By interacting organism › Bacteria › Methylococcaceae

Associationobservedoriginal resultmeasured

Claim · model-written summary

Methylomicrobium, Nitrospira and iron-cycling bacteria increased in abundance in the rice rhizosphere.

Taxon: riceOryza sativat0
Interactor: MethylomicrobiumMethylomicrobiume3other
Second interactor: NitrospiraNitrospirae3other
Outcome: abundancee3
Direction: increasede3
Qualifier: iron-cycling bacteria (e.g., Sideroxydans)e3

Verbatim

t0
“rice rhizosphere microbial community reassembly”
✓ located verbatim in the source · title, characters 30–77

e3
“Key taxa, such as methanotrophs (e.g., Methylomicrobium), nitrifiers (e.g., Nitrospira), and iron-cycling bacteria (e.g., Sideroxydans), not only increased in abundance”
✓ located verbatim in the source · abstract, characters 1181–1349

Title

Reovirus infection results in rice rhizosphere microbial community reassembly through metabolite-mediated recruitment and exclusion

Zhanbiao Li; Wandi Luo; Huiting Xie; et al. Microbiome 2025. doi:10.1186/s40168-025-02188-6

Other claims from this paper (8)

Intervention effectobservedoriginal resultmeasured

Claim · model-written summary

PC increased rhizosphere abundance of Methylosarcina.

Taxon: riceOryza sativat0
Treatment: Phanerochaete chrysosporiumt0
Interactor: MethylosarcinaMethylosarcinae0symbiont
Second interactor: Phanerochaete chrysosporiumPhanerodontia chrysosporiumt0symbiont
Outcome: abundancee0
Direction: increasinge0

Not reportedComparator

Verbatim

e0
“increasing the abundance of four beneficial bacterial genera, including Mycobacterium, Desulfovirga, Methylosarcina, and Ferruginibacter”
✓ located verbatim in the source · abstract, characters 627–763

t0
“Phanerochaete chrysosporium reduces heavy metal uptake in rice”
✓ located verbatim in the source · title, characters 0–62

Title

Phanerochaete chrysosporium reduces heavy metal uptake in rice by affecting rhizosphere microbes and root metabolism

Renyan Duan; Yu Zhang; Qian Dai; et al. Ecotoxicology and Environmental Safety 2025. doi:10.1016/j.ecoenv.2025.118403

Other claims from this paper (13)

Intervention effect Phanerochaete chrysosporium reduced Sb concentration in rice grains.
Intervention effect Phanerochaete chrysosporium reduced As concentration in rice grains.
Intervention effect Phanerochaete chrysosporium reduced Cr concentration in rice grains.
Intervention effect Phanerochaete chrysosporium reduced Pb concentration in rice grains.
Intervention effect Phanerochaete chrysosporium reduced Zn concentration in rice grains.
Intervention effect PC increased rhizosphere abundance of Mycobacterium.
Intervention effect PC increased rhizosphere abundance of Desulfovirga.
Intervention effect PC increased rhizosphere abundance of Ferruginibacter.
Intervention effect PC significantly altered root organic acids concentration.
Intervention effect PC significantly altered root choline concentration.
Intervention effect PC significantly altered root amino acids concentration.
Observation PC affected histidine, pyrimidine, alanine/aspartate/glutamate, and glycine/serine/threonine metabolism pathways.
Mechanism Authors suggest PC reduces rice heavy-metal uptake by changing root metabolism and rhizosphere microbiome composition.

Intervention effectobservedoriginal resultpositivemeasured

Claim · model-written summary

l -alanine enhanced Methylococcus geothermalis proliferation.

