From 00eb65c830102316e3c0aea6225d443161c37544 Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Tue, 21 Jul 2026 20:15:52 -0700
Subject: [PATCH] Rhodopseudomonas-Geobacter magnetite redox: curate causal
 graph
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Add directed `downstream` causal edges to the four existing
ecological_interactions of CommunityMech:000268, from the Edison
causal-graph run (PaperQA3; PMID:25814583 Byrne et al. 2015 Science,
+ doi:10.1126/science.aaa4834).

Wiring — the reversible magnetite "battery" loop:
- Phototrophic Magnetite Fe(II) Oxidation -> Anaerobic Magnetite Fe(III)
  Reduction (TIE-1 photo-oxidation of Fe(II) supplies the Fe(III) acceptor
  G. sulfurreducens reduces).
- Anaerobic Magnetite Fe(III) Reduction -> Phototrophic Magnetite Fe(II)
  Oxidation (Geobacter regenerates the Fe(II) donor for TIE-1; reversible
  in co-cultures) — closing the 2<->3 redox loop.
- Phototrophic ... Oxidation, Anaerobic ... Reduction, and Magnetite-Mediated
  Electron Sharing all -> Biogeochemical Battery Function (the two
  half-reactions + electron sharing constitute the emergent, reusable
  mineral electron store).

InteractionDownstream carries target + causal description only; evidence
stays on the parent nodes (existing PMID:25814583 snippets). Schema
validates; no new snippets or terms. Record HTML page regenerated.

First causal record curated via a normal `just research-community-causal`
run after the .env-precedence fix (#245) — no `env -u` workaround.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 ...s_Geobacter_Magnetite_Redox_Coculture.html | 36 +++++++++++++++++++
 ...s_Geobacter_Magnetite_Redox_Coculture.yaml | 27 ++++++++++++++
 2 files changed, 63 insertions(+)

diff --git a/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html b/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html
index fa81c477..9b5d63d0 100644
--- a/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html
+++ b/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html
@@ -409,6 +409,7 @@ <h1>Rhodopseudomonas-Geobacter Magnetite Redox Coculture</h1>
                     </span>
                 </div>
                 
+                
             </div>
         </section>
 
@@ -643,6 +644,15 @@ <h3>Magnetite-Mediated Electron Sharing</h3>
                 
 
                 
+                <div class="interaction-flow">
+                    <strong>Downstream Effects:</strong>
+                    
+                    <div class="flow-item">
+                        <span class="flow-arrow">→</span> Biogeochemical Battery Function
+                    </div>
+                    
+                </div>
+                
 
                 
                 <h4>Evidence</h4>
@@ -718,6 +728,19 @@ <h3>Phototrophic Magnetite Fe(II) Oxidation</h3>
                 
 
                 
+                <div class="interaction-flow">
+                    <strong>Downstream Effects:</strong>
+                    
+                    <div class="flow-item">
+                        <span class="flow-arrow">→</span> Anaerobic Magnetite Fe(III) Reduction
+                    </div>
+                    
+                    <div class="flow-item">
+                        <span class="flow-arrow">→</span> Biogeochemical Battery Function
+                    </div>
+                    
+                </div>
+                
 
                 
                 <h4>Evidence</h4>
@@ -784,6 +807,19 @@ <h3>Anaerobic Magnetite Fe(III) Reduction</h3>
                 
 
                 
+                <div class="interaction-flow">
+                    <strong>Downstream Effects:</strong>
+                    
+                    <div class="flow-item">
+                        <span class="flow-arrow">→</span> Phototrophic Magnetite Fe(II) Oxidation
+                    </div>
+                    
+                    <div class="flow-item">
+                        <span class="flow-arrow">→</span> Biogeochemical Battery Function
+                    </div>
+                    
+                </div>
+                
 
                 
                 <h4>Evidence</h4>
diff --git a/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml b/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml
index 24cdbe9a..e372d2d0 100644
--- a/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml
+++ b/kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml
@@ -143,6 +143,12 @@ ecological_interactions:
     term:
       id: GO:0006826
       label: iron ion transport
+  downstream:
+  - target: Biogeochemical Battery Function
+    description: >
+      Magnetite-mediated electron sharing between the phototrophic Fe(II)
+      oxidizer and the anaerobic Fe(III) reducer manifests as the emergent,
+      reusable mineral electron-storage system (the "battery").
   evidence:
   - reference: PMID:25814583
     supports: SUPPORT
@@ -178,6 +184,16 @@ ecological_interactions:
     term:
       id: GO:0015979
       label: photosynthesis
+  downstream:
+  - target: Anaerobic Magnetite Fe(III) Reduction
+    description: >
+      Light-driven oxidation of magnetite Fe(II) to Fe(III) supplies the
+      oxidized Fe(III) that G. sulfurreducens subsequently uses as its anaerobic
+      electron acceptor.
+  - target: Biogeochemical Battery Function
+    description: >
+      TIE-1 phototrophic Fe(II) oxidation is one half of the reversible redox
+      cycling that charges magnetite toward its oxidized state.
   evidence:
   - reference: PMID:25814583
     supports: SUPPORT
@@ -213,6 +229,17 @@ ecological_interactions:
     term:
       id: GO:0006826
       label: iron ion transport
+  downstream:
+  - target: Phototrophic Magnetite Fe(II) Oxidation
+    description: >
+      G. sulfurreducens reduction of magnetite Fe(III) regenerates the reduced
+      Fe(II) electron donor for TIE-1, closing the reversible redox loop (the
+      process is reversible in co-cultures).
+  - target: Biogeochemical Battery Function
+    description: >
+      Fe(III) reduction is the complementary half-reaction that restores the
+      mineral's reduced electron-storage capacity, making the magnetite store
+      reusable.
   evidence:
   - reference: PMID:25814583
     supports: SUPPORT