Sampling is the origin, sub-culturing is the cultivation (#183, #543) - #548
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Sampling is the origin, sub-culturing is the cultivation (#183, #543)#548realmarcin wants to merge 1 commit into
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Cyprus_Copper_Sulphide_Bioleaching_Consortium: sampled from packed bioleaching column SC3 at the Skouriotissa Mine, then maintained at 28 °C without agitation and sub-cultured ten times at 5% inoculum every two months in MAM with 0.25 g of unsterilised chalcopyrite, before being split onto chalcocite as well. The mineral is in the setup rather than only among environmental factors because it is the growth substrate and the experimental variable at once — the study is about how mineral type drives composition. It is also deliberately unsterilised, which is a choice about what the community is allowed to encounter. Static, recorded for the same reason as the thermophilic cellulose and TCE records: a mineral-attached acidophile consortium grows on a settled solid surface, so "without agitation" is a design decision, not an omission. No system_type or working_volume — the source names neither for the sub-cultures. The packed column is the field source, not the laboratory setup; recording it would describe where the community was found rather than how it was grown. This completes the three "likely curatable" predictions in #543, and it is the closest call of them. The community originates in a column at a mine, which is the shape that made Avena_Rhizosphere unenrichable. What separates them is that this one was carried into the laboratory and propagated for ten passages. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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What
Cyprus_Copper_Sulphide_Bioleaching_Consortium— sampled from packed bioleaching column SC3 at the Skouriotissa Mine, then maintained at 28 °C without agitation and sub-cultured ten times at 5% inoculum every two months in MAM with 0.25 g of unsterilised chalcopyrite, before being split onto chalcocite as well.The mineral is part of the setup
It is the growth substrate and the experimental variable at once — the study exists to ask how mineral type drives composition. It is also deliberately unsterilised, which is a choice about what the community is allowed to encounter, not an oversight.
Static, again on purpose
Same reasoning as the thermophilic cellulose (#537) and TCE (#541) records: a mineral-attached acidophile consortium grows on a settled solid surface, so "without agitation" is a design decision. Recorded rather than dropped, because a missing agitation field reads as an omission.
What is not recorded
No
system_typeorworking_volume— the source names neither for the sub-cultures. The packed column is the field source, not the laboratory setup; recording it would describe where the community was found rather than how it was grown.The closest call in #543 so far
This completes the three "likely curatable" predictions. It is also the one that nearly went the other way: the community originates in a column at a mine, which is precisely the shape that made
Avena_Rhizosphereunenrichable.What separates them is a single fact — this one was carried into the laboratory and propagated for ten passages. Sampling is the origin; sub-culturing is the cultivation. A record whose paper only describes the first has nothing for this slot.
#543 scorecard
Five of thirteen candidates now verified by reading: 2 refused (
Avena_Rhizosphere,OMM12), 1 partial (Cheese_Rind, in vitro arm only), 3 curated (Acetylene_Fueled,Rifle_Aquifer, this one). The predicted classification has held on every one checked.Checks
just validate— no issuesjust validate-references— 0 issues; both snippets verbatimjust validate-strict,just lint,just check-docs-current— exit 0uv run pytest tests/— 2375 passed, 16 skippedPart of #183. Advances #543.
🤖 Generated with Claude Code