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Horonobe and Mizunami Underground Research Laboratory Subsurface Microbiome

Community ID CommunityMech:000218
Ecological State STABLE
Environment deep subsurface groundwater (URL)
ENVO:01001004

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 NCBITaxon:131567
PRIMARY_PRODUCER PRIMARY_DEGRADER
N/A
  • PMID:39696556 - SUPPORT (IN_VIVO)
    "methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL"
Mizunami granitic URL groundwater microbiome NCBITaxon:131567
PRIMARY_DEGRADER
N/A
  • PMID:39696556 - SUPPORT (IN_VIVO)
    "High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL"

Ecological Interactions

Ecological interaction network for Horonobe and Mizunami Underground Research Laboratory Subsurface Microbiome 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

Lithology-Driven Community Divergence

NICHE_PARTITIONING

Evidence

  • PMID:39696556 - SUPPORT (IN_VIVO)
    "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 Functional Core

CROSS_FEEDING

Metabolites: dihydrogen (CHEBI:18276), carbon dioxide (CHEBI:16526), sulfate (CHEBI:16189)

Biological Processes:

Evidence

  • PMID:39696556 - SUPPORT (IN_VIVO)
    "hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs"

Genotypic Homogeneity Across Depths in Horonobe

COLONIZATION_FACILITATION

Evidence

  • PMID:39696556 - SUPPORT (IN_VIVO)
    "near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL"
  • PMID:39696556 - SUPPORT (IN_VIVO)
    "the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period"

Trans-Continental Genotypic Overlap

COLONIZATION_FACILITATION

Evidence

  • PMID:39696556 - SUPPORT (IN_VIVO)
    "Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA"

External Resources

Name Repository Resource ID
Primary publication for the Horonobe and Mizunami URL microbiome
PubMed record for the Amano et al. 2024 Environmental Microbiome paper. 		OTHER PMID:39696556
  • PMID:39696556 - SUPPORT (IN_VIVO)
    "microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock"
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
  • PMID:39696556 - SUPPORT (IN_VIVO)
    "defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan"
Sampling duration four-year multi-year campaign N/A
  • PMID:39696556 - SUPPORT (IN_VIVO)
    "the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs"
Hydrological regime low current hydraulic conductivity; paleo-glacial mobility N/A
  • PMID:39696556 - SUPPORT (IN_VIVO)
    "current low hydraulic conductivity and groundwater compositional heterogeneity"