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Richmond Mine AMD Biofilm

Community ID CommunityMech:000059
Ecological State STABLE
Environment acid mine drainage
ENVO:00002186

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
  • PMID:10966399 - SUPPORT (IN_VIVO)
    "The most abundant of the 16S rRNA genes detected were from organisms related to Leptospirillum species"
  • PMID:10966399 - SUPPORT (IN_VIVO)
    "The most abundant of the 16S rRNA genes detected were from organisms related to Leptospirillum species."
Ferroplasma acidarmanus NCBITaxon:97393
PRIMARY_PRODUCER
DOMINANT
  • PMID:15066799 - SUPPORT (IN_VIVO)
    "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"
  • doi:10.1186/1467-4866-5-13 - SUPPORT (IN_VIVO)
    "Molecular analyses of 232 small subunit ribosomal RNA (16S rRNA) gene sequences from six sites during a sampling time when lower temperature (<32°C), higher pH (>0.8) conditions predominated show the dominance of Fe-oxidizing prokaryotes such as Ferroplasma and Leptospirillum in the primary drainage communities"
Leptospirillum ferrodiazotrophum NCBITaxon:412449
PRIMARY_PRODUCER SYNTROPHIC_PARTNER
COMMON
  • PMID:16204553 - SUPPORT (IN_VITRO)
    "Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph"
  • doi:10.1186/1467-4866-5-13 - SUPPORT (IN_VIVO)
    "Molecular analyses of 232 small subunit ribosomal RNA (16S rRNA) gene sequences from six sites during a sampling time when lower temperature (<32°C), higher pH (>0.8) conditions predominated show the dominance of Fe-oxidizing prokaryotes such as Ferroplasma and Leptospirillum in the primary drainage communities"
Acidithiobacillus ferrooxidans NCBITaxon:920
PRIMARY_PRODUCER
RARE
  • doi:10.1186/1467-4866-5-13 - SUPPORT (IN_VIVO)
    "Several novel lineages were identified within the archaeal Thermoplasmatales order associated with the pyrite slump, and the Red Pool (pH 1.4) contained the only population of Acidithiobacillus"
  • PMID:19077236 - SUPPORT (IN_VITRO)
    "BACKGROUND: Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining)"
Micrarchaeota (ARMAN-1/2) NCBITaxon:1801631
CROSS_FEEDER
COMMON
  • PMID:20421484 - SUPPORT (IN_VIVO)
    "Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems"
  • doi:10.1073/pnas.0914294107 - SUPPORT (IN_VIVO)
    "always present in communities associated with acid mine drainage (AMD) at Iron Mountain in northern California with pH < 1.5, and are usually found in low abundance (5–25%) in the community"
Parvarchaeota (ARMAN-4/5) NCBITaxon:1462422
CROSS_FEEDER
COMMON
  • doi:10.1038/s41396-017-0002-z - SUPPORT (IN_VIVO)
    "Despite their small genomes (0.64–1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation"
  • doi:10.1038/s41396-017-0002-z - SUPPORT (IN_VIVO)
    "these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation"

Ecological Interactions

Ecological interaction network for Richmond Mine AMD Biofilm Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).
Taxon
Cross-feeding
Mutualism
Syntrophy
Competition
Commensalism
Niche partitioning
Colonization facilitation
Strain competition
Predation

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

Source Taxon: Leptospirillum group II

Target Taxon: Ferroplasma acidarmanus

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 - PARTIAL (IN_VIVO)
    "oxidation of approximately 1 × 105 to 2 × 105 moles pyrite/day"

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)

Target Taxon: Parvarchaeota (ARMAN-4/5)

Metabolites: organic molecular entity (CHEBI:50860)

Biological Processes:

Evidence

Iron and Sulfur Oxidation at Higher pH Refugia

COMPETITION

Source Taxon: Acidithiobacillus ferrooxidans

Target Taxon: Leptospirillum group II

Metabolites: Fe(II) (CHEBI:29033), Fe(III) (CHEBI:29034), elemental sulfur (CHEBI:27568)

Biological Processes:

Evidence

  • doi:10.1186/1467-4866-5-13 - SUPPORT (IN_VIVO)
    "Several novel lineages were identified within the archaeal Thermoplasmatales order associated with the pyrite slump, and the Red Pool (pH 1.4) contained the only population of Acidithiobacillus"
  • PMID:19077236 - SUPPORT (IN_VITRO)
    "BACKGROUND: Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining)"

