Australian Lead Zinc Polymetallic Tailings Consortium

Community ID CommunityMech:000004

Ecological State PERTURBED

Environment mine tailing
ENVO:00000072

A stratified microbial community from abandoned polymetallic mine tailings in Western Australia, characterized by vertical zonation of acidophilic and anaerobic organisms across steep pH and redox gradients. This system represents a naturally acidifying sulfidic tailings dump where oxidative weathering of Pb-Zn sulfide minerals drives extreme environmental heterogeneity and microhabitat specialization. The upper oxidized layer (pH 1.5-3.0) is dominated by iron- and sulfur-oxidizing acidophiles including Acidithiobacillus ferrooxidans (dual Fe/S oxidation) and Leptospirillum ferriphilum (specialized Fe oxidation), which generate ferric iron and sulfuric acid that mobilize lead, zinc, copper, and iron from sulfide minerals including galena (PbS), sphalerite (ZnS), and chalcopyrite (CuFeS₂). The intermediate chemocline exhibits dramatic pH transitions (pH 3-5) where Ferroplasma acidarmanus thrives in highly acidic microniches while facultative acidophiles transition to neutral conditions. The deeper sediment layer (pH 5-7) harbors anaerobic metal-reducing bacteria including Geobacter metallireducens that reduce ferric iron to ferrous iron using organic carbon, creating redox cycling between oxic and anoxic zones. Metagenome-assembled genomes (MAGs) reveal extensive microhabitat partitioning, with distinct populations specializing in surface oxidation, chemocline transitions, or deep anaerobic processes. Metal concentrations reach toxic levels (Pb: hundreds mg/kg, Zn: thousands mg/kg, Cu: hundreds mg/kg, Fe: up to 30% w/w), selecting for metal-resistant populations. This abandoned tailings system demonstrates natural biogeochemical cycling without active mining, with microbial communities driving ongoing metal mobilization (upper layers) and potential natural attenuation (deeper layers). The MAG-resolved metagenomics approach reveals cryptic microbial diversity including novel acidophilic lineages adapted to polymetallic stress, providing insights into bioremediation strategies and microbial evolution in extreme anthropogenic environments.

Taxonomy

Taxon	Ontology ID	Functional Roles	Abundance
Acidithiobacillus ferrooxidans	NCBITaxon:920	PRIMARY_DEGRADER	DOMINANT
PMID:22092956 - SUPPORT (IN_VIVO) "Weathering of waste rock, high in S and Fe, had resulted in a varying elemental dispersal down a face of the tailings hill" PMID:23574280 - SUPPORT (IN_VIVO) "Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively" doi:10.1128/aem.02458-10 - SUPPORT (IN_VIVO) "Although Acidithiobacillus ferrooxidans and Leptospirillum spp"
Leptospirillum ferriphilum	NCBITaxon:178606	PRIMARY_DEGRADER	DOMINANT
PMID:23574280 - SUPPORT (IN_VIVO) "Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively" doi:10.1128/aem.02458-10 - SUPPORT (IN_VIVO) "Although Acidithiobacillus ferrooxidans and Leptospirillum spp"
Ferroplasma acidarmanus	NCBITaxon:97393	PRIMARY_DEGRADER CROSS_FEEDER	ABUNDANT
doi:10.1128/aem.02883-07 - SUPPORT (IN_VIVO) "Bacterial diversity in mine tailing microbial communities has not been thoroughly investigated despite the correlations that have been observed between the relative microbial diversity and the success of revegetation efforts at tailing sites" PMID:23574280 - SUPPORT (IN_VIVO) "16S rRNA pyrosequencing revealed a contrasting microbial composition between the six tailings: Proteobacteria-related sequences dominated T1-T3 with relative abundance ranging from 56 to 93%, whereas Ferroplasma-related sequences dominated T4-T6 with relative abundance ranging from 28 to 58%"
Geobacter metallireducens	NCBITaxon:28232	SECONDARY_FERMENTER	COMMON
doi:10.1016/j.scitotenv.2021.151468 - SUPPORT (IN_VIVO) "We revealed Cd-induced adenine and cytosine hypermethylation using specific antibodies in dot blots and found that the methylation level of adenine compared to cytosine changed even to a bigger extent" doi:10.1016/j.jhazmat.2023.130774 - SUPPORT (IN_VIVO) "Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers"
Sulfobacillus thermosulfidooxidans	NCBITaxon:28034	PRIMARY_DEGRADER	RARE
doi:10.3390/min14030255 - SUPPORT (IN_VITRO) "The study examined the solubilisation process using a mesophilic mixed bacterial culture, including Acidithiobacillus ferrooxidans (AF), Acidithiobacillus thiooxidans (AT), Leptospirillum ferrooxidans (LF), and the thermophilic species Sulfobacillus thermosulfidooxidans (ST)" doi:10.1186/s12863-016-0330-4 - SUPPORT (IN_VIVO) "At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A"
Acidiphilium cryptum	NCBITaxon:524	CROSS_FEEDER	COMMON
doi:10.1128/aem.02883-07 - SUPPORT (IN_VIVO) "Bacterial diversity in mine tailing microbial communities has not been thoroughly investigated despite the correlations that have been observed between the relative microbial diversity and the success of revegetation efforts at tailing sites" doi:10.1128/aem.00294-14 - SUPPORT (IN_VIVO) "However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Lead and Zinc Mobilization from Sulfide Minerals

