Industrial Bioleaching Reactor Consortium

The 2014 adapted chalcopyrite culture showed initial A. caldus predominance by qPCR at 20 percent pulp density. This positive population result does not identify A. caldus as a ferrous-iron oxidizer: the 2023 study describes sulfur-oxidizing potential for A. caldus BR_03, not its ownership of the A-plasma rusticyanin finding. The studies concern different communities. Relative predominance does not establish the proposed pH, substrate-depletion or competitive mechanism of succession.

Participating Taxa: Acidithiobacillus caldus

Evidence

• PMID:24242252 - SUPPORT (IN_VITRO)
  "A. caldus was the predominant species in the initial stage"

The 2023 genome analysis assigns sulfur-oxidizing potential to A. caldus BR_03. PARTIAL - this supports its proposed role in sulfur transformations, not measured taxon-specific sulfuric-acid flux, a fixed biologically maintained pH or a comparative rate advantage over mesophiles. The 2023 reactor pH was operationally adjusted. The separate 2019 pH experiment reports early attached A. caldus abundance; it does not establish all mechanistic claims for this composite roster.

Participating Taxa: Acidithiobacillus caldus

Metabolites: sulfur (CHEBI:26833 · MediaIngredientMech · CMMMech), sulfuric acid (CHEBI:26836 · MediaIngredientMech · CMMMech)

Biological Processes:

• sulfur compound metabolic process (GO:0006790 · PathwayMech)

Evidence

• doi:10.3390/biology12111411 - SUPPORT (COMPUTATIONAL)
  "This bacterium is a sulfur-oxidizing acidophile"

The 2014 20-percent-pulp chalcopyrite experiment reports S. acidophilus, rather than A. caldus, as predominant in the middle stage. The positive qPCR population result does not selectively establish a mixotrophic transition, superior iron-oxidation efficiency, a molasses response or competitive niche partitioning. Those causal mechanisms cannot be assigned from the succession observation alone.

Participating Taxa: Sulfobacillus acidophilus

Evidence

• PMID:24242252 - SUPPORT (IN_VITRO)
  "S. acidophilus rather than A. caldus became the predominant species in the middle stage"

PARTIAL - the 2023 study describes iron-oxidation potential in the F. acidiphilum BR_01 and Acidiplasma BR_02 genomes from a 45 C continuous CO2 reactor. The related Acidiplasma MBA-1 genome study supports an aerobic iron-oxidizing capability. These findings do not transfer the 2014 F. thermophilum late-stage abundance result to either canonical participant, prove their late-stage copper contribution, or establish a universal heavy-metal tolerance threshold. Exact community identity remains unresolved under #1509.

Participating Taxa: Ferroplasma acidiphilum, Acidiplasma sp.

Metabolites: Fe(II) (CHEBI:29033 · MediaIngredientMech · CMMMech), Fe(III) (CHEBI:29034 · MediaIngredientMech · CMMMech)

Evidence

• doi:10.3390/biology12111411 - PARTIAL (COMPUTATIONAL)
  "is capable of oxidizing ferrous iron and reducing molecular oxygen"
• doi:10.1134/S0026261716060059 - PARTIAL (COMPUTATIONAL)
  "oxidizing ferrous iron under oxic conditions and utilizing organic compounds"

After more than two years of serial adaptation, the 2014 mixed culture extracted 60.4 percent of copper from chalcopyrite at 20 percent pulp density in 25 days. This measured consortium outcome is retained. The two canonical participants listed here are a supported subset, not the complete culture: the paper also reports F. thermophilum, which is not represented by the canonical F. acidiphilum/Acidiplasma entries. Ferric-iron regeneration is a proposed process context, not an A. caldus iron-oxidation loop or a selectively measured contribution of the 2023 MAGs. Resolve the exact roster and missing valid regeneration structure under #1509.

