Iberian Pit Lake Stratified Community

Community ID CommunityMech:000034

Ecological State STABLE

Environment acid mine drainage
ENVO:00002186

A permanently stratified (meromictic) acidic pit lake community from the Iberian Pyrite Belt in southwestern Spain/Portugal, distinguished by dramatic vertical metabolic zonation and subsurface anaerobic processes in an extreme acid mine drainage environment. The pit lake ecosystem exhibits three distinct layers: an upper oxic mixolimnion (pH 2.2-3.1, 0-3m depth), a chemocline transition zone (11m), and an anoxic monimolimnion (pH 3.0-4.5, 35m depth). The upper layer is dominated by acidophilic green algae (Coccomyxa onubensis) and heterotrophic bacteria (Acidiphilium), while the chemocline hosts intense sulfate reduction and iron cycling by specialized Proteobacteria (Desulfomonile, Candidatus Acidulodesulfobacterium). The deep anoxic layer harbors archaeal heterotrophs (Thermoplasmatales, 46% of sequences) that scavenge organic carbon and perform sulfide oxidation using trace oxygen, along with iron-reducing bacteria (Geobacter) and subsurface methanogens (Methanobrevibacter, Methanospirillum). The permanent stratification creates steep geochemical gradients with iron concentrations increasing from 2 mM Fe³⁺ in surface waters to 113 mM Fe²⁺ at depth, sulfate ranging from 26-126 mM, and oxygen transitioning from oxic to completely anoxic conditions. This system represents a natural laboratory for studying coupled aerobic-anaerobic metabolism, metal cycling, biosulfidogenesis, and subsurface methanogenesis under polyextreme conditions (acidity, metals, anoxia). The Iberian Pyrite Belt pit lakes demonstrate how microbial stratification can support complex biogeochemical cycling and potential natural attenuation of toxic metals through sulfide precipitation.

Taxonomy

Taxon	Ontology ID	Functional Roles	Abundance
Leptospirillum	NCBITaxon:179	PRIMARY_DEGRADER	COMMON
PMID:23840525 - SUPPORT (IN_VIVO) "The microorganisms detected in NSC were characteristic of acid mine drainage (AMD), including iron oxidizing bacteria (Leptospirillum, Acidithiobacillus ferrooxidans) and facultative iron reducing bacteria and archaea (Acidithiobacillus ferrooxidans, Acidiphilium, Actinobacteria, Acidimicrobiales, Ferroplasma) detected in the bottom layer" PMID:36123522 - PARTIAL (IN_VIVO) "Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer"
Acidithiobacillus ferrooxidans	NCBITaxon:920	PRIMARY_DEGRADER	COMMON
PMID:23840525 - SUPPORT (IN_VIVO) "The microorganisms detected in NSC were characteristic of acid mine drainage (AMD), including iron oxidizing bacteria (Leptospirillum, Acidithiobacillus ferrooxidans) and facultative iron reducing bacteria and archaea (Acidithiobacillus ferrooxidans, Acidiphilium, Actinobacteria, Acidimicrobiales, Ferroplasma) detected in the bottom layer"
Acidiphilium	NCBITaxon:522	CROSS_FEEDER SECONDARY_FERMENTER	COMMON
PMID:23840525 - SUPPORT (IN_VIVO) "The microorganisms detected in NSC were characteristic of acid mine drainage (AMD), including iron oxidizing bacteria (Leptospirillum, Acidithiobacillus ferrooxidans) and facultative iron reducing bacteria and archaea (Acidithiobacillus ferrooxidans, Acidiphilium, Actinobacteria, Acidimicrobiales, Ferroplasma) detected in the bottom layer"
Desulfomonile	NCBITaxon:2357	PRIMARY_DEGRADER SECONDARY_FERMENTER	DOMINANT
PMID:36123522 - PARTIAL (IN_VIVO) "Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer" PMID:36123522 - SUPPORT (IN_VIVO) "Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies."
Candidatus Acidulodesulfobacterium	NCBITaxon:2597222	PRIMARY_DEGRADER SECONDARY_FERMENTER	ABUNDANT
PMID:36123522 - SUPPORT (IN_VIVO) "In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation" PMID:36123522 - PARTIAL (IN_VIVO) "Ca. Acidulodesulfobacterium"
Thermoplasmatales	NCBITaxon:2301	CROSS_FEEDER SECONDARY_FERMENTER	DOMINANT
PMID:36123522 - PARTIAL (IN_VIVO) "Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer" PMID:36123522 - PARTIAL (IN_VIVO) "Heterotrophic archaeal populations" PMID:36123522 - PARTIAL (IN_VIVO) "Thermoplasmatales dominated in the deep layer"
Methanobrevibacter	NCBITaxon:2172	SECONDARY_FERMENTER	RARE
doi:10.3390/microorganisms8091275 - SUPPORT (IN_VIVO) "In the monimolimnion of FC, sequences affiliated with the putative sulfate-reducing genus Desulfomonile were dominant (58%), whereas in the more acidic and metal-enriched LZ, elemental sulfur-reducing Acidianus and Thermoplasma spp., and disproportionating Desulfocapsa spp" doi:10.1111/gbi.12065 - SUPPORT (IN_VIVO) "DNA microarray hybridization confirmed the presence of members of methane oxidizers, sulfate‐reducers, metal and sulfur oxidizers, and methanogenic Euryarchaeota"
Coccomyxa onubensis	NCBITaxon:1125364	PRIMARY_PRODUCER	DOMINANT
PMID:36123522 - SUPPORT (IN_VIVO) "We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline" PMID:36123522 - PARTIAL (IN_VIVO) "active green alga Coccomyxa onubensis dominated the upper layer and chemocline"

