Skip to content

Bound wet-up viral mortality and groundwater genomic causal claims (batch49) #1492

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 wet-up viral mortality and groundwater genomic causal claims (batch49) #1492

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
107 changes: 76 additions & 31 deletions docs/communities/Grassland_Soil_WetUp_Virus_Host_Community.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -570,13 +570,20 @@ <h2>Ecological Interactions</h2>

<div class="interaction-card">
<div class="interaction-header">
<h3>Lytic Virus Activity Dominates Wet-Up Response</h3>
<span class="interaction-type">PREDATION</span>
<h3>Lytic-Dominated Viral Response Inferred After Wet-Up</h3>
</div>
<p class="prewrap interaction-description">After wet-up, lytic rather than lysogenic cycles dominate, with viral richness declining by 50 percent within 24 hours and viral biomass increasing four-fold within one week.</p>
<p class="prewrap interaction-description">Laboratory wet-up microcosms showed viral richness loss and increasing viral-DNA biomass proxies, with isotope incorporation supporting active viral DNA replication. The authors infer a predominantly lytic response from these measurements and lifestyle markers. This positive evidence does not exclude nonintegrating temperate lifestyles or directly count every productive infection. The abstract reports a 50% richness decline within 24 h and a four-fold biomass increase within one week; the main Results summarize richness loss over the week. Those time-window summaries need not conflict; no independent reconstruction of the time course is claimed here.</p>




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

soil DNA viruses (virions),

grassland soil bacterial hosts

</p>



Expand All @@ -599,8 +606,8 @@ <h3>Lytic Virus Activity Dominates Wet-Up Response</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Viral Lysis Drives Microbial Death
<p class="prewrap causal-description">Wet-up lytic viral activity produces measurable host-cell lysis by one week after rewetting.</p>
<span class="flow-arrow">→</span> Estimated Viral Contribution to Microbial Death
<p class="prewrap causal-description">PARTIAL - productive lytic infection would cause host death. Viral replication, particle dynamics and lifestyle markers support this contribution, but the magnitude is inferred using burst-size and recovery assumptions rather than directly resolved infection-to-death events.</p>
</div>

</div>
Expand All @@ -616,7 +623,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/37730729/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37730729</a>

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

<div class="snippet">"viruses in lytic cycles dominate the response to wet-up"</div>
Expand All @@ -629,7 +636,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/37730729/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37730729</a>

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

<div class="snippet">"Viral richness decreases by 50% within 24 h post wet-up, while viral biomass increases four-fold within one week"</div>
Expand All @@ -642,10 +649,10 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Viral Lysis Drives Microbial Death</h3>
<h3>Estimated Viral Contribution to Microbial Death</h3>
<span class="interaction-type">PREDATION</span>
</div>
<p class="prewrap interaction-description">Viruses drive measurable and continuous cell lysis, accounting for up to 46 percent of microbial death one week after wet-up.</p>
<p class="prewrap interaction-description">The study estimates a viral contribution to bacterial mortality from extracellular viral DNA and a separately estimated bacterial-death denominator. Its cumulative one-week estimate ranges from below 1% to 46.6% as assumed burst size changes from 200 to 1 virions per cell. This is a model-dependent inference, not directly counted lysis of 46% of all microbes. The estimate depends on viral genome length, extraction recovery, particle persistence and assumptions about bacterial rRNA gene copies. Canonical virus-to-bacterium direction denotes the proposed aggregate predatory process, not resolved strain-specific host links.</p>


<p><strong>Source Taxon:</strong> soil DNA viruses (virions)</p>
Expand Down Expand Up @@ -675,8 +682,8 @@ <h3>Viral Lysis Drives Microbial Death</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Lysis-Coupled Biomass Turnover and CO2 Efflux
<p class="prewrap causal-description">Virus-driven bacterial death contributes to microbial biomass turnover and the post-wet-up CO2 efflux from seasonally dry soil.</p>
<span class="flow-arrow">→</span> Inferred Lysis Contribution to Biomass Turnover and CO2 Efflux
<p class="prewrap causal-description">HYPOTHESIZED - lysis-released cellular carbon could support turnover and community respiration. The study does not isolate the viral share of CO2 efflux or selectively establish this carbon-transfer mediation.</p>
</div>

