Skip to content

Bound regolith, lupin and MAMC causal claims (batch64) #1565

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
realmarcin wants to merge 1 commit into from
Closed

Bound regolith, lupin and MAMC causal claims (batch64) #1565

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
224 changes: 106 additions & 118 deletions docs/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.html
View file
Open in desktop

Large diffs are not rendered by default.

209 changes: 202 additions & 7 deletions docs/communities/Lupinus_SC7_Rhizosphere_SynCom.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -941,11 +941,38 @@ <h2>Ecological Interactions</h2>
<div class="interaction-header">
<h3>SC-7 high-complexity lupin response</h3>
</div>
<p class="prewrap interaction-description">The most complex consortium, SC-7, was the SynCom associated with the highest lupin growth increase and broad host transcriptional responses, but the assay varied richness and membership simultaneously and therefore does not separate a pure diversity effect from the effect of particular strains.
</p>
<p class="prewrap interaction-description">The twelve-strain SC-7 inoculum produced the strongest reported lupin growth response in both gnotobiotic FlowPot and non-sterile CAS-soil experiments. The panel varied richness and strain composition together, so a pure diversity effect is not isolated. The twelve listed canonical participants match the inoculated strain codes in main Table 1, including both Streptomyces strains; they do not represent the missing host or all background soil taxa. Input membership does not establish dominance or equal abundance at harvest.</p>




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

Bradyrhizobium sp. CAR08,

Micromonospora sp. Lupac 08,

Caulobacter sp. LARHSG274,

Kribbella sp. LARHCF250,

Pseudomonas sp. LARHCG127,

Pseudoxanthomonas sp. LARHCG66,

Rhizobium sp. LARHSG275,

Sphingopyxis sp. LARHCG72,

Stenotrophomonas sp. LARHCG68,

Streptomyces sp. LARHCF249,

Streptomyces sp. LARHCF252,

Variovorax sp. LARHSF232

</p>



Expand Down Expand Up @@ -994,11 +1021,38 @@ <h4>Evidence</h4>
<div class="interaction-header">
<h3>SC-7-associated host transcriptional reprogramming</h3>
</div>
<p class="prewrap interaction-description">SC-7 inoculation was associated with up-regulated lupin root pathways for signaling, hormone perception, primary and secondary metabolism, defense responses, and growth regulation.
</p>
<p class="prewrap interaction-description">RNA-seq of living lupin roots from the FlowPot experiment associated SC-7 with changes in signaling, hormone perception, defense, and primary and secondary metabolic gene sets. Some pathways were upregulated and others downregulated; this is differential expression and enrichment, not direct hormone production, nitrogen-fixation rate or a demonstrated mediator of growth. Leghemoglobin expression and genomic plant-growth annotations do not independently establish functional flux. The inoculated twelve-strain roster does not resolve each strain contribution.</p>




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

Bradyrhizobium sp. CAR08,

Micromonospora sp. Lupac 08,

Caulobacter sp. LARHSG274,

Kribbella sp. LARHCF250,

Pseudomonas sp. LARHCG127,

Pseudoxanthomonas sp. LARHCG66,

Rhizobium sp. LARHSG275,

Sphingopyxis sp. LARHCG72,

Stenotrophomonas sp. LARHCG68,

Streptomyces sp. LARHCF249,

Streptomyces sp. LARHCF252,

Variovorax sp. LARHSF232

</p>



Expand Down Expand Up @@ -1033,11 +1087,38 @@ <h4>Evidence</h4>
<div class="interaction-header">
<h3>Complex SynCom root and rhizosphere reshaping</h3>
</div>
<p class="prewrap interaction-description">More complex Lupinus SynCom inocula, including SC-7, were associated with root-associated microbiome shifts, moderate rhizosphere effects, and limited bulk-soil effects across sterile and non-sterile tests.
</p>
<p class="prewrap interaction-description">In non-sterile CAS soil, the SynCom panel including SC-7 was associated with compartment-specific relative microbiome profiles, with the largest reported changes in roots and limited bulk-soil changes. SC-7 had lower root Shannon diversity than uninoculated controls. These results must remain separate from gnotobiotic colonization and FlowPot RNA-seq. Genus-level relative profiles are not absolute exclusion or unambiguous persistence of each inoculated strain; changes after computational removal of inoculant-associated ASVs are not a biological knockout. The Results sentence reporting no significant compartment treatment effects conflicts with its reported PERMANOVA p=0.001, so no blanket significance claim is certified here.</p>




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

Bradyrhizobium sp. CAR08,

Micromonospora sp. Lupac 08,

Caulobacter sp. LARHSG274,

Kribbella sp. LARHCF250,

Pseudomonas sp. LARHCG127,

Pseudoxanthomonas sp. LARHCG66,

Rhizobium sp. LARHSG275,

Sphingopyxis sp. LARHCG72,

Stenotrophomonas sp. LARHCG68,

Streptomyces sp. LARHCF249,

Streptomyces sp. LARHCF252,

Variovorax sp. LARHSF232

</p>



Expand Down Expand Up @@ -1127,7 +1208,7 @@ <h2>Associated Datasets</h2>
</section>

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>

<div class="discussion">
<h3>
Expand All @@ -1144,6 +1225,21 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which SC-7 functions mediate host growth and compartment-specific community changes?
</h3>
<p class="prewrap">Preserve all three observations and zero arrows. FlowPot root transcriptomics, gnotobiotic strain profiles and non-sterile CAS-soil relative microbiota are different endpoints. Co-occurrence hubs, no agar inhibition zones and gene annotations do not demonstrate facilitation, coexistence, nitrogen-fixation flux or a growth mediator. Main Table1 verifies twelve input strain codes, not dominance or genome/culture identity; two Streptomyces strains share a genus CURIE and must retain distinct preferred names. The existing richness-versus-membership gap stays open. Main text has conflicting PERMANOVA wording/p-value and six-week incubation/eight-week harvest wording; no reanalysis or supplement/raw-data audit was performed. #1564 tracks these and missing-host/role metadata.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#SC-7 high-complexity lupin response</code>, <code>ecological_interactions#SC-7-associated host transcriptional reprogramming</code>, <code>ecological_interactions#Complex SynCom root and rhizosphere reshaping</code></p>




</div>

</section>
Expand Down Expand Up @@ -1601,6 +1697,39 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Bradyrhizobium sp. CAR08",

"Micromonospora sp. Lupac 08",

"Caulobacter sp. LARHSG274",

"Kribbella sp. LARHCF250",

"Pseudomonas sp. LARHCG127",

"Pseudoxanthomonas sp. LARHCG66",

"Rhizobium sp. LARHSG275",

"Sphingopyxis sp. LARHCG72",

"Stenotrophomonas sp. LARHCG68",

"Streptomyces sp. LARHCF249",

"Streptomyces sp. LARHCF252",

"Variovorax sp. LARHSF232"

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

})();

(function() {
Expand All @@ -1625,6 +1754,39 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Bradyrhizobium sp. CAR08",

"Micromonospora sp. Lupac 08",

"Caulobacter sp. LARHSG274",

"Kribbella sp. LARHCF250",

"Pseudomonas sp. LARHCG127",

"Pseudoxanthomonas sp. LARHCG66",

"Rhizobium sp. LARHSG275",

"Sphingopyxis sp. LARHCG72",

"Stenotrophomonas sp. LARHCG68",

"Streptomyces sp. LARHCF249",

"Streptomyces sp. LARHCF252",

"Variovorax sp. LARHSF232"

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

})();

(function() {
Expand All @@ -1649,6 +1811,39 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Bradyrhizobium sp. CAR08",

"Micromonospora sp. Lupac 08",

"Caulobacter sp. LARHSG274",

"Kribbella sp. LARHCF250",

"Pseudomonas sp. LARHCG127",

"Pseudoxanthomonas sp. LARHCG66",

"Rhizobium sp. LARHSG275",

"Sphingopyxis sp. LARHCG72",

"Stenotrophomonas sp. LARHCG68",

"Streptomyces sp. LARHCF249",

"Streptomyces sp. LARHCF252",

"Variovorax sp. LARHSF232"

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

})();


Expand Down
Loading