diff --git a/kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml b/kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml new file mode 100644 index 00000000..bc33fbda --- /dev/null +++ b/kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml @@ -0,0 +1,313 @@ +name: TYQ1 Nematode Biocontrol SynCom +description: 'An 8-member synthetic community centered on keystone species Rhizobium pusense TYQ1, + which is enriched during root-knot nematode (Meloidogyne incognita) infection of cucumber (Cucumis + sativus cv. Zhongnong 26). TYQ1 recruits 7 biomarker species that enhance biofilm formation and + metabolic cross-feeding, creating a tightly interconnected network for synergistic nematode + suppression. The community was identified through stress-induced enrichment analysis and validated + across 12 soil types, demonstrating that keystone species recruitment can guide functional microbial + community assembly to synergistically enhance plant health. + + ' +ecological_state: ENGINEERED +community_origin: ENGINEERED +community_category: RHIZOSPHERE +engineering_design: + objective: Assemble a functional synthetic community centered on stress-induced keystone species + for synergistic root-knot nematode suppression in cucumber + assembly_strategy: Stress-induced enrichment identification of keystone Rhizobium pusense TYQ1 + followed by recruitment of biomarker species + perturbation_design: 'Tested across 3 soil types (Beijing sandy loam, Shandong silty loam, + Zhejiang loam) and validated across 12 soil types. Pathogen challenge with 300 J2s Meloidogyne + incognita per seedling.' + measurement_endpoints: + - 16S rRNA amplicon sequencing + - Biofilm formation assays + - Metabolic interaction network analysis + - Nematode suppression assays + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: stress-induced recruitment of keystone species can guide functional microbial community + assembly to synergistically enhance plant health + explanation: Documents the engineering rationale for the TYQ1-centered SynCom +environment_term: + preferred_term: cucumber rhizosphere + term: + id: ENVO:00005801 + label: rhizosphere + notes: 'Rhizosphere of Cucumis sativus cv. Zhongnong 26 (RKN-susceptible cucumber). Root-knot + nematode infection restructured the rhizosphere bacterial community regardless of soil type. + + ' +taxonomy: +- taxon_term: + preferred_term: Rhizobium pusense TYQ1 + term: + id: NCBITaxon:655028 + label: Rhizobium pusense + notes: 'Keystone species and central metabolic hub. Directly inhibits root-knot nematodes and + coordinates biofilm formation across the community. Its enrichment causes restructuring of + the rhizobacterial community, leading to recruitment of 7 biomarker species. + + ' + strain_designation: + strain_name: TYQ1 + isolation_source: Cucumber rhizosphere under RKN stress + functional_role: + - PRIMARY_DEGRADER + abundance_level: DOMINANT + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: This strain not only directly inhibited RKNs but also caused the restructuring of the + rhizobacterial community, thereby leading to the enrichment of multiple biomarker species + explanation: Documents TYQ1 as keystone species with direct nematicidal and community-restructuring + roles +- taxon_term: + preferred_term: Sphingomonas panni SP + term: + id: NCBITaxon:165696 + label: Sphingomonas panni + notes: Biomarker species recruited by TYQ1 enrichment (OTU2477). + strain_designation: + strain_name: SP + isolation_source: Cucumber rhizosphere under RKN stress + functional_role: + - CROSS_FEEDER + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming + ability of the community and established a tightly interconnected metabolic interaction network + explanation: Documents SP as recruited biomarker contributing to biofilm and metabolic network +- taxon_term: + preferred_term: Sphingomonas xanthus SX + term: + id: NCBITaxon:13687 + label: Sphingomonas + notes: 'Biomarker species recruited by TYQ1 enrichment (OTU1716). Genus-level NCBITaxon used + as species-level ID not available. + + ' + strain_designation: + strain_name: SX + isolation_source: Cucumber rhizosphere under RKN stress + functional_role: + - CROSS_FEEDER + abundance_level: DOMINANT + abundance_value: '>1% relative abundance' + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming + ability of the community and established a tightly interconnected metabolic interaction network + explanation: Documents SX as recruited biomarker contributing to biofilm and metabolic network +- taxon_term: + preferred_term: Acidovorax soli AS + term: + id: NCBITaxon:459536 + label: Acidovorax soli + notes: Biomarker species recruited by TYQ1 enrichment (OTU2167). + strain_designation: + strain_name: AS + isolation_source: Cucumber rhizosphere under RKN stress + functional_role: + - CROSS_FEEDER + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming + ability of the community and established a tightly interconnected metabolic interaction network + explanation: Documents AS as recruited biomarker contributing to biofilm and metabolic network +- taxon_term: + preferred_term: Acidovorax facilis AF + term: + id: NCBITaxon:12916 + label: Acidovorax facilis + notes: Biomarker species with significant nematicidal activity (OTU2649). + strain_designation: + strain_name: AF + isolation_source: Cucumber rhizosphere under RKN stress + functional_role: + - PRIMARY_DEGRADER + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: the TYQ1-centered synthetic community exhibited more efficient and stable inhibition + of RKNs + explanation: Documents AF as a member with significant nematicidal activity +- taxon_term: + preferred_term: Novosphingobium subterraneum NS + term: + id: NCBITaxon:165699 + label: Novosphingobium subterraneum + notes: Biomarker species recruited by TYQ1 enrichment (OTU613). + strain_designation: + strain_name: NS + isolation_source: Cucumber rhizosphere under RKN stress + functional_role: + - CROSS_FEEDER + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming + ability of the community and established a tightly interconnected metabolic interaction network + explanation: Documents NS as recruited biomarker contributing to biofilm and metabolic network +- taxon_term: + preferred_term: Xenophilus aerolatus XA + term: + id: NCBITaxon:507237 + label: Xenophilus aerolatus + notes: Biomarker species recruited by TYQ1 enrichment (OTU2715). + strain_designation: + strain_name: XA + isolation_source: Cucumber rhizosphere under RKN stress + functional_role: + - CROSS_FEEDER + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming + ability of the community and established a tightly interconnected metabolic interaction network + explanation: Documents XA as recruited biomarker contributing to biofilm and metabolic network +- taxon_term: + preferred_term: Microbacterium arborescens MA + term: + id: NCBITaxon:2028 + label: Microbacterium arborescens + notes: Biomarker species recruited by TYQ1 enrichment (OTU11267). + strain_designation: + strain_name: MA + isolation_source: Cucumber rhizosphere under RKN stress + functional_role: + - CROSS_FEEDER + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming + ability of the community and established a tightly interconnected metabolic interaction network + explanation: Documents MA as recruited biomarker contributing to biofilm and metabolic network +ecological_interactions: +- name: Keystone-Mediated Community Recruitment + description: 'TYQ1 enrichment during root-knot nematode infection causes restructuring of the + rhizobacterial community, leading to enrichment of 7 biomarker species. RKN infection + restructured the rhizosphere bacterial community in RKN-susceptible cucumber plants regardless + of soil type. + + ' + interaction_type: MUTUALISM + source_taxon: + preferred_term: Rhizobium pusense TYQ1 + term: + id: NCBITaxon:655028 + label: Rhizobium pusense + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: root-knot nematode (RKN) infection restructured the rhizosphere bacterial community in + RKN-susceptible cucumber plants, regardless of the soil type + explanation: Documents stress-induced community restructuring mediated by TYQ1 +- name: Synergistic Biofilm Formation + description: 'All 7 recruited biomarker species show mutual attraction to TYQ1 and enhance + biofilm-forming ability of the community. Biofilm formation is a key mechanism for community + cohesion and nematode suppression. + + ' + interaction_type: MUTUALISM + source_taxon: + preferred_term: Rhizobium pusense TYQ1 + term: + id: NCBITaxon:655028 + label: Rhizobium pusense + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming + ability of the community and established a tightly interconnected metabolic interaction network + explanation: Documents synergistic biofilm enhancement across the SynCom +- name: Metabolic Cross-Feeding Network + description: 'TYQ1 serves as the central metabolic hub in a tightly interconnected metabolic + interaction network with the 7 biomarker species, enabling metabolic cross-feeding that supports + community function. + + ' + interaction_type: CROSS_FEEDING + source_taxon: + preferred_term: Rhizobium pusense TYQ1 + term: + id: NCBITaxon:655028 + label: Rhizobium pusense + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming + ability of the community and established a tightly interconnected metabolic interaction network + explanation: Documents TYQ1 as central metabolic hub in cross-feeding network +- name: Synergistic Nematode Suppression + description: 'The complete 8-member TYQ1-centered SynCom exhibits more efficient and stable + root-knot nematode inhibition than individual members alone, demonstrating emergent synergistic + biocontrol activity. + + ' + interaction_type: MUTUALISM + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: the TYQ1-centered synthetic community exhibited more efficient and stable inhibition + of RKNs + explanation: Documents synergistic nematode suppression by the complete SynCom +associated_datasets: +- name: 16S Amplicon Sequencing (Rhizosphere) + dataset_type: AMPLICON_16S + repository: NCBI_BIOPROJECT + accession: PRJNA1313845 + url: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1313845 + description: 16S rRNA amplicon sequencing data from cucumber rhizosphere under RKN infection + across multiple soil types. + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: root-knot nematode (RKN) infection restructured the rhizosphere bacterial community in + RKN-susceptible cucumber plants, regardless of the soil type + explanation: Documents amplicon-based community profiling across soil types +- name: 16S Amplicon Sequencing (SynCom Validation) + dataset_type: AMPLICON_16S + repository: NCBI_BIOPROJECT + accession: PRJNA1313795 + url: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1313795 + description: 16S rRNA amplicon sequencing data from SynCom validation experiments. + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: the TYQ1-centered synthetic community exhibited more efficient and stable inhibition + of RKNs + explanation: Documents SynCom validation sequencing data +- name: Transcriptomics + dataset_type: METATRANSCRIPTOME + repository: NCBI_BIOPROJECT + accession: PRJNA1314495 + url: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1314495 + description: Transcriptomic data for understanding gene expression in TYQ1-centered SynCom during + nematode biocontrol. + evidence: + - reference: PMID:41660888 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: stress-induced recruitment of keystone species can guide functional microbial community + assembly to synergistically enhance plant health + explanation: Documents transcriptomic analysis of the SynCom