diff --git a/docs/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.html b/docs/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.html index e0ef3f547..9439f6ef5 100644 --- a/docs/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.html +++ b/docs/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.html @@ -578,8 +578,7 @@

Ecological Interactions

Ammonium Cross-Feeding By Nitrogen-Fixing R. palustris

CROSS_FEEDING -

Rhodopseudomonas palustris fixes dinitrogen and excretes ammonium as the essential nitrogen source for E. coli in the anaerobic synthetic mutualism. -

+

In the tested anaerobic cocultures, nitrogen-fixing R. palustris supplies ammonium required by E. coli. Effective exchange depends on the donor and recipient context: engineered ammonium-excreting partners support growth, whereas WT-based emergence depends on recipient adaptation. This is not a claim that every wild-type pairing readily supports the same exchange.

Source Taxon: Rhodopseudomonas palustris

@@ -622,8 +621,7 @@

Ammonium Cross-Feeding By Nitrogen-Fixing R. palustris

→ Reciprocal Carbon-Nitrogen Cross-Feeding -

Ammonium excreted by nitrogen-fixing R. palustris supplies the nitrogen currency needed by E. coli in the reciprocal coculture. -

+

Ammonium transfer supports E. coli nitrogen acquisition and thereby its contribution to reciprocal coculture growth in the tested donor/recipient contexts; the rate and emergence of this exchange are strain dependent.

@@ -655,8 +653,7 @@

Evidence

E. coli Fermentation Product Cross-Feeding

CROSS_FEEDING -

E. coli ferments glucose and excretes organic acids that serve as essential carbon sources for R. palustris, forming the carbon-transfer half of the reciprocal exchange. -

+

E. coli fermentation supplies acetate, lactate and succinate that R. palustris can use as carbon sources in the studied cocultures. The paper excludes formate from these consumed organic-acid carbon sources; ethanol excretion is not evidence that ethanol supplies the partner. This is the carbon-transfer half of the demonstrated reciprocal exchange.

Source Taxon: Escherichia coli

@@ -687,8 +684,7 @@

E. coli Fermentation Product Cross-Feeding

→ Reciprocal Carbon-Nitrogen Cross-Feeding -

E. coli fermentation products provide the essential carbon flow to R. palustris that balances R. palustris ammonium transfer back to E. coli. -

+

The usable organic-acid products of E. coli fermentation supply carbon to R. palustris, enabling the carbon-transfer arm of the reciprocal carbon/nitrogen exchange; not every excreted fermentation product is a partner carbon source.

@@ -707,7 +703,7 @@

Evidence

- SUPPORT (IN_VITRO) -
"E. coli ferments glucose, a carbon source that R. palustris cannot consume, and excretes ethanol and organic acids"
+
"The organic acids, with the exception of formate, serve as the sole carbon sources for R. palustris"
@@ -720,7 +716,7 @@

Evidence

Reciprocal Carbon-Nitrogen Cross-Feeding

CROSS_FEEDING -

R. palustris supplies ammonium while E. coli supplies fermentation products.

+

Reciprocal exchange of ammonium and usable organic-acid carbon supports the tested R. palustris-E. coli cocultures. Engineered donor contexts and adapted recipient contexts are distinct routes to coexistence, not a universal wild-type phenotype. Enhanced recipient uptake is the authors mechanistic interpretation of emergence; no new gene-design or feedback node is added here.

@@ -790,6 +786,45 @@

Evidence

+
+

Knowledge gaps & discussions (1)

+ +
+

+ KNOWLEDGE_GAP + OPEN + How general is reciprocal exchange across donor and recipient backgrounds? +

+

The complete primary manuscript distinguishes engineered ammonium donors from WT-based emergence and shows that recipient adaptation can enable coculture growth without increased donor ammonium excretion. Retain both observed transfer directions, but do not generalize growth rates, readiness of exchange or inferred uptake feedback to arbitrary wild-type pairings. Species-level canonical taxonomy is unchanged. No new genetic design or experimental protocol is curated.

