µM siderophore remaining in solution.
X-ray absorption spectroscopy (Figures 8-10). Gallium K-edge extended X-ray absorption fine structure (EXAFS) spectra were collected at room temperature at Stanford Synchrotron Radiation Lightsource (SSRL) or the Advanced Photon Source. Spectra were collected for most Ga(III)-siderophore sorbed to mineral surfaces, free Ga sorbed to mineral surfaces, and aqueous Ga(III)-PDMA and Ga(III)-protochelin complexes. Spectra were energy calibrated, averaged, background-subtracted, splined, and least square fit (Kelly, Hesterberg et al. 2008) using the SixPACK interface (Webb 2005), which makes use of the IFEFFIT code (Newville 2001). Using the standards above, linear combination fitting with the spectra of the Ga(III)-sorbed to minerals surfaces and the aqueous Ga(III)-siderophore complexes (Kruft et al. 2013) was used to analyze the spectra of Ga(III)-siderophore complex reacted with corresponding mineral surface to better understand surface complexation structures for on the mineral surface.
