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) diff --git a/kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml b/kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml index 64a666e9..ee26916c 100644 --- a/kb/communities/ORNL_PMI_Populus_PD10_SynCom.yaml +++ b/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