Calcite mineral
Calcium carbonate mineral with ideal formula CaCO3, distinct from its polymorphs vaterite and aragonite, calcium as an element, limestone or marble resources, and manufactured calcium carbonate products. The September 2026 IMA list gives grandfathered status and original-description year 1836, not a new-mineral approval accession. Curated laboratory experiments identify calcite in bacterial-treatment solids; neither metal-removal percentages nor criticality designations are inherited by this mineral from their target metals.
Microbial & Biochemical Mechanisms (2)
Calcite formation in a calcium-supplemented DW018 terbium assay
biomineralization
Microbial
Associated Organisms:
Lysinibacillus (NCBITaxon:400634)
Washed urease-producing Lysinibacillus sp. DW018 biomass produced calcite-assigned diffraction peaks after 2 h in a calcium- and urea-supplemented synthetic Tb(III) solution. SEM-EDS associated Ca and Tb with the cell-bearing product, but does not establish Tb substitution into the calcite lattice, a pure calcite product, or phase-specific Tb uptake. Early solution Tb depletion occurred before the resolved calcite peaks and also without added calcium. Calcite formation therefore does not establish the cause or necessity of the rapid Tb-removal response.
Experimental Context & Analytical Limits:
DW018 was isolated from ionic rare-earth tailings in Gannan, China, and assigned by the authors to Lysinibacillus using 16S rRNA analysis; the genus identifier does not identify this strain or establish a species assignment. The experiment used synthetic solution rather than tailings leachate or actual wastewater. Log-phase cells were harvested at 4000 rpm, washed three times in sterile water and resuspended in sterile saline. The standard 30 mL assay had final OD600 1.0, reported 400 micromolar Tb(III), 25 mM CaCl2 and 2% urea, at 37 degrees C; the Tb salt counter-ion and percentage basis for urea are not specified. Each experiment was repeated three times. The adsorption comparator replaced both CaCl2 and urea with water; a separate calcium-dose arm included no added Ca. The final recommended no-added-Ca/0.5% urea recipe is distinct from the standard Ca-supplemented calcite experiment. No matched-pH cell-free or killed-biomass phase-control result is reported. XRD solids were centrifuged at 8000 rpm for 10 min, washed, pre-cooled at -20 and -80 degrees C, freeze-dried for 24 h and ground; SEM specimens additionally underwent glutaraldehyde fixation, phosphate buffer washing and ethanol dehydration. Prepared ex situ solids do not establish the unaltered in-solution amorphous precursor or Tb coordination. The supernatant fluorescence assay measured depletion after centrifugation, not a purified Tb product or an industrial recovery operation.
DW018 was isolated from ionic rare-earth tailings in Gannan, China, and assigned by the authors to Lysinibacillus using 16S rRNA analysis; the genus identifier does not identify this strain or establish a species assignment. The experiment used synthetic solution rather than tailings leachate or actual wastewater. Log-phase cells were harvested at 4000 rpm, washed three times in sterile water and resuspended in sterile saline. The standard 30 mL assay had final OD600 1.0, reported 400 micromolar Tb(III), 25 mM CaCl2 and 2% urea, at 37 degrees C; the Tb salt counter-ion and percentage basis for urea are not specified. Each experiment was repeated three times. The adsorption comparator replaced both CaCl2 and urea with water; a separate calcium-dose arm included no added Ca. The final recommended no-added-Ca/0.5% urea recipe is distinct from the standard Ca-supplemented calcite experiment. No matched-pH cell-free or killed-biomass phase-control result is reported. XRD solids were centrifuged at 8000 rpm for 10 min, washed, pre-cooled at -20 and -80 degrees C, freeze-dried for 24 h and ground; SEM specimens additionally underwent glutaraldehyde fixation, phosphate buffer washing and ethanol dehydration. Prepared ex situ solids do not establish the unaltered in-solution amorphous precursor or Tb coordination. The supernatant fluorescence assay measured depletion after centrifugation, not a purified Tb product or an industrial recovery operation.
Curated Evidence Points:
Support
Source:
bian2024
Sections 2.5/2.7 and 3.5.1, Figure 7 (p. 8), support the calcite assignment in the 2 h MICP product, contrasted with starting cells, 10 min MICP and adsorption traces. Section 3.5.2 and Figure 8 (p. 9) show cell-bearing crystals and Ca/Tb elemental maps. These are one experiment's complementary observations, not independent replications or a quantitative phase analysis. Figure 1 and Section 3.2 support only the authors' genus-level designation for DW018.