+ +

Attaches to: ecological_interactions#Ammonium Cross-Feeding By Nitrogen-Fixing R. palustris, ecological_interactions#E. coli Fermentation Product Cross-Feeding, ecological_interactions#Reciprocal Carbon-Nitrogen Cross-Feeding

+ + + +
+ 1 evidence item(s) + +
+
+ IN_VITRO + SUPPORT + + + + PMID:32788711 + + +
+

multiple combinations of recipient and producer genotypes can lead to stable coexistence

+

Discussion limits coexistence to genotype/environment combinations, rather than all pairings.

+
+ +
+ + +
+ +
diff --git a/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html b/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html index df9895946..8476fb407 100644 --- a/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html +++ b/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html @@ -585,7 +585,7 @@

Ecological Interactions

Ecological interaction network for Rhodopseudomonas-Geobacter Magnetite Redox Coculture - Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, syntrophy, niche partitioning). + Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -593,18 +593,8 @@

Ecological Interactions

Cross-feeding -
-
- Syntrophy -
-
- Niche partitioning + aria-hidden="true" data-symbol="symbolTriangle2" + data-color="#929caa"> Other
@@ -613,17 +603,19 @@

Ecological Interactions

Magnetite-Mediated Electron Sharing

- CROSS_FEEDING
-

Rhodopseudomonas palustris TIE-1 withdraws electrons from magnetite during phototrophic Fe(II) oxidation, while Geobacter sulfurreducens returns electrons to magnetite through anaerobic Fe(III) reduction. -

+

The two recorded bacteria exchange electrons with a shared mixed-valence magnetite reservoir: R. palustris TIE-1 withdraws electrons during phototrophic Fe(II) oxidation, whereas G. sulfurreducens supplies electrons during Fe(III) reduction. This is mineral-mediated redox cycling, not a direct nutrient transfer from TIE-1 to Geobacter.

-

Source Taxon: Rhodopseudomonas palustris TIE-1

+

Participating Taxa: -

Target Taxon: Geobacter sulfurreducens

+ Rhodopseudomonas palustris TIE-1, + + Geobacter sulfurreducens + +

@@ -645,17 +637,6 @@

Magnetite-Mediated Electron Sharing

-

Biological Processes:

- -
@@ -663,8 +644,7 @@

Magnetite-Mediated Electron Sharing

→ Biogeochemical Battery Function -

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"). -

+

Opposed microbial electron withdrawal and supply allow magnetite to function as the shared redox reservoir under the tested externally controlled conditions.

@@ -707,17 +687,19 @@

Evidence

Phototrophic Magnetite Fe(II) Oxidation

- NICHE_PARTITIONING
-

Under light, R. palustris TIE-1 oxidizes Fe(II) in magnetite nanoparticles, decreasing the reduced fraction of the mixed-valence mineral. -

+

Under light, R. palustris TIE-1 oxidizes magnetite Fe(II), withdrawing stored electrons and discharging the mineral. In the coculture cycle this is one community redox step, not a demonstrated pairwise fitness benefit or resource-partitioning experiment.

-

Source Taxon: Rhodopseudomonas palustris TIE-1

+

Participating Taxa: -

Target Taxon: Geobacter sulfurreducens

+ Rhodopseudomonas palustris TIE-1, + + Geobacter sulfurreducens + +

@@ -753,14 +735,12 @@

Phototrophic Magnetite Fe(II) Oxidation

→ Anaerobic Magnetite Fe(III) Reduction -

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. -

+

Oxidation regenerates magnetite Fe(III) that Geobacter can subsequently reduce when electron donor is supplied under the tested reducing conditions; the observed cycle depends on external conditions.

→ Biogeochemical Battery Function -

TIE-1 phototrophic Fe(II) oxidation is one half of the reversible redox cycling that charges magnetite toward its oxidized state. -

+

Phototrophic Fe(II) oxidation withdraws electrons from magnetite and discharges the mineral reservoir; it does not charge an oxidized electron store.

