Silicate minerals as a direct source of limiting nutrients: Siderophore synthesis and uptake promote ferric iron bioavailability from olivine and microbial growth

TL;DR

Siderophore synthesis enables *Shewanella oneidensis* MR-1 to acquire iron directly from olivine and grow to >10⁹ cells/mL in iron-depleted medium, whereas a siderophore-synthesis deletion mutant shows a severe growth penalty unless supplied with siderophores. XPS and SEM evidence suggest siderophores strip a nanometre-scale ferric oxide surface layer, enhancing silicate dissolution and iron bioavailability at low micromolar concentrations.

Key findings

• MR-1 grew to >10⁹ cells/mL with olivine as the sole iron source; ΔMR-1 exhibited a pronounced growth penalty and extended lag phase, and CAS assays confirmed no de novo siderophore production. When ΔMR-1 received siderophore-replete MR-1 filtrate at 0 h or 24 h, it reached >10⁹ cells/mL, comparable to MR-1.
• With deferoxamine amendments, ΔMR-1 growth rate and stationary-phase density depended on siderophore concentration: ≥25 µM was required for growth rates and densities on par with MR-1, while concentrations below 5–10 µM significantly limited growth; stationary-phase densities followed a logarithmic relationship with siderophore concentration. These growth-limiting concentrations (≤5–10 µM) are lower than the hundreds to thousands of micromolar used in previous abiotic mineral-dissolution experiments.
• SEM showed etch-pit/scouring dissolution features on olivine exposed to siderophores (MR-1 or filtrate-amended ΔMR-1), absent in abiotic controls and ΔMR-1 without siderophore amendments. XPS of non-siderophore-exposed olivine gave Fe 2p₁/₂ peak positions of 709.37–710.30 eV, straddling ferrous and ferric end-members, whereas MR-1-exposed samples consistently showed ferrous-range spectra with poor signal-to-noise, suggesting depletion of a ferric surface layer.
• Ferrozine assays on filtered experimental solutions were below detection limit, suggesting the Mtr pathway for iron reduction did not play a significant role. The proposed mechanism is that siderophores remove a protective nanometre-thick ferric oxide coating, enhancing silicate dissolution and nutrient bioavailability.

Methods

• Oxic batch growth experiments used *S. oneidensis* MR-1 and the siderophore-synthesis deletion mutant ΔMR-1 (ΔSO3031) in 50 mL iron-depleted pH 7 M-1 minimal medium (50 mM MOPS buffer; 18 mM N-acetyl glucosamine as carbon source/electron donor), amended with 0.05 g olivine grains (150–300 µm; composition Mg₁.₇₆Fe₀.₂₄SiO₄, Fo88) as the sole iron source. Cultures were inoculated with 1.3×10⁹ cells (initial density 2.6×10⁷ cells/mL) and incubated at 30°C with shaking at 120 rpm.
• Filtrate amendment experiments were conducted in triplicate: MR-1; ΔMR-1 plus 5 mL siderophore-replete MR-1 filtrate at 0 h; ΔMR-1 plus filtrate at 24 h; ΔMR-1 with no siderophores; and killed controls. Commercial deferoxamine experiments used ΔMR-1 at 0, 0.05, 0.2, 1, 5, 10, 25, 50, and 100 µM; concentrations of 0, 0.05, 1, 50, and 100 µM were run in triplicate over full growth, while 0.2, 5, 10, and 25 µM were run in duplicate and measured only for final stationary-phase densities.
• Growth was monitored by OD₆₀₀ correlated to cell counts. Mineral surfaces were analyzed by SEM, XRF, and XPS; dissolved Fe(II) was measured by ferrozine assay on duplicate filtered samples (n = 2) from MR-1 and ΔMR-1 experiments with 50 µM deferoxamine at 45 h.

Limitations

• Stated: SEM images provide only a qualitative indication of dissolution and not a quantified measure along mineral surfaces; EDX maps did not provide conclusive elemental mobility or surface chemistry due to high detection limits; interactions between siderophore synthesis and amorphous silicate layers remain unclear; further work is needed on dissolution kinetics, iron release, and partitioning of iron between dissolved and cell-bound pools.
• Stated: XPS spectra from MR-1 experiments had poor signal-to-noise ratios, and structural differences between native putrebactin (cyclic di-hydroxamate) and deferoxamine (tris-hydroxamate) may cause different ligand:metal ratios and iron-mobility dynamics.
• Evident from the text: the study uses a single organism and a single silicate mineral under oxic, defined laboratory conditions; it does not directly measure siderophore concentrations at mineral surfaces or quantify dissolution rates; ferrozine measurements were below detection limit, limiting conclusions about Fe(II) dynamics.