From 53677c07dd76a968148276c83fdf885c61614596 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 11 Aug 2026 05:19:16 -0700 Subject: [PATCH] THOR: nutrient level is the setting, and one record refused (#183, #543) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit THOR_Rhizosphere_Model_Community: liquid culture in half-strength tryptic soy broth at 28 °C with vigorous shaking, strains propagated on 1/10-strength TSA, interactions assayed across LB, half-strength TSB and soybean root exudate. The dilutions are in the record because they are chosen, not incidental. The paper's finding is that antagonism among the three members is medium-dependent and appears predominantly under the lower-nutrient condition, so a setup saying "TSB" would drop the half-strength — which is where the interactions are. No system_type or working_volume: the source says "liquid culture" and names the broth, never the vessel or the fill, and the assays run on plates as well as in liquid, so one vessel value would misdescribe half the experiments. Also filed #543. Avena_Rhizosphere_CrossKingdom_SIP_Community ranked top of the candidate list — 95k of full text, 100% member coverage — and must not be curated at all: it is stable-isotope probing of native rhizosphere soil, and the community was never grown in a vessel. No field in the record distinguishes that case. community_origin fails (three NATURAL records are legitimately cultivated, all verified), ecological_state fails (two of them are STABLE), and community_category fails (a RHIZOSPHERE record already carries a setup). The check has to be a human reading the source, which is worth knowing before anyone batches the remaining 13 full-text candidates. Co-Authored-By: Claude Opus 5 --- .../THOR_Rhizosphere_Model_Community.yaml | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/kb/communities/THOR_Rhizosphere_Model_Community.yaml b/kb/communities/THOR_Rhizosphere_Model_Community.yaml index 1f61cc99..bfc62b99 100644 --- a/kb/communities/THOR_Rhizosphere_Model_Community.yaml +++ b/kb/communities/THOR_Rhizosphere_Model_Community.yaml @@ -221,6 +221,44 @@ ecological_interactions: evidence_source: IN_VITRO snippet: production of more robust biofilms by the three members together than individually explanation: Supports biofilm formation as an emergent three-member community phenotype. +cultivation_setup: +- cultivation_mode: BATCH + operating_temperature: 28.0 + operating_temperature_unit: °C + instrument_detail: >- + Liquid culture in half-strength tryptic soy broth at 28 °C with vigorous shaking, with + strains propagated on 1/10-strength tryptic soy agar. Interactions were also assayed on + plates and across three media - LB, half-strength TSB, and soybean root exudate - because + which interactions appear depends on the medium: the inhibition among these strains shows + up predominantly under the lower-nutrient condition. + notes: >- + No `system_type` or `working_volume`. The source says "liquid culture" and names the + broth, never the vessel or the fill, and the interaction assays run on both plates and in + liquid - so a single vessel value would misdescribe half the experiments rather than + approximate them. + + Nutrient level is recorded as part of the setup rather than as an environmental factor + because it is a manipulated variable here: dilute TSA and TSB are chosen, and the paper's + point is that antagonism among the three members is medium-dependent. A record showing + only "TSB" would lose the half-strength, which is where the interactions are. + + Media and temperature are stated for the strains generally, which for a three-member + model community assembled from those strains is also the coculture's condition; the + coculture sentences name the same media (#529). + evidence: + - reference: PMID:30837345 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Bacterial strains were propagated on 1/10-strength tryptic soy agar (TSA) and grown + in liquid culture in 1/2-strength tryptic soy broth (TSB) at 28°C with vigorous shaking + explanation: Temperature, agitation, and the two dilute media the community is grown on. + - reference: PMID:30837345 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Rhizosphere isolates were grown alone or in coculture with P. koreensis CI12 in soybean + root exudate + explanation: Cocultures were run in root exudate as well as defined broth. + environmental_factors: - name: Rhizosphere Origin value: Field-grown soybean root/rhizosphere-associated isolates