@@ -790,17 +770,19 @@

Evidence

Anaerobic Magnetite Fe(III) Reduction

- NICHE_PARTITIONING
-

Geobacter sulfurreducens reduces Fe(III) in magnetite, reversing the TIE-1-driven oxidation and restoring the mineral's reduced electron-storage capacity. -

+

G. sulfurreducens reduces magnetite Fe(III), storing supplied electrons as reduced Fe(II) and charging the mineral. The demonstrated reversal requires suitable electron-donor and environmental conditions; it is not evidence of direct reciprocal nutrient exchange.

+ -

Source Taxon: Geobacter sulfurreducens

+

Participating Taxa: + Rhodopseudomonas palustris TIE-1, -

Target Taxon: Rhodopseudomonas palustris TIE-1

+ Geobacter sulfurreducens + +

@@ -822,17 +804,6 @@

Anaerobic Magnetite Fe(III) Reduction

-

Biological Processes:

- -
@@ -840,14 +811,12 @@

Anaerobic Magnetite Fe(III) Reduction

→ Phototrophic Magnetite Fe(II) Oxidation -

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). -

+

Reduction regenerates magnetite Fe(II) that TIE-1 can oxidize during a subsequent illuminated phase, closing the experimentally demonstrated conditional redox cycle.

→ Biogeochemical Battery Function -

Fe(III) reduction is the complementary half-reaction that restores the mineral's reduced electron-storage capacity, making the magnetite store reusable. -

+

Fe(III) reduction charges magnetite with electrons and restores the reduced electron reservoir for later phototrophic discharge.

@@ -877,13 +846,19 @@

Evidence

Biogeochemical Battery Function

- SYNTROPHY
-

The paired Fe(II)-oxidizing and Fe(III)-reducing activities make magnetite function as a reusable mineral electron-storage system for the coculture. -

+

Repeated microbial reduction and oxidation make magnetite a reusable electron reservoir in the tested cocultures: reduction charges it and oxidation discharges it. External light and electron-donor supply drive the cycle; this is not a self-sustaining loop or a demonstrated syntrophic fitness relationship.

+ +

Participating Taxa: + + Rhodopseudomonas palustris TIE-1, + + Geobacter sulfurreducens + +

@@ -917,19 +892,6 @@

Evidence

-
  • -
    - - doi:10.1126/science.aaa4834 - - - SUPPORT (IN_VITRO) -
    - -
    "magnetite, which contains both Fe(II) and Fe(III), can serve as both an electron acceptor and donor"
    - -
    • -
    @@ -975,6 +937,45 @@

    Associated Datasets

    +
    +

    Knowledge gaps & discussions (1)

    + +
    +

    + KNOWLEDGE_GAP + OPEN + Which ecological benefits follow from the demonstrated mineral redox cycle? +

    +

    The full primary paper supports repeated coculture redox reversals with externally controlled light and electron-donor conditions. Preserve the real feedback directions, but distinguish mineral electron storage from direct nutrient cross-feeding, competition-based niche partitioning and product-removal syntrophy. Current SYNTROPHY does not require obligacy; the missing evidence is the relevant metabolic/fitness feedback. Redox chemistry is not iron-ion transport. The DOI cache contains an editorial summary, so graph evidence now uses the primary PMID abstract. Non-graph functional roles remain for issue1759.

    + +

    Attaches to: ecological_interactions#Magnetite-Mediated Electron Sharing, ecological_interactions#Phototrophic Magnetite Fe(II) Oxidation, ecological_interactions#Anaerobic Magnetite Fe(III) Reduction, ecological_interactions#Biogeochemical Battery Function

    + + + +
    + 1 evidence item(s) + +
    +
    + IN_VITRO + SUPPORT + + + + PMID:25814583 + + +
    +

    This process is reversible in co-cultures

    +

    Primary abstract supports reversal, not direct nutrient exchange or self-sustaining reciprocal fitness.

