Industrial Bioleaching Reactor Consortium

Community ID CommunityMech:000035

Ecological State ENGINEERED

Environment bioreactor
ENVO:01000605

An industrial-scale moderately thermophilic acidophilic microbial consortium operating in continuous and batch bioreactors for metal extraction from sulfide ores and concentrates. This consortium represents a unique system with complete genomic characterization of six key organisms: Acidiplasma sp., Acidithiobacillus caldus, Cuniculiplasma divulgatum, Ferroplasma acidiphilum, Ferroplasma sp., and Thermoplasmatales archaeon. The community operates at moderate thermophilic temperatures (40-50°C) and extremely low pH (1.5-2.0), oxidizing ferrous iron and reduced sulfur compounds to generate ferric iron (Fe³⁺) and sulfuric acid for dissolving chalcopyrite (CuFeS₂) and other metal sulfides. Comparative analysis across batch versus continuous reactor modes reveals distinct population dynamics, with Acidithiobacillus caldus dominating early stages (up to 60% at pH >2), Sulfobacillus benefaciens in mid-stages (62-66%), and Ferroplasma thermophilum in late stages (66% under acidic, metal-rich conditions). The adapted consortium achieves exceptional copper extraction of 60.4% from 20% pulp density chalcopyrite concentrate in 25 days, producing 22.90 g/L dissolved copper. Operating under controlled carbon sources (CO₂, molasses) and temperature gradients (40-50°C), this system demonstrates how operational parameters shape microbial community structure and metal recovery efficiency. The availability of six complete reference genomes (PRJNA976529) enables genomic-level investigation of biooxidation mechanisms, making this the most comprehensively characterized industrial bioleaching consortium for biotechnological applications in extractive metallurgy.

Taxonomy

Taxon	Ontology ID	Functional Roles	Abundance
Acidithiobacillus caldus	NCBITaxon:33059	PRIMARY_PRODUCER PRIMARY_DEGRADER	DOMINANT
doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community" 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%" doi:10.1007/s00253-008-1792-8 - SUPPORT (IN_VITRO) "To compare oxidative dissolution rates of chalcopyrite by different consortia of moderately thermophilic acidophiles, various defined mixed cultures of three bacteria Acidithiobacillus caldus s2, Leptospirillum ferriphilum YSK, and Sulfobacillus sp. LN and one archaeon Ferroplasma thermophilum L1 were studied in batch shake flask cultures incubated at 45 degrees C"
Ferroplasma acidiphilum	NCBITaxon:74969	PRIMARY_PRODUCER SYNTROPHIC_PARTNER	DOMINANT
doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community" 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%"
Ferroplasma sp.	NCBITaxon:2591003	PRIMARY_PRODUCER SYNTROPHIC_PARTNER	ABUNDANT
doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community" 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%"
Acidiplasma sp.	NCBITaxon:1872114	PRIMARY_DEGRADER SYNTROPHIC_PARTNER	ABUNDANT
doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community" doi:10.1134/S0026261716060059 - SUPPORT (IN_VIVO) "The genome of Acidiplasma sp. MBA-1 is the first genome of this genus deposited to a public database DDBJ/EMBL/GenBank (accession no"
Cuniculiplasma divulgatum	NCBITaxon:1673428	SECONDARY_FERMENTER SYNTROPHIC_PARTNER	ABUNDANT
doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community" PMID:30499003 - WRONG_STATEMENT (IN_VIVO) "Cuniculiplasmataceae" doi:10.1007/s00792-018-1071-2 - SUPPORT (IN_VIVO) "Recently, the order Thermoplasmatales was expanded through the cultivation and description of species Cuniculiplasma divulgatum and corresponding family Cuniculiplasmataceae"
Thermoplasmatales archaeon	NCBITaxon:2268204	PRIMARY_DEGRADER	COMMON
doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "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"
Sulfobacillus benefaciens	NCBITaxon:453960	PRIMARY_DEGRADER SYNTROPHIC_PARTNER	DOMINANT
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%"
Leptospirillum ferriphilum	NCBITaxon:178606	PRIMARY_PRODUCER	RARE
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%"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Thermophilic Ferrous Iron Oxidation in Early Reactor Stages

CROSS_FEEDING

Source Taxon: Acidithiobacillus caldus

Metabolites: Fe(II) (CHEBI:29033), Fe(III) (CHEBI:29034)

Biological Processes:

oxidation-reduction process (GO:0055114)
iron ion transport (GO:0006826)
carbon fixation (GO:0015977)

Downstream Effects:

→ Chalcopyrite Dissolution by Ferric Iron

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%"
doi:10.1007/s00253-008-1792-8 - SUPPORT (IN_VITRO)

"Mutualistic interactions between physiologically distinct moderately thermophilic acidophiles, involving transformations of iron and sulfur and transfer of organic compound, were considered to play a critical role in promoting chalcopyrite dissolution"

Thermophilic Sulfur Oxidation to Sulfuric Acid

MUTUALISM

Source Taxon: Acidithiobacillus caldus

Metabolites: sulfur (CHEBI:26833), sulfuric acid (CHEBI:26836)

Biological Processes:

oxidation-reduction process (GO:0055114)
sulfur compound metabolic process (GO:0006790)

Evidence

doi:10.1007/s13213-019-01453-y - SUPPORT (IN_VITRO)

"Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus were the dominant species during the early stage"

Mid-Stage Mixotrophic Iron Oxidation

CROSS_FEEDING

Source Taxon: Sulfobacillus benefaciens

Metabolites: Fe(II) (CHEBI:29033), Fe(III) (CHEBI:29034), organic molecular entity (CHEBI:50860)

Biological Processes:

oxidation-reduction process (GO:0055114)
organic substance metabolic process (GO:0071704)

Evidence

PMID:24242252 - SUPPORT (IN_VITRO)

"caldus became the predominant species in the middle stage"

Late-Stage Extreme Acidophile Iron Oxidation

CROSS_FEEDING

Source Taxon: Ferroplasma acidiphilum

Target Taxon: Acidiplasma sp.

Metabolites: Fe(II) (CHEBI:29033), Fe(III) (CHEBI:29034)

Biological Processes:

oxidation-reduction process (GO:0055114)
iron ion transport (GO:0006826)

Downstream Effects:

→ Chalcopyrite Dissolution by Ferric Iron

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%"

Chalcopyrite Dissolution by Ferric Iron

MUTUALISM

Source Taxon: Acidithiobacillus caldus

Target Taxon: Ferroplasma acidiphilum

Metabolites: chalcopyrite (CHEBI:50885), copper(2+) (CHEBI:29036), Fe(III) (CHEBI:29034), Fe(II) (CHEBI:29033)

Biological Processes:

oxidation-reduction process (GO:0055114)

Downstream Effects:

→ Thermophilic Ferrous Iron Oxidation in Early Reactor Stages

Evidence

PMID:24242252 - SUPPORT (IN_VITRO)

"Thereafter, these samples were combined and then inoculated into a basal salts solution in which different substrates (ferrous sulfate, elemental sulfur, and chalcopyrite) served as energy sources"
PMID:24242252 - SUPPORT (IN_VITRO)

"Thereafter, these samples were combined and then inoculated into a basal salts solution in which different substrates (ferrous sulfate, elemental sulf"

Organic Matter Scavenging by Cuniculiplasma

COMMENSALISM

Source Taxon: Cuniculiplasma divulgatum

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

Biological Processes:

organic substance metabolic process (GO:0071704)
heterotrophic metabolism (GO:0019318)

Evidence

PMID:30499003 - WRONG_STATEMENT (IN_VIVO)

"Cuniculiplasmataceae"
doi:10.1007/s00792-018-1071-2 - SUPPORT (IN_VIVO)

"Co-existence of Cuniculiplasmataceae with archaeal Richmond Mine acidophilic nanoorganisms ('ARMAN')-related archaea representing an intriguing group within the "microbial dark matter" suggests their common fundamental environmental strategy and metabolic networking"

Early-Stage Iron Oxidation with Leptospirillum

SYNTROPHY

Source Taxon: Leptospirillum ferriphilum

Target Taxon: Acidithiobacillus caldus

Metabolites: Fe(II) (CHEBI:29033), Fe(III) (CHEBI:29034)

Biological Processes:

oxidation-reduction process (GO:0055114)

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%"

Ferroplasma Species Complementarity

CROSS_FEEDING

Source Taxon: Ferroplasma sp.

Target Taxon: Ferroplasma acidiphilum

Metabolites: Fe(II) (CHEBI:29033)

Biological Processes:

oxidation-reduction process (GO:0055114)

Evidence

doi:10.3390/biology12111411 - PARTIAL (IN_VIVO)

"Acidithiobacillus"

Thermoplasmatales Archaeal Community Structure

MUTUALISM

Source Taxon: Thermoplasmatales archaeon

Target Taxon: Acidiplasma sp.

Biological Processes:

oxidation-reduction process (GO:0055114)

Evidence

doi:10.3390/biology12111411 - PARTIAL (IN_VIVO)

"Acidithiobacillus"

Environmental Factors

Factor	Value	Unit
Moderate Thermophilic Temperature Range	40-50	°C
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%" doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature"
Extreme Acidity and pH Succession	1.5-2.0 (final); 3.79 (initial)	pH units
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%"
High Pulp Density Through Adaptation	1-20% (adapted to 20% after >2 years)	% w/v
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%"
Aeration and CO2 Enrichment	200 ml/h/L with 1% CO2	ml/h/L
PMID:24242252 - SUPPORT (IN_VITRO) "Thereafter, these samples were combined and then inoculated into a basal salts solution in which different substrates (ferrous sulfate, elemental sulfur, and chalcopyrite) served as energy sources" doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature"
Carbon Source Variation	CO2, molasses, organic matter	qualitative
doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor" 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%"
Reactor Configuration and Operational Mode	Batch and continuous modes	qualitative
doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor" PMID:24242252 - SUPPORT (IN_VITRO) "After that, the mixed cultures growing on different substrates were pooled equally, resulting in a final mixed culture"
Leaching Time and Succession Phases	0-25+ days with distinct phases	days
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%" doi:10.3390/biology12111411 - SUPPORT (IN_VIVO) "At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature"
Ferric Iron Concentration Gradient	>15 g/L in late stages	g/L
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%"