MUTUALISM

Source Taxon: Acidithiobacillus ferrooxidans

Target Taxon: Leptospirillum ferriphilum

Metabolites: galena (CHEBI:82328), sphalerite (CHEBI:82332), Fe(III) (CHEBI:29034), lead(2+) (CHEBI:49807), zinc(2+) (CHEBI:29105), sulfuric acid (CHEBI:26836)

Biological Processes:

oxidation-reduction process (GO:0055114)
iron ion transport (GO:0006826)
response to metal ion (GO:0010038)

Downstream Effects:

→ Stratified Iron Redox Cycling

Evidence

doi:10.1128/aem.02458-10 - SUPPORT (IN_VIVO)

"Analysis of spatial and temporal variations in the microbial community in the abandoned tailings impoundment of a Pb-Zn mine revealed distinct microbial populations associated with the different oxidation stages of the tailings"
PMID:22092956 - SUPPORT (IN_VIVO)

"Weathering of waste rock, high in S and Fe, had resulted in a varying elemental dispersal down a face of the tailings hill"

Stratified Iron Redox Cycling

COMMENSALISM

Source Taxon: Leptospirillum ferriphilum

Target Taxon: Geobacter metallireducens

Metabolites: Fe(II) (CHEBI:29033), Fe(III) (CHEBI:29034), ferrihydrite (CHEBI:82823)

Biological Processes:

oxidation-reduction process (GO:0055114)
iron ion transport (GO:0006826)
dissimilatory iron reduction (GO:0019568)

Downstream Effects:

→ Lead and Zinc Mobilization from Sulfide Minerals

Evidence

doi:10.1016/j.jhazmat.2023.130774 - SUPPORT (IN_VIVO)

"Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers"
doi:10.1016/j.scitotenv.2021.151468 - SUPPORT (IN_VIVO)

"DNA hypermethylation caused by environmental pollutants like cadmium (Cd) has already been demonstrated in many invertebrates, including earthworms"

Microhabitat Specialization Along pH Gradient

COMMENSALISM

Source Taxon: Ferroplasma acidarmanus

Target Taxon: Acidithiobacillus ferrooxidans

Metabolites: hydron (CHEBI:15378)

Biological Processes:

response to pH (GO:0009268)
cellular pH homeostasis (GO:0030641)
response to metal ion (GO:0010038)

Evidence

doi:10.1128/aem.02883-07 - SUPPORT (IN_VIVO)

"Phylotype richness in these communities decreased from 42 in the OS control to 24 in the moderately acidic samples and 8 in the extremely acidic tailing samples"
doi:10.1128/aem.00294-14 - SUPPORT (IN_VIVO)

"Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions."

Copper Mobilization and Toxicity Interactions

COMPETITION

Source Taxon: Acidithiobacillus ferrooxidans

Metabolites: chalcopyrite (CHEBI:50831), copper(2+) (CHEBI:29036)

Biological Processes:

copper ion transport (GO:0006825)
response to copper ion (GO:0046688)
oxidation-reduction process (GO:0055114)

Evidence

doi:10.3390/min14030255 - SUPPORT (IN_VITRO)

"The study examined the solubilisation process using a mesophilic mixed bacterial culture, including Acidithiobacillus ferrooxidans (AF), Acidithiobacillus thiooxidans (AT), Leptospirillum ferrooxidans (LF), and the thermophilic species Sulfobacillus thermosulfidooxidans (ST)"
PMID:22092956 - SUPPORT (IN_VIVO)

"Weathering of waste rock, high in S and Fe, had resulted in a varying elemental dispersal down a face of the tailings hill"

Thermophilic Bioleaching in Solar-Heated Microniches

MUTUALISM

Source Taxon: Sulfobacillus thermosulfidooxidans

Target Taxon: Acidithiobacillus ferrooxidans

Metabolites: Fe(II) (CHEBI:29033), Fe(III) (CHEBI:29034), sulfuric acid (CHEBI:26836)

Biological Processes:

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

Evidence

doi:10.3390/min14030255 - SUPPORT (IN_VITRO)

"The study examined the solubilisation process using a mesophilic mixed bacterial culture, including Acidithiobacillus ferrooxidans (AF), Acidithiobacillus thiooxidans (AT), Leptospirillum ferrooxidans (LF), and the thermophilic species Sulfobacillus thermosulfidooxidans (ST)"
doi:10.1186/s12863-016-0330-4 - SUPPORT (IN_VIVO)

"At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A"

Heterotrophic Carbon Scavenging and Iron Reduction

COMMENSALISM

Source Taxon: Acidiphilium cryptum

Target Taxon: Acidithiobacillus ferrooxidans

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

Biological Processes:

organic substance catabolic process (GO:1901575)
oxidation-reduction process (GO:0055114)

Evidence

doi:10.1128/aem.02883-07 - SUPPORT (IN_VIVO)

"Bacterial diversity in mine tailing microbial communities has not been thoroughly investigated despite the correlations that have been observed between the relative microbial diversity and the success of revegetation efforts at tailing sites"
doi:10.1128/aem.00294-14 - PARTIAL (IN_VIVO)

"pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings"

Environmental Factors

Factor	Value	Unit
pH Stratification	1.5-7.0	pH units (depth-dependent)
doi:10.1128/aem.02883-07 - SUPPORT (IN_VIVO) "Phylotype richness in these communities decreased from 42 in the OS control to 24 in the moderately acidic samples and 8 in the extremely acidic tailing samples" doi:10.1016/j.jhazmat.2023.130774 - SUPPORT (IN_VIVO) "The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties"
Lead Concentration	200-800	mg/kg solid phase; 5-50 mg/L dissolved
doi:10.1128/aem.02458-10 - SUPPORT (IN_VIVO) "Analysis of spatial and temporal variations in the microbial community in the abandoned tailings impoundment of a Pb-Zn mine revealed distinct microbial populations associated with the different oxidation stages of the tailings" doi:10.1128/aem.02883-07 - SUPPORT (IN_VIVO) "This study employed phylogenetic analyses of 16S rRNA genes to compare the bacterial communities present in highly disturbed, extremely (pH 2.7) and moderately (pH 5.7) acidic lead-zinc mine tailing samples from a semiarid environment with those from a vegetated off-site (OS) control sample (pH 8)"
Zinc Concentration	2000-8000	mg/kg solid phase; 50-500 mg/L dissolved
doi:10.1128/aem.02458-10 - SUPPORT (IN_VIVO) "were consistently present in the acidic tailings, acidophilic archaea, mostly Ferroplasma acidiphilum , were predominant in the oxidized zones and the oxidation front, indicating their importance to generation of acid mine drainage." PMID:23574280 - SUPPORT (IN_VIVO) "In an attempt to link the microbial community composition and function in mine tailings to the generation of acid mine drainage, we simultaneously explored the geochemistry and microbiology of six tailings collected from a lead/zinc mine, i.e"
Copper Concentration	300-1200	mg/kg solid phase; 20-150 mg/L dissolved
PMID:22092956 - SUPPORT (IN_VIVO) "We investigated bacterial community assemblages and functions down a hill slope contaminated by tailings from a volcanogenic massive sulphide mine in arid Western Australia" doi:10.1186/s12863-016-0330-4 - SUPPORT (IN_VIVO) "A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap"
Iron Concentration	Up to 30%	% w/w solid phase; 1000-10000 mg/L dissolved
doi:10.1016/j.jhazmat.2023.130774 - SUPPORT (IN_VIVO) "Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers" PMID:22092956 - SUPPORT (IN_VIVO) "Weathering of waste rock, high in S and Fe, had resulted in a varying elemental dispersal down a face of the tailings hill"
Oxygen Stratification	Oxic to anoxic	depth-dependent gradient
doi:10.1016/j.jhazmat.2023.130774 - SUPPORT (IN_VIVO) "Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers" doi:10.1016/j.scitotenv.2021.151468 - SUPPORT (IN_VIVO) "DNA hypermethylation caused by environmental pollutants like cadmium (Cd) has already been demonstrated in many invertebrates, including earthworms"
Arid Climate with Wetting-Drying Cycles	Semi-arid	climate classification
PMID:22092956 - SUPPORT (IN_VIVO) "We investigated bacterial community assemblages and functions down a hill slope contaminated by tailings from a volcanogenic massive sulphide mine in arid Western Australia" doi:10.1128/aem.02883-07 - SUPPORT (IN_VIVO) "This study employed phylogenetic analyses of 16S rRNA genes to compare the bacterial communities present in highly disturbed, extremely (pH 2.7) and moderately (pH 5.7) acidic lead-zinc mine tailing samples from a semiarid environment with those from a vegetated off-site (OS) control sample (pH 8)"
MAG Diversity and Specialization	100-200	estimated distinct MAG populations
doi:10.1016/j.jhazmat.2023.130774 - SUPPORT (IN_VIVO) "Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds" doi:10.1186/s40793-021-00380-3 - SUPPORT (IN_VIVO) "By taking advantage of high-throughput sequencing and up-to-date metagenomic binning technology, we reconstructed the microbial community structure and potential coupled iron and nitrogen metabolism pathways in the tailings"
Time Since Abandonment	Decades	years since mining cessation
doi:10.1128/aem.02883-07 - SUPPORT (IN_VIVO) "This study employed phylogenetic analyses of 16S rRNA genes to compare the bacterial communities present in highly disturbed, extremely (pH 2.7) and moderately (pH 5.7) acidic lead-zinc mine tailing samples from a semiarid environment with those from a vegetated off-site (OS) control sample (pH 8)" PMID:22092956 - SUPPORT (IN_VIVO) "Weathering of waste rock, high in S and Fe, had resulted in a varying elemental dispersal down a face of the tailings hill"