    +
    + +
    + + +
    + +
    @@ -1321,7 +1322,7 @@

    Evidence

    (function() { var intId = "interaction:0"; - var intType = "CROSS_FEEDING"; + var intType = "UNKNOWN"; var metabolites = []; @@ -1334,10 +1335,6 @@

    Evidence

    var processes = []; - - processes.push("iron ion transport"); - - var evidenceCount = 2; nodes.push({ @@ -1351,23 +1348,26 @@

    Evidence

    }); - var srcKey = "Rhodopseudomonas palustris TIE-1"; - if (taxonNodeIds[srcKey]) { - links.push({ source: taxonNodeIds[srcKey], target: intId }); - } + var participantKeys = [ - var tgtKey = "Geobacter sulfurreducens"; - if (taxonNodeIds[tgtKey]) { - links.push({ source: intId, target: taxonNodeIds[tgtKey] }); - } + "Rhodopseudomonas palustris TIE-1", + + "Geobacter sulfurreducens" + + ]; + participantKeys.forEach(function(key) { + if (taxonNodeIds[key]) { + links.push({ source: taxonNodeIds[key], target: intId }); + } + }); })(); (function() { var intId = "interaction:1"; - var intType = "NICHE_PARTITIONING"; + var intType = "UNKNOWN"; var metabolites = []; @@ -1395,23 +1395,26 @@

    Evidence

    }); - var srcKey = "Rhodopseudomonas palustris TIE-1"; - if (taxonNodeIds[srcKey]) { - links.push({ source: taxonNodeIds[srcKey], target: intId }); - } + var participantKeys = [ - var tgtKey = "Geobacter sulfurreducens"; - if (taxonNodeIds[tgtKey]) { - links.push({ source: intId, target: taxonNodeIds[tgtKey] }); - } + "Rhodopseudomonas palustris TIE-1", + + "Geobacter sulfurreducens" + + ]; + participantKeys.forEach(function(key) { + if (taxonNodeIds[key]) { + links.push({ source: taxonNodeIds[key], target: intId }); + } + }); })(); (function() { var intId = "interaction:2"; - var intType = "NICHE_PARTITIONING"; + var intType = "UNKNOWN"; var metabolites = []; @@ -1424,10 +1427,6 @@

    Evidence

    var processes = []; - - processes.push("iron ion transport"); - - var evidenceCount = 1; nodes.push({ @@ -1441,23 +1440,26 @@

    Evidence

    }); - var srcKey = "Geobacter sulfurreducens"; - if (taxonNodeIds[srcKey]) { - links.push({ source: taxonNodeIds[srcKey], target: intId }); - } + var participantKeys = [ - var tgtKey = "Rhodopseudomonas palustris TIE-1"; - if (taxonNodeIds[tgtKey]) { - links.push({ source: intId, target: taxonNodeIds[tgtKey] }); - } + "Rhodopseudomonas palustris TIE-1", + + "Geobacter sulfurreducens" + + ]; + participantKeys.forEach(function(key) { + if (taxonNodeIds[key]) { + links.push({ source: taxonNodeIds[key], target: intId }); + } + }); })(); (function() { var intId = "interaction:3"; - var intType = "SYNTROPHY"; + var intType = "UNKNOWN"; var metabolites = []; @@ -1466,7 +1468,7 @@

    Evidence

    var processes = []; - var evidenceCount = 2; + var evidenceCount = 1; nodes.push({ id: intId, @@ -1481,6 +1483,19 @@

    Evidence

    + var participantKeys = [ + + "Rhodopseudomonas palustris TIE-1", + + "Geobacter sulfurreducens" + + ]; + participantKeys.forEach(function(key) { + if (taxonNodeIds[key]) { + links.push({ source: taxonNodeIds[key], target: intId }); + } + }); + })(); diff --git a/docs/communities/Rice_Acid_Soil_Bioinoculant_SynCom.html b/docs/communities/Rice_Acid_Soil_Bioinoculant_SynCom.html index eb0c192cf..ea3360f1f 100644 --- a/docs/communities/Rice_Acid_Soil_Bioinoculant_SynCom.html +++ b/docs/communities/Rice_Acid_Soil_Bioinoculant_SynCom.html @@ -525,66 +525,6 @@

