Polydymite mineral
Polydymite is the cubic nickel thiospinel mineral species, with IMA formula Ni2+Ni3+2S4 (Ni3S4), distinct from Fe-bearing violarite, other nickel sulfides, elemental nickel and mixed ores. The September 2026 IMA-CNMNC list gives grandfathered status and original-description year 1876; that year is not a unique approval accession. The curated mechanism concerns a synthetic mineral-assigned component of laboratory precipitates. No nickel criticality designation or industrial deployment is inherited.
Microbial & Biochemical Mechanisms (1)
Polydymite-assigned minor phase in processed nickel-sulfide culture solids
biomineralization
Microbial
Associated Organisms:
Nitratidesulfovibrio vulgaris str. Hildenborough (NCBITaxon:882)
Processed Hildenborough culture precipitates contain particles assigned to polydymite, alongside other nickel sulfides. Abiotic products also contain the assigned phase, and oxidation during preparation remains a plausible source. The observation does not demonstrate that live cells specifically synthesized polydymite before harvest.
Experimental Context & Analytical Limits:
Mansor2019 Methods pp.3–4: the reported culture is Desulfovibrio vulgaris DSM 644, Hildenborough/ATCC 29579; current authority name is Nitratidesulfovibrio vulgaris str. Hildenborough. Anoxic modified metal toxicity medium contained lactate, sulfate, yeast extract, tryptone and HEPES, initially pH 7.2. NiCl2 and FeSO4 stocks supplied a nominal total of 500 micromolar Ni plus Fe across No Fe, 5:1, 1:1 and 1:5 Ni/Fe arms. No Fe means no intentionally added Fe stock, not a demonstrated trace-Fe-free medium. After 72 h pre-growth at 30 degrees C with shaking, 1% volume inoculum was transferred into 100 mL metal-amended medium; the actual mineral-incubation temperature and shaking rate are not restated separately. Biotic products were sampled after 6–25 days. XRD pellets were rinsed and dried on glass; TEM pellets underwent detergent, lysozyme and proteinase K treatment for 1 h at 45 degrees C, followed by washing, shipping and up to 1 h sonication. The abiotic comparison instead titrated 50 mL of 15 mM sodium sulfide at 2 mL/h into 50 mL double-strength medium, aged 5–36 days and harvested solids by filtration. This gives a nominal 7.5 mM final chemically added sulfide, not a measured biotic sulfide concentration. Final bulk pH was approximately 7.1 in biotic arms versus approximately 8.0–8.2 in abiotic arms; the arms are not matched for pH, sulfide delivery, sampling times or harvesting. These are laboratory salt-solution experiments, not treatment of an industrial waste or natural ore.
Mansor2019 Methods pp.3–4: the reported culture is Desulfovibrio vulgaris DSM 644, Hildenborough/ATCC 29579; current authority name is Nitratidesulfovibrio vulgaris str. Hildenborough. Anoxic modified metal toxicity medium contained lactate, sulfate, yeast extract, tryptone and HEPES, initially pH 7.2. NiCl2 and FeSO4 stocks supplied a nominal total of 500 micromolar Ni plus Fe across No Fe, 5:1, 1:1 and 1:5 Ni/Fe arms. No Fe means no intentionally added Fe stock, not a demonstrated trace-Fe-free medium. After 72 h pre-growth at 30 degrees C with shaking, 1% volume inoculum was transferred into 100 mL metal-amended medium; the actual mineral-incubation temperature and shaking rate are not restated separately. Biotic products were sampled after 6–25 days. XRD pellets were rinsed and dried on glass; TEM pellets underwent detergent, lysozyme and proteinase K treatment for 1 h at 45 degrees C, followed by washing, shipping and up to 1 h sonication. The abiotic comparison instead titrated 50 mL of 15 mM sodium sulfide at 2 mL/h into 50 mL double-strength medium, aged 5–36 days and harvested solids by filtration. This gives a nominal 7.5 mM final chemically added sulfide, not a measured biotic sulfide concentration. Final bulk pH was approximately 7.1 in biotic arms versus approximately 8.0–8.2 in abiotic arms; the arms are not matched for pH, sulfide delivery, sampling times or harvesting. These are laboratory salt-solution experiments, not treatment of an industrial waste or natural ore.
Curated Evidence Points:
Support
Source:
mansor2019
Table 2, Results p.5 and Figure 4d assign a minor irregular-particle component in Ni-rich products to polydymite, using lattice fringes near 3.34 angstrom. The No Fe culture products also contain precursor particles and vaesite. This is a source-assigned minor component of mixed recovered solids, not a phase-pure product.
