Add propanotrophic chlorinated-ethene cometabolism community#73
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Curate a new community YAML (CommunityMech:000271) from Faghihinezhad, Eshghdoostkhatami, Cupples 2026 Journal of Environmental Management, doi:10.1016/j.jenvman.2026.129957, "Characterization of multiple trichloroethene, cis-dichloroethene and 1,1-dichloroethene degrading propanotrophic communities". System: propane-enriched aerobic mixed cultures derived from three KBS-LTER agricultural soils (T2, T3, T4) and an impacted-site sediment (West Coast Naval Station, Site 1), evaluated for cometabolic biodegradation of TCE, cDCE, and 1,1-DCE over successive transfers. Members and roles: - Rhodococcus opacus and R. wratislaviensis (PRIMARY_DEGRADER, DOMINANT in TCE-amended enrichments) - Mycolicibacterium and Mycobacterium (PRIMARY_DEGRADER, dominant in cDCE-amended enrichments) - Pseudonocardia (PRIMARY_DEGRADER, dominant in 1,1-DCE-degrading cultures; carries truncated prmA so transformation enzyme unclear - PARTIAL) - Pseudonocardia broussonetiae (Site-1-specific MAG) - Methylibium and an unclassified Burkholderiaceae (CROSS_FEEDER, RARE non-actinobacterial propane-monooxygenase MAGs from cDCE enrichments) Interactions captured: - Propane-cometabolic TCE degradation by Rhodococcus (CROSS_FEEDING via group-5 prmABCD) - Propane-cometabolic cDCE degradation by Mycolicibacterium and Mycobacterium (CROSS_FEEDING via group-6 SDIMO with prmACDB ordering - PARTIAL since expression not examined) - Substrate-specific selection across the three chlorinated ethenes (COMPETITION at COMMUNITY_LEVEL) - 1,1-DCE-driven inhibition of propanotrophs (COMPETITION at COMMUNITY_LEVEL) Plus four environmental factors: propane growth substrate, chlorinated-ethene concentration ranges, inoculum source, aerobic shaken incubation. Storage: - Full-text PDF tracked at references_pdfs/Faghihinezhad_2026_propanotrophic_TCE_cDCE_DCE.pdf (new directory; no prior PDF storage convention in the repo). - references_cache/DOI_10.1016_j.jenvman.2026.129957.md now carries the full-text extracted from the PDF (content_type: full_text), enabling snippet validation against methods/results passages that the abstract alone does not cover. All snippets validate as substrings of the cached full text; `just validate-references-all` reports 39 errors (unchanged from main - the new community adds zero). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
Adds a new curated CommunityMech community record (CommunityMech:000271) describing propane-enriched, aerobic propanotrophic mixed cultures capable of cometabolic degradation of TCE, cDCE, and (in subsets) 1,1-DCE, backed by a cached full-text reference for DOI:10.1016/j.jenvman.2026.129957.
Changes:
- Adds a new community YAML capturing members/roles, ecological interactions, and environmental factors for the propanotrophic chlorinated-ethene cometabolism enrichments.
- Adds a new
references_cachefull-text markdown file for the cited 2026 J. Environmental Management article to support evidence snippets.
Reviewed changes
Copilot reviewed 1 out of 3 changed files in this pull request and generated 6 comments.
| File | Description |
|---|---|
| kb/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml | New curated community definition (members, interactions, environmental factors, evidence). |
| references_cache/DOI_10.1016_j.jenvman.2026.129957.md | New cached full-text reference backing snippet validation for the community curation. |
Comments suppressed due to low confidence (2)
kb/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml:321
- This second trichloroethene entry also uses CHEBI:18045; the repo convention elsewhere is CHEBI:16602 for trichloroethene. Please update this term for consistency across curated communities.
- preferred_term: trichloroethene
term:
id: CHEBI:18045
label: trichloroethene
kb/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.yaml:271
- This interaction description states that Mycolicibacterium and Mycobacterium both carry propane monooxygenase operons driving cDCE oxidation. The cached text explicitly reports prm operon-containing MAGs as Mycobacterium (and others), but does not indicate Mycolicibacterium MAGs/operons. Please adjust the wording (e.g., describe Mycolicibacterium as dominant by read-based taxonomy without asserting operon carriage) or add evidence that directly supports operon presence in Mycolicibacterium.
- name: Propane-Cometabolic cDCE Degradation by Mycolicibacterium and Mycobacterium
description: Mycolicibacterium dominates and Mycobacterium follows in all
four cDCE-amended enrichments; both genera carry propane monooxygenase
operons (with prmACDB ordering for the Mycobacterium MAGs, suggestive of
group-6 SDIMOs) that drive cometabolic cDCE oxidation while propane is
the growth substrate.
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Six review points from Copilot: - Cache cleanup: re-extract the PDF text with control-byte removal and paragraph-aware wrapping. The previous version of the cache contained 6 NUL bytes + 6 other ASCII control bytes (which could flip the file to binary in some tools) and was stored as a single ~109 kB line. Now: 0 NUL/control bytes, sentence-respecting paragraph layout wrapped at 100 columns, same content, all snippets still validate. - CHEBI ID for trichloroethene: 18045 -> 16602 to match the repo- standard term used by 4 other chlorinated-ethene communities (Dehalococcoides Syntrophomonas / Pelobacter / Desulfovibrio cocultures and KB1). - Mycolicibacterium notes: drop the unsourced claim that this genus carries prmACDB-ordered group-6 SDIMO operons. The paper's MAG-level results report propane monooxygenase operons on Rhodococcus, Mycobacterium, and Pseudonocardia MAGs, plus two Proteobacterial MAGs; the prmACDB ordering is specifically attributed to Mycobacterium. Updated notes flag that Mycolicibacterium dominance is from community-composition analysis, not MAG-level prm operons. - TCE-cometabolism description softened: the previous wording "the group-5 propane monooxygenase (prmABCD) is implicated as the enzyme that fortuitously oxidizes TCE" is stronger than the abstract supports (functional gene analysis identified the operons but expression was not examined). Now: states that Rhodococcus MAGs carry the prmABCD operon and that both group 5 and putative group 6 monooxygenases were identified in the community, with the caveat that expression was not examined and the in-vivo TCE-oxidizing enzyme is not directly demonstrated. - 1,1-DCE-inhibition description softened: drop the unsupported "rather than its irreversible transformation products" assertion. The evidence supports inhibitory/toxic effects at elevated concentrations but does not distinguish parent compound vs. transformation products; description now reflects that limitation explicitly. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Curate a new community YAML (`CommunityMech:000271`) from Faghihinezhad, Eshghdoostkhatami, Cupples 2026 Journal of Environmental Management, `doi:10.1016/j.jenvman.2026.129957` — "Characterization of multiple trichloroethene, cis-dichloroethene and 1,1-dichloroethene degrading propanotrophic communities".
System: propane-enriched aerobic mixed cultures derived from three KBS-LTER agricultural soils (T2, T3, T4) and an impacted-site sediment (West Coast Naval Station, Site 1), evaluated for cometabolic biodegradation of TCE, cDCE, and 1,1-DCE over successive transfers.
Members and roles
Interactions
Plus four environmental factors: propane growth substrate, chlorinated-ethene concentrations, inoculum source, aerobic shaken incubation.
Storage
Test plan
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