PSY Transgenic Rice Rhizosphere Methane-Mitigating Community

Community ID CommunityMech:000216

Ecological State ENGINEERED

Environment PSY transgenic rice paddy rhizosphere — ontology label: rhizosphere
ENVO:00005801 · HabitatMech ↗

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 — ontology label: Bacteria	NCBITaxon:2 · TaxonMech · TraitMech	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 — ontology label: Archaea	NCBITaxon:2157 · TaxonMech · TraitMech	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 — ontology label: Bacteria	NCBITaxon:2 · TaxonMech · TraitMech	CROSS_FEEDER	N/A
PMID:41582156 - SUPPORT (IN_VIVO) "decreased activity of H2-producing genes"

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.

Taxon

Competition

Other

Proposed H2 Oxidation Competition with Methanogenesis

COMPETITION

HYPOTHESIZED - PSY1 rhizospheres had higher transcription of bacterial H2-consuming hydrogenases, supporting the proposal that bacterial H2 use restricts substrate for hydrogenotrophic methanogens. This is not a measured H2 pool or isolated pairwise competition experiment. Individual genome-scale models predict increased H2 oxidation mainly with higher O2; elevated exudate compounds have little direct effect on oxidation but support biomass. Canonical Bacteria and Archaea IDs denote the named functional guilds, not all members of those domains.

Source Taxon: rhizosphere H2-oxidizing bacteria

Target Taxon: hydrogenotrophic methanogens

Metabolites: dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech), methane (CHEBI:16183 · MediaIngredientMech · CMMMech)

Biological Processes:

methanogenesis (GO:0015948 · PathwayMech)

Downstream Effects:

→ Reduced Methane Emissions and Proposed H2 Limitation

HYPOTHESIZED - Greater bacterial H2 consumption could reduce substrate available for hydrogenotrophic methanogenesis and contribute to lower methane. Transcript patterns and individual metabolic models support this mechanism indirectly; H2 depletion, pairwise competition and the fraction of methane reduction mediated by this route were not directly isolated.

Evidence

PMID:41582156 - PARTIAL (IN_VIVO)

"increased activity of bacterial H2 oxidation pathways"
PMID:41582156 - PARTIAL (IN_VIVO)

"decreased CH4 emissions are due to a lower amount of H2 available for hydrogenotrophic methanogenesis"

PSY Root Exudate Effects and Proposed Bacterial Substrate Preference

The living rice host, not an abiotic source, produces exudates with altered composition. Axenic seedling metabolomics found enriched gluconeogenic compounds, largely amino acids, without a significant total-carbon difference. Adding whole PSY1 or PSY2 exudates to soil caused lower CH4 than Kitaake exudates; water controls produced no detected CH4. HYPOTHESIZED - Genomic substrate preferences and PSY1 transcript associations suggest selective support of H2-consuming bacteria, but a specific amino-acid transfer or uptake-mediated mechanism was not isolated. Seedling exudates are not direct samples of mature soil-grown root flux.

Participating Taxa: rhizosphere H2-oxidizing bacteria

Metabolites: amino acid (CHEBI:33709 · MediaIngredientMech · CMMMech)

Biological Processes:

gluconeogenesis (GO:0006094 · PathwayMech)
amino acid catabolic process (GO:0009063 · PathwayMech)

Downstream Effects:

→ Proposed H2 Oxidation Competition with Methanogenesis

PARTIAL - Altered exudate composition may support biomass and activity of H2-consuming guilds enriched for gluconeogenic-acid use, indirectly contributing to the proposed H2 competition. The model predicts little direct effect of exudate enrichment on H2 oxidation itself; increased oxidation responds mainly to O2. Whole-exudate methane suppression is experimentally supported but does not resolve this specific mediator.