Taxon: riceOryza sativat0
Treatment: l -alaninee0
Interactor: Methylococcus geothermalisMethylococcus geothermalise0other
Outcome: Methylococcus geothermalis and Methylocystis parvus proliferatione0
Direction: enhancee0

Not reportedComparator

Verbatim

e0
“l -alanine as a key growth-supporting metabolite secreted by P. frigoritolerans AE95, which was experimentally validated to enhance Methylococcus geothermalis and Methylocystis parvus proliferation”
✓ located verbatim in the source · abstract, characters 946–1143

t0
“rice”
✓ located verbatim in the source · title, characters 77–81

Title

Dual functionality of Peribacillus frigoritolerans in methane mitigation and rice immunity

Hyeonu Yang; Seonghan Jang; Su Yeon Lee; et al. Plant Stress 2025. doi:10.1016/j.stress.2025.101174

Other claims from this paper (5)

Observation Peribacillus frigoritolerans AE95 promoted methanotroph growth in vitro.
Intervention effect Applying AE95 to rice roots reduced methane emission by up to 66.8 %.
Mechanism Metabolic modeling predicted l -alanine secretion as a growth-supporting metabolite.
Intervention effect P. frigoritolerans elicited rice innate immunity against Xanthomonas oryzae pv. oryzae.
Intervention effect l -alanine supplementation elicited rice innate immunity against Xanthomonas oryzae pv. oryzae.

Mechanismauthor interpretationoriginal resultpositivesignificant (as stated)measured

Claim · model-written summary

Methylobacter abundance may explain increased dissolved organic carbon and lower Cd availability to rice.

Taxon: riceOryza sativae0
Interactor: MethylobacterMethylobactere0other
Outcome: Cd availability for ricee0
Direction: decreasede0
Value: r = 0.694e0

Verbatim

e0
“higher relative abundance of Methylobacter observed in azolla incorporation treatment may account for dissolved organic carbon increase (r = 0.694; P < 0.05), and hence decreased the Cd availability for rice”
✓ located verbatim in the source · abstract, characters 535–742

Title

Azolla incorporation under flooding reduces grain cadmium accumulation by decreasing soil redox potential

Chen Liu; Bin Guo; Hua Li; et al. Scientific Reports 2021. doi:10.1038/s41598-021-85648-x

Other claims from this paper (7)

Mechanism The authors infer nitrogen mineralization may contribute to increased rice yield.
Association Lower soluble Cd reduced OsNramp5 expression in rice roots.
Association Lower soluble Cd increased OsHMA3 levels in rice roots.
Intervention effect Azolla incorporation decreased rice grain Cd concentrations by 80.3%.
Intervention effect Azolla incorporation increased rice production by 13.4%.
Observation Azolla absorbed a negligible amount of Cd.
Recommendation The authors recommend intercropping azolla with early rice and incorporating it before late rice transplantation for safe double rice production.

Observationobservedoriginal resultmeasured

Claim · model-written summary

Methylomonas was the most active methanotroph group in the roots of Phragmites australis.

Taxon: Phragmites australisPhragmites australise0
Organ / stage: root samplese0
Interactor: MethylomonasMethylomonase1symbiont
Outcome: most active groupe1

Verbatim

e0
“from root samples of three emergent macrophytes, including Phragmites australis, Typha angustifolia, and Schoenoplectus triqueter (syn. Scirpus triqueter L.) from a eutrophic wetland”
✓ located verbatim in the source · abstract, characters 419–601

e1
“A type I methanotroph, Methylomonas, was the most active group in P. australis, whereas Methylocystis, a type II methanotroph, was the dominant group in S. triqueter”
✓ located verbatim in the source · abstract, characters 834–999

Title

Diversity of active root-associated methanotrophs of three emergent plants in a eutrophic wetland in northern China

Jing Cui; Ji Zhao; Zheng Wang; et al. AMB Express 2020. doi:10.1186/s13568-020-00984-x

Other claims from this paper (6)

Observationobservedoriginal resultmeasured

Claim · model-written summary

At the DNA level, Methylomonas was predominant in the roots of all three emergent macrophytes.

