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Regenerate HTML with CultureMech and MediaIngredientMech links
Update community HTML pages to display new growth media linkage: - CultureMech media IDs with clickable links - MediaIngredientMech ingredient IDs with clickable links - Ingredient composition with source attribution - Updated 21 community pages with growth_media sections Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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‎docs/communities/At_RSPHERE_SynCom.html‎

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@@ -942,6 +942,303 @@ <h2>Environmental Factors</h2>
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<!-- Growth Media -->
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<section>
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<h2>Growth Media</h2>
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<div class="metadata">
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<h3>
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R2A Agar for bacterial isolation and maintenance
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<span style="font-size: 0.9rem; color: var(--text-muted);">
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(CultureMech:002706)
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</span>
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</h3>
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<p style="margin: 0.5rem 0;">
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<a href="https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:002706" class="term-link" target="_blank" rel="noopener">
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View in CultureMech →
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</a>
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</p>
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<div class="metadata-grid" style="margin-top: 1rem;">
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<div class="metadata-item">
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<span class="metadata-label">pH</span>
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<span class="metadata-value">7.2</span>
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</div>
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<div class="metadata-item">
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<span class="metadata-label">Temperature</span>
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<span class="metadata-value">28 degrees Celsius</span>
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</div>
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<div class="metadata-item">
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<span class="metadata-label">Atmosphere</span>
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<span class="metadata-value">AEROBIC</span>
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</div>
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</div>
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<h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
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<table>
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<thead>
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<tr>
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<th>Component</th>
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<th>Concentration</th>
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<th>Unit</th>
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<th>CHEBI</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><strong>Yeast extract</strong></td>
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<td>0.5</td>
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<td>G_PER_L</td>
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<td>
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N/A
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</td>
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</tr>
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<tr>
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<td><strong>Proteose peptone no. 3</strong></td>
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<td>0.5</td>
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<td>G_PER_L</td>
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<td>
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N/A
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</td>
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</tr>
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<tr>
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<td><strong>Casamino acids</strong></td>
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<td>0.5</td>
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<td>G_PER_L</td>
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<td>
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N/A
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</td>
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</tr>
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<tr>
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<td><strong>Glucose</strong></td>
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<td>0.5</td>
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<td>G_PER_L</td>
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<td>
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N/A
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</td>
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</tr>
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<tr>
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<td><strong>Starch</strong></td>
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<td>0.5</td>
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<td>G_PER_L</td>
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<td>
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N/A
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</td>
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</tr>
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<tr>
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<td><strong>Sodium pyruvate</strong></td>
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<td>0.3</td>
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<td>G_PER_L</td>
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<td>
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N/A
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</td>
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</tr>
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<tr>
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<td><strong>K2HPO4</strong></td>
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<td>0.3</td>
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<td>G_PER_L</td>
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<td>
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N/A
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</td>
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</tr>
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<tr>
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<td><strong>MgSO4 x 7 H2O</strong></td>
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<td>0.05</td>
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<td>G_PER_L</td>
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<td>
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N/A
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</td>
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</tr>
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<tr>
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<td><strong>Agar</strong></td>
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<td>15</td>
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<td>G_PER_L</td>
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<td>
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N/A
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</td>
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</tr>
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</tbody>
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</table>
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<p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
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<strong>Preparation notes:</strong> Low-nutrient medium used for isolation and maintenance of soil and rhizosphere bacteria from Arabidopsis roots. R2A supports slow-growing oligotrophic bacteria common in soil environments.
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</p>
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<div style="margin-top: 1rem;">
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<h4 style="color: var(--text);">Evidence</h4>
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<div class="evidence-item">
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<a href="https://doi.org/10.1038/nature16192"
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class="pmid-link" target="_blank" rel="noopener">
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doi:10.1038/nature16192
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</a>
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<p class="snippet">"We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing"</p>
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</div>
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</div>
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</div>
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<div class="metadata">
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<h3>
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Half-strength Murashige-Skoog medium for Arabidopsis growth
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</h3>
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<div class="metadata-grid" style="margin-top: 1rem;">
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<div class="metadata-item">
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<span class="metadata-label">pH</span>
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<span class="metadata-value">5.7</span>
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</div>
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<div class="metadata-item">
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<span class="metadata-label">Temperature</span>
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<span class="metadata-value">22 degrees Celsius</span>
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</div>
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</div>
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<h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
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<table>
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<thead>
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<tr>
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<th>Component</th>
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<th>Concentration</th>
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<th>Unit</th>
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<th>CHEBI</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td><strong>Murashige-Skoog basal salts</strong></td>
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<td>0.5</td>
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<td>x (half-strength)</td>
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<td>
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N/A
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</td>
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</tr>
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<tr>
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<td><strong>Sucrose</strong></td>
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<td>1</td>
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<td>%</td>
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<td>
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<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17992"
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class="term-link" target="_blank" rel="noopener">
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CHEBI:17992
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</a>
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</td>
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</tr>
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<tr>
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<td><strong>Agar</strong></td>
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<td>0.8</td>
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<td>%</td>
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<td>
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N/A
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</td>
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</tr>
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</tbody>
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</table>
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<p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
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<strong>Preparation notes:</strong> Gnotobiotic plant growth system with 0.5× MS medium supplemented with 1% sucrose and 0.8% agar. Seeds surface-sterilized prior to inoculation. Plates oriented vertically to allow root observation and bacterial colonization tracking.
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</p>
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<div style="margin-top: 1rem;">
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<h4 style="color: var(--text);">Evidence</h4>
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<div class="evidence-item">
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<a href="https://doi.org/10.1038/nature16192"
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class="pmid-link" target="_blank" rel="noopener">
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doi:10.1038/nature16192
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</a>
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<p class="snippet">"Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiota on their cognate host organs, but are also capable of ectopic leaf or root colonization"</p>
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</div>
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</div>
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</div>
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</section>
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</main>
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