Evidence

PMID:41582156 - SUPPORT (IN_VITRO)

"Soils treated with Kitaake exudates exhibited consistently higher CH4 emissions than those treated with PSY1 or PSY2 exudates"
PMID:41582156 - PARTIAL (OTHER)

"their activities are likely stimulated by elevated levels of gluconeogenic acids, primarily amino acids, in PSY root exudates"

Reduced H2-Producing Transcripts and Modeled H2 Supply

PSY1 rhizospheres showed lower expression of H2-producing hydrogenases and nitrogenase markers than Kitaake at specified sampling stages. Individual dFBA models predict less H2 production with enriched PSY1 exudate compounds, even where producer biomass increases. This distinguishes gene-expression measurements and modeled flux from reduced producer abundance or directly measured H2 supply. It is not by itself a -/- competition phenotype.

Participating Taxa: rhizosphere H2-producing bacteria

Metabolites: dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech)

Downstream Effects:

→ Reduced Methane Emissions and Proposed H2 Limitation

HYPOTHESIZED - Lower H2-generating activity could restrict substrate supply for hydrogenotrophic methanogenesis. Gene-expression patterns and predicted H2 flux are consistent with this direction, but do not measure the shared H2 pool or isolate the causal contribution to greenhouse CH4 reduction.

Evidence

PMID:41582156 - SUPPORT (IN_VIVO)

"decreased activity of H2-producing genes"
PMID:41582156 - PARTIAL (COMPUTATIONAL)

"suppressed H2 production in the PSY rhizosphere"

Reduced Methane Emissions and Proposed H2 Limitation

Greenhouse rice grown in agronomic soil emitted less cumulative CH4 with PSY1 (about 38%) and PSY2 (about 58%) than Kitaake over 70 days. Repeated timepoints were integrated at tub level, not as repeat observations of the same destructively sampled plant. Microbial omics and metabolic modeling focused on PSY1. HYPOTHESIZED - Lower H2 production and greater bacterial consumption restrict hydrogenotrophic methanogenesis; inferred oxygenation and methane oxidation may also contribute. Lower measured CH4 is demonstrated, but the H2-mediated fraction, oxygen concentration and in-situ H2 pool are unresolved.

Metabolites: dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech), methane (CHEBI:16183 · MediaIngredientMech · CMMMech)

Biological Processes:

methanogenesis (GO:0015948 · PathwayMech)

Evidence

PMID:41582156 - SUPPORT (IN_VIVO)

"reduce cumulative CH4 emissions by 38% (PSY1) and 58% (PSY2) over 70 days of growth compared with controls."
PMID:41582156 - PARTIAL (COMPUTATIONAL)

"Metabolic modeling using metagenomic and metabolomic data predicts elevated H2 oxidation and suppressed H2 production"

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN How should the demonstrated whole-exudate methane response be linked without equating it with resolved amino-acid or hydrogen mediation?

Three existing arrows remain explicitly partial or hypothesized. The direct exudate-to-methane link merits extension review; a one-community Edison dry run is not a report or spend authorization. Individual dFBA models are not a coupled methanogen competition experiment. Preserve living-host effects, greenhouse CH4 and soil-exudate perturbations while separating PSY1 omics, seedling sampling, oxygen inference, transcripts and model flux. Specific compounds, H2 addback and field transfer need further evidence.

Attaches to: ecological_interactions#Proposed H2 Oxidation Competition with Methanogenesis, ecological_interactions#PSY Root Exudate Effects and Proposed Bacterial Substrate Preference, ecological_interactions#Reduced H2-Producing Transcripts and Modeled H2 Supply, ecological_interactions#Reduced Methane Emissions and Proposed H2 Limitation

1 evidence item(s)

IN_VITRO SUPPORT PMID:41582156

Soils treated with Kitaake exudates exhibited consistently higher CH4 emissions than those treated with PSY1 or PSY2 exudates

Direct whole-exudate soil amendment supports a methane response, not attribution to individual amino acids.

