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| 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 | ||
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The
Sphingomonas xanthus SXentry uses a genus-level NCBITaxon ID (NCBITaxon:13687, labelSphingomonas) while thepreferred_termclaims a species-level identification (Sphingomonas xanthus). This is internally inconsistent and can mislead downstream consumers (e.g., taxonomy summaries). Either update the taxon name to genus-level (e.g.,Sphingomonas sp./Sphingomonas sp. SX) to match the ID+label, or switch to a species-level NCBITaxon ID if available.