From b7b8e195d7ae8197d13a319b4a618946b6c74af8 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 11 Aug 2026 08:00:13 -0700 Subject: [PATCH] Sampling is the origin, sub-culturing is the cultivation (#183, #543) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 --- ...opper_Sulphide_Bioleaching_Consortium.yaml | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml b/kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml index 40dd4f33..0bafc010 100644 --- a/kb/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.yaml +++ b/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)