Pelagibacter ubique: Difference between revisions

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{{Biorealm Genus}}
{{Biorealm Genus}}
[[Image:Pelagibacter.jpg‎|frame|none|right|''Pelagibacter ubique''. Image courtesy of [http://ober-proteomics.pnl.gov/bioapps/organisms.stm Office of Biological & Environmental Research] ]].


==Classification==
==Classification==
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==References==
==References==
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]
(?) Cascio, Jamais. World Changing. [http://www.worldchanging.com/archives/003334.html Genetic Efficiency and the Carbon Cycle.] 19 August 2005. Accessed 26 August 2007.


(1) [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=198252&lvl=3&lin=f&keep=1&srchmode=1&unlock United States of America. National Library of Medicine (NLM) and National Institutes of Health (NIH). National Center for Biotechnology Information (NCBI): Pelagibacter ubique. Accessed 26 August 2007.]
(?) Comprehensive Microbial Resource. [http://cmr.tigr.org/tigr-scripts/CMR/GenomePage.cgi?org=ntcp06 Candidatus Pelagibacter ubique HTCC1062 Genome Page.] Last updated 27 September 2006. Accessed 26 August 2007.


(2)[http://ober-proteomics.pnl.gov/bioapps/organisms.stm Giovannoni, Stephen, and Douglas Barofsky, comps. United States of America. U.S. Department of Energy. Biological and Environmental Research - PNNL Proteomics. Biological Applications - Organisms: ''Pelagibacter ubique''. Last updated May 2007. Accessed 26 August 2007.]
(?) European Bioinfomatics Institute. [http://www.edi.ac.uk/2can/genomes/bacteria/Candidatus_Pelagibacter_ubique.html Bacteria Genomes - CANDIDATUS PELAGIBACTER UBIQUE.] Accessed 26 August 2007.


(3) [http://www.mcb.oregonstate.edu/giovannoni/projects/subproject/sar11.htm Giovannoni, Dr. Stephen. "SAR 11." Giovannoni Lab. Oregon State University. Accessed 26 August 2007.]
(?) Giovannoni, Stephen. Oregon State University. [http://www.mcb.oregonstate.edu/giovannoni/projects/subproject/sar11.htm Giovannoni Lab: SAR 11.] Accessed 26 August 2007.


Edited by [mailto:ldizon@yahoo.com Liza Dizon], student of [mailto:ralarsen@ucsd.edu Rachel Larsen]
(?) Giovannoni, Stephen, and Douglas Barofsky, comps. U.S. Department of Energy. Biological and Environmental Research - PNNL Proteomics. [http://ober-proteomics.pnl.gov/bioapps/organisms.stm Biological Applications - Organisms: ''Pelagibacter ubique''.] Last updated May 2007. Accessed 26 August 2007.
 
(?) Giovannoni, S.J., Bibbs, L., Cho, J.-C., Stapels, M.D., Desiderio, R., Vergin, K.L., Rappe, M.S., Laney, S., Wilhelm, L.J., Tripp, H.J., Mathur, E.J., and Barofsky, D.F. [http://www.mcb.oregonstate.edu/giovannoni/publications/subpublication/nature04032.pdf Proteorhodopsin in the ubiquitous marine bacterium SAR11.] Nature 438 (3 November 2005): 82-85.
 
(?) Giovannoni S.J., Morris, R. M., Rappe, M. S., Connon, S. A., Vergin, K. L., Siebold, W. A., and Carlson, C. A. [http://www.mcb.oregonstate.edu/giovannoni/publications/subpublication/natureMorrisSAR11.pdf SAR11 clade dominates ocean surface bacterioplankton communities.] Nature 420 (December 2002): 806-810.
 
(?) Giovannoni, S.J., Rappe, M. S., Connan, S. A., and Vergin, K. L. [http://www.mcb.oregonstate.edu/giovannoni/publications/subpublication/nature00917_r.pdf Cultivation of the ubiquitous SAR11 marine bacterioplankton clade.] Nature 418 (8 August 2002): 630-631.
 
(?) Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D., Bibbs, L., Eads, J., Richardson, T.H., Noordewier, M., Rappe, M.S., Short, J., Carrington, J.C., and Mathur, E.J. [www.sciencemag.org Genome Streamlining in a Cosmopolitan Oceanic Bacterium.] Science 309 (19 August 2005): 1242-1245.
 
(?) Genomics: GTL. U.S. Department of Energy Office of Science. Systems for Biology for Energy and Environment: Genomes to Life Contractor-Grantee Workschop 2005. [http://genomicsgtl.energy.gov/pubs/2005abstracts/html/file71.shtml Microbial Genomics - ''Pelagibacter ubique'': A Post-Genomic Investigation of Carbon Metabolism and Photochemistry in an Extraordinarily Abundant Oceanic Bacterium.] February 2005. Accessed 26 August 2007.
 
(?) Kyoto Encyclopedia of Genes and Genomes. [http://www.genome.jp/kegg-bin/show_organism?org=pub Candidatus Pelagibacter ubique.] Accessed 26 August 2007.
 
(?) Monterey Bay Aquarium Research Institute (MBARI). Giovannoni, Stephen. [http://www.mbari.org/seminars/2005/spring2005/spril15_giovannoni.htm ''Pelagibacter ubique'': A Perfect engineering solution?] Seminar: Pacific Forum. 15 April 2005. Accessed 26 August 2007.
 
(?) National Library of Medicine (NLM) and National Institutes of Health (NIH). [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=198252&lvl=3&lin=f&keep=1&srchmode=1&unlock National Center for Biotechnology Information (NCBI): Pelagibacter ubique.] Accessed 26 August 2007.
 
(?) Pease, Roland. BBC News. [http://newsvote.bbc.co.uk/mpapps/pagetools/print/news.bbc.co.uk/1/hi/sci/tech/4166076.stm Ocean bug has 'smallest genome'.] Last updated 19 August 2005. Accessed 26 August 2007.
 
Edited by [mailto:ldizon@ucsd.com Liza Dizon], student of [mailto:ralarsen@ucsd.edu Rachel Larsen]

Revision as of 06:09, 29 August 2007

A Microbial Biorealm page on the genus Pelagibacter ubique

Pelagibacter ubique. Image courtesy of Office of Biological & Environmental Research

.

Classification

Higher order taxa

Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; SAR11 cluster; Candidatus Pelagibacter; Candidatus Pelagibacter ubique

Species

NCBI: Taxonomy

Pelagibacter ubique

Description and significance

Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced. Describe how and where it was isolated. Include a picture or two (with sources) if you can find them.

Genome structure

Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence? Does it have any plasmids? Are they important to the organism's lifestyle?

Cell structure and metabolism

Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.

Ecology

Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.

Pathology

How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.

Application to Biotechnology

Does this organism produce any useful compounds or enzymes? What are they and how are they used?

Current Research

Enter summaries of the most recent research here--at least three required

References

(?) Cascio, Jamais. World Changing. Genetic Efficiency and the Carbon Cycle. 19 August 2005. Accessed 26 August 2007.

(?) Comprehensive Microbial Resource. Candidatus Pelagibacter ubique HTCC1062 Genome Page. Last updated 27 September 2006. Accessed 26 August 2007.

(?) European Bioinfomatics Institute. Bacteria Genomes - CANDIDATUS PELAGIBACTER UBIQUE. Accessed 26 August 2007.

(?) Giovannoni, Stephen. Oregon State University. Giovannoni Lab: SAR 11. Accessed 26 August 2007.

(?) Giovannoni, Stephen, and Douglas Barofsky, comps. U.S. Department of Energy. Biological and Environmental Research - PNNL Proteomics. Biological Applications - Organisms: Pelagibacter ubique. Last updated May 2007. Accessed 26 August 2007.

(?) Giovannoni, S.J., Bibbs, L., Cho, J.-C., Stapels, M.D., Desiderio, R., Vergin, K.L., Rappe, M.S., Laney, S., Wilhelm, L.J., Tripp, H.J., Mathur, E.J., and Barofsky, D.F. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438 (3 November 2005): 82-85.

(?) Giovannoni S.J., Morris, R. M., Rappe, M. S., Connon, S. A., Vergin, K. L., Siebold, W. A., and Carlson, C. A. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420 (December 2002): 806-810.

(?) Giovannoni, S.J., Rappe, M. S., Connan, S. A., and Vergin, K. L. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418 (8 August 2002): 630-631.

(?) Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D., Bibbs, L., Eads, J., Richardson, T.H., Noordewier, M., Rappe, M.S., Short, J., Carrington, J.C., and Mathur, E.J. [www.sciencemag.org Genome Streamlining in a Cosmopolitan Oceanic Bacterium.] Science 309 (19 August 2005): 1242-1245.

(?) Genomics: GTL. U.S. Department of Energy Office of Science. Systems for Biology for Energy and Environment: Genomes to Life Contractor-Grantee Workschop 2005. Microbial Genomics - Pelagibacter ubique: A Post-Genomic Investigation of Carbon Metabolism and Photochemistry in an Extraordinarily Abundant Oceanic Bacterium. February 2005. Accessed 26 August 2007.

(?) Kyoto Encyclopedia of Genes and Genomes. Candidatus Pelagibacter ubique. Accessed 26 August 2007.

(?) Monterey Bay Aquarium Research Institute (MBARI). Giovannoni, Stephen. Pelagibacter ubique: A Perfect engineering solution? Seminar: Pacific Forum. 15 April 2005. Accessed 26 August 2007.

(?) National Library of Medicine (NLM) and National Institutes of Health (NIH). National Center for Biotechnology Information (NCBI): Pelagibacter ubique. Accessed 26 August 2007.

(?) Pease, Roland. BBC News. Ocean bug has 'smallest genome'. Last updated 19 August 2005. Accessed 26 August 2007.

Edited by Liza Dizon, student of Rachel Larsen