Ion-Adsorption REE Indigenous Community

Community ID CommunityMech:000036

Ecological State STABLE

Environment weathering crust
ENVO:00002230

A highly diverse indigenous microbial community in ion-adsorption rare earth element (REE) deposits in weathering profiles of South China, demonstrating remarkable selectivity for heavy rare earth elements (HREE) through bacterial teichoic acid binding. This natural community comprises over 700 genera spanning bacterial (84.2% dominated by Proteobacteria 46.9%, Acidobacteria 14.6%, Actinobacteria 9.0%, Firmicutes 6.3%) and fungal (Ascomycota 47.8%, Basidiomycota 40.4%) lineages distributed through weathering profiles up to 40 meters depth. The community exhibits unique HREE vs LREE fractionation capability, with Gram-positive bacteria (Bacillus, Micrococcus) preferentially adsorbing HREE (82-85% efficiency) compared to LREE (70-78%), driven by teichoic acids in cell walls that provide selective phosphate binding sites for heavier lanthanides. Removal of teichoic acids reduces REE adsorption from 65.5% to 17.8%, confirming their critical role. The community accelerates REE mineralization in supergene weathering environments through bioweathering of granite, dissolution of REE-bearing minerals, and biosorption-mediated HREE enrichment. Ion-adsorption deposits represent the world's main source of strategically critical HREE (Dy, Y, Tb, Eu) used in permanent magnets and phosphors, with over 40 deposit sites in South China. The indigenous microbial community functions across pH gradients (4.3-7.0), exhibits oligotrophic K-strategist adaptations (Acidobacteria), and demonstrates co-localization of ytterbium with phosphate-rich cell walls. This natural HREE fractionation system offers a sustainable model for selective REE recovery and explains the geological genesis of commercially valuable HREE-enriched clay deposits.

Taxonomy

Taxon	Ontology ID	Functional Roles	Abundance
Proteobacteria	NCBITaxon:1224	PRIMARY_DEGRADER CROSS_FEEDER	DOMINANT
Acidobacteria	NCBITaxon:57723	PRIMARY_DEGRADER	ABUNDANT
Actinobacteria	NCBITaxon:201174	PRIMARY_DEGRADER	ABUNDANT
Bacillus	NCBITaxon:1386	PRIMARY_DEGRADER	COMMON
Micrococcus	NCBITaxon:1269	PRIMARY_DEGRADER	COMMON
Ascomycota	NCBITaxon:4890	PRIMARY_DEGRADER CROSS_FEEDER	DOMINANT
Basidiomycota	NCBITaxon:5204	PRIMARY_DEGRADER	DOMINANT

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Teichoic Acid-Mediated HREE Selective Biosorption

COMMENSALISM

Source Taxon: Bacillus

Target Taxon: Micrococcus

Metabolites: dysprosium(3+) (CHEBI:49782), yttrium(3+) (CHEBI:49976), ytterbium(3+) (CHEBI:33342), phosphate (CHEBI:18367)

Biological Processes:

metal ion transport (GO:0030001)
cellular response to metal ion (GO:0071248)

Downstream Effects:

→ HREE Enrichment in B Horizon

Evidence

PMID:35708325 - SUPPORT (IN_VIVO)

"Taking advantage of bacteria strains isolated from the profile, Gram-positive bacteria affiliated with Bacillus and Micrococcus preferentially adsorbed HREEs, and teichoic acids in the cell wall served as the main sites for HREE adsorption, leading to an enrichment of HREEs in the deposit"
PMID:35708325 - SUPPORT (IN_VIVO)

"teichoic acids in the cell walls of G+ bacteria lead to REE fractionation; removal of teichoic acid decreased REE adsorption from 65.5% to only 17.8%"
PMID:35708325 - SUPPORT (IN_VIVO)

"Yb is colocalized with P, where both elements are relatively rich along the cell wall"

Bioweathering and REE Mineral Dissolution

CROSS_FEEDING

Source Taxon: Proteobacteria

Target Taxon: Actinobacteria

Metabolites: citric acid (CHEBI:30769), oxalic acid (CHEBI:16995), organic molecular entity (CHEBI:50860)

Biological Processes:

organic substance catabolic process (GO:1901575)

Downstream Effects:

→ Teichoic Acid-Mediated HREE Selective Biosorption

Evidence

PMID:35708325 - SUPPORT (IN_VIVO)

"These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene REE mineralization but also provide insights into efficient utilization of mineral resources via a biological pathway"
PMID:35708325 - SUPPORT (IN_VIVO)

"Both fungi and bacteria can contribute to the REE mineralization in regolith-hosted deposits"

HREE Enrichment in B Horizon

MUTUALISM

Source Taxon: Bacillus

Metabolites: dysprosium(3+) (CHEBI:49782), yttrium(3+) (CHEBI:49976), terbium(3+) (CHEBI:33375)

Biological Processes:

metal ion transport (GO:0030001)

Evidence

PMID:35708325 - SUPPORT (IN_VIVO)

"Taking advantage of bacteria strains isolated from the profile, Gram-positive bacteria affiliated with Bacillus and Micrococcus preferentially adsorbed HREEs, and teichoic acids in the cell wall served as the main sites for HREE adsorption, leading to an enrichment of HREEs in the deposit"
PMID:35708325 - SUPPORT (IN_VIVO)

"selective adsorption of REEs by teichoic acids in the cell walls of Gram-positive bacteria can contribute to the fractionation between HREEs and LREEs"

Fungal Bioweathering and Mineral Dissolution

MUTUALISM

Source Taxon: Ascomycota

Target Taxon: Basidiomycota

Metabolites: citric acid (CHEBI:30769), oxalic acid (CHEBI:16995)

Biological Processes:

organic substance catabolic process (GO:1901575)

Downstream Effects:

→ Teichoic Acid-Mediated HREE Selective Biosorption

Evidence

PMID:35708325 - SUPPORT (IN_VIVO)

"Both fungi and bacteria can contribute to the REE mineralization in regolith-hosted deposits"
PMID:35708325 - SUPPORT (IN_VIVO)

"These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene REE mineralization but also provide insights into efficient utilization of mineral resources via a biological pathway"

Oligotrophic REE Mobilization and Deep Profile Colonization

COMMENSALISM

Source Taxon: Acidobacteria

Target Taxon: Proteobacteria

Metabolites: organic molecular entity (CHEBI:50860)

Biological Processes:

organic substance catabolic process (GO:1901575)

Evidence

PMID:35708325 - SUPPORT (IN_VIVO)

"Acidobacteria are considered to have an oligotrophic (K-strategist) lifestyle, which facilitates their living in the low-nutrient environments in regolith-hosted REE deposits"
PMID:35708325 - SUPPORT (IN_VIVO)

"However, little is known about the roles of microorganisms in the formation of exogenic deposits such as regolith-hosted REE deposits that are of HREE enrichment and provide over 90% of global HREE demand"

Environmental Factors

Factor	Value	Unit
Weathering Profile Depth	0-40	meters
pH Gradient	4.3-7.0	pH units
REE Concentration and HREE Enrichment	776	ppm total REE
Geographic Distribution	40+	deposit sites
Microbial Diversity	700+	genera
Temperature	15-25	°C
Economic Significance	80-90%	% global HREE supply