    Ecological Interactions

    -
    -
    -

    Al-Resistant Rice Rhizosphere SynCom Assembly

    -
    -

    Highly aluminium-resistant bacterial strains isolated from the rice rhizosphere were assembled into a synthetic community for acidic-soil bioinoculation tests. -

    - - - - - - - - -

    Biological Processes:

    - - - - -
    - Downstream Effects: - -
    - → Rhizodeposited Carbon-Fueled SynCom Proliferation -

    The assembled Al-resistant SynCom entered the rice rhizosphere, where host rhizodeposition supported its successful proliferation. -

    -
    - -
    - - - -

    Evidence

    - - -
    -

    Rhizodeposited Carbon-Fueled SynCom Proliferation

    @@ -617,8 +557,7 @@

    Rhizodeposited Carbon-Fueled SynCom Proliferation

    → Extracellular Al-Toxicity Mitigation -

    SynCom proliferation in the rice rhizosphere preceded community-level mitigation of soil acidification and aluminium toxicity. -

    +

    HYPOTHESIZED: root-carbon-supported proliferation supplies an active community capable of extracellular acid/Al mitigation. The accessible primary abstract reports both processes but does not isolate proliferation as the mediator; chronology alone is not causal proof.

    @@ -685,14 +624,12 @@

    Extracellular Al-Toxicity Mitigation

    → Topsoil Legacy Phosphorus Usage -

    Relief of acidic-soil aluminium stress was part of the plant-microbe coordination that enabled greater use of legacy phosphorus in topsoil. -

    +

    HYPOTHESIZED: mitigation of acidic-soil Al stress could help plant-microbe coordination improve access to legacy phosphorus. This direction is an authors proposed route, not quantitatively resolved mediation in the accessible abstract.

    → Acidic-Field Rice Yield Increase -

    Reduced soil acidification and aluminium toxicity contributed to the SynCom-mediated rice yield increase measured in acidic fields. -

    +

    PARTIAL: reduced acidification and Al toxicity are proposed contributors to the positive SynCom field-yield response, but the accessible abstract does not separate their contribution from other community effects.

    @@ -723,8 +660,7 @@

    Evidence

    Topsoil Legacy Phosphorus Usage

    -

    Functional coordination between rice and the SynCom increased access to topsoil legacy phosphorus under acidic field conditions. -

    +

    HYPOTHESIZED: plant-SynCom coordination offers a route to greater use of legacy phosphorus in acidic topsoil. The accessible primary abstract presents this as a promising application, not a quantified phosphorus flux or an isolated causal mediator of yield.

    @@ -748,8 +684,7 @@

    Topsoil Legacy Phosphorus Usage

    → Acidic-Field Rice Yield Increase -

    Improved use of legacy topsoil phosphorus helped connect Al-toxicity resistance to the observed acidic-field yield response. -

    +

    HYPOTHESIZED: improved legacy-phosphorus access could contribute to yield, but the accessible abstract does not demonstrate that this pathway mediates the measured 26.36% field response.

    @@ -765,7 +700,7 @@

    Evidence

    PMID:37783790 - - SUPPORT (IN_VIVO) + - PARTIAL (IN_VIVO)
    "The functional coordination between plants and microbes offers a promising way to increase the usage of legacy phosphorus in topsoil."
    @@ -780,8 +715,7 @@

    Evidence

    Acidic-Field Rice Yield Increase

    -

    The Al-resistant rhizosphere SynCom increased rice yield in acidic fields and improved growth, yield, soil-acidity resistance, and aluminium-toxicity resistance. -

    +

    The primary study reports a 26.36% rice-yield increase with the Al-resistant SynCom in acidic fields. This positive intervention outcome is distinct from proof of any single phosphorus- or Al-mediated causal pathway.

    @@ -808,19 +742,6 @@

    Acidic-Field Rice Yield Increase

    Evidence