Partial
Source:
mansor2019
Discussion pp.7–8 explicitly raises oxidation during mounting or transport as an explanation for polydymite in Fe-poor abiotic samples, including possible formation under very low oxygen. That preparation alternative cannot be dismissed for the culture solids. In Fe-containing experiments the source uses polydymite/violarite because their reflections overlap; those mixed assignments are not counted as unambiguous pure polydymite evidence.
Partial
Source:
mansor2019_si
Table S1 places polydymite and violarite 220 reflections at approximately 3.34 and 3.35 angstrom, respectively. The annotated Figure 4c panel instead labels the 3.38 angstrom reflection 100p, conflicting with the main-text 220 assignment. The Figure 5b diffraction annotation also contains indices that do not align consistently with the tabulated thiospinel assignments. These unresolved labels and phase overlap limit detailed structural claims; source-level particle assignment is retained without a new crystallographic identification.
Partial
Source:
mansor2019
Methods pp.3–4, Table 2 and Figures 2–4: no independent bottle-replicate count or killed-cell, cell-free metabolite, pH-matched or sulfide-flux-matched comparison is reported. Table 2 n values count EDS analyses and the particle-size histograms count individual particles, not independent cultures. EDS is explicitly semi-quantitative; XRD mostly shows poorly crystalline mixtures. No phase-specific yield, isolated product purity, Ni recovery mass balance or long-term stability challenge is demonstrated.
Partial
Source:
mansor2019
Discussion pp.8–12 and Figures 9–11 propose acidic cell-surface microenvironments, secreted organics and altered nucleation/growth as explanations. Local pH, specific metabolites and enzymes were not directly measured in this experiment; Figure 9 is a proposed sequence and Figure 10 a literature-derived solubility model, not direct observations of a cell-local pathway. Preparation can affect phase identity: the authors observed later oxidation of some Fe-rich samples and analyzed grids within 24 h. Their short air-drying comparison does not establish that all phase formation preceded harvest. No industrial deployment or universal microbial requirement is inferred.
Context_only
Source:
dsm644
The DSMZ catalogue links DSM 644 to Hildenborough and ATCC 29579 under the current Nitratidesulfovibrio name. Together with NCBI strain entry 882 this grounds the reported strain label; it is not a genomic authentication of the inoculum or a separate precipitation experiment.
Sources & References
-
ima202609: IMA-CNMNC (September 2026). The New IMA List of Minerals. Definitions p.1; Polydymite row p.175: Ni2+Ni3+2S4, G (grandfathered), original-description year 1876.
https://cnmnc.units.it/files/editor/IMA_Master_List_(2026-09).pdf (accessed 2026-10-14) -
mansor2019: Mansor, M., Winkler, C., Hochella, M. F. Jr. and Xu, J. (2019). Nanoparticulate Nickel-Hosting Phases in Sulfidic Environments: Effects of Ferrous Iron and Bacterial Presence on Mineral Formation Mechanism and Solid-Phase Nickel Distribution. Frontiers in Earth Science 7:151. DOI 10.3389/feart.2019.00151. Full primary PDF, Methods pp.3–4, Results pp.4–6, Figures 1–11, Tables 1–2 and Discussion pp.6–13.
https://doi.org/10.3389/feart.2019.00151 (accessed 2026-10-14) -
mansor2019_si: Mansor et al. (2019), associated Supplementary Material, Table_1 DOCX. DOI 10.3389/feart.2019.00151.s001; Frontiers Figshare article 8323754, file 15598037. Nine annotated diffraction panels and Table S1.
https://doi.org/10.3389/feart.2019.00151.s001 (accessed 2026-10-14) -
taxonomy_hildenborough: NCBI Taxonomy 882 — Nitratidesulfovibrio vulgaris str. Hildenborough, strain rank; historical Desulfovibrio vulgaris ATCC 29579 name retained as equivalent.
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=882&mode=Info (accessed 2026-10-14) -
dsm644: DSMZ catalogue DSM 644 — Nitratidesulfovibrio vulgaris, Hildenborough; lists ATCC 29579, NCIMB 8303 and VKM B-1760. Current name and collection equivalence, not an independent authentication of the experimental inoculum.
https://www.dsmz.de/collection/catalogue/details/culture/DSM-644 (accessed 2026-10-14)
Curation History
| Timestamp | Curator | Action | Summary |
|---|---|---|---|
2026-10-14T10:05:48Z |
codex (GPT-6) | CREATE | Created an evidence-backed mineral record from current IMA identity and full Mansor2019 primary study with its diffraction supplement; retained mixed-phase, abiotic, preparation, replication and mechanistic uncertainties. This shares one experiment with the other round68 nickel-sulfide owners. |
Record source: data/records/polydymite.yaml