Humboldtine mineral
Humboldtine is the iron(II) oxalate dihydrate mineral Fe(C2O4).2H2O, listed as a grandfathered species, with original-description year 1821, in the September 2026 IMA compilation. It is distinct from elemental iron, dissolved iron-oxalate complexes, other metal oxalates and the heterogeneous siderite- and pyrrhotite-bearing experimental feeds. No criticality designation is inherited from iron.
Microbial & Biochemical Mechanisms (2)
Humboldtine formation in Aspergillus niger cultures on two iron-bearing rocks
biomineralization
Microbial
Associated Organisms:
Aspergillus niger (NCBITaxon:5061)
Humboldtine-assigned crystals formed during laboratory culture of Aspergillus niger Ch 4/07 on siderite-bearing and altered pyrrhotite-bearing rocks. Powder diffraction supports the product identity, while the reported absence of iron-oxalate crystals in uninoculated controls supports a fungal contribution under these conditions. Organic-acid dissolution followed by iron-oxalate precipitation is the proposed explanation; neither a specific enzyme nor a measured iron-redox pathway is established. No isolated product yield, complete conversion or industrial deployment is demonstrated.
Experimental Context & Analytical Limits:
Ch 4/07 was isolated from weathered Proconesos marble at Chersonesos, Crimea; the authors identify it by ITS accession KF768341. The siderite feed from Dalnegorsk was chiefly Mg/Mn-bearing siderite with pyrite, muscovite, quartz and montmorillonite. The Pyrrhotite Gorge feed was largely replaced by poorly crystalline iron oxides/hydroxides and also contained quartz, kaolinite, albite and locally biotite. Neither feed was a pure mineral reagent. Autoclaved fragments about 1 by 0.5 by 0.5 cm were incubated in Petri dishes with 15 mL autoclaved Czapek-Dox medium: NaNO3 3.0, KH2PO4 1.0, MgSO4.7H2O 0.5, KCl 0.5, FeSO4.7H2O 0.015 and glucose 30.0 g/L. The medium therefore supplied some iron itself. Initial pH was 5.5; temperature is reported only as room temperature. Conidia and mycelial fragments from ten-day agar cultures were added, without a stated inoculum density. Triplicate syntheses and uninoculated controls ran for 3-18 days, with observations on days 3, 5, 7, 10, 14 and 18. No no-rock, killed-biomass, cell-free-metabolite or matched-pH comparison is reported, and iron origins were not mass-balanced.
Ch 4/07 was isolated from weathered Proconesos marble at Chersonesos, Crimea; the authors identify it by ITS accession KF768341. The siderite feed from Dalnegorsk was chiefly Mg/Mn-bearing siderite with pyrite, muscovite, quartz and montmorillonite. The Pyrrhotite Gorge feed was largely replaced by poorly crystalline iron oxides/hydroxides and also contained quartz, kaolinite, albite and locally biotite. Neither feed was a pure mineral reagent. Autoclaved fragments about 1 by 0.5 by 0.5 cm were incubated in Petri dishes with 15 mL autoclaved Czapek-Dox medium: NaNO3 3.0, KH2PO4 1.0, MgSO4.7H2O 0.5, KCl 0.5, FeSO4.7H2O 0.015 and glucose 30.0 g/L. The medium therefore supplied some iron itself. Initial pH was 5.5; temperature is reported only as room temperature. Conidia and mycelial fragments from ten-day agar cultures were added, without a stated inoculum density. Triplicate syntheses and uninoculated controls ran for 3-18 days, with observations on days 3, 5, 7, 10, 14 and 18. No no-rock, killed-biomass, cell-free-metabolite or matched-pH comparison is reported, and iron origins were not mass-balanced.
Curated Evidence Points:
Support
Source:
zelenskaya2021
Sections 2.1-3.2 and Figure 1a-d show PXRD-assigned humboldtine on siderite at day five and on altered pyrrhotite at day seven, at reported pH 3.5 plus or minus 0.5. PXRD used CoKalpha radiation and ICDD PDF-2 2016; SEM and EDX provide morphology and elemental context. Remaining substrate reflections preclude interpreting the patterns as pure product or complete conversion. Figures 2-3 show later crystal growth, splitting and dissolution features. Figure 4 and the Results report no iron-oxalate crystals in the uninoculated controls; the control figure caption does not give a sampling day and no quantitative control phase balance is supplied.
Partial
Source:
zelenskaya2021
The claim that formation begins earlier on pyrrhotite relies on day-three prismatic Fe-rich crystals seen by SEM/EDX, before the day-seven PXRD assignment. Morphology and elemental iron alone are not an independent early phase confirmation. The claimed slower crystallization, influence of impurity ions and coupled Fe(II)/Fe(III) reactions remain interpretations without quantitative dissolution rates, oxalate concentrations, redox measurements or independently varied impurity controls. The reported pyrrhotite-medium pH falls to 2 at day 14 and returns to 3.5 plus or minus 0.5 at day 18; the latter is called an initial value in Results, whereas the Methods' initial medium pH is 5.5.