</div>
Expand All @@ -692,7 +699,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/37730729/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37730729</a>

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

<div class="snippet">"up to 46% of microbial death driven by viral lysis one week following wet-up"</div>
Expand All @@ -705,17 +712,20 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Lysis-Coupled Biomass Turnover and CO2 Efflux</h3>
<span class="interaction-type">PREDATION</span>
<h3>Inferred Lysis Contribution to Biomass Turnover and CO2 Efflux</h3>
</div>
<p class="prewrap interaction-description">Viral lysis contributes to turnover of soil microbial biomass and the widely reported CO2 efflux following wet-up of seasonally dry soils.</p>
<p class="prewrap interaction-description">HYPOTHESIZED - lysis can release cellular material that contributes to soil biomass turnover and potentially fuels respiration after wet-up. The paper interprets its viral dynamics and mortality estimates in this ecosystem context; it does not selectively isolate virus-driven CO2 flux or establish this pathway as the cause of the whole wet-up respiration pulse.</p>


<p><strong>Source Taxon:</strong> soil DNA viruses (virions)</p>


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

<p><strong>Target Taxon:</strong> grassland soil bacterial hosts</p>
soil DNA viruses (virions),

grassland soil bacterial hosts

</p>



Expand All @@ -742,7 +752,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/37730729/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37730729</a>

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

<div class="snippet">"viruses contribute to turnover of soil microbial biomass and the widely reported CO2 efflux following wet-up of seasonally dry soils"</div>
Expand All @@ -758,6 +768,25 @@ <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>
How much wet-up mortality and respiratory carbon flux are caused by viruses?
</h3>
<p class="prewrap">Resolve burst size, genome-length conversion, extraction efficiency, persistent particles and the assumed six bacterial 16S copies per cell before assigning a fixed mortality fraction. The Results and Discussion give slightly different lower bounds, both below 1%; no equation or analysis-code reimplementation is claimed. Separate early osmotic mortality from later viral effects. Genomic lifestyle markers do not exclude nonintegrating temperate infections, and coarse host predictions do not identify every infected strain. Direct viral perturbations and carbon tracing are needed for the proposed CO2 mediation. Abstract and main-body richness summaries use different time windows, which need not be contradictory. Preserve all positive time-course evidence while retaining these uncertainty labels; non-graph metadata is not recertified.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Lytic-Dominated Viral Response Inferred After Wet-Up</code>, <code>ecological_interactions#Estimated Viral Contribution to Microbial Death</code>, <code>ecological_interactions#Inferred Lysis Contribution to Biomass Turnover and CO2 Efflux</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -993,7 +1022,7 @@ <h2>Environmental Factors</h2>

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

var processes = [];
Expand All @@ -1006,7 +1035,7 @@ <h2>Environmental Factors</h2>

nodes.push({
id: intId,
label: "Lytic Virus Activity Dominates Wet-Up Response",
label: "Lytic-Dominated Viral Response Inferred After Wet-Up",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1017,6 +1046,19 @@ <h2>Environmental Factors</h2>



var participantKeys = [

"soil DNA viruses (virions)",

"grassland soil bacterial hosts"

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

})();

(function() {
Expand All @@ -1034,7 +1076,7 @@ <h2>Environmental Factors</h2>

nodes.push({
id: intId,
label: "Viral Lysis Drives Microbial Death",
label: "Estimated Viral Contribution to Microbial Death",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1059,7 +1101,7 @@ <h2>Environmental Factors</h2>

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


Expand All @@ -1072,7 +1114,7 @@ <h2>Environmental Factors</h2>

nodes.push({
id: intId,
label: "Lysis-Coupled Biomass Turnover and CO2 Efflux",
label: "Inferred Lysis Contribution to Biomass Turnover and CO2 Efflux",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1081,17 +1123,20 @@ <h2>Environmental Factors</h2>
});


var srcKey = "soil DNA viruses (virions)";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "grassland soil bacterial hosts";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"soil DNA viruses (virions)",

"grassland soil bacterial hosts"

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

})();

Expand Down
Loading