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Stratified Iron Redox Cycling

MUTUALISM

Source Taxon: Leptospirillum

Target Taxon: Acidithiobacillus ferrooxidans

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

Biological Processes:

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

Downstream Effects:

→ Biosulfidogenesis and Metal Precipitation

Evidence

PMID:36123522 - SUPPORT (IN_VIVO)

"Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals"
PMID:36123522 - PARTIAL (IN_VIVO)

"iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria"

Biosulfidogenesis and Metal Precipitation

MUTUALISM

Source Taxon: Desulfomonile

Target Taxon: Candidatus Acidulodesulfobacterium

Metabolites: sulfate (CHEBI:16189), hydrogen sulfide (CHEBI:16136), copper sulfide (CHEBI:75219)

Biological Processes:

dissimilatory sulfate reduction (GO:0019419)
sulfide oxidation (GO:0070221)

Downstream Effects:

→ Subsurface Heterotrophic Carbon Scavenging

Evidence

PMID:36123522 - SUPPORT (IN_VIVO)

"We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation"
PMID:36123522 - PARTIAL (IN_VIVO)

"sulfide mineral precipitation in the deep layer"

Algal Primary Production and Carbon Export

CROSS_FEEDING

Source Taxon: Coccomyxa onubensis

Target Taxon: Acidiphilium

Metabolites: organic molecular entity (CHEBI:50860), carbon dioxide (CHEBI:16526), Fe(II) (CHEBI:29033)

Biological Processes:

photosynthesis (GO:0015979)
carbon fixation (GO:0015977)

Evidence

PMID:36123522 - SUPPORT (IN_VIVO)

"We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline"
PMID:36123522 - PARTIAL (IN_VIVO)

"active green alga Coccomyxa onubensis dominated the upper layer and chemocline"

Subsurface Heterotrophic Carbon Scavenging

CROSS_FEEDING

Source Taxon: Thermoplasmatales

Biological Processes:

organic substance catabolic process (GO:1901575)
tricarboxylic acid cycle (GO:0006099)

Downstream Effects:

→ Subsurface Methanogenesis

Evidence

PMID:36123522 - SUPPORT (IN_VIVO)

"We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation"
PMID:36123522 - PARTIAL (IN_VIVO)

"quantity and quality of organic carbon reaching the deep layer"

Subsurface Methanogenesis

CROSS_FEEDING

Source Taxon: Methanobrevibacter

Metabolites: methane (CHEBI:16183), hydrogen (CHEBI:18276)

Biological Processes:

methanogenesis (GO:0015948)

Evidence

doi:10.3390/microorganisms8091275 - SUPPORT (IN_VIVO)

"Furthermore, the detection of reads classified as methanogens and Desulfosporosinus spp., although at low relative abundance, represents one of the lowest pH values (2.9 in LZ) at which these taxa have been reported, to our knowledge"
PMID:36123522 - SUPPORT (IN_VIVO)

"Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling"

Environmental Factors

Factor	Value	Unit
Upper Layer pH	2.2-3.1	pH units
PMID:36123522 - SUPPORT (IN_VIVO) "We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline"
Deep Layer pH	3.0-4.5	pH units
PMID:36123522 - SUPPORT (IN_VIVO) "Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria"
Oxygen Stratification	Oxic to anoxic	stratification gradient
PMID:36123522 - SUPPORT (IN_VIVO) "We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation" PMID:36123522 - PARTIAL (IN_VIVO) "oxygen additions to the groundwater enabling sulfur oxidation"
Iron Concentration Gradient	2-113	mM Fe
PMID:36123522 - SUPPORT (IN_VIVO) "The chemocline had activity for iron(II) oxidation carried out by populations of Ca"
Sulfate Concentration	26-126	mM
PMID:36123522 - SUPPORT (IN_VIVO) "Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals"
Permanent Stratification	Meromictic	lake type
PMID:36123522 - SUPPORT (IN_VIVO) "Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria" doi:10.1007/s10230-008-0059-z - SUPPORT (IN_VIVO) "A marked vertical trend of increasing temperature and dissolved metal concentrations is observed in the monimolimnia of some meromictic pit lakes of the Iberian"
Microbial Diversity Gradient	72-206	ASVs per sample
PMID:36123522 - SUPPORT (IN_VIVO) "Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling"