From 6d9991c13c6238c3fc92f0e7273e369798bc1eb3 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 11 Aug 2026 09:34:23 -0700 Subject: [PATCH] The medium is the experiment, and the guess fails twice (#183, #543) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom: the fungus as an 8 mm plug and B. altitudinis B4 at 50 μL of OD600 0.4, co-cultured in P20 liquid medium made WITHOUT thiamine, with single-partner treatments as controls; plate assays at 28 °C in the dark. The omission is the point. S. clintonianus is a thiamine auxotroph, so a medium lacking thiamine is what makes it dependent on the bacterium. Recording "P20" without "without thiamine" would describe a system in which the interaction cannot be observed at all — the same shape as the fumarate deliberately kept out of the syntrophy record, where one component decides whether the partnership is necessary. No system_type or working_volume: the source gives neither for the co-culture, and both liquid co-culture and 60 mm plate assays appear, so one vessel value would misdescribe half the work. Second failure of the "likely refuse" group in #543, and it failed differently from the first. ORNL_PMI_Populus was assembled in liquid and never met a plant; here the two partners are co-cultured in liquid with the plant simply absent from the assay. Two falsifications from two readings means the remaining three in that group are not being classified without reading either. Co-Authored-By: Claude Opus 5 --- ...illus_Thiamine_Ectomycorrhizal_SynCom.yaml | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml b/kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml index 039bdc62..b9410b62 100644 --- a/kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml +++ b/kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml @@ -326,6 +326,43 @@ growth_media: at 28°C in the dark explanation: Plate format, plug size, temperature and light regime for the assay. +cultivation_setup: +- cultivation_mode: BATCH + operating_temperature: 28.0 + operating_temperature_unit: °C + instrument_detail: >- + The fungus as an 8 mm plug and B. altitudinis B4 at 50 μL of OD600 0.4, co-cultured in + P20 liquid medium made without thiamine, alongside single-partner treatments as controls. + Plate work ran at 28 °C in the dark. + notes: >- + The medium is the experiment. P20 without thiamine is what makes S. clintonianus - a + thiamine auxotroph - dependent on the bacterium, so recording the medium without the + omission would describe a system in which the interaction cannot be observed. This is the + same shape as the fumarate deliberately excluded from the syntrophy record: a single + component decides whether the partnership is necessary. + + No `system_type` or `working_volume`: the source gives neither for the co-culture, and + both the liquid co-culture and the 60 mm plate assays appear, so one vessel value would + misdescribe half the work. + + Predicted a likely refusal in #543 on the assumption that a plant-associated SynCom lives + on the plant. Wrong again, and differently: the two partners are co-cultured in liquid, + with the plant absent. Second of the five in that group to fail, which is why the + remaining three are not being classified without reading. + evidence: + - reference: PMID:41454778 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: clintonianus (8 mm) and B. altitudinis B4 (50 μL, OD600 = 0.4) were co-cultured in + P20 liquid medium (without thiamine) + explanation: The two members were grown together, in a medium lacking the vitamin at issue. + - reference: PMID:41454778 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Fungal plugs (8 mm) were placed in the center of the plate (60 mm) and incubated at + 28°C in the dark + explanation: Temperature and light regime for the plate assays. + environmental_factors: - name: Thiamine limitation of the fungal partner value: fungus cannot effectively obtain or synthesize thiamine