A depth-stratified microbial community in Lac Pavin, a deep, permanently stratified lake in central France. Genome-resolved analyses across the oxygen gradient reveal enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and the anoxic zone and sediments, with oxygen shaping non-CPR bacterial and archaeal metabolic strategies. RuBisCO genes are detected throughout the water column and sediments, including form II/III and form III-related enzymes encoded by Candidate Phyla Radiation (CPR) bacteria in the water column and DPANN archaea in the sediments. Methane oxidation and its byproducts are largely spatially separated from methane production, which is mediated by diverse sediment methanogens that vary on the centimeter scale.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| water-column Candidate Phyla Radiation (CPR) bacteria — ontology label: Patescibacteria group | NCBITaxon:1783273 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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N/A |
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| sediment DPANN archaea — ontology label: Nanobdellati | NCBITaxon:1783276 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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N/A |
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| sediment methanogenic archaea — ontology label: Archaea | NCBITaxon:2157 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
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N/A |
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Ecological Interactions
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
Depth-Associated Carbon Metabolic Potential
Genome-resolved metagenomics associates Calvin-cycle potential with shallower lake zones and Wood-Ljungdahl/reverse-TCA potential with anoxic water and sediments. PARTIAL - depth and oxygen co-vary with light and other geochemistry; this is genetic potential, not measured carbon-fixation flux or an isolated oxygen effect. The listed Archaea participant represents only the canonical archaeal component; most non-CPR bacterial lineages in this analysis are absent from the record roster.
Participating Taxa: sediment methanogenic archaea
Metabolites: carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)
Biological Processes:
- carbon fixation (GO:0015977 · PathwayMech)
Evidence
-
PMID:36694212 - PARTIAL (COMPUTATIONAL)"enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments"
Spatial Separation Of Methane-Cycle Genetic Potential
Methane-monooxygenase genetic potential is concentrated near the lake interface, with low-abundance occurrences in anoxic water, whereas mcr genes are mainly sediment-associated and also occur in the anoxic zone. This is largely separated potential, not strictly exclusive compartments or measured methane flux. Genome recovery is incomplete, so nondetection is not proof of absence. The listed sediment-methanogen aggregate does not resolve the missing bacterial methane oxidizers.
Participating Taxa: sediment methanogenic archaea
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech)
Biological Processes:
- methanogenesis (GO:0015948 · PathwayMech)
Evidence
-
PMID:36694212 - PARTIAL (COMPUTATIONAL)"the oxidation of methane and its byproducts is largely spatially separated from methane production"
CPR And DPANN RuBisCO-Associated CO2 Incorporation Potential
CPR water-column genomes encode form II/III and III-c RuBisCO, and sediment DPANN genomes include form III-related enzymes. PARTIAL - these variants suggest CO2 incorporation through a free-nucleotide pathway, not complete Calvin-cycle autotrophy or measured CO2 fixation. CPR gene repertoires show weak depth differentiation overall; host-mediated selection is a hypothesis, not an established consequence of the carbon-fixation node.
Participating Taxa: water-column Candidate Phyla Radiation (CPR) bacteria, sediment DPANN archaea
Metabolites: carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)
Biological Processes:
- carbon fixation (GO:0015977 · PathwayMech)
Evidence
-
PMID:36694212 - PARTIAL (COMPUTATIONAL)"we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments"
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PMID:36694212 - PARTIAL (COMPUTATIONAL)"Both form II/III and all form III RuBisCO likely function by incorporating carbon dioxide with a free nucleotide"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which depth-associated capacities are expressed and mediate carbon flux?
Drop both common-gradient arrows: co-varying genomic distributions do not establish carbon fixation as a cause of methane-cycle separation or CPR/DPANN RuBisCO distributions. Retain all three positive observations as potential. The 738 genomes cover only part of the community; nondetection and incomplete genomes cannot establish pathway absence. Oxygen, light and other geochemistry co-vary. CPR repertoires are weakly differentiated by depth, with host selection proposed. Canonical participants are incomplete: Archaea represents only the listed archaeal component, not all carbon-fixing bacteria or methane oxidizers. #1553 tracks roles and missing taxonomy/non-graph evidence. Main text/captions read, not raw genomes, separate supplements or figure pixels.
Attaches to: ecological_interactions#Depth-Associated Carbon Metabolic Potential, ecological_interactions#Spatial Separation Of Methane-Cycle Genetic Potential, ecological_interactions#CPR And DPANN RuBisCO-Associated CO2 Incorporation Potential
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the Lac Pavin stratified lake community
PubMed record for the 2023 Microbiome paper on geochemical gradient impacts on Lac Pavin microbial community function. |
OTHER | PMID:36694212 |
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DOI landing page
DOI link to the Microbiome paper. |
OTHER | doi:10.1186/s40168-022-01416-7 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Oxygen gradient | oxic interface to anoxic sediments | N/A |
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Cross-Mech Suite Links
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