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