Add Rice-Duckweed Bacillus biocontrol SynCom (closes #23)#26
Conversation
8-member Bacillus-dominated SynCom from rice-duckweed agroecosystem (PMID:41736136). Division-of-labor architecture with auxin, siderophore, lipopeptide, and polyketide specialists for concurrent growth promotion and sheath blight biocontrol (70% disease reduction). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Pull request overview
This PR adds a new knowledge-base entry (kb/communities/Rice_Duckweed_Bacillus_SynCom.yaml) describing an 8-member Bacillus-dominated synthetic community assembled from a rice-duckweed agroecosystem. The community features a division-of-labor biocontrol architecture that simultaneously promotes rice growth and suppresses Rhizoctonia solani sheath blight (70% disease index reduction), as documented in PMID:41736136.
Changes:
- Adds a new community YAML file with 4 representative genus-level taxonomy entries, 2 ecological interactions, engineering design metadata, and leave-one-member perturbation details.
- Documents the division-of-labor metabolic specialization (auxin production, siderophore-linked iron mobilization, lipopeptide/polyketide antagonism) with ontology-linked metabolites (IAA, acetoin, 2,3-butanediol, surfactin).
- Includes environmental factors capturing the rice-duckweed agroecosystem greenhouse context.
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| term: | ||
| id: CHEBI:29681 | ||
| label: surfactin | ||
| notes: Lipopeptide antibiotic contributing to biocontrol |
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The description of the "Antimicrobial Biocontrol of Sheath Blight" interaction (lines 156–158) states that SynCom members produce "lipopeptides (surfactin, bacillomycin, fengycin) and polyketides (difficidin)", but only surfactin is listed in the metabolites section (lines 171–176). Bacillomycin, fengycin, and difficidin are entirely absent from the metabolites list, even though they are specifically named and documented by the qRT-PCR measurement endpoints (line 31) and the notes on the lipopeptide/polyketide taxonomy entries (lines 93, 110–111). These missing metabolites should be added to make the metabolites section consistent with the description.
| notes: Lipopeptide antibiotic contributing to biocontrol | |
| notes: Lipopeptide antibiotic contributing to biocontrol | |
| - preferred_term: bacillomycin | |
| term: | |
| label: bacillomycin | |
| notes: Lipopeptide antibiotic contributing to biocontrol | |
| - preferred_term: fengycin | |
| term: | |
| label: fengycin | |
| notes: Lipopeptide antibiotic contributing to biocontrol | |
| - preferred_term: difficidin | |
| term: | |
| label: difficidin | |
| notes: Polyketide antibiotic contributing to biocontrol |
| - preferred_term: indole-3-acetic acid | ||
| term: | ||
| id: CHEBI:16411 | ||
| label: indol-3-yl-acetic acid |
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The label for CHEBI:16411 is indol-3-yl-acetic acid at line 134, but across the codebase the consistent label used for this CHEBI term is indole-3-acetic acid (as seen in kb/communities/Chlamydomonas_Methylobacterium_Mutualism.yaml:125, kb/communities/Pseudonitzschia_Sulfitobacter_Association.yaml:93, and kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml:332). While indol-3-yl-acetic acid is a valid IUPAC synonym, the codebase convention is to use indole-3-acetic acid as the label for this term. This should be corrected for consistency.
| label: indol-3-yl-acetic acid | |
| label: indole-3-acetic acid |
Summary
kb/communities/Rice_Duckweed_Bacillus_SynCom.yamlfor an 8-member Bacillus-dominated SynCom from a rice-duckweed agroecosystem (PMID:41736136, doi:10.1186/s40168-026-02360-6)just validate)Closes #23
Test plan
just validate kb/communities/Rice_Duckweed_Bacillus_SynCom.yamlpasses with no issues🤖 Generated with Claude Code