[codex] curate 50 synthetic communities

kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml

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+id: CommunityMech:000114
+name: Aerobic Denitrification Disturbance-Stable SynCom
+description: A three-member aerobic denitrification SMC that maintains function under dibutyl phthalate
+  and levofloxacin disturbances through division of labor.
+ecological_state: ENGINEERED
+community_origin: SYNTHETIC
+community_category: BIOREMEDIATION
+engineering_design:
+  objective: Resolve how synthetic denitrifying communities maintain functional stability under environmental
+    disturbances.
+  assembly_strategy: Pseudomonas aeruginosa N2, Acinetobacter baumannii N1, and Aeromonas hydrophila were
+    assembled as an aerobic denitrification SMC.
+  perturbation_design: Dibutyl phthalate and levofloxacin disturbance treatments.
+  measurement_endpoints:
+  - denitrification efficiency
+  - interspecific communication
+  - energy flux
+  - electron transfer
+  - EPS production
+  evidence:
+  - &id001
+    reference: PMID:40020349
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Understanding how synthetic microbial community (SMC) respond to environmental disturbances
+      is the key to realizing SMC engineering applications.
+    explanation: Supports the defined synthetic community design and represented community context.
+environment_term:
+  preferred_term: laboratory bioreactor
+  term:
+    id: ENVO:01001405
+    label: laboratory bioreactor
+  notes: Aerobic denitrification synthetic microbial community under pollutant disturbances.
+taxonomy:
+- taxon_term:
+    preferred_term: Pseudomonas aeruginosa
+    term:
+      id: NCBITaxon:287
+      label: Pseudomonas aeruginosa
+  functional_role:
+  - CROSS_FEEDER
+  evidence:
+  - *id001
+- taxon_term:
+    preferred_term: Acinetobacter baumannii
+    term:
+      id: NCBITaxon:470
+      label: Acinetobacter baumannii
+  functional_role:
+  - CROSS_FEEDER
+  evidence:
+  - *id001
+- taxon_term:
+    preferred_term: Aeromonas hydrophila
+    term:
+      id: NCBITaxon:644
+      label: Aeromonas hydrophila
+  functional_role:
+  - CROSS_FEEDER
+  evidence:
+  - *id001
+ecological_interactions:
+- name: Disturbance-Stable Division of Labor
+  description: Members redistribute functional dominance and metabolic pathways to maintain denitrification.
+  interaction_type: CROSS_FEEDING
+  evidence:
+  - *id001
+environmental_factors:
+- name: defined synthetic community design
+  value: Pseudomonas aeruginosa N2, Acinetobacter baumannii N1, and Aeromonas hydrophila were assembled
+    as an aerobic denitrification SMC.
+  description: Dibutyl phthalate and levofloxacin disturbance treatments.
+  evidence:
+  - *id001

kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml

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+id: CommunityMech:000113
+name: Aerobic Denitrification Quorum-Quenching SynCom
+description: A three-member aerobic denitrification SynCom whose quorum-quenching and AHL-mediated interactions
+  improve nitrate removal.
+ecological_state: ENGINEERED
+community_origin: SYNTHETIC
+community_category: BIOREMEDIATION
+engineering_design:
+  objective: Improve aerobic denitrification efficiency by engineering member interactions in a synthetic
+    microbial community.
+  assembly_strategy: Acinetobacter baumannii N1, Pseudomonas aeruginosa N2, and Aeromonas hydrophila were
+    assembled as an SMC.
+  perturbation_design: Single-culture, co-culture, and three-member SMC denitrification systems were compared.
+  measurement_endpoints:
+  - nitrate reduction
+  - nitrite accumulation
+  - AHL signaling
+  - electron transfer
+  evidence:
+  - &id001
+    reference: PMID:38277828
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: a synthetic microbial community (SMC) composed of denitrifiers Acinetobacter baumannii N1
+      (AC), Pseudomonas aeruginosa N2 (PA) and Aeromonas hydrophila (AH) were constructed.
+    explanation: Supports the defined synthetic community design and represented community context.
+environment_term:
+  preferred_term: laboratory bioreactor
+  term:
+    id: ENVO:01001405
+    label: laboratory bioreactor
+  notes: Aerobic denitrification synthetic microbial community for nitrate wastewater removal.
+taxonomy:
+- taxon_term:
+    preferred_term: Acinetobacter baumannii
+    term:
+      id: NCBITaxon:470
+      label: Acinetobacter baumannii
+  functional_role:
+  - CROSS_FEEDER
+  evidence:
+  - *id001
+- taxon_term:
+    preferred_term: Pseudomonas aeruginosa
+    term:
+      id: NCBITaxon:287
+      label: Pseudomonas aeruginosa
+  functional_role:
+  - CROSS_FEEDER
+  evidence:
+  - *id001
+- taxon_term:
+    preferred_term: Aeromonas hydrophila
+    term:
+      id: NCBITaxon:644
+      label: Aeromonas hydrophila
+  functional_role:
+  - CROSS_FEEDER
+  evidence:
+  - *id001
+ecological_interactions:
+- name: AHL-Mediated Aerobic Denitrification
+  description: AHL signaling and quorum quenching coordinate electron transfer and nitrate reduction.
+  interaction_type: CROSS_FEEDING
+  evidence:
+  - *id001
+environmental_factors:
+- name: defined synthetic community design
+  value: Acinetobacter baumannii N1, Pseudomonas aeruginosa N2, and Aeromonas hydrophila were assembled
+    as an SMC.
+  description: Single-culture, co-culture, and three-member SMC denitrification systems were compared.
+  evidence:
+  - *id001

kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml

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+id: CommunityMech:000092
+name: Arabidopsis Coumarin Root SynCom
+description: A reduced Arabidopsis root-isolate SynCom used to detect rhizosphere community shifts caused
+  by phytoalexin, flavonoid, and coumarin exudates.
+ecological_state: ENGINEERED
+community_origin: SYNTHETIC
+community_category: RHIZOSPHERE
+engineering_design:
+  objective: Determine how Arabidopsis specialized metabolites shape root-associated bacterial community
+    composition.
+  assembly_strategy: Reduced synthetic community of Arabidopsis thaliana root-isolated bacteria.
+  perturbation_design: Plant mutants deficient in secreted phytoalexins, flavonoids, and coumarins.
+  measurement_endpoints:
+  - community shifts
+  - rhizosphere colonization
+  - metabolite-dependent recruitment
+  evidence:
+  - &id001
+    reference: PMID:31152139
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: We employed a reduced synthetic community (SynCom) of Arabidopsis thaliana root-isolated
+      bacteria to detect community shifts that occur in the absence of the secreted small-molecule phytoalexins,
+      flavonoids, and coumarins.
+    explanation: Supports the defined synthetic community design and represented community context.
+environment_term:
+  preferred_term: rhizosphere
+  term:
+    id: ENVO:00005801
+    label: rhizosphere
+  notes: Arabidopsis root SynCom used to test plant specialized metabolite effects on rhizosphere assembly.
+taxonomy:
+- taxon_term:
+    preferred_term: Arabidopsis root-isolated bacteria
+    term:
+      id: NCBITaxon:2
+      label: Bacteria
+  functional_role:
+  - CROSS_FEEDER
+  evidence:
+  - *id001
+ecological_interactions:
+- name: Coumarin-Dependent Recruitment
+  description: Plant exuded specialized metabolites structure which bacteria persist in the rhizosphere.
+  interaction_type: COLONIZATION_FACILITATION
+  evidence:
+  - *id001
+environmental_factors:
+- name: defined synthetic community design
+  value: Reduced synthetic community of Arabidopsis thaliana root-isolated bacteria.
+  description: Plant mutants deficient in secreted phytoalexins, flavonoids, and coumarins.
+  evidence:
+  - *id001

kb/communities/Arabidopsis_Phyllosphere_SynCom7.yaml

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+id: CommunityMech:000091
+name: Arabidopsis Phyllosphere SynCom7
+description: A seven-strain reduced-complexity Arabidopsis phyllosphere SynCom used to test host genetic
+  effects on microbiota composition.
+ecological_state: ENGINEERED
+community_origin: SYNTHETIC
+community_category: OTHER
+engineering_design:
+  objective: Identify Arabidopsis host genetic factors that alter phyllosphere community composition and
+    abundance.
+  assembly_strategy: Seven bacterial strains representing abundant phyllosphere phyla were inoculated
+    onto gnotobiotic Arabidopsis mutants.
+  perturbation_design: Host mutant panel affecting surface structure, cell wall, defense, secondary metabolism,
+    and pathogen recognition.
+  measurement_endpoints:
+  - community composition
+  - member abundance
+  - host genotype effects
+  evidence:
+  - &id001
+    reference: PMID:24743269
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: the model plant Arabidopsis thaliana was used in a gnotobiotic system and inoculated with
+      a reduced complexity synthetic bacterial community composed of seven strains representing the most
+      abundant phyla in the phyllosphere.
+    explanation: Supports the defined synthetic community design and represented community context.
+environment_term:
+  preferred_term: phyllosphere
+  term:
+    id: ENVO:01001442
+    label: phyllosphere
+  notes: Gnotobiotic Arabidopsis phyllosphere inoculated with a seven-strain bacterial community.
+taxonomy:
+- taxon_term:
+    preferred_term: Arabidopsis phyllosphere bacteria
+    term:
+      id: NCBITaxon:2
+      label: Bacteria
+  functional_role:
+  - CROSS_FEEDER
+  evidence:
+  - *id001
+ecological_interactions:
+- name: Host-Genotype-Structured Assembly
+  description: Arabidopsis host genotype shifts the abundance and composition of the phyllosphere SynCom.
+  interaction_type: NICHE_PARTITIONING
+  evidence:
+  - *id001
+environmental_factors:
+- name: defined synthetic community design
+  value: Seven bacterial strains representing abundant phyllosphere phyla were inoculated onto gnotobiotic
+    Arabidopsis mutants.
+  description: Host mutant panel affecting surface structure, cell wall, defense, secondary metabolism,
+    and pathogen recognition.
+  evidence:
+  - *id001

kb/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.yaml

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+id: CommunityMech:000118
+name: Bacillus-Bradyrhizobium Straw Humification SynCom
+description: A two-member Bacillus siamensis and Bradyrhizobium japonicum SynCom that promotes maize straw
+  humification and soil organic carbon.
+ecological_state: ENGINEERED
+community_origin: SYNTHETIC
+community_category: LIGNOCELLULOSE
+engineering_design:
+  objective: Accelerate straw humification and improve soil organic carbon through a functionally stable
+    SynCom.
+  assembly_strategy: Keystone taxa from dilution microcosms were assembled as Bacillus siamensis B and
+    Bradyrhizobium japonicum G.
+  perturbation_design: Cross-feeding assays, enzyme activity assays, and field straw-return experiments.
+  measurement_endpoints:
+  - straw humification
+  - soil organic carbon
+  - cellulase activity
+  - xylanase activity
+  - nitrogenase activity
+  evidence:
+  - &id001
+    reference: PMID:41264879
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: From these taxa, we constructed a two-membered SynCom (Bacillus siamensis B and Bradyrhizobium
+      japonicum G).
+    explanation: Supports the defined synthetic community design and represented community context.
+environment_term:
+  preferred_term: soil
+  term:
+    id: ENVO:00001998
+    label: soil
+  notes: Cropland soil receiving maize straw and two-member SynCom inoculation.
+taxonomy:
+- taxon_term:
+    preferred_term: Bacillus siamensis
+    term:
+      id: NCBITaxon:1178515
+      label: Bacillus siamensis
+  functional_role:
+  - PRIMARY_DEGRADER
+  evidence:
+  - *id001
+- taxon_term:
+    preferred_term: Bradyrhizobium japonicum
+    term:
+      id: NCBITaxon:375
+      label: Bradyrhizobium japonicum
+  functional_role:
+  - CROSS_FEEDER
+  evidence:
+  - *id001
+ecological_interactions:
+- name: Straw Humification Cross-Feeding
+  description: Bacillus and Bradyrhizobium cross-feed to promote straw-degrading enzymes and humification.
+  interaction_type: CROSS_FEEDING
+  evidence:
+  - *id001
+environmental_factors:
+- name: defined synthetic community design
+  value: Keystone taxa from dilution microcosms were assembled as Bacillus siamensis B and Bradyrhizobium
+    japonicum G.
+  description: Cross-feeding assays, enzyme activity assays, and field straw-return experiments.
+  evidence:
+  - *id001