Participating Taxa: Acidithiobacillus caldus, Sulfobacillus acidophilus

Metabolites: chalcopyrite (CHEBI:86202 · MediaIngredientMech · CMMMech), copper(2+) (CHEBI:29036 · MediaIngredientMech · CMMMech), Fe(III) (CHEBI:29034 · MediaIngredientMech · CMMMech), Fe(II) (CHEBI:29033 · MediaIngredientMech · CMMMech)

Evidence

• PMID:24242252 - SUPPORT (IN_VITRO)
  "At that pulp density, the culture extracted 60.4% of copper from the chalcopyrite in 25 days."

The C. divulgatum BR_06 genome in the 2023 reactor sample contains annotated central-carbon and protease functions. PARTIAL - these support organic-carbon metabolic potential, not measured transfer from specific lysed partners, detoxification of other members, vitamin donation or a 20-percent-pulp chalcopyrite niche. The separate Cuniculiplasmataceae review is ecological background, not direct evidence for this reactor mechanism.

Participating Taxa: Cuniculiplasma divulgatum

Metabolites: organic molecular entity (CHEBI:50860 · MediaIngredientMech · CMMMech), peptide (CHEBI:16670 · MediaIngredientMech · CMMMech)

Evidence

• doi:10.3390/biology12111411 - PARTIAL (COMPUTATIONAL)
  "A large number of proteases"

The 2014 culture contained L. ferriphilum before adaptation above 4 percent pulp density, after which it was not detected. This positive culture-composition comparison does not prove extinction or isolate pulp density from correlated organics, reagents and adaptation history. Its known iron-oxidizing capability is context, not directly measured flux in every stage, and the 2023 iron-oxidizer profiles concern another system.

Participating Taxa: Leptospirillum ferriphilum

Metabolites: Fe(II) (CHEBI:29033 · MediaIngredientMech · CMMMech), Fe(III) (CHEBI:29034 · MediaIngredientMech · CMMMech)

Evidence

• PMID:24242252 - SUPPORT (IN_VITRO)
  "The results show that the culture consisted mainly of four species, including Leptospirillum ferriphilum, Acidithiobacillus caldus, Sulfobacillus acidophilus, and Ferroplasma thermophilum, before adapting to a pulp density of 4%"
• PMID:24242252 - SUPPORT (IN_VITRO)
  "L. ferriphilum could not be detected when the pulp density was greater than 4%."

The 2023 metagenome from the 45 C continuous CO2 reactor contained F. acidiphilum BR_01 and Ferroplasma BR_04 genomes. This positive co-detection and the reactor profiles do not demonstrate functional redundancy, improved community performance from complementarity, or their presence in the distinct high-pulp 2014 culture. Exact canonical strain mappings remain part of #1509.

Participating Taxa: Ferroplasma sp., Ferroplasma acidiphilum

Metabolites: Fe(II) (CHEBI:29033 · MediaIngredientMech · CMMMech)

Evidence

• doi:10.3390/biology12111411 - PARTIAL (IN_VITRO)
  "16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group)"
• doi:10.3390/biology12111411 - SUPPORT (COMPUTATIONAL)
  "BR_04 and BR_01"

The 2023 reactor comparison reports increasing Acidiplasma relative abundance from 40 to 50 C and higher A-plasma abundance at 45 C. Preserve this operationally associated population pattern without labeling it a demonstrated pairwise niche interaction. Reactor mode and carbon source also matter; single reactor runs per condition and relative profiles do not isolate competitive mechanisms or assign absolute growth rates to each group.

Participating Taxa: Thermoplasmatales archaeon, Acidiplasma sp.

Biological Processes:

• response to temperature stimulus (GO:0009266 · PathwayMech)

Evidence

• doi:10.3390/biology12111411 - SUPPORT (COMPUTATIONAL)
  "A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in the bio-oxidation process"
• doi:10.3390/biology12111411 - SUPPORT (IN_VITRO)
  "Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant at 45 °C."