← Back to Communities

Richmond Mine AMD Biofilm

Ecological State STABLE
Environment acid mine drainage
ENVO:00002186
Source File Richmond_Mine_AMD_Biofilm.yaml

A thick, subaerial biofilm community from the Richmond Mine at Iron Mountain, California, representing one of the most extreme acid mine drainage (AMD) environments on Earth. This predominantly lithotrophic biofilm thrives at extraordinarily low pH (0.5-1.0) with temperatures ranging from 30-50°C and metal ion concentrations in the decagrams per liter range. The community is dominated by iron-oxidizing bacteria (Leptospirillum spp.) and archaea (Ferroplasma acidarmanus) that drive pyrite dissolution through ferric iron generation. Leptospirillum group II comprises 71% of detected clones, with Ferroplasma reaching up to 85% of cells in highly acidic microniches. The biofilm also contains nitrogen-fixing Leptospirillum group III (L. ferrodiazotrophum), making it a keystone species in this nitrogen-limited ecosystem. Ultra-small ARMAN archaea (Micrarchaeota and Parvarchaeota) with genome sizes ~1 Mb represent novel lineages found at 5-25% relative abundance. The community oxidizes approximately 1-2 × 10⁵ moles of pyrite per day, generating extreme acidity and solubilizing metals including iron (up to 24 g/L), zinc (several g/L), and copper (hundreds mg/L). This natural biofilm serves as a model system for understanding microbial life at pH extremes and has implications for biomining, bioremediation, and astrobiology.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Leptospirillum group II NCBITaxon:419541
PRIMARY_PRODUCER
DOMINANT
Ferroplasma acidarmanus NCBITaxon:97393
PRIMARY_PRODUCER
DOMINANT
Leptospirillum ferrodiazotrophum NCBITaxon:412449
PRIMARY_PRODUCER SYNTROPHIC_PARTNER
COMMON
Acidithiobacillus ferrooxidans NCBITaxon:920
PRIMARY_PRODUCER
RARE
Micrarchaeota (ARMAN-1/2) NCBITaxon:1801631
CROSS_FEEDER
COMMON
Parvarchaeota (ARMAN-4/5) NCBITaxon:1462422
CROSS_FEEDER
COMMON

Ecological Interactions

Ferrous Iron Oxidation by Leptospirillum

CROSS_FEEDING

Source Taxon: Leptospirillum group II

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

Biological Processes:

Downstream Effects:
→ Pyrite Dissolution

Evidence

  • PMID:10966399 - SUPPORT (IN_VIVO)
    "Nearest relatives to the majority of sequences came from iron-oxidizing acidophiles, and it appears that iron oxidation is the predominant metabolic characteristic of the organisms in the slime"
  • doi:10.1186/1467-4866-5-13 - SUPPORT (IN_VIVO)
    "The detachment of thiosulfate () as a leaving group in pyrite oxidation should result in the formation and persistence of tetrathionate in low pH ferric iron-rich AMD solutions"

Ferrous Iron Oxidation by Ferroplasma

CROSS_FEEDING

Source Taxon: Ferroplasma acidarmanus

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

Biological Processes:

Downstream Effects:
→ Pyrite Dissolution

Evidence

  • PMID:15066799 - SUPPORT (IN_VITRO)
    "All four Ferroplasma isolates were capable of growing chemoorganotrophically on yeast extract or a range of sugars and chemomixotrophically on ferrous iron and yeast extract or sugars, and isolate "Ferroplasma acidarmanus" Fer1(T) required much higher levels of organic carbon"
  • "However, during the last few years, new studies of a number of acidic environments, particularly mining waste waters, acidic pools, etc., in diverse geographical locations have revealed the presence of new cell wall‐lacking archaea related to the recently described, acidophilic, ferrous‐iron oxidizing Ferroplasma acidiphilum"

Pyrite Dissolution

MUTUALISM

Metabolites: pyrite (CHEBI:51905), sulfate (CHEBI:16189), sulfuric acid (CHEBI:26836)

Biological Processes:

Downstream Effects:
→ Ferrous Iron Oxidation by Leptospirillum

Evidence

  • doi:10.1186/1467-4866-5-13 - SUPPORT (IN_VIVO)
    "The detachment of thiosulfate () as a leaving group in pyrite oxidation should result in the formation and persistence of tetrathionate in low pH ferric iron-rich AMD solutions"
  • doi:10.1186/1467-4866-5-13 - SUPPORT (IN_VIVO)
    "they ensure a continual supply of ferric iron essential for pyrite dissolution"

Nitrogen Fixation by Leptospirillum Group III

MUTUALISM

Source Taxon: Leptospirillum ferrodiazotrophum

Metabolites: dinitrogen (CHEBI:17997), ammonia (CHEBI:16134)

Biological Processes:

Evidence

  • PMID:16204553 - SUPPORT (IN_VITRO)
    "Based on the prediction that this organism is solely responsible for nitrogen fixation in the community, we pursued a selective isolation strategy to obtain the organism in pure culture"
  • PMID:19429552 - SUPPORT (IN_VIVO)
    "Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics"

Organic Carbon Scavenging by ARMAN

CROSS_FEEDING

Source Taxon: Micrarchaeota (ARMAN-1/2)

Metabolites: organic molecular entity (CHEBI:50860)

Biological Processes:

Evidence

Environmental Factors

Factor Value Unit
Extreme Acidity 0.5-1.0 pH
Temperature 30-50 °C
Metal Concentrations Fe: 24 g/L; Zn: several g/L; Cu: hundreds mg/L g/L or mg/L
Pyrite Oxidation Rate 1-2 × 10⁵ moles pyrite/day
Oxygen Availability Aerobic to microaerobic qualitative