A natural alkaline geothermal microbial mat community from Mushroom Spring in Yellowstone National Park. The community is structured around thermophilic Synechococcus cyanobacteria, filamentous anoxygenic phototrophs related to Roseiflexus and Chloroflexus, and an undermat community that includes Thermodesulfovibrio-like sulfate reducers. It is a DOE-relevant model for high-temperature photosynthesis, diel carbon and nitrogen cycling, metagenome-resolved community metabolism, and carbon flow in phototrophic microbial mats.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Mushroom Spring Synechococcus spp. — ontology label: Synechococcus | NCBITaxon:1129 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
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N/A |
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| Mushroom Spring Roseiflexus spp. — ontology label: Roseiflexus | NCBITaxon:120961 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
CROSS_FEEDER
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DOMINANT |
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| Mushroom Spring Chloroflexus spp. — ontology label: Chloroflexus | NCBITaxon:1107 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
CROSS_FEEDER
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N/A |
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| Mushroom Spring Thermodesulfovibrio sp. — ontology label: Thermodesulfovibrio | NCBITaxon:28261 · TaxonMech · TraitMech |
SECONDARY_FERMENTER
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COMMON |
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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.
Putative Diel Phototrophic Carbon Fixation
Metatranscriptomics measured diel expression in Roseiflexus and Chloroflexus populations: bacteriochlorophyll and reaction-center transcripts were more abundant at night, whereas key 3-hydroxypropionate carbon-fixation genes were expressed during the day. PARTIAL - The authors infer daytime photomixotrophic carbon fixation from these RNA patterns; direct fixation flux or resource partitioning between the genera is not established by the available abstract.
Participating Taxa: Mushroom Spring Roseiflexus spp., Mushroom Spring Chloroflexus spp.
Metabolites: carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)
Biological Processes:
- photosynthesis (GO:0015979 · PathwayMech)
- carbon fixation (GO:0015977 · PathwayMech)
Evidence
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PMID:23575369 - PARTIAL (COMPUTATIONAL)"expressed key genes involved in the 3-hydroxypropionate (3-OHP) carbon dioxide fixation bi-cycle during the day"
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PMID:23575369 - SUPPORT (COMPUTATIONAL)"Transcripts for genes involved in the biosynthesis of bacteriochlorophylls"
Putative Diel Phototroph Storage Polymer Cycling
PARTIAL - Diel expression of storage-polymer synthesis and degradation genes supports the authors proposed model: nighttime polyhydroxyalkanoate and wax-ester synthesis with glycogen fermentation, followed by daytime use of stored carbon and electron reserves. Polymer turnover and flux through this model are inferred from transcripts in the available abstract, not directly measured here.
Participating Taxa: Mushroom Spring Roseiflexus spp., Mushroom Spring Chloroflexus spp.
Biological Processes:
- fermentation (GO:0006113 · PathwayMech)
- carbon fixation (GO:0015977 · PathwayMech)
HYPOTHESIZED - The source model proposes that daytime polyhydroxyalkanoate and wax-ester degradation supplies carbon and electron reserves that support photomixotrophic carbon fixation through the 3-OHP bi-cycle. This metabolic link targets putative carbon fixation, not a demonstrated effect of polymer degradation on gene expression.
Evidence
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PMID:23575369 - PARTIAL (COMPUTATIONAL)"storage polymers, including glycogen, polyhydroxyalkanoates and wax esters"
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PMID:23575369 - PARTIAL (COMPUTATIONAL)"in daytime, polyhydroxyalkanoates and wax esters are degraded"
Upper-Mat and Undermat Nitrogen Fixation Potential
PARTIAL - The undermat study contrasts previously demonstrated Synechococcus nitrogen fixation with putative Thermodesulfovibrio diazotrophy supported by nifHDK and accessory genes. Thermodesulfovibrio nitrogen fixation was not demonstrated in this study. This is a comparison of spatially associated capacities, not nitrogen transfer between these taxa or exclusive layer occupancy. Limited nitrate/nitrite gene recovery in abundant-member partial genomes does not establish pathway absence.
Participating Taxa: Mushroom Spring Synechococcus spp., Mushroom Spring Thermodesulfovibrio sp.
Biological Processes:
- nitrogen fixation (GO:0009399 · PathwayMech)
Evidence
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PMID:28634470 - PARTIAL (COMPUTATIONAL)"Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat"
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PMID:28634470 - PARTIAL (COMPUTATIONAL)"nitrate/nitrite metabolism was limited"
Stratified Chlorophototrophic Community Structure
Amplicon and metagenomic sequencing resolve a diverse but extremely uneven Mushroom Spring undermat and a stratified phototrophic mat. Upper-layer members also occur in the undermat: the layers differ in relative abundance, not exclusive occupancy. This positive community-structure result does not establish nitrogen transfer or show that stratification causes nitrogen fixation.
Participating Taxa: Mushroom Spring Synechococcus spp., Mushroom Spring Roseiflexus spp., Mushroom Spring Chloroflexus spp., Mushroom Spring Thermodesulfovibrio sp.
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:28634470 - SUPPORT (COMPUTATIONAL)"diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring"
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PMID:28634470 - SUPPORT (COMPUTATIONAL)"Metagenome binning recovered partial genomes of all abundant community members"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
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Mushroom Spring Chloroflexi diel metatranscriptomics publication
PubMed-indexed metatranscriptomic study of phototrophic Chloroflexi in the Mushroom Spring microbial mat over a diel period. |
METATRANSCRIPTOMICS | OTHER | PMID:23575369 |
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Mushroom Spring undermat genome-centric publication
PubMed-indexed genome-centric metagenomic analysis of abundant members in the Mushroom Spring undermat community. |
METAGENOMICS | OTHER | PMID:28634470 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which observations distinguish activity and causal mediation from inferred potential?
Preserve measured RNA and community structure. The 2013 carbon-flow model is explicit in the accessible abstract; full-text XML failed and publisher access was restricted, so do not claim a complete Methods audit. The 2017 main body supports inferred Thermodesulfovibrio diazotrophy, with maturation genes relevant beyond nifHDK alone. Incomplete genomes limit absence claims. Distinct sampling campaigns and overlapping layers do not establish spatially directed nitrogen exchange or a stratification-to-fixation causal link.
Attaches to: ecological_interactions#Putative Diel Phototrophic Carbon Fixation, ecological_interactions#Putative Diel Phototroph Storage Polymer Cycling, ecological_interactions#Upper-Mat and Undermat Nitrogen Fixation Potential, ecological_interactions#Stratified Chlorophototrophic Community Structure
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Geothermal spring temperature and chemistry | neutral to alkaline geothermal spring mat | N/A |
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| Diel light regime | day-night light cycle | N/A |
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| Mat depth | upper phototrophic layer and orange undermat | N/A |
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Cross-Mech Suite Links
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