Context_only
Source:
zelenskaya2021
Section 4 and Figure 5 describe a separate search in lichen-dominated biofilms from Kola Peninsula and Karelia iron ores, in which iron oxalates were not found and goethite was reported instead. This field observation limits transfer of the culture result to natural biofilms; it neither refutes the laboratory phase assignment nor establishes universal absence of humboldtine in nature. Earlier disputed lichen iron-oxalate claims cited in the Introduction are not adopted here.
Context_only
Source:
genbank_niger
KF768341.1 labels strain Ch 4/07 and species taxon 5061, supporting the reported ITS-based provenance. It is not a genome, a strain TaxID or independent authentication of the experimental culture.
Context_only
Source:
ncbi_taxonomy
NCBI verifies the species name and identifier, not a mineral-forming trait.
Organism- and feed-dependent humboldtine assignments in brown-rot fungal cultures
biomineralization
Microbial
Associated Organisms:
Serpula himantioides (NCBITaxon:80602), Coniophora puteana (NCBITaxon:80637), Amyloporia xantha (NCBITaxon:1333629), Serpula lacrymans (NCBITaxon:85982)
A separate laboratory comparison reports humboldtine in selected brown-rot fungal cultures on siderite- and altered pyrrhotite-bearing rocks. Phase assignments depend on the organism, feed and analytical method. Serpula lacrymans is included as a tested comparator without reported iron-oxalate products, not as a demonstrated producer. The study supports culture-associated mineral formation, without establishing a specific biochemical pathway, comparative recovery efficiency or deployment. The source name Antrodia xantha is retained in context; its sequence and current NCBI Taxonomy XML use Amyloporia xantha.
Experimental Context & Analytical Limits:
Table 2 identifies LE-BIN 1368 Serpula himantioides (KY352492), LE-BIN 1370 Coniophora puteana (KY433978), LE-BIN 1029 Antrodia xantha (KY433983) and LE-BIN 1192 Serpula lacrymans (KY352493). Table 3 describes Dalnegorsk Mg/Mn-bearing siderite with pyrite, muscovite, quartz and montmorillonite, and Pyrrhotite Gorge ore largely replaced by poorly crystalline iron oxides/hydroxides with other silicate phases. These are the same feed types/localities as the 2021 study, not purified siderite or pyrrhotite and not proof of identical individual specimens. Approximately 1 by 0.5 by 0.5 cm blocks received 20 mL liquid glucose-peptone medium in plastic Petri dishes, initial pH 5.5, at room temperature for 30 days. Inocula were mycelial fragments from ten-day glucose-peptone agar cultures; syntheses were in triplicate with uninoculated controls. Inoculum density and substrate sterilization are not specified. The listed agar-medium recipe includes FeSO4.7H2O 0.005 g/L; the liquid formulation is not separately tabulated, so a background-medium iron contribution is not excluded. No iron-source balance, oxalate assay, isolated-product mass, killed-biomass or cell-free comparison is reported. The paper specifies uninoculated controls but supplies no separate iron-arm control results or phase plots.
Table 2 identifies LE-BIN 1368 Serpula himantioides (KY352492), LE-BIN 1370 Coniophora puteana (KY433978), LE-BIN 1029 Antrodia xantha (KY433983) and LE-BIN 1192 Serpula lacrymans (KY352493). Table 3 describes Dalnegorsk Mg/Mn-bearing siderite with pyrite, muscovite, quartz and montmorillonite, and Pyrrhotite Gorge ore largely replaced by poorly crystalline iron oxides/hydroxides with other silicate phases. These are the same feed types/localities as the 2021 study, not purified siderite or pyrrhotite and not proof of identical individual specimens. Approximately 1 by 0.5 by 0.5 cm blocks received 20 mL liquid glucose-peptone medium in plastic Petri dishes, initial pH 5.5, at room temperature for 30 days. Inocula were mycelial fragments from ten-day glucose-peptone agar cultures; syntheses were in triplicate with uninoculated controls. Inoculum density and substrate sterilization are not specified. The listed agar-medium recipe includes FeSO4.7H2O 0.005 g/L; the liquid formulation is not separately tabulated, so a background-medium iron contribution is not excluded. No iron-source balance, oxalate assay, isolated-product mass, killed-biomass or cell-free comparison is reported. The paper specifies uninoculated controls but supplies no separate iron-arm control results or phase plots.
Curated Evidence Points:
Support
Source:
vlasov2023
Table 4 reports humboldtine by SEM/EDX and PXRD for S. himantioides on siderite at pH 3 and pyrrhotite at pH 2.5; Figures 6b-c show the assigned crystals. For A. xantha, Table 4 reports humboldtine by both methods on siderite at pH 2, and Figure 3f displays that diffraction pattern. Figure 7b also labels whewellite in this siderite specimen, whereas the table lists only humboldtine. The caption to Figure 3 explicitly notes substrate reflections; neither pattern nor morphology establishes a pure humboldtine product.