Partial
Source:
bian2024
Sections 2.5, 3.3 and 3.4.3 and Figures 2/5 show rapid supernatant depletion, including strong removal with no added Ca; the reported 98.28% at 10 min is solution removal, not calcite-specific recovery. Figure 7 lacks resolved calcite peaks in the 10 min trace. Section 3.5.1's inference that absent peaks exclude amorphous compounds is not supported by diffraction and conflicts with Section 3.5.2's proposed amorphous mixed Ca-Tb material. Figure 9 cannot identify that phase, and Figure 8 mapping cannot prove crystal-lattice entry. FTIR shifts in Figure 10 do not establish a unique molecular pathway. Tables 1-2 measure heat-pretreated cell viability and urease activity, whereas Figure 3 measures simultaneous hot reaction; these are not matched proof that living cells or active urease are unnecessary.
Calcite assigned in ureolytic geothermal-brine treatment solids
biomineralization
Microbial
Associated Organisms:
Sporosarcina pasteurii (NCBITaxon:1474)
Prepared S. pasteurii DSM 33 biomass with urea generated mixed carbonate-bearing solids during treatment of one natural geothermal brine. The authors assigned calcite together with vaterite and magnesite by powder XRD. This mineral-level observation shares the Rehmanji2025 experiment with cmmmech:vaterite and cmmmech:lithium-bearing-geothermal-brine; those records are not independent replications. It does not identify the proportion of Ca, Mg, Mn or Sr entering calcite, demonstrate a pure calcite yield, or recover lithium into a separate product.
Experimental Context & Analytical Limits:
DSM 33 cells were grown in TSB with 500 mM urea at 28 degrees C and 180 rpm, harvested in mid-log phase at 3200 g for 15 min and PBS-washed. Unsterilized natural brine from an unnamed Cornish geothermal project was treated under reported non-growth conditions: 100 mL in 250 mL flasks, initial OD600 0.05-0.4, 500 mM added urea, 28 degrees C, static for 24 h, in triplicate. The source-designated B. subtilis ATCC-2385 comparator and a separate brine-plus-urea/no-added-cell arm provide treatment comparisons, but no matched-pH chemical or killed-cell phase-control series is reported. The comparator strain designation remains unverified. Section 4.6 sampled 15 mL at 24 h, centrifuged at 3200 g for 15 min and dried the pellet at 60 degrees C for 24 h for XRD; the reported dry-pellet quantity is not a mass-balance mineral yield. Phase assignments concern processed mixed solids, without quantitative refinement or an in situ phase time course. Cow-urine/CaCl2 assays and spent-yeast biomass cultivation are separate arms. Laboratory flask treatment and slurry tests do not establish industrial deployment.
DSM 33 cells were grown in TSB with 500 mM urea at 28 degrees C and 180 rpm, harvested in mid-log phase at 3200 g for 15 min and PBS-washed. Unsterilized natural brine from an unnamed Cornish geothermal project was treated under reported non-growth conditions: 100 mL in 250 mL flasks, initial OD600 0.05-0.4, 500 mM added urea, 28 degrees C, static for 24 h, in triplicate. The source-designated B. subtilis ATCC-2385 comparator and a separate brine-plus-urea/no-added-cell arm provide treatment comparisons, but no matched-pH chemical or killed-cell phase-control series is reported. The comparator strain designation remains unverified. Section 4.6 sampled 15 mL at 24 h, centrifuged at 3200 g for 15 min and dried the pellet at 60 degrees C for 24 h for XRD; the reported dry-pellet quantity is not a mass-balance mineral yield. Phase assignments concern processed mixed solids, without quantitative refinement or an in situ phase time course. Cow-urine/CaCl2 assays and spent-yeast biomass cultivation are separate arms. Laboratory flask treatment and slurry tests do not establish industrial deployment.
Curated Evidence Points:
Support
Source:
rehmanji2025
Sections 2.1-2.2, 4.1-4.2 and 4.5-4.7 and Figures 1-2 support prepared biomass, the natural-brine experiment, carbonate-bearing solids and ex situ characterization. The narrow claim is calcite's source-assigned presence in the mixed treatment product.
