The amendments are the coculture, not a treatment on it (#183) - #541
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The amendments are the coculture, not a treatment on it (#183)#541realmarcin wants to merge 1 commit into
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Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture: 60 mL serum bottles with 25 mL artificial bay water medium under N2, static, 34 °C, each strain inoculated at 10% v/v, with TCE and acetylene both at 0.1 mM. Both amendments are in instrument_detail because they are the coculture's mechanism rather than a condition applied to it. Acetylene is Pelobacter's electron donor and carbon source, and Pelobacter is what feeds the dechlorinating partner; TCE is what that partner reduces. Take either out and there is no consortium to describe. Static for the same reason as the JN4/GD17 record: strict anaerobes on volatile substrates in a sealed bottle, where agitation would work against both the gas balance and the syntrophic exchange. The serial transfers are described rather than forced into cultivation_mode, which has no value for them — cocultures were carried forward at 5% v/v once 20 μmol TCE had gone to vinyl chloride and 36 μmol acetylene was depleted. The monoculture conditions in the same paper — strains 195 and BAV1 on defined medium under H2/CO2, SFB93 alone on ABW — are not recorded (#529), the fifth time in this batch. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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This was referenced Aug 11, 2026
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What
Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture— 60 mL serum bottles with 25 mL artificial bay water medium under an N₂ headspace, static, 34 °C, each strain inoculated at 10% v/v, with TCE and acetylene both at 0.1 mM.Why both amendments are in
instrument_detailThey are the coculture's mechanism, not a condition applied to it. Acetylene is Pelobacter's electron donor and carbon source; Pelobacter is what feeds the dechlorinating partner; TCE is what that partner reduces. Remove either and there is no consortium left to describe.
Recording them as
environmental_factorsalone would read as "this community was exposed to TCE", which inverts the relationship.Static, again on purpose
Same reasoning as the JN4/GD17 record: strict anaerobes on volatile substrates in a sealed bottle, where agitation works against both the gas balance and the syntrophic exchange. Recorded rather than dropped, because a missing agitation field otherwise reads as an omission.
The serial transfers are described, not forced into an enum
Cocultures were carried forward at 5% v/v once 20 μmol TCE had gone to vinyl chloride and 36 μmol acetylene was depleted.
CultivationModeEnumhas no value for serial batch transfer, so it goes innotesrather than being approximated bySEMI_CONTINUOUS, which would imply continuous feeding.Monocultures excluded
Strains 195 and BAV1 on defined medium under H₂/CO₂ (80:20), and SFB93 alone on ABW, are all in the same paper and none are recorded here — #529 for the fifth time in this batch. The supporting snippet settles it directly: it names "Bacterial cocultures of strains 195 and SFB93".
Checks
just validate— no issuesjust validate-references— 0 issues; snippet verbatimjust validate-strict,just lint,just check-docs-current— exit 0uv run pytest tests/— 2375 passed, 16 skippedPart of #183.
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