https://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&feed=atom&action=historySilicibacter pomeroyi - Revision history2024-03-29T14:48:57ZRevision history for this page on the wikiMediaWiki 1.39.6https://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=54887&oldid=prevBarichD at 19:12, 19 August 20102010-08-19T19:12:23Z<p></p>
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</table>BarichDhttps://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=19678&oldid=prevGillenk at 16:59, 27 July 20072007-07-27T16:59:07Z<p></p>
<a href="https://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=19678&oldid=16635">Show changes</a>Gillenkhttps://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=16635&oldid=prevLkhachat: /* References */2007-06-05T07:07:53Z<p><span dir="auto"><span class="autocomment">References</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>4. Entrez Genome Project. http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=281 </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>4. Entrez Genome Project. http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=281 </div></td></tr>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>5. Gonzalez JM, Covert JS, Whitman WB, Henriksen JR, Mayer F, Scharf B, Schmitt R, Buchan A, Fuhrman JA, Kiene RP, Moran MA. <del style="font-weight: bold; text-decoration: none;">“Silicibacter </del>pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfonioproprionate-demethylating bacteria from marine environments.” Int J Syst Evol Microbiol. 2003. Volume 53. p. 1261-9.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>5. Gonzalez JM, Covert JS, Whitman WB, Henriksen JR, Mayer F, Scharf B, Schmitt R, Buchan A, Fuhrman JA, Kiene RP, Moran MA. <ins style="font-weight: bold; text-decoration: none;">“''Silicibacter </ins>pomeroyi<ins style="font-weight: bold; text-decoration: none;">'' </ins>sp. nov. and <ins style="font-weight: bold; text-decoration: none;">''</ins>Roseovarius nubinhibens<ins style="font-weight: bold; text-decoration: none;">'' </ins>sp. nov., dimethylsulfonioproprionate-demethylating bacteria from marine environments.” Int J Syst Evol Microbiol. 2003. Volume 53. p. 1261-9.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>http://ijs.sgmjournals.org/cgi/content/full/53/5/1261 </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>http://ijs.sgmjournals.org/cgi/content/full/53/5/1261 </div></td></tr>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>8. Johnson, A., Moran, M. & Miller, W. “Investigating carbon monoxide (CO) consumption in the marine bacteria Silicibacter pomeroyi with coxL gene expression.” Geophysical Research Abstracts. 2007. Volume 9. p. 4535.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>8. Johnson, A., Moran, M. & Miller, W. “Investigating carbon monoxide (CO) consumption in the marine bacteria <ins style="font-weight: bold; text-decoration: none;">''</ins>Silicibacter pomeroyi<ins style="font-weight: bold; text-decoration: none;">'' </ins>with coxL gene expression.” Geophysical Research Abstracts. 2007. Volume 9. p. 4535.</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>9. Kiene, R. P., Linn, L. J. & Bruton, J. A. “New and important roles for DMSP in marine microbial communities.” J Sea Res. 2000. Volume 43. p. 209–224.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>9. Kiene, R. P., Linn, L. J. & Bruton, J. A. “New and important roles for DMSP in marine microbial communities.” J Sea Res. 2000. Volume 43. p. 209–224.</div></td></tr>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>11. Moran M.A., Buchan A., Gonzalez J.M., Heidelberg J.F., Whitman W.B., Kiene R.P., Henriksen J.R., King G.M., Belas R., Fuqua C., Brinkac L., Lewis M., Johri S., Weaver B., Pai G., Eisen J.A., Rahe E., Sheldon WM, Ye W., Miller T.R., Carlton J., Rasko D.A., Paulsen I.T., Ren Q., Daugherty S.C., Deboy R.T., Dodson R.J., Durkin A.S., Madupu R., Nelson W.C., Sullivan S.A., Rosovitz M.J., Haft D.H., Selengut J., Ward N. “Genome sequence of <del style="font-weight: bold; text-decoration: none;">silicibacter </del>pomeroyi reveals adaptions to the marine environment.” Nature. 2004. Volume 432. p. 910-3.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>11. Moran M.A., Buchan A., Gonzalez J.M., Heidelberg J.F., Whitman W.B., Kiene R.P., Henriksen J.R., King G.M., Belas R., Fuqua C., Brinkac L., Lewis M., Johri S., Weaver B., Pai G., Eisen J.A., Rahe E., Sheldon WM, Ye W., Miller T.R., Carlton J., Rasko D.A., Paulsen I.T., Ren Q., Daugherty S.C., Deboy R.T., Dodson R.J., Durkin A.S., Madupu R., Nelson W.C., Sullivan S.A., Rosovitz M.J., Haft D.H., Selengut J., Ward N. “Genome sequence of <ins style="font-weight: bold; text-decoration: none;">''Silicibacter </ins>pomeroyi<ins style="font-weight: bold; text-decoration: none;">'' </ins>reveals adaptions to the marine environment.” Nature. 2004. Volume 432. p. 910-3.</div></td></tr>
