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Repair diatom, phenol, Phormidium and phosphite causal claims (batch84) #1702

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64 changes: 59 additions & 5 deletions docs/communities/Phaeodactylum_Aliivibrio_Diel_Coculture.html
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Expand Up @@ -613,7 +613,7 @@ <h2>Ecological Interactions</h2>
<div class="interaction-header">
<h3>Aliivibrio Surface Colonization of Phaeodactylum</h3>
</div>
<p class="prewrap interaction-description">SEM imaging showed A. fischeri colonizing P. tricornutum cell surfaces in the 30% marine broth co-culture, with filamentous structures likely corresponding to EPS from one or both partners.</p>
<p class="prewrap interaction-description">SEM showed A. fischeri attached to P. tricornutum surfaces in the 30% marine-broth coculture. Filamentous structures were interpreted as likely EPS from one or both partners; neither their chemical identity nor their producer was established by microscopy. Preserve the physical association without treating it as proof of nutrient transfer or the cause of photosynthetic decline.</p>


<p><strong>Source Taxon:</strong> Aliivibrio fischeri MCCC 1H00019</p>
Expand Down Expand Up @@ -652,10 +652,10 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Amino Acid Resource Competition</h3>
<h3>Proposed Amino Acid Resource Competition</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">Rather than supporting a direct growth-promotion effect of A. fischeri on P. tricornutum, the EASW/30% marine broth co-culture showed nutrient depletion and pigment dynamics consistent with early competition for amino-acid resources.</p>
<p class="prewrap interaction-description">HYPOTHESIZED - Nutrient and pigment profiles led the authors to propose early amino-acid competition. Nitrate-N and orthophosphate were measured, but amino-acid depletion and partner-resolved exchange were not. Medium-matched axenic HAC controls support a negative coculture effect on late photosynthetic performance; moderate broth enrichment itself supported axenic growth. These observations do not isolate amino-acid competition as the mechanism or show bacterial growth promotion by bioluminescence.</p>



Expand Down Expand Up @@ -685,7 +685,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42668638/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42668638</a>

- SUPPORT (IN_VITRO)
- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"These results are more consistent with a competitive effect in co-culture than with a growth-promoting role of A. fischeri."</div>
Expand Down Expand Up @@ -714,6 +714,60 @@ <h4>Evidence</h4>

<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which processes connect bacterial association to diatom physiological and diel responses?
</h3>
<p class="prewrap">Keep SEM attachment and medium-controlled late physiological decline as positive findings. Matched late physiological controls exist, but no day-8 axenic transcriptome was collected; age, nutrients and growth phase confound attribution of Co8d transcription to bacteria alone. Light-dark rhythmic gene counts do not establish endogenous clock disruption. Biomass-flux changes (+81%/-87%) are transcript-constrained model predictions, not measured intracellular or interspecies flux. EPS decline admits synthesis, dilution and catabolism explanations. Dedicated physiological/diel/model response structure remains issue #1698, with a one-community Edison dry run and no paid report; no new arrow is inferred from the two existing nodes.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Aliivibrio Surface Colonization of Phaeodactylum</code>, <code>ecological_interactions#Proposed Amino Acid Resource Competition</code></p>



<details class="evidence-list">
<summary class="muted small">2 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42668638/" rel="nofollow noreferrer">PMID:42668638</a>


</div>
<p class="snippet small prewrap">Scanning electron microscopy (SEM) analysis demonstrated significant colonization of P. tricornutum cell surfaces by A. fischeri</p>
<p class="muted small prewrap">Supports bacterial attachment to the diatom cell surface in co-culture.</p>
</div>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">PARTIAL</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42668638/" rel="nofollow noreferrer">PMID:42668638</a>


</div>
<p class="snippet small prewrap">The observed nutrient depletion patterns and pigment dynamics suggest early-phase competition for amino acid resources between P. tricornutum and A. fischeri</p>
<p class="muted small prewrap">Supports the authors&#39; competition interpretation; nutrient/pigment observations do not directly identify exchanged or limiting amino acids.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1116,7 +1170,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Amino Acid Resource Competition",
label: "Proposed Amino Acid Resource Competition",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
103 changes: 82 additions & 21 deletions docs/communities/Phenol_Carboxylation_Consortium.html
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Expand Up @@ -616,8 +616,7 @@ <h2>Ecological Interactions</h2>
<h3>Phenol Oxidation by Syntrophorhabdus</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Syntrophorhabdus aromaticivorans strain UI(T) oxidizes phenol in the M. hungatei coculture and forms 4-hydroxybenzoate and benzoate as transient intermediates, initiating methanogenic aromatic-compound mineralization by the defined pair.
</p>
<p class="prewrap interaction-description">S. aromaticivorans UI(T) oxidized phenol in coculture with M. hungatei. Transient 4-hydroxybenzoate and benzoate were measured and subsequently consumed. PARTIAL - These intermediates support a proposed carboxylation/dehydroxylation route, but the paper explicitly leaves the actual enzymes and mechanism unresolved; they are not demonstrated interspecies carbon cargo.</p>


<p><strong>Source Taxon:</strong> Syntrophorhabdus aromaticivorans strain UI(T)</p>
Expand All @@ -634,7 +633,7 @@ <h3>Phenol Oxidation by Syntrophorhabdus</h3>
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15882"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:15882</a>),

benzoate
benzoic acid
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=30746"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:30746</a>),

Expand Down Expand Up @@ -663,9 +662,8 @@ <h3>Phenol Oxidation by Syntrophorhabdus</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Community Aromatic Mineralization to Acetate and Methane
<p class="prewrap causal-description">Phenol oxidation by strain UI(T) supplies the aromatic-intermediate flux that the syntrophic coculture carries through to acetate and methane.
</p>
<span class="flow-arrow">→</span> Community Aromatic Conversion to Acetate and Methane
<p class="prewrap causal-description">Phenol conversion by UI(T), coupled to partner electron disposal, supplies the measured coculture acetate/methane endpoint. Preserve this positive direction without asserting transfer of aromatic intermediates to the methanogen or complete substrate disappearance in the 100-day assay.</p>
</div>

</div>
Expand Down Expand Up @@ -701,6 +699,19 @@ <h4>Evidence</h4>

</li>

<li class="evidence-item">
<div>

<a href="https://pubmed.ncbi.nlm.nih.gov/18281436/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:18281436</a>

- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"The actual mechanisms employed by strain UIT cells for the metabolism of phenol remain unclear"</div>

</li>

</ul>

</div>
Expand All @@ -710,8 +721,7 @@ <h4>Evidence</h4>
<h3>M. hungatei H2 Scavenging and Methanogenesis</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Methanospirillum hungatei provides the methanogenic sink for the S. aromaticivorans syntrophy. Inhibition of methanogenesis with 2-BES and exposure to high hydrogen partial pressure both stopped aromatic-substrate degradation, supporting H2 scavenging as a required syntrophic electron sink.
</p>
<p class="prewrap interaction-description">M. hungatei supplied a methanogenic electron sink: 5 mM 2-BES blocked aromatic degradation, and elevated H2 stopped phenol and 4-hydroxybenzoate degradation. These perturbations support low-H2 syntrophy under the methanogenic conditions, not merely co-occurrence. Hydrogen was detected, while the authors did not exclude formate or other carriers. Dependence is conditional: AQDS enabled acetate production without methane in BES-treated culture; attempts at axenic isolation with AQDS failed.</p>


<p><strong>Source Taxon:</strong> Methanospirillum hungatei</p>
Expand Down Expand Up @@ -758,14 +768,12 @@ <h3>M. hungatei H2 Scavenging and Methanogenesis</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Phenol Oxidation by Syntrophorhabdus
<p class="prewrap causal-description">M. hungatei H2 scavenging keeps the electron sink active for strain UI(T); when methanogenesis was blocked or hydrogen partial pressure was raised, phenol and 4-hydroxybenzoate degradation stopped.
</p>
<p class="prewrap causal-description">Methanogenic electron disposal maintains conditions allowing UI(T) phenol oxidation; BES inhibition and high-H2 inhibition support this direction. This applies to the methanogenic treatment, not an absolute requirement for this partner when an alternative acceptor such as AQDS is supplied.</p>
</div>

<div class="flow-item">
<span class="flow-arrow">→</span> Community Aromatic Mineralization to Acetate and Methane
<p class="prewrap causal-description">Methanogenic H2 scavenging is the partner process that lets aromatic oxidation continue through to acetate and methane in the coculture.
</p>
<span class="flow-arrow">→</span> Community Aromatic Conversion to Acetate and Methane
<p class="prewrap causal-description">The active methanogenic sink allows aromatic conversion to continue and supplies the methane component of the acetate/methane endpoint. AQDS-treated inhibited cultures produced acetate without methane, separating conversion from the methanogenic product.</p>
</div>

</div>
Expand Down Expand Up @@ -807,11 +815,10 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Community Aromatic Mineralization to Acetate and Methane</h3>
<h3>Community Aromatic Conversion to Acetate and Methane</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">The S. aromaticivorans-M. hungatei coculture couples strain UI(T) aromatic substrate oxidation to methanogenic electron disposal, consuming phenol, p-cresol, isophthalate, 4-hydroxybenzoate, and benzoate for growth and producing acetate and methane as end products.
</p>
<p class="prewrap interaction-description">The defined UI(T)-M. hungatei coculture utilized phenol, p-cresol, isophthalate, 4-hydroxybenzoate and benzoate for growth and produced acetate and methane. Preserve these positive conversion and product measurements. Acetate remains an organic product, and Table 2 reports residual substrate at 100 days; this is not complete mineralization or universal complete removal. Absence of fermentative growth in the tested inhibited cultures does not negate the AQDS alternative-electron-acceptor result.</p>



Expand Down Expand Up @@ -844,7 +851,7 @@ <h3>Community Aromatic Mineralization to Acetate and Methane</h3>
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17879"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17879</a>),

benzoate
benzoic acid
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=30746"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:30746</a>),

Expand Down Expand Up @@ -925,6 +932,60 @@ <h4>Evidence</h4>

<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which enzymes and electron carriers implement the observed syntrophic phenol conversion?
</h3>
<p class="prewrap">Preserve all three existing positive causal arrows and the BES/high-H2 perturbations. Intermediates suggest a route but do not identify its enzymes; the authors allow hydrogen and/or formate transfer. AQDS replaces the methanogenic electron sink under the tested inhibited condition, without establishing a pure isolate. Acetate/methane conversion is not complete carbon mineralization. The alternative Desulfovibrio culture is a separate experimental condition, not a third member of this canonical pair; no new topology is required for these repairs.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Phenol Oxidation by Syntrophorhabdus</code>, <code>ecological_interactions#M. hungatei H2 Scavenging and Methanogenesis</code>, <code>ecological_interactions#Community Aromatic Conversion to Acetate and Methane</code></p>



<details class="evidence-list">
<summary class="muted small">2 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">PARTIAL</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/18281436/" rel="nofollow noreferrer">PMID:18281436</a>


</div>
<p class="snippet small prewrap">The actual mechanisms employed by strain UIT cells for the metabolism of phenol remain unclear</p>
<p class="muted small prewrap">Primary Discussion distinguishes intermediate measurements from the unresolved enzymatic route.</p>
</div>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/18281436/" rel="nofollow noreferrer">PMID:18281436</a>


</div>
<p class="snippet small prewrap">The addition of 5 mM 2-BES to a coculture with M. hungatei completely inhibited the degradation of isophthalate, phenol, and 4-hydroxybenzoate.</p>
<p class="muted small prewrap">Blocking methanogenesis stopped aromatic-substrate degradation in the M. hungatei coculture.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1189,7 +1250,7 @@ <h4 style="color: var(--text);">Evidence</h4>

metabolites.push("phenol");

metabolites.push("benzoate");
metabolites.push("benzoic acid");

metabolites.push("4-hydroxybenzoate");

Expand All @@ -1200,7 +1261,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("phenol-containing compound metabolic process");


var evidenceCount = 2;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1287,7 +1348,7 @@ <h4 style="color: var(--text);">Evidence</h4>

metabolites.push("4-hydroxybenzoate");

metabolites.push("benzoate");
metabolites.push("benzoic acid");

metabolites.push("acetate");

Expand All @@ -1308,7 +1369,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Community Aromatic Mineralization to Acetate and Methane",
label: "Community Aromatic Conversion to Acetate and Methane",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
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