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"

Growth Media

submerged Capay rice-paddy soil in greenhouse pots, fertigated

pH 6.59

Preparation notes: Soil crushed to 2 mm, homogenized and stored until planting, then 2000 g per pot, 18 pots per 23-gallon tub, five tubs per genotype. Tubs were flooded before transplanting and kept submerged with deionized water every other day -- paddy conditions, which is what makes this record about methane cycling. From day 15 the deionized water was replaced with fertigation at N 77, P 20, K 75, Ca 27, Mg 17, S 68, Fe 1.5, Cu 0.02, Mn 0.5, Mo 0.01, Zn 0.1 and B 0.5 ppm; the source gives that composition inside square brackets, which validate-references strips (#622), so it is prose here rather than a quote. ph 6.59 is the mean soil pH reported for the field site, not a controlled setpoint. atmosphere is UNSET: the source never describes THIS experiment's soil as anoxic -- every 'anaerobic'/'anoxic' mention is background about rice paddies in general, a metabolic term, or a cited study, and one passage has methanogenesis inhibited 'until conditions become anoxic'. The pots also sit on greenhouse benches in room air, so ANAEROBIC would mislabel the system even where the soil is reduced. Submergence is what is stated, and it is quoted above (#649). NO GREENHOUSE TEMPERATURE OR PHOTOPERIOD IS REPORTED for the pot phase; the 28/24 C, 14 h:10 h figures belong to the germination incubators and are recorded on the other medium, not here.

Evidence

PMID:41582156

"Soil from a rice field in Davis (38.543224 degrees North and -121.810536 West) was collected in July 2022 and in July and December 2023 using a front-end loader to gather down to a depth of ~6–10 inches."

PMID:41582156

"The soil at the field site belongs to the Capay soil series, a fine, smectitic, thermic Typic Haploxerert."

PMID:41582156

"Soil pH was 6.59 on average."

PMID:41582156

"For both experiments, all soils were transported back to the greenhouse, crushed to a 2 mm particle size, thoroughly homogenized, and stored until planting. Then, the soil was transferred into new 5.5 × 5.5 inch pots (2000 g per pot), which were then placed into five 23 gallon tubs per genotype (18 pots each)."

PMID:41582156

"Prior to seedling transplantation, enough water was added to the tubs to submerge the soils."

PMID:41582156

"Axenic seedlings were then transplanted into the watered pots (one seedling per pot) in the greenhouse, where they were irrigated with deionized water every other day to keep the soil submerged."

PMID:41582156

"Each tub contained only one plant genotype to avoid root exudate compositional changes. We also kept a separate tub with unplanted pots and bulk soil controls."

1x Murashige and Skoog salts with 1% sucrose, pH 5.65 (germination only)

pH 5.65

Temperature 28 °C

Atmosphere AEROBIC

Preparation notes: Seeds dehulled, surface-sterilised in 20% bleach for 30 min, washed with autoclaved water. Solid: sown on plates, sealed with Micropore tape for gas exchange, held vertically 7 days. Hydroponic: germinated on water plates 2 days in darkness, then 5 days in flasks. This medium produces the AXENIC seedlings that are transplanted into the soil pots; it is not the medium the rhizosphere community grows in, and is recorded separately for that reason.

Evidence

PMID:41582156

"Rice seeds were dehulled, surface-sterilized in 20% bleach for 30 minutes, and thoroughly washed with autoclaved water. The seeds were grown in 1× Murashige and Skoog (1× MS) salt mixture with 1% sucrose (pH 5.65), either as a solid medium containing 0.3% Gellex (Gellan Gum, Caisson Laboratories) or hydroponically in flasks with 100 mL of the same media without Gellex."

PMID:41582156

"For solid medium conditions, seeds were sown on plates, sealed with Micropore tape for gas exchange, and placed vertically for 7 days."

PMID:41582156

"The incubators used for rice germination and growth were set with a 14-h-light/10-h-dark photoperiod at 28 °C/24 °C."

Cross-Mech Suite Links

Explore related entities across the CultureBotAI X-Mech knowledge bases:

HabitatMech: PSY transgenic rice paddy rhizosphere ↗ TaxonMech: rhizosphere H2-oxidizing bacteria ↗ TraitMech: rhizosphere H2-oxidizing bacteria ↗ TaxonMech: hydrogenotrophic methanogens ↗ TraitMech: hydrogenotrophic methanogens ↗ TaxonMech: rhizosphere H2-producing bacteria ↗ TraitMech: rhizosphere H2-producing bacteria ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