Taxon: three emergent macrophytese0
Organ / stage: rootse3
Interactor: MethylomonasMethylomonase3symbiont
Outcome: predominante3
Qualifier: at the DNA levele3

Verbatim

e0
“from root samples of three emergent macrophytes, including Phragmites australis, Typha angustifolia, and Schoenoplectus triqueter (syn. Scirpus triqueter L.) from a eutrophic wetland”
✓ located verbatim in the source · abstract, characters 419–601

e3
“However, at the DNA level, Methylomonas was predominant in the roots of all three plants”
✓ located verbatim in the source · abstract, characters 1085–1173

Title

Diversity of active root-associated methanotrophs of three emergent plants in a eutrophic wetland in northern China

Jing Cui; Ji Zhao; Zheng Wang; et al. AMB Express 2020. doi:10.1186/s13568-020-00984-x

Other claims from this paper (6)

Mechanismauthor interpretationoriginal resultpositivemeasured

Claim · model-written summary

Methylomonas and Methylocystis likely contribute to aerobic methane oxidation in the eutrophic wetland roots.

Taxon: three emergent macrophytese0
Interactor: MethylomonasMethylomonase5symbiont
Second interactor: MethylocystisMethylocystise5symbiont
Outcome: aerobic methane oxidatione5
Qualifier: in a eutrophic wetlande5

Verbatim

e0
“from root samples of three emergent macrophytes, including Phragmites australis, Typha angustifolia, and Schoenoplectus triqueter (syn. Scirpus triqueter L.) from a eutrophic wetland”
✓ located verbatim in the source · abstract, characters 419–601

e5
“These results indicate that members of the genera Methylomonas (type I) and Methylocystis (type II) can significantly contribute to aerobic methane oxidation in a eutrophic wetland”
✓ located verbatim in the source · abstract, characters 1306–1486

Title

Diversity of active root-associated methanotrophs of three emergent plants in a eutrophic wetland in northern China

Jing Cui; Ji Zhao; Zheng Wang; et al. AMB Express 2020. doi:10.1186/s13568-020-00984-x

Other claims from this paper (6)

Observationobservedoriginal resultmeasured

Claim · model-written summary

Type I methanotrophs had higher diversity than type II methanotrophs in the rice rhizobiome.

Taxon: RiceOryza sativat0
Interactor: Type I methanotrophsMethylococcaceaee0other
Outcome: diversitye0
Direction: highere0
Value: n=12e0
Comparator: type II methanotrophse0

Verbatim

e0
“Type I methanotrophs (n=12) had higher diversity than type II methanotrophs (n=6).”
✓ located verbatim in the source · abstract, characters 871–953

t0
“Rice”
✓ located verbatim in the source · title, characters 79–83

Title

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

Madangchanok Imchen; Ranjith Kumavath; Aline B. M. Vaz; et al. Frontiers in Microbiology 2019. doi:10.3389/fmicb.2019.02103

Other claims from this paper (8)

Association Plant growth promoting bacterial abundance and diversity increased over rice growth stages.
Association Rice rhizobiome alpha diversity and complexity increased significantly.
Observation Hydrogenotrophic methanogens dominated throughout rice cultivation.
Observation Type II methanotrophs had significantly higher abundance than type I methanotrophs.
Association Type I methanotrophs were enriched during water logged rice stages.
Observation Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria.
Observation Nitrosospira dominated ammonia oxidizing bacteria.
Observation Nitrospira dominated nitrite oxidizing bacteria.

Associationobservedoriginal resultmeasured

Claim · model-written summary

Type I methanotrophs were enriched during water logged rice stages.

Taxon: RiceOryza sativat0
Organ / stage: water logged stagese0
Interactor: type I methanotrophsMethylococcaceaee0other
Outcome: type I methanotrophs being enrichede0
Direction: enrichede0

Verbatim

e0
“Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages.”
✓ located verbatim in the source · abstract, characters 1019–1129

t0
“Rice”
✓ located verbatim in the source · title, characters 79–83

Title

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

Madangchanok Imchen; Ranjith Kumavath; Aline B. M. Vaz; et al. Frontiers in Microbiology 2019. doi:10.3389/fmicb.2019.02103

Other claims from this paper (8)

Methylococcaceae 9 claims

9 claims