From 21f9ca949f9db2782a02706b144aa88be597dba5 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 11 Aug 2026 02:16:10 -0700 Subject: [PATCH] Syntrophy setup, and the fumarate that must not be in it (#183) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Syntrophobacter_Methanobacterium_Syntrophy: 1 L flasks with 550 mL medium, in triplicate, 37 °C, under a pressurised N2/CO2 (80:20) gas phase at 172 kPa. The headspace is not merely an anaerobic blanket — syntrophic propionate oxidation is thermodynamically feasible only while the partner keeps H2 and formate low, so the gas composition and pressure are part of the experiment. The cited sentence says "all organisms", which here covers the cocultures as well as the axenic controls, so these are the community's conditions. That is the #529 check passing on the wording rather than on a member-name count. Deliberately excluded: the 20 mM propionate and 60 mM fumarate supplement, which the source attaches to "the medium for the pure cultures". Fumarate is an electron acceptor that lets S. fumaroxidans grow without a partner, so carrying it into the coculture's setup would describe a condition that abolishes the syntrophy this record exists to document. Same shape as the precultures excluded from the last three records, but with a sharper consequence. Also fixes two reference-validation failures already on main for this record. The snippets wrote strain designations as `MPOB T`, `JF1 T`, `MF T`; the cached text renders the superscript type-strain marker closed up, `MPOBT`, `JF1T`, `MFT`. A rendering artefact, not a misquotation — the record now validates at zero issues rather than two. Co-Authored-By: Claude Opus 5 --- ...ophobacter_Methanobacterium_Syntrophy.html | 4 +- ...ophobacter_Methanobacterium_Syntrophy.yaml | 38 +++++++++++++++++-- 2 files changed, 37 insertions(+), 5 deletions(-) diff --git a/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html b/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html index 607b1841..92d62231 100644 --- a/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html +++ b/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html @@ -1058,7 +1058,7 @@

Evidence

-

"Syntrophobacter fumaroxidans MPOB T (DSM 10017) was cultivated under anoxic conditions in basal medium as described previously"

+

"Syntrophobacter fumaroxidans MPOBT (DSM 10017) was cultivated under anoxic conditions in basal medium as described previously"

@@ -1084,7 +1084,7 @@

Evidence

-

"Cocultures of S. fumaroxidans with Methanospirillum hungatei strain JF1 T (DSM 864) or Methanobacterium formicicum MF T (DSM 1535) were grown with 30 mM of propionate without electron acceptor"

+

"Cocultures of S. fumaroxidans with Methanospirillum hungatei strain JF1T (DSM 864) or Methanobacterium formicicum MFT (DSM 1535) were grown with 30 mM of propionate without electron acceptor"

diff --git a/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml b/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml index 8067e882..8728e37a 100644 --- a/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml +++ b/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml @@ -250,6 +250,38 @@ ecological_interactions: were used in its sulfidogenic metabolism explanation: Confirms the importance of formate as an interspecies electron carrier in addition to H2 +cultivation_setup: +- cultivation_mode: BATCH + system_type: FLASK + working_volume: 550.0 + working_volume_unit: mL + operating_temperature: 37.0 + operating_temperature_unit: °C + instrument_detail: >- + 1 L flasks holding 550 mL of medium, in triplicate, under a pressurised N2/CO2 (80:20) + gas phase at 172 kPa. The headspace is not just an anaerobic blanket: syntrophic + propionate oxidation is thermodynamically feasible only while the partner keeps H2 and + formate low, so the gas composition and pressure are part of the experiment. + notes: >- + The cited sentence says "all organisms", which in this paper covers the cocultures as + well as the axenic controls - so these are the community's conditions and not a member's. + That is the #529 check passing on the wording rather than on a member-name count, as it + did for the JN4/GD17 record. + + What is NOT recorded: the 20 mM propionate and 60 mM fumarate supplement, which the + source attaches specifically to "the medium for the pure cultures". Fumarate is an + electron acceptor that lets S. fumaroxidans grow without a partner, so carrying it into + the coculture's setup would describe a condition that removes the syntrophy this record + exists to document. + evidence: + - reference: PMID:29611893 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: All organisms were batch cultured in triplicate at 37°C in 1 l flasks with 550 ml + medium under anaerobic conditions provided by a pressurised (172 kPa; 1.7 atm) gas phase + of N2/CO2 (80:20, vol/vol) + explanation: Mode, vessel, working volume, temperature and the pressurised anaerobic headspace. + environmental_factors: - name: Exogenous Formate Dosage value: 5-10 mM promotes; 50 mM inhibits @@ -393,7 +425,7 @@ growth_media: - reference: PMID:29611893 supports: SUPPORT evidence_source: IN_VITRO - snippet: Syntrophobacter fumaroxidans MPOB T (DSM 10017) was cultivated under anoxic conditions + snippet: Syntrophobacter fumaroxidans MPOBT (DSM 10017) was cultivated under anoxic conditions in basal medium as described previously explanation: Establishes anoxic basal-medium cultivation for the propionate-oxidizing partner. - reference: PMID:29611893 @@ -404,8 +436,8 @@ growth_media: - reference: PMID:29611893 supports: SUPPORT evidence_source: IN_VITRO - snippet: Cocultures of S. fumaroxidans with Methanospirillum hungatei strain JF1 T (DSM 864) or - Methanobacterium formicicum MF T (DSM 1535) were grown with 30 mM of propionate without electron + snippet: Cocultures of S. fumaroxidans with Methanospirillum hungatei strain JF1T (DSM 864) or + Methanobacterium formicicum MFT (DSM 1535) were grown with 30 mM of propionate without electron acceptor explanation: Confirms the S. fumaroxidans-M. formicicum coculture and propionate substrate concentration. discussions: