My #543 prediction was wrong, and that is the useful part (#183, #543)

kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml

@@ -190,6 +190,51 @@ ecological_interactions:
       conjugal transfer genes found in the same genus, likely belonging to
       another plasmid, evidence of intra-plasmid competition
     explanation: Supports the CRISPR-spacer-based plasmid competition.
+cultivation_setup:
+- cultivation_mode: BATCH
+  operating_temperature: 28.0
+  operating_temperature_unit: °C
+  instrument_detail: >-
+    The consortium was sampled from packed bioleaching column SC3 at the Skouriotissa Mine in
+    Cyprus, then maintained in the laboratory: incubated at 28 °C without agitation and
+    sub-cultured ten times at 5% inoculum every two months in MAM with 0.25 g of unsterilised
+    research-grade chalcopyrite. It was then split and sub-cultured onto chalcocite as well as
+    chalcopyrite, since the mineral is the variable the study is about.
+  notes: >-
+    The mineral is in the setup rather than only among environmental factors because it is
+    the substrate the community is grown on and the experimental variable at once - the whole
+    question is how mineral type drives composition. It is also deliberately unsterilised,
+    which is a choice about what the community is allowed to encounter.
+
+    Static, and worth recording for the same reason as the thermophilic cellulose and TCE
+    records: a mineral-attached acidophile consortium is grown on a settled solid surface, so
+    "without agitation" is a design decision rather than an omission.
+
+    No `system_type` or `working_volume`. The source names neither the vessel nor the fill for
+    the sub-cultures; the packed column it came from is the field source, not the laboratory
+    setup, and recording it would describe where the community was found rather than how it
+    was grown.
+
+    Third of the three "likely curatable" predictions in #543, and it holds - but only just.
+    The community originates in a column at a mine, which is exactly the shape that made
+    Avena_Rhizosphere unenrichable. What separates them is that this one was then carried into
+    the laboratory and propagated for ten passages; the sampling is the origin, the
+    sub-culturing is the cultivation.
+  evidence:
+  - reference: PMID:41381092
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Before the experiment, the microbial enrichment was incubated at 28°C without agitation
+      and sub‐cultured 10 times with a 5% inoculum every 2 months in MAM with 0.25 g unsterilized
+      research grade chalcopyrite
+    explanation: Temperature, static operation, transfer regime, medium and mineral substrate.
+  - reference: PMID:41381092
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: microbial consortia from a copper bioleaching column in Cyprus were cultivated on
+      chalcopyrite (CuFeS2) and then sub‐cultured on chalcocite (Cu2S) and chalcopyrite
+    explanation: The community was cultivated in the laboratory, and the mineral was varied.
+
 environmental_factors:
 - name: Mineral substrate
   value: chalcopyrite (CuFeS2) and chalcocite (Cu2S)

kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml

@@ -566,6 +566,45 @@ ecological_interactions:
     snippet: To unravel the underlying metabolic interactions, flux balance analysis was used to model
       microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities
     explanation: Supports metabolite exchange interactions in community assembly
+cultivation_setup:
+- cultivation_mode: BATCH
+  operating_temperature: 30.0
+  operating_temperature_unit: °C
+  instrument_detail: >-
+    Serial-dilution passaging of the ten-member community in liquid culture. Each strain was
+    grown alone for 48 h, normalised to the lowest OD600 in that medium, then equal volumes
+    were mixed so the starting inoculum held all ten at roughly equal concentration.
+    Triplicate cultures were incubated 48 h at 30 °C with shaking at 200 rpm and passaged
+    every 48 h at 1:10 into fresh medium.
+  notes: >-
+    Two media were run in parallel, R2A and MOPS, because the study's question is whether the
+    same ten strains form different stable communities in different environments. Recording
+    one would misrepresent the design, so both are named here rather than a single
+    growth_media entry standing in for them.
+
+    No `system_type` or `working_volume`. The 10 mL test tubes named in the source are for the
+    individual seed cultures; the source does not say what the community passages were run in,
+    and carrying the seed-culture vessel across would be the preculture error (#529).
+
+    Predicted a likely refusal in #543, on the assumption that a plant-associated SynCom lives
+    on the plant. That was wrong: this community was assembled and passaged in liquid medium
+    and never put on a Populus root in this study. Recorded because the prediction failing is
+    the useful part - the remaining candidates there need the same reading rather than
+    inheriting the guess.
+  evidence:
+  - reference: PMID:33995895
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Equal volumes of the normalized culture were mixed together, and the community was
+      transferred into fresh medium using a 1:10 dilution
+    explanation: The community itself was passaged, not just its members.
+  - reference: PMID:33995895
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Triplicate cultures, for both media, were incubated for 48 h at 30 °C with shaking
+      at 200 rpm
+    explanation: Temperature, agitation and the 48 h passage interval, for the community cultures.
+
 environmental_factors:
 - name: Growth medium context
   value: two media environments