Environmental Factors

Factor Value Unit
Extreme Acidity 0.5-1.0 pH
  • PMID:10966399 - SUPPORT (IN_VIVO)
    "An unusually thick ( approximately 1 cm) slime developed on a slump of finely disseminated pyrite ore within an extreme acid mine drainage site at Iron Mountain, near Redding, Calif"
  • doi:10.1186/1467-4866-5-13 - SUPPORT (IN_VIVO)
    "Extremely acidic effluent (pH between 0.5 and 0.9) resulting from oxidation of approximately 1 × 105 to 2 × 105 moles pyrite/day contains up to 24 g/1 Fe, several g/1 Zn and hundreds of mg/l Cu"
Temperature 30-50 °C
  • 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)
    "Molecular analyses of 232 small subunit ribosomal RNA (16S rRNA) gene sequences from six sites during a sampling time when lower temperature (<32°C), higher pH (>0.8) conditions predominated show the dominance of Fe-oxidizing prokaryotes such as Ferroplasma and Leptospirillum in the primary drainage communities"
Metal Concentrations Fe: 24 g/L; Zn: several g/L; Cu: hundreds mg/L g/L or mg/L
  • doi:10.1186/1467-4866-5-13 - SUPPORT (IN_VIVO)
    "Extremely acidic effluent (pH between 0.5 and 0.9) resulting from oxidation of approximately 1 × 105 to 2 × 105 moles pyrite/day contains up to 24 g/1 Fe, several g/1 Zn and hundreds of mg/l Cu"
  • PMID:10966399 - SUPPORT (IN_VIVO)
    "The predominant metabolic feature of bacteria of this subdivision is anaerobic sulfate or metal reduction"
Pyrite Oxidation Rate 1-2 × 10⁵ moles pyrite/day
  • doi:10.1186/1467-4866-5-13 - SUPPORT (IN_VIVO)
    "Extremely acidic effluent (pH between 0.5 and 0.9) resulting from oxidation of approximately 1 × 105 to 2 × 105 moles pyrite/day contains up to 24 g/1 Fe, several g/1 Zn and hundreds of mg/l Cu"
Oxygen Availability Aerobic to microaerobic qualitative
  • PMID:10966399 - SUPPORT (IN_VIVO)
    "Unexpectedly, sequences that affiliated within the delta subdivision of the Proteobacteria were detected"

Growth Media

Modified Mineral Salts Medium for Ferroplasma acidarmanus (CultureMech:000423)

View in CultureMech →

pH 1.5
Temperature 37 °C
Atmosphere MICROAEROBIC

Composition

Component Concentration Unit CHEBI
Iron(II) sulfate 44.2 g/L CHEBI:29033
Yeast extract 0.1 % wt/vol N/A
Ammonium sulfate 0.4 g/L CHEBI:62946
Magnesium sulfate heptahydrate 0.4 g/L CHEBI:32599
Monopotassium phosphate 0.05 g/L CHEBI:63036
KNO3 0.25 G_PER_L N/A
KH2PO4 0.1 G_PER_L N/A
MgSO4 x 7 H2O 0.05 G_PER_L N/A
CaCl2 x 2 H2O 0.01 G_PER_L N/A
EDTA 5 G_PER_L N/A
CuCl2 x 5 H2O 0.1 G_PER_L N/A
FeSO4 x 7 H2O 2 G_PER_L N/A
ZnSO4 x 7 H2O 0.1 G_PER_L N/A
NiCl2 x 6 H2O 0.02 G_PER_L N/A
CoCl2 x 6 H2O 0.2 G_PER_L N/A
Na2MoO4 0.03 G_PER_L N/A
MnCl2 x 4 H2O 0.03 G_PER_L N/A

Preparation notes: Medium for cultivation of Ferroplasma acidarmanus isolated from Richmond Mine AMD. F. acidarmanus grows chemomixotrophically on ferrous iron + yeast extract or sugars. This isolate requires much higher levels of organic carbon (0.1% wt/vol yeast extract) compared to F. acidiphilum (0.02-0.04%). Capable of facultative anaerobic growth by coupling chemoorganotrophic growth on yeast extract to reduction of ferric iron. Optimum pH 1.0-1.7, capable of growth at pH 0. Temperature optimum 35-42°C. Microaerophilic, tolerates low oxygen concentrations. Note: This medium supports pure culture growth of isolated F. acidarmanus, but the intact Richmond Mine biofilm community has not been successfully replicated in laboratory culture.

Evidence

PMID:15066799

"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"

PMID:15066799

"The temperature optima for the four isolates were between 35 and 42 degrees C and the pH optima were 1.0 to 1.7, and "F. acidarmanus" Fer1(T) was capable of growing at pH 0"

PMID:15066799

"All four isolates were facultative anaerobes, coupling chemoorganotrophic growth on yeast extract to the reduction of ferric iron"

Nitrogen-Free Medium for Leptospirillum ferrodiazotrophum (CultureMech:015436)

View in CultureMech →

pH 1.7
Temperature 33 °C
Atmosphere AEROBIC

Composition

Component Concentration Unit CHEBI
Iron(II) sulfate 30 g/L CHEBI:29033
Magnesium sulfate 0.4 g/L CHEBI:32599
Monopotassium phosphate 0.05 g/L CHEBI:63036

Preparation notes: Nitrogen-free medium developed for selective isolation of Leptospirillum ferrodiazotrophum (Leptospirillum group III), the nitrogen-fixing member of Richmond Mine biofilm. Richmond Mine AMD biofilm sample naturally abundant in group III was homogenized, filtered, and serially diluted into nitrogen-free liquid medium. Culture grew autotrophically to maximum density ~10^6 cells/ml, oxidizing ferrous iron as sole energy source. Ammonium sulfate deliberately omitted to select for diazotrophic organisms capable of nitrogen fixation. This selective isolation strategy was guided by metagenomic data showing a single nif operon on a Leptospirillum group III genome fragment. Axenic culture confirmed by 16S rRNA-ITS clone library analysis. Note: This medium supports L. ferrodiazotrophum but not the complete biofilm community.

Evidence

PMID:16204553

"An AMD biofilm sample naturally abundant in Leptospirillum group III cells was homogenized, filtered, and serially diluted into a nitrogen-free liquid medium. The resulting culture in the terminal dilution grew autotrophically to a maximum cell density of approximately 10(6) cells/ml, oxidizing ferrous iron as the sole energy source"

PMID:16204553

"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:16204553

"Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph"