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Qualify CPR lipid hypotheses and retain unresolved source gaps (batch 27) #1367

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141 changes: 96 additions & 45 deletions docs/communities/Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community.html
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Expand Up @@ -559,7 +559,7 @@ <h2>Ecological Interactions</h2>
<div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
<svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
<title id="network-svg-title">Ecological interaction network for Crystal Geyser CO2-Rich Aquifer Autotrophic CPR Lysolipid Community</title>
<desc id="network-svg-desc">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, commensalism).</desc>
<desc id="network-svg-desc">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).</desc>
</svg>
<div class="network-legend">
<div class="legend-item">
Expand All @@ -572,28 +572,28 @@ <h2>Ecological Interactions</h2>
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolWye"
data-color="#cf7830"></svg> Commensalism
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>


<div class="interaction-card">
<div class="interaction-header">
<h3>Autotrophy-Based Deep Biosphere</h3>
<span class="interaction-type">CROSS_FEEDING</span>
<h3>Predominantly Autotrophic Carbon Supply</h3>
</div>
<p class="prewrap interaction-description">Microbial lipid stable-carbon-isotope compositions show that bacterial and archaeal CO2 fixation in the deep subsurface provides the organic carbon for the complex communities residing there.</p>
<p class="prewrap interaction-description">Stable carbon isotope compositions, community metagenomes and geological constraints support a predominantly autotrophic origin of biomass across the sampled aquifers. Bacterial and archaeal carbon fixation supplies the community organic-carbon pool; isotope mass-balance estimates depend on fractionation assumptions and allow heterotrophic reuse. This does not trace a particular producer-to-CPR carbon or lipid transfer.</p>




<p><strong>Participating Taxa:</strong>

deep-aquifer CO2-fixing bacteria and archaea

</p>



<p><strong>Metabolites:</strong>
Expand Down Expand Up @@ -623,9 +623,8 @@ <h3>Autotrophy-Based Deep Biosphere</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Lipid Redistribution to CPR Symbionts
<p class="prewrap causal-description">Autotrophic bacterial and archaeal production supplies deep-subsurface organic carbon to the complex community that includes lipid-limited CPR putative symbionts.
</p>
<span class="flow-arrow">→</span> Putative CPR Lipid Acquisition
<p class="prewrap causal-description">HYPOTHESIZED - autotrophically fixed carbon can supply bacterial lipid production and the community material available for CPR acquisition. The isotope, lipid and genomic observations support this proposed carbon route but do not trace transfer from a particular producer to CPR cells.</p>
</div>

</div>
Expand Down Expand Up @@ -654,17 +653,21 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Lipid Redistribution to CPR Symbionts</h3>
<span class="interaction-type">SYNTROPHY</span>
<h3>Putative CPR Lipid Acquisition</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">CPR bacteria possess regular lipid membranes despite lacking complete lipid biosynthesis pathways; lipids likely originate from other community members, with the partner bacteria/archaea also adapting to high in situ pressure via increased fatty acid unsaturation.</p>
<p class="prewrap interaction-description">HYPOTHESIZED - CPR-associated membrane lipids together with missing known complete lipid-biosynthesis pathways support acquisition of lipids or precursors from coexisting bacteria. Scavenging degraded biomass and direct host-derived acquisition remain alternatives; neither a donor nor uptake flux was resolved. The broad producer participant represents community context, not proof of archaeal-to-CPR donation. Some Nealsonbacteria retain near-complete pathways, so unknown ACP-independent biosynthesis cannot be excluded. Product-removal syntrophy was not demonstrated.</p>


<p><strong>Source Taxon:</strong> deep-aquifer CO2-fixing bacteria and archaea</p>


<p><strong>Participating Taxa:</strong>

<p><strong>Target Taxon:</strong> deep-aquifer CPR bacteria</p>
deep-aquifer CPR bacteria,

deep-aquifer CO2-fixing bacteria and archaea

</p>



Expand Down Expand Up @@ -699,9 +702,8 @@ <h3>Lipid Redistribution to CPR Symbionts</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> CPR Lysolipid Enrichment as Curvature Adaptation
<p class="prewrap causal-description">Imported or redistributed community lipids form CPR bacterial membranes, whose lysolipid enrichment is a candidate response to high curvature.
</p>
<span class="flow-arrow">→</span> CPR-Associated Lysolipids and Proposed Curvature Adaptation
<p class="prewrap causal-description">HYPOTHESIZED - acquired community lipids or precursors could provide material for CPR-associated lysolipid membranes and their proposed curvature adaptation. Lipid correlations and mixed-fraction spectroscopy do not demonstrate that acquisition causes lysolipid enrichment or that enrichment improves curvature tolerance.</p>
</div>

</div>
Expand All @@ -717,7 +719,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/32203118/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:32203118</a>

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

<div class="snippet">"CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes"</div>
Expand All @@ -730,10 +732,10 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/32203118/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:32203118</a>

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

<div class="snippet">"adapt to high in situ pressure by increasing fatty acid unsaturation"</div>
<div class="snippet">"the redistribution of lipids into putative symbionts within this community"</div>

</li>

Expand All @@ -743,10 +745,10 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/32203118/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:32203118</a>

- SUPPORT (IN_VIVO)
- PARTIAL (OTHER)
</div>

<div class="snippet">"the redistribution of lipids into putative symbionts within this community"</div>
<div class="snippet">"Thus, we suggest that most CPR bacteria derive their membrane lipids, including lysolipids, from coexisting bacteria."</div>

</li>

Expand All @@ -756,14 +758,19 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>CPR Lysolipid Enrichment as Curvature Adaptation</h3>
<span class="interaction-type">COMMENSALISM</span>
<h3>CPR-Associated Lysolipids and Proposed Curvature Adaptation</h3>
</div>
<p class="prewrap interaction-description">Unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes.</p>
<p class="prewrap interaction-description">Lipidomics, organism-lipid correlations and FTIR of CPR-enriched size fractions support lysolipid-rich membranes in some CPR bacteria. These fractions are mixed communities, not purified CPR isolates; the initial fraction also contained abundant Sulfurimonas. Reduced curvature stress in small cells is a proposed adaptive explanation, not a tested membrane-mechanical or fitness effect. No unaffected-donor relationship is established.</p>




<p><strong>Participating Taxa:</strong>

deep-aquifer CPR bacteria

</p>



<p><strong>Metabolites:</strong>
Expand Down Expand Up @@ -800,7 +807,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/32203118/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:32203118</a>

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

<div class="snippet">"An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes"</div>
Expand All @@ -816,6 +823,25 @@ <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 sources and uptake routes supply CPR lipids, and do lysolipids causally relieve membrane curvature stress?
</h3>
<p class="prewrap">The complete primary main body supports mostly autotrophic community carbon, missing known biosynthesis pathways and CPR-associated lysolipids. Correlated relative abundances, mixed size fractions and FTIR do not resolve donors or transfer rates. Degraded-biomass scavenging, direct host acquisition and unknown biosynthetic routes remain distinguishable hypotheses. Selective uptake/biosynthesis perturbations, tracing and membrane-mechanical measurements would test the proposed chain. The separate archaeal lipid discussion must not establish archaeal donation to CPR. No figure images or supplementary files were inspected. Non-graph taxon-role and pressure-adaptation overstatements remain in #1366.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Predominantly Autotrophic Carbon Supply</code>, <code>ecological_interactions#Putative CPR Lipid Acquisition</code>, <code>ecological_interactions#CPR-Associated Lysolipids and Proposed Curvature Adaptation</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1051,7 +1077,7 @@ <h2>Environmental Factors</h2>

(function() {
var intId = "interaction:0";
var intType = "CROSS_FEEDING";
var intType = "UNKNOWN";
var metabolites = [];


Expand All @@ -1068,7 +1094,7 @@ <h2>Environmental Factors</h2>

nodes.push({
id: intId,
label: "Autotrophy-Based Deep Biosphere",
label: "Predominantly Autotrophic Carbon Supply",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1079,11 +1105,22 @@ <h2>Environmental Factors</h2>



var participantKeys = [

"deep-aquifer CO2-fixing bacteria and archaea"

];
participantKeys.forEach(function(key) {
if (taxonNodeIds[key]) {
links.push({ source: taxonNodeIds[key], target: intId });
}
});

})();

(function() {
var intId = "interaction:1";
var intType = "SYNTROPHY";
var intType = "CROSS_FEEDING";
var metabolites = [];


Expand All @@ -1102,7 +1139,7 @@ <h2>Environmental Factors</h2>

nodes.push({
id: intId,
label: "Lipid Redistribution to CPR Symbionts",
label: "Putative CPR Lipid Acquisition",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1111,23 +1148,26 @@ <h2>Environmental Factors</h2>
});


var srcKey = "deep-aquifer CO2-fixing bacteria and archaea";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "deep-aquifer CPR bacteria";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"deep-aquifer CPR bacteria",

"deep-aquifer CO2-fixing bacteria and archaea"

];
participantKeys.forEach(function(key) {
if (taxonNodeIds[key]) {
links.push({ source: taxonNodeIds[key], target: intId });
}
});

})();

(function() {
var intId = "interaction:2";
var intType = "COMMENSALISM";
var intType = "UNKNOWN";
var metabolites = [];


Expand All @@ -1144,7 +1184,7 @@ <h2>Environmental Factors</h2>

nodes.push({
id: intId,
label: "CPR Lysolipid Enrichment as Curvature Adaptation",
label: "CPR-Associated Lysolipids and Proposed Curvature Adaptation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1155,6 +1195,17 @@ <h2>Environmental Factors</h2>



var participantKeys = [

"deep-aquifer CPR bacteria"

];
participantKeys.forEach(function(key) {
if (taxonNodeIds[key]) {
links.push({ source: taxonNodeIds[key], target: intId });
}
});

})();


Expand Down
29 changes: 29 additions & 0 deletions ...cords/Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community/2026-10-06T041950Z-codex-5086e8.yaml
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@@ -0,0 +1,29 @@
history_version: 1
target:
kind: record
path: kb/communities/Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community.yaml
slug: Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community
session:
id: 2026-10-06T041950Z-codex-5086e8
timestamp: '2026-10-06T04:19:50Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1365
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Retain the positive isotope/genomic carbon-source evidence with its fractionation
and recipient-resolution limits; no arbitrary exchange type on primary production.; Retain
source-proposed bacterial lipid acquisition as partial cross-feeding, not measured donor
flux, obligatory lipid dependence or product-removal syntrophy.; Retain CPR-associated
lysolipid measurements and a qualified curvature hypothesis without pure-isolate attribution
or a commensal fitness sign.
details: Source-based self-adversarial graph qualification; no new nodes/arrows. reports/causal_graph_review/decisions/20261006-three-records-batch27.yaml
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