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PSY Transgenic Rice Rhizosphere Methane-Mitigating Community

Community ID CommunityMech:000216
Ecological State ENGINEERED
Environment PSY transgenic rice paddy rhizosphere
ENVO:00002233

A rice rhizosphere microbial community whose H2 cycling and methanogenesis are reshaped by host overexpression of PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) genes. Two independent transgenic rice genotypes (PSY1 and PSY2) reduced cumulative CH4 emissions by 38 percent and 58 percent over 70 days relative to controls. Genome-resolved metatranscriptomic, metagenomic, metabolomic, and metabolic modeling data from PSY rhizosphere soils show lower ratios of CH4 production versus consumption gene activities (largely hydrogenotrophic), decreased H2-producing gene activity, and increased bacterial H2 oxidation pathways. Assembled genomes of rhizosphere H2-oxidizing bacteria are enriched in gluconeogenic-acid utilization genes, and their activity is likely stimulated by elevated gluconeogenic-acid amino acids in PSY rice root exudates, lowering H2 available for hydrogenotrophic methanogens.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
rhizosphere H2-oxidizing bacteria NCBITaxon:2
PRIMARY_DEGRADER CROSS_FEEDER
N/A
  • PMID:41582156 - SUPPORT (IN_VIVO)
    "Assembled genomes of rhizosphere H2-oxidizing bacteria are enriched in genes utilizing gluconeogenic acids"
hydrogenotrophic methanogens NCBITaxon:2157
PRIMARY_PRODUCER
N/A
  • PMID:41582156 - SUPPORT (IN_VIVO)
    "lower ratios of gene activities for (mostly hydrogenotrophic) CH4 production versus consumption"
rhizosphere H2-producing bacteria NCBITaxon:2
CROSS_FEEDER
N/A
  • PMID:41582156 - SUPPORT (IN_VIVO)
    "decreased activity of H2-producing genes"

Ecological Interactions

Ecological interaction network for PSY Transgenic Rice Rhizosphere Methane-Mitigating Community 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

H2 Oxidation Outcompetes Hydrogenotrophic Methanogenesis

COMPETITION

Source Taxon: rhizosphere H2-oxidizing bacteria

Target Taxon: hydrogenotrophic methanogens

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

Biological Processes:

Evidence

  • PMID:41582156 - SUPPORT (IN_VIVO)
    "increased activity of bacterial H2 oxidation pathways"
  • PMID:41582156 - SUPPORT (IN_VIVO)
    "decreased CH4 emissions are due to a lower amount of H2 available for hydrogenotrophic methanogenesis"

Root Exudate Gluconeogenic Acid Cross-Feeding

CROSS_FEEDING

Metabolites: amino acid (CHEBI:33709)

Biological Processes:

Evidence

  • PMID:41582156 - SUPPORT (IN_VIVO)
    "their activities are likely stimulated by elevated levels of gluconeogenic acids, primarily amino acids, in PSY root exudates"

Reduced H2 Producer Activity

COMPETITION

Metabolites: dihydrogen (CHEBI:18276)

Evidence

  • PMID:41582156 - SUPPORT (IN_VIVO)
    "suppressed H2 production in the PSY rhizosphere"

External Resources

Name Repository Resource ID
Primary publication for the PSY rice rhizosphere methane-mitigating community
PubMed record for the Shi et al. 2026 Nature Communications paper linking PSY transgenic rice to altered rhizosphere H2 cycling and reduced methane emissions. 		OTHER PMID:41582156
  • PMID:41582156 - SUPPORT (IN_VIVO)
    "elevated H2 oxidation and suppressed H2 production in the PSY rhizosphere"
DOI landing page
DOI link to the Nature Communications paper. 		OTHER doi:10.1038/s41467-026-68640-9

Environmental Factors

Factor Value Unit
PSY transgene background PSY1 vs PSY2 vs control rice N/A
  • PMID:41582156 - SUPPORT (IN_VIVO)
    "two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY)"
Growth period 70 days of growth N/A
  • PMID:41582156 - SUPPORT (IN_VIVO)
    "70 days of growth compared with controls"