Partial
Source:
vlasov2023
For C. puteana on siderite at pH 5.5, Table 4 assigns humboldtine by SEM/EDX but gives a dash for PXRD; the prose's formation claim is retained with that weaker phase confirmation. On pyrrhotite at pH 2, the table lists humboldtine by both methods and also calcium oxalates by PXRD. A. xantha on pyrrhotite at pH 4 instead has whewellite, with no humboldtine assignment. S. lacrymans has dashes for both iron-feed arms, including pH; these are not invented numeric zero yields or demonstrated permanent inability of the species to form humboldtine.
Partial
Source:
vlasov2023
Section 4 compares brown-rot fungi with earlier A. niger experiments, including the 2021 article, rather than supplying a matched same-medium A. niger iron-feed arm in Table 4. Different media, volumes and durations prevent inferring superior rates or yields. Organic-acid production and biomass growth are proposed explanations, without a measured causal time course here. Figures 1-2 concern calcium oxalates in the Rogoselga adit; they are not field humboldtine evidence.
Context_only
Source:
ncbi_taxonomy
Official taxonomy XML verifies all four species IDs and uses Amyloporia xantha for 1333629. The browser heading agrees, although its current-name field retains Antrodia xantha. This naming discrepancy does not establish a different strain or an additional experiment.
Context_only
Source:
genbank_himantioides
KY352492.1 links LE-BIN 1368 to species taxon 80602.
Context_only
Source:
genbank_puteana
KY433978.1 links LE-BIN 1370 to species taxon 80637.
Context_only
Source:
genbank_xantha
KY433983.1 labels Amyloporia xantha LE-BIN 1029 and species taxon 1333629.
Context_only
Source:
genbank_lacrymans
KY352493.1 links comparator LE-BIN 1192 to species taxon 85982. These ITS/ribosomal accessions identify deposited sequences, not strain-specific TaxIDs, genomes or independent culture authentication.
Sources & References
-
ima_2026_09: IMA-CNMNC. The New IMA List of Minerals, September 2026. Humboldtine row, PDF page 97; introductory column definitions.
https://cnmnc.units.it/files/editor/IMA_Master_List_(2026-09).pdf (accessed 2026-10-11) -
zelenskaya2021: Zelenskaya, Izatulina, Frank-Kamenetskaya and Vlasov (2021). Iron Oxalate Humboldtine Crystallization by Fungus Aspergillus niger. Crystals 11:1591. Complete article, Sections 2-4 and Figures 1-5.
https://doi.org/10.3390/cryst11121591 (accessed 2026-10-11) -
vlasov2023: Vlasov, Zelenskaya, Izatulina, Janson and Frank-Kamenetskaya (2023). Oxalate Crystallization under the Action of Brown Rot Fungi. Crystals 13:432. Complete article, Tables 1-5 and Figures 1-7.
https://doi.org/10.3390/cryst13030432 (accessed 2026-10-11) -
ncbi_taxonomy: NCBI Taxonomy XML records for species 5061, 80602, 80637, 85982 and 1333629. Scientific names, ranks and name relationships.
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=5061,80602,80637,85982,1333629&retmode=xml (accessed 2026-10-11) -
genbank_niger: GenBank KF768341.1. Aspergillus niger strain Ch 4/07 ribosomal/ITS sequence.
https://www.ncbi.nlm.nih.gov/nuccore/KF768341.1 (accessed 2026-10-11) -
genbank_himantioides: GenBank KY352492.1. Serpula himantioides strain LE-BIN 1368 ITS sequence.
https://www.ncbi.nlm.nih.gov/nuccore/KY352492.1 (accessed 2026-10-11) -
genbank_puteana: GenBank KY433978.1. Coniophora puteana strain LE-BIN 1370 ribosomal/ITS sequence.
https://www.ncbi.nlm.nih.gov/nuccore/KY433978.1 (accessed 2026-10-11) -
genbank_xantha: GenBank KY433983.1. Amyloporia xantha strain LE-BIN 1029 ribosomal/ITS sequence.
https://www.ncbi.nlm.nih.gov/nuccore/KY433983.1 (accessed 2026-10-11) -
genbank_lacrymans: GenBank KY352493.1. Serpula lacrymans strain LE-BIN 1192 ribosomal/ITS sequence.
https://www.ncbi.nlm.nih.gov/nuccore/KY352493.1 (accessed 2026-10-11)
Curation History
| Timestamp | Curator | Action | Summary |
|---|---|---|---|
2026-10-11T22:59:12Z |
codex (GPT-6; codex) | CREATE | Added humboldtine mineral identity and two laboratory fungal formation studies, preserving feed mixtures, method-dependent assignments, organism-specific comparisons, control gaps and field-context limits. |
Record source: data/records/humboldtine.yaml