A multi-year, depth-resolved groundwater microbiome study of the Horonobe (sedimentary rock) and Mizunami (granitic rock) Underground Research Laboratories in Japan, sampling defined intervals between 140 and 400 m below the surface over four years. Draft genomes were reconstructed for more than 90 percent of all detected organisms. The Horonobe and Mizunami microbiomes are dissimilar at the community level, but hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds, and sulfate reduction are well represented in both, while methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and tunnel proximity select for candidate phyla radiation bacteria in the Mizunami URL. Approximately one third of genomically defined organisms have near-identical genotypes at multiple depths within Horonobe, and closely-related species recur in three other USA subsurface environments, constraining expectations of global subsurface biodiversity.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Horonobe sedimentary URL groundwater microbiome — ontology label: cellular organisms | NCBITaxon:131567 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
PRIMARY_DEGRADER
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N/A |
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| Mizunami granitic URL groundwater microbiome — ontology label: cellular organisms | NCBITaxon:131567 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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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.
Site-Associated URL Community Divergence
Groundwater metagenomes distinguish the sedimentary Horonobe and granitic Mizunami microbiomes. Host rock, location, groundwater chemistry and tunnel/flow context covary, so the comparison supports a site-associated pattern and a proposed lithological explanation, not an isolated lithology effect or demonstrated competitive niche partitioning. The two canonical habitat-level participants share a broad cellular-organisms CURIE but denote different sampled communities.
Participating Taxa: Horonobe sedimentary URL groundwater microbiome, Mizunami granitic URL groundwater microbiome
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)
Evidence
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PMID:39696556 - SUPPORT (COMPUTATIONAL)"The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock"
Shared Deep-Subsurface Genomic Functional Potential
Genome marker annotations in both URLs support widespread coding potential for hydrogen metabolism, Rubisco-based carbon fixation, nitrogen reduction and sulfate reduction. The positive genomic result is not measurement of pathway expression, biogeochemical flux, or exchange between every organism carrying those genes. A functional repertoire is not itself cross-feeding.
Participating Taxa: Horonobe sedimentary URL groundwater microbiome, Mizunami granitic URL groundwater microbiome
Metabolites: dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech), sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech)
Biological Processes:
- carbon fixation (GO:0015977 · PathwayMech)
- sulfate reduction (GO:0019420 · PathwayMech)
Evidence
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PMID:39696556 - SUPPORT (COMPUTATIONAL)"hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs"
Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis
CROSS_FEEDINGPARTIAL - in Horonobe samples farther from tunnels, the authors propose that putative autotrophic sulfate-reducing Syntrophobacterales may produce hydrogen supporting Methanospirillum methanogenesis. Genomic capacities and community profiles motivate this model, without directly measuring partner-resolved hydrogen transfer, necessity or simultaneous sulfate reduction and hydrogen export. The canonical Horonobe community placeholder does not resolve those partners as individual grounded taxa.
Participating Taxa: Horonobe sedimentary URL groundwater microbiome
Metabolites: dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech), sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech), methane (CHEBI:16183 · MediaIngredientMech · CMMMech)
Biological Processes:
- sulfate reduction (GO:0019420 · PathwayMech)
- methanogenesis (GO:0015948 · PathwayMech)
Evidence
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PMID:39696556 - PARTIAL (COMPUTATIONAL)"predicted to be autotrophic sulfate-reducers that may also produce H2, supporting methanogenesis by abundant Methanospirillum"
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PMID:39696556 - PARTIAL (COMPUTATIONAL)"methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL"
Genotypic Homogeneity Across Depths in Horonobe
Near-identical genotypes recur across Horonobe depths for approximately one third of genomically defined organisms. Coverage-qualified iRep estimates for a subset support replication, not direct absolute growth rates for all taxa. Historical groundwater mobility is a proposed explanation for present genotype similarity; the data do not directly establish migration, colonization facilitation or mutation rates, and current low conductivity and heterogeneous chemistry argue against assuming ongoing intersite dispersal.
Participating Taxa: Horonobe sedimentary URL groundwater microbiome
Biological Processes:
- growth (GO:0040007 · PathwayMech)
Evidence
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PMID:39696556 - SUPPORT (COMPUTATIONAL)"near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL"
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PMID:39696556 - PARTIAL (COMPUTATIONAL)"the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period"
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PMID:39696556 - SUPPORT (COMPUTATIONAL)"in situ growth was detected for some bacteria, albeit at slow rates"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which processes connect URL genomic potential to activity and dispersal?
Remove both overview-to-hydrogen arrows: contrasting sites provides context, and membership of a shared functional repertoire provides inclusion, neither an experimentally resolved upstream cause of the proposed transfer. Expression, isotope/flux measurements and partner perturbations would test the retained hydrogen hypothesis. Distinct rpS3 and genome-ANI species definitions yield different overlap counts and must not be conflated. Broad habitat placeholders are not organism-resolved donor/recipient groundings. Methanoperedens iron-coupling, tunnel-associated mobilization and historical dispersal are additional proposals, not newly demonstrated branches or an exhaustive mechanism expansion. Non-graph metadata is preserved, not recertified.
Attaches to: ecological_interactions#Site-Associated URL Community Divergence, ecological_interactions#Shared Deep-Subsurface Genomic Functional Potential, ecological_interactions#Horonobe Sulfate-Reducer Hydrogen Support of Methanogenesis, ecological_interactions#Genotypic Homogeneity Across Depths in Horonobe
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the Horonobe and Mizunami URL microbiome
PubMed record for the Amano et al. 2024 Environmental Microbiome paper. |
OTHER | PMID:39696556 |
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DOI landing page
DOI link to the Environmental Microbiome paper. |
OTHER | doi:10.1186/s40793-024-00649-3 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Depth interval | 140 to 400 m below surface | N/A |
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| Sampling duration | four-year multi-year campaign | N/A |
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| Hydrological regime | low current hydraulic conductivity; paleo-glacial mobility | N/A |
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