Support
Source:
rehmanji2025_si
Figure S7 (p. 24) explicitly labels calcite as phase 2 alongside vaterite and magnesite. Table S1 describes the brine composition; the XRD operating table is on p. 5 with its S5 caption on p. 6. Figure S5 (pp. 21-22) is the separate no-added-cell comparison. These observations are not pure-phase mineral yields.
Partial
Source:
rehmanji2025
The main text misreferences the XRD plot as S6, which actually shows growth and pH. Its initial 10-minute claim conflicts with Figure 1's hour axis and Section 4.2's hour sampling schedule. Mg/Mn percentage claims do not consistently match Figure 1, whose B. subtilis Mn series also declines. No removal percentage or ten-minute rate is assigned to calcite. Section 4.4 does not clearly specify solid/liquid separation for each ICP-OES metal aliquot, preventing a stronger dissolved-only interpretation.
Partial
Source:
rehmanji2025_si
Figure S5's inoculated Mn/Sr series differs from Figure 1 and is not pooled with it. Table S7 saturation indices differ from the ranges quoted in Section 2.2, including negative magnesite entries; modeled saturation cannot confirm a mineral phase. Table S2 omits the Li wavelength and S9 labels aqueous Li retention as recovery. No lithium product, mineral-specific incorporation or conversion between mg/L and mg/kg is inferred.
Sources & References
-
ima_2026_09: IMA-CNMNC. The New IMA List of Minerals, September 2026; definitions pp. 1-2 and Calcite row p. 35, Ca(CO3), G, 1836.
https://cnmnc.units.it/files/editor/IMA_Master_List_(2026-09).pdf (accessed 2026-10-14) -
handbook_calcite: Handbook of Mineralogy, Calcite, CaCO3; Mineral Data Publishing, version 1, 2001-2005. Mineral identity and polymorphism.
https://www.handbookofmineralogy.org/pdfs/calcite.pdf (accessed 2026-10-14) -
bian2024: Bian, Dong, Ning, Song and Hu (2024). Recovery of terbium by Lysinibacillus sp. DW018 isolated from ionic rare earth tailings based on microbial induced calcium carbonate precipitation. Frontiers in Microbiology 15:1416731. Sections 2.1-2.9, 3.2-3.5 and 4; Figures 1-10, Tables 1-2.
https://doi.org/10.3389/fmicb.2024.1416731 (accessed 2026-10-14) -
ncbi_lysinibacillus: NCBI Taxonomy 400634, Lysinibacillus, genus. Parent-rank context only for the source-designated isolate DW018, not an authenticated strain ID.
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=400634&mode=Info (accessed 2026-10-14) -
rehmanji2025: Rehmanji, Skeffington, Hudson-Edwards and Newsome (2025). Circular economy approaches to microbially-induced carbonate precipitation for bioprocessing of geothermal brine for lithium recovery. RSC Advances 15:43263-43274; DOI 10.1039/d5ra06824j. Sections 2.1-2.2, 4.1-4.2 and 4.4-4.7; Figures 1-2.
https://doi.org/10.1039/d5ra06824j (accessed 2026-10-14) -
rehmanji2025_si: Rehmanji et al. (2025), supporting information to DOI 10.1039/d5ra06824j, 27-page RA-015-D5RA06824J-s001.pdf. Tables S1-S2/S5/S7 and Figures S1-S7; actual XRD figure is S7 p. 24, not the main text's S6 reference.
https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12590475/supplementaryFiles (accessed 2026-10-14) -
dsm33: DSMZ catalogue, Sporosarcina pasteurii DSM 33, type strain, strain 22.
https://www.dsmz.de/collection/catalogue/details/culture/DSM-33 (accessed 2026-10-14) -
ncbi_pasteurii: NCBI Taxonomy 1474, Sporosarcina pasteurii, species.
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1474&mode=Info (accessed 2026-10-14)
Curation History
| Timestamp | Curator | Action | Summary |
|---|---|---|---|
2026-10-14T12:19:25Z |
codex (GPT-6; codex) | CREATE | Created mineral identity and two laboratory carbonate-formation mechanisms from complete primary evidence; preserved no-added-calcium Tb removal, mixed-product and coordination limits, source contradictions and shared brine experiment lineage. |
Record source: data/records/calcite.yaml