Pelagibacter ubique

Pelagibacter ubique
Scientific classification (Candidatus)
Kingdom:	Bacteria
Phylum:	Proteobacteria
Class:	Alphaproteobacteria
Order:	Rickettsiales
Family:	"Pelagibacteraceae"
Genus:	Pelagibacter
Species:	P. ubique
Binomial name
Candidatus Pelagibacter ubique Rappé et al. 2002

Pelagibacter, with the single species P. ubique, was isolated in 2002 and given a specific name,^[1] although it has not yet been validly published according to the bacteriological code.^[2] It is an abundant member of the SAR11 clade in the phylum Alphaproteobacteria. SAR11 members are highly dominant organisms found in both salt and fresh water worldwide — possibly the most numerous bacteria in the world (perhaps 10²⁸ individual cells) and were originally known only from their rRNA genes, which were first identified in environmental samples from the Sargasso Sea in 1990 by Stephen Giovannoni's laboratory in the Department of Microbiology at Oregon State University and later found in oceans worldwide.^[3]

It is rod or crescent shaped and one of the smallest self-replicating cells known, with a length of 0.37-0.89 µm and a diameter of only 0.12-0.20 µm. It recycles dissolved organic carbon. It undergoes regular seasonal cycles in abundance - in summer reaching ~50% of the cells in the temperate ocean. Thus it plays a major role in the Earth's carbon cycle.

Its discovery was the subject of "Oceans of Microbes", Episode 5 of "Intimate Strangers: Unseen Life on Earth" by PBS ^[4]

Cultivation

Several strains of Pelagibacter ubique have been cultured thanks to improved isolation techniques.^[5] The most studied strain is HTCC1062 (high-throughput cultivation collection).^[1]

The factors that regulate SAR11 populations are still largely unknown. They have sensors for nitrogen, phosphate, and iron limitation, and a very unusual requirement for reduced sulfur compounds. It is hypothesised that they have been molded by evolution in a low nutrient ecosystem, such as the Sargasso Sea where it was first discovered.^[6]

Genome

The genome of P. ubique strain HTCC1062 was completely sequenced in 2005 showing that P. ubique has the smallest genome (1,308,759 bp) of any free living organism.^[7] The only species with smaller genomes are endocellular symbionts and parasites, such as Mycoplasma genitalium or Nanoarchaeum equitans^[7]

Non-coding RNAs have been identified in P. ubique through a bioinformatics screen of the published genome and metagenomic data. Examples of ncRNA found in this organisms include the SAM-V riboswitch, and other cis-regulatory elements like the rpsB motif.^[8][9]

Name

See also: Bacterial taxonomy

The name of the genus (Pelagibacter) stems from the Latin masculin noun pelagus ("sea") combined with the suffix -bacter (rod, bacterium), to mean "bacterium of the sea". The connecting vowel is an "i" and not an "o", as the first term is the Latin "pelagus" and not the Greek original πέλαγος (pelagos) (the word pelagus is a Greek word used in Latin poetry, it is a 2nd declension noun with an Greek-like irregular nominative plural pelagē and not pelagi^[10]). The name of the specific epithet (ubique) is a Latin adverb meaning "everywhere"; it should be noted species with the status Candidatus are not validly published so do not have to be grammatically correct, such as having specific epithets having to be adjectives or nouns in apposition in the nominative case or genitive nouns according to rule 12c of the IBCN.^[11]

The term "Candidatus" is used for proposed species for which the lack of information (cf.^[12]) prevents it from being a validated species according to the bacteriological code,^[13][14] such as deposition in two public cell repositories