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</table>Lkhachathttps://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=16621&oldid=prevLkhachat: /* Genome structure */2007-06-05T07:06:48Z<p><span dir="auto"><span class="autocomment">Genome structure</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The genomic sequence of ''Silicibacter pomeroyi'' is 4,109,442 base pairs long. It contains a megaplasmid that is 491,611 base pairs long (11). The megaplasmid has no rRNA operons (10). The genome sequence also has 4,283 coding sequences (CDS). Table 1 provides a summary of the elements contained in the genome of this organism. ''S. pomeroyi'' has a linear chromosome while DSS-3 has a circular chromosome. ''S. pomeroyi'' and DSS-3 are different strains of the same species (11). The existence of any prophages in the bacterial genome has not been detected. A unique and noteworthy characteristic of ''S. pomeroyi'' is that it has “the highest proportion of genes coding for signal transduction,” which gives the organism an “enhanced ability to sense and respond to conditions outside the cell” (11). It has both heterotrophic and lithoheterotrophic characteristics, which means that it relies on inorganic compounds such as carbon monoxide and sulfphide for energy. ''S. pomeroyi'' has genes that are specialized in the uptake of compounds derived from algae, allow for fast growth, and facilitate the use of metabolites by the bacterium to reduce microzones. The ''Silicibacter'' genus is also known to possess numerous peptide transporters, which indicate the importance of proteins as carbon source for these species (11). Another distinctive feature of this bacterium is its six ABC-type transporter systems since “no other sequenced genome has more than three” (11). These transporter systems are likely to be used by ''S. pomeroyi'' for the purpose of cell growth regulation. S. pomeroyi also has five tranport sysems for DMSP transport, “four transporters for ammonium and one for urea” (11). Its genome houses genes that facilitate integration of ammonium and urea, which are useful sources of nitrogen (11). </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The genomic sequence of ''Silicibacter pomeroyi'' is 4,109,442 base pairs long. It contains a megaplasmid that is 491,611 base pairs long (11). The megaplasmid has no rRNA operons (10). The genome sequence also has 4,283 coding sequences (CDS). Table 1 provides a summary of the elements contained in the genome of this organism. ''S. pomeroyi'' has a linear chromosome while DSS-3 has a circular chromosome. ''S. pomeroyi'' and DSS-3 are different strains of the same species (11). The existence of any prophages in the bacterial genome has not been detected. A unique and noteworthy characteristic of ''S. pomeroyi'' is that it has “the highest proportion of genes coding for signal transduction,” which gives the organism an “enhanced ability to sense and respond to conditions outside the cell” (11). It has both heterotrophic and lithoheterotrophic characteristics, which means that it relies on inorganic compounds such as carbon monoxide and sulfphide for energy. ''S. pomeroyi'' has genes that are specialized in the uptake of compounds derived from algae, allow for fast growth, and facilitate the use of metabolites by the bacterium to reduce microzones. The ''Silicibacter'' genus is also known to possess numerous peptide transporters, which indicate the importance of proteins as carbon source for these species (11). Another distinctive feature of this bacterium is its six ABC-type transporter systems since “no other sequenced genome has more than three” (11). These transporter systems are likely to be used by ''S. pomeroyi'' for the purpose of cell growth regulation. <ins style="font-weight: bold; text-decoration: none;">''</ins>S. pomeroyi<ins style="font-weight: bold; text-decoration: none;">'' </ins>also has five tranport sysems for DMSP transport, “four transporters for ammonium and one for urea” (11). Its genome houses genes that facilitate integration of ammonium and urea, which are useful sources of nitrogen (11). </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>In addition, the ''S. pomeroyi'' genome contains two cox operons that encode aerobic carbon monoxide dehydrogenases. These enzymes are used to oxidize carbon monoxide to carbone dioxide. There are also three rRNA operons present in the genome, which explains the organism’s ability to quickly respond to modifications depending on the availability of resources. When there is plenty of carbon and energy available, ''S. pomeroyi'' stores carbon and energy via the polyhydroxyalkanoic acid synthesis pathway. This organism does not display any evidence of pathways for autotrophy, which implies that it obtains its energy through carboxidotrophy, which is the process of utilizing carbon monoxide. The genome of ''S. pomeroyi'' also lacks genes that encode phototrophy (10). The genome contains “31 genes that encode elements for motility” (11). The organism achieves motility by rotating its complex flagellum11. A growing body of evidence also suggests the presence of a large number of genes that encode “the production, degradation, and efflux of toxins and metabolites” (10) in marine organisms such as ''S. pomeroyi''. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>In addition, the ''S. pomeroyi'' genome contains two cox operons that encode aerobic carbon monoxide dehydrogenases. These enzymes are used to oxidize carbon monoxide to carbone dioxide. There are also three rRNA operons present in the genome, which explains the organism’s ability to quickly respond to modifications depending on the availability of resources. When there is plenty of carbon and energy available, ''S. pomeroyi'' stores carbon and energy via the polyhydroxyalkanoic acid synthesis pathway. This organism does not display any evidence of pathways for autotrophy, which implies that it obtains its energy through carboxidotrophy, which is the process of utilizing carbon monoxide. The genome of ''S. pomeroyi'' also lacks genes that encode phototrophy (10). The genome contains “31 genes that encode elements for motility” (11). The organism achieves motility by rotating its complex flagellum11. A growing body of evidence also suggests the presence of a large number of genes that encode “the production, degradation, and efflux of toxins and metabolites” (10) in marine organisms such as ''S. pomeroyi''.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Cell structure and metabolism==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Cell structure and metabolism==</div></td></tr>
</table>Lkhachathttps://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=16605&oldid=prevLkhachat at 07:04, 5 June 20072007-06-05T07:04:54Z<p></p>
<a href="https://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=16605&oldid=11726">Show changes</a>Lkhachathttps://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=11726&oldid=prevLkhachat: /* Pathology */2007-05-30T02:49:24Z<p><span dir="auto"><span class="autocomment">Pathology</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Pathology==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Pathology==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">How does this organism </del>cause <del style="font-weight: bold; text-decoration: none;">disease? Human</del>, <del style="font-weight: bold; text-decoration: none;">animal</del>, <del style="font-weight: bold; text-decoration: none;">plant hosts? Virulence factors, as well as patient symptoms</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">''S. pomeroyi'' is not known to </ins>cause <ins style="font-weight: bold; text-decoration: none;">any diseases in humans</ins>, <ins style="font-weight: bold; text-decoration: none;">plants</ins>, <ins style="font-weight: bold; text-decoration: none;">or animals. It is an environmental microbe</ins>.</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Application to Biotechnology==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Application to Biotechnology==</div></td></tr>
</table>Lkhachathttps://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=11725&oldid=prevLkhachat: /* Ecology */2007-05-30T02:49:00Z<p><span dir="auto"><span class="autocomment">Ecology</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Ecology==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Ecology==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Describe any interactions with other organisms </del>(<del style="font-weight: bold; text-decoration: none;">included eukaryotes</del>), <del style="font-weight: bold; text-decoration: none;">contributions </del>to the <del style="font-weight: bold; text-decoration: none;">environment</del>, <del style="font-weight: bold; text-decoration: none;">effect on environment, etc</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">''Silicibacter pomeroyi'' contributes to the environment by degrading DMSP in order to produce dimethylsulfide </ins>(<ins style="font-weight: bold; text-decoration: none;">DMS</ins>)<ins style="font-weight: bold; text-decoration: none;">. DMS is a sulfur compound that makes a major contribution to the sulfur supply in the atmosphere. It also plays an important role in the regulation of the climate by forming clouds and scattering the radiation coming from the sun3. The sulfur obtained from DMSP is integrated into proteins of bacteria; as a result</ins>, <ins style="font-weight: bold; text-decoration: none;">DMSP acts as a major source of sulfur for marine bacterioplankton This organism is also known </ins>to <ins style="font-weight: bold; text-decoration: none;">carry out </ins>the <ins style="font-weight: bold; text-decoration: none;">DMSP-demethylation/demethiolation pathway. This pathway produces methanethiol (MeSH)</ins>, <ins style="font-weight: bold; text-decoration: none;">which expedites the incorporation of sulfur obtained from the degradation of DMSP into bacterial proteins6</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Pathology==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Pathology==</div></td></tr>
</table>Lkhachathttps://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=11724&oldid=prevLkhachat: /* Cell structure and metabolism */2007-05-30T02:48:20Z<p><span dir="auto"><span class="autocomment">Cell structure and metabolism</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Cell structure and metabolism==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Cell structure and metabolism==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Figure 2 shows the phase-contrast micrograph, tramission electron micrograph, and scanning electron micrograph of <del style="font-weight: bold; text-decoration: none;">silicibacter </del>pomeroyi. Analysis of this organism using these different micrographs has allowed scientists to detect blebs that are present in the outer <del style="font-weight: bold; text-decoration: none;">membrane</del>. These blebs may be responsible for the “degradation of insoluble <del style="font-weight: bold; text-decoration: none;">substrates</del>.<del style="font-weight: bold; text-decoration: none;">” </del>The bacterium also is seen to contain poly-β-hydroxybutyrate (PHB) inclusion bodies. The importance of the blebs and PHB bodies lies in the fact that they help <del style="font-weight: bold; text-decoration: none;">silicibacter </del>pomeroyi to pick up and store nutrients <del style="font-weight: bold; text-decoration: none;">allowing </del>it to survive in environments with low nutrient salt and high oxygen <del style="font-weight: bold; text-decoration: none;">concentrations (Gonz)</del>. <del style="font-weight: bold; text-decoration: none;">It </del>uses organic acids <del style="font-weight: bold; text-decoration: none;">and </del>amino acids <del style="font-weight: bold; text-decoration: none;">for growth </del>and <del style="font-weight: bold; text-decoration: none;">grows </del>at 10-40°C temperature range. <del style="font-weight: bold; text-decoration: none;">However</del>, <del style="font-weight: bold; text-decoration: none;">silicibacter </del>pomeroyi <del style="font-weight: bold; text-decoration: none;">does </del>not <del style="font-weight: bold; text-decoration: none;">have the ability </del>to ferment glucose or reduce <del style="font-weight: bold; text-decoration: none;">nitrate (Gonzalez)</del>, but it can degrade aromatic <del style="font-weight: bold; text-decoration: none;">compounds (Buchan)</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Figure 2 shows the phase-contrast micrograph, tramission electron micrograph, and scanning electron micrograph of <ins style="font-weight: bold; text-decoration: none;">''Silicibacter </ins>pomeroyi<ins style="font-weight: bold; text-decoration: none;">''</ins>. Analysis of this organism using these different micrographs has allowed scientists to detect blebs that are present in the outer <ins style="font-weight: bold; text-decoration: none;">membrane4</ins>. These blebs may be responsible for the “degradation of insoluble <ins style="font-weight: bold; text-decoration: none;">substrates”5</ins>. The bacterium also is seen to contain poly-β-hydroxybutyrate (PHB) inclusion bodies. The importance of the blebs and PHB bodies lies in the fact that they help <ins style="font-weight: bold; text-decoration: none;">''Silicibacter </ins>pomeroyi<ins style="font-weight: bold; text-decoration: none;">'' </ins>to pick up and store nutrients<ins style="font-weight: bold; text-decoration: none;">, which allow </ins>it to survive in environments with low nutrient salt and high oxygen <ins style="font-weight: bold; text-decoration: none;">concentrations4</ins>. <ins style="font-weight: bold; text-decoration: none;">This organism </ins>uses organic acids<ins style="font-weight: bold; text-decoration: none;">, </ins>amino acids<ins style="font-weight: bold; text-decoration: none;">, </ins>and <ins style="font-weight: bold; text-decoration: none;">other compounds such as ethanol, glycerol, acetate, DMSP, glucose, pyruvate, succinate, etc. to grow </ins>at 10-40°C temperature range. <ins style="font-weight: bold; text-decoration: none;">It requires NaCl for growth. Although vitamins are not required</ins>, <ins style="font-weight: bold; text-decoration: none;">enhanced growth was observed in their presence. ''S. </ins>pomeroyi<ins style="font-weight: bold; text-decoration: none;">'' is </ins>not <ins style="font-weight: bold; text-decoration: none;">able </ins>to <ins style="font-weight: bold; text-decoration: none;">either </ins>ferment glucose or reduce <ins style="font-weight: bold; text-decoration: none;">nitrate4</ins>, but it can degrade aromatic <ins style="font-weight: bold; text-decoration: none;">compounds1,2. It hydrolyzes gelatin but not cellulose or starch. In the presence of arginine, ''S</ins>. pomeroyi<ins style="font-weight: bold; text-decoration: none;">'' can also oxidize thiosulfate. It </ins>has <ins style="font-weight: bold; text-decoration: none;">the capacity to produce both oxidase and catalse. It forms cream-colored</ins>, <ins style="font-weight: bold; text-decoration: none;">circular colonies on marine agar. A noteworthy characteristic of this bacterium is its ability to separate its outer membrane from </ins>the <ins style="font-weight: bold; text-decoration: none;">cytoplasm4</ins>.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Silicibacter </del>pomeroyi has <del style="font-weight: bold; text-decoration: none;">a polar flagellum</del>, <del style="font-weight: bold; text-decoration: none;">which rotates in </del>the <del style="font-weight: bold; text-decoration: none;">clockwise direction</del>. </div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2" class="diff-side-added"></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Ecology==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Ecology==</div></td></tr>
</table>Lkhachathttps://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=11723&oldid=prevLkhachat: /* Genome structure */2007-05-30T02:47:00Z<p><span dir="auto"><span class="autocomment">Genome structure</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Genome structure==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Genome structure==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The genomic sequence of <del style="font-weight: bold; text-decoration: none;">silicibacter </del>pomeroyi is 4,109,442 base pairs long. It contains a megaplasmid that is 491,611 base pairs long. The genome sequence also has 4,283 coding sequences (CDS). <del style="font-weight: bold; text-decoration: none;">The DSS-3 strain of </del>''<del style="font-weight: bold; text-decoration: none;">Silicibacter </del>pomeroyi'' has a circular chromosome. A unique and noteworthy characteristic of S. pomeroyi is that it has “the highest proportion of genes coding for signal transduction,” which gives the organism an “enhanced ability to sense and respond to conditions outside the <del style="font-weight: bold; text-decoration: none;">cell” (citation)</del>. <del style="font-weight: bold; text-decoration: none;">This is a </del>lithoheterotrophic <del style="font-weight: bold; text-decoration: none;">and heterotrophic organism </del>that <del style="font-weight: bold; text-decoration: none;">uses </del>inorganic compounds such as carbon monoxide and <del style="font-weight: bold; text-decoration: none;">sulfide</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The genomic sequence of <ins style="font-weight: bold; text-decoration: none;">''Silicibacter </ins>pomeroyi<ins style="font-weight: bold; text-decoration: none;">'' </ins>is 4,109,442 base pairs long. It contains a megaplasmid that is 491,611 base pairs long. The genome sequence also has 4,283 coding sequences (CDS). ''<ins style="font-weight: bold; text-decoration: none;">S. </ins>pomeroyi'' <ins style="font-weight: bold; text-decoration: none;">has a linear chromosome while its DSS-3 strain </ins>has a circular chromosome. A unique and noteworthy characteristic of <ins style="font-weight: bold; text-decoration: none;">''</ins>S. pomeroyi<ins style="font-weight: bold; text-decoration: none;">'' </ins>is that it has “the highest proportion of genes coding for signal transduction,” which gives the organism an “enhanced ability to sense and respond to conditions outside the <ins style="font-weight: bold; text-decoration: none;">cell</ins>.<ins style="font-weight: bold; text-decoration: none;">” It has both heterotrophic and </ins>lithoheterotrophic <ins style="font-weight: bold; text-decoration: none;">characteristics, which means </ins>that <ins style="font-weight: bold; text-decoration: none;">it relies on </ins>inorganic compounds such as carbon monoxide and <ins style="font-weight: bold; text-decoration: none;">sulfphide for energy. ''S. pomeroyi'' has genes that are specialized in the uptake of compounds derived from algae, allow for fast growth, and facilitate the use of metabolites by the bacterium to reduce microzones. The ''Silicibacter'' genus is also known to possess numerous peptide transporters, which indicate the importance of proteins as carbon source for these species7. Another distinctive feature of this bacterium is its six ABC-type transporter systems since “no other sequenced genome has more than three”7. These transporter systems are primarily used by S. pomeroyi for the purpose of cell growth regulation. ''S. pomeroyi'' also has five tranport sysems for DMSP transport, “four transporters for ammonium and one for urea”7. Its genome also houses genes that facilitate integration of ammonium and urea, which are useful sources of nitrogen7. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">The ''S. pomeroyi'' genome contains two operans that encode aerobic carbon monoxide dehydrogenases. These dehydrogenases are used to oxidize carbon monoxide to carbone dioxide. There are also three rRNA operons present in its genome, which explains the organism’s ability to quickly respond to modifications in the availability of resources. When there is plenty of carbon and energy available, ''S. pomeroyi'' stores it via the polyhydroxyalkanoic acid synthesis pathway. This organism does not display any evidence of pathways for autotrophy, which implies that it obtains its energy through carboxidotrophy. The genome of ''S. pomeryi'' contains “31 genes that encode elements for motility,” which the organism achieves by rotating its complex flagellum7</ins>.</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Cell structure and metabolism==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Cell structure and metabolism==</div></td></tr>
</table>Lkhachathttps://microbewiki.kenyon.edu/index.php?title=Silicibacter_pomeroyi&diff=11722&oldid=prevLkhachat: /* Description and significance */2007-05-30T02:44:19Z<p><span dir="auto"><span class="autocomment">Description and significance</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Description and significance==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Description and significance==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''Silicibacter pomeroyi'' is among organisms that are capable of degrading sulfur compounds found in marine environments. In fact, this bacteria has the ability not only to degrade but also to demehtylate and cleave dimethylsulfoniopropionate (DMSP). It is a rod-shaped, Gram-negative bacterium that lives in marine environments and uses oxygen for its metabolic activities, such as to obtain energy. ''Silicibacter pomeroyi'' has a single but complex flagellum that rotates in the clockwise direction4, which accounts for its motility (Moran). This important characteristic enables the organism to place itself in favorable environments (Moran). Its surface is covered with blebs and its interior contains poly-β-hydroxybutyrate inclusions. It was isolated in Georgia from coastal sea water. This organism should be given a lot of attention because it plays an important role in climate regulation and greatly contributes to the “global atmospheric sulfur pool”4. By degrading DMSP, ''Silicibacter pomeroyi'' causes the formation of dimethylsulfide (DMS), which is a volatile sulfur compound that greatly adds to the sulfur supply in the atmosphere. DMS also influences climate regulation by forming clouds and backscattering solar radiation3,8. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>''Silicibacter pomeroyi'' is among organisms that are capable of degrading sulfur compounds found in marine environments. In fact, this bacteria has the ability not only to degrade but also to demehtylate and cleave dimethylsulfoniopropionate (DMSP). It is a rod-shaped, Gram-negative bacterium that lives in marine environments and uses oxygen for its metabolic activities, such as to obtain energy. ''Silicibacter pomeroyi'' has a single but complex flagellum that rotates in the clockwise direction4, which accounts for its motility (Moran). This important characteristic enables the organism to place itself in favorable environments (Moran). Its surface is covered with blebs and its interior contains poly-β-hydroxybutyrate inclusions. It was isolated in Georgia from coastal sea water. This organism should be given a lot of attention because it plays an important role in climate regulation and greatly contributes to the “global atmospheric sulfur pool”4. By degrading DMSP, ''Silicibacter pomeroyi'' causes the formation of dimethylsulfide (DMS), which is a volatile sulfur compound that greatly adds to the sulfur supply in the atmosphere. DMS also influences climate regulation by forming clouds and backscattering solar radiation3,8. </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In addition, this bacterium also metabolizes DMSP through the demethylation/ demethiolation pathway to produce methanethiol (MeSH). The significance of MeSH lies in its critical role in the incorporation of DMSP sulfur into bacterial proteins. In the presence of MeSH, DMSP is quickly integraded into the bacterial proteins6.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In addition, this bacterium also metabolizes DMSP through the demethylation/ demethiolation pathway to produce methanethiol (MeSH). The significance of MeSH lies in its critical role in the incorporation of DMSP sulfur into bacterial proteins. In the presence of MeSH, DMSP is quickly integraded into the bacterial proteins6.</div></td></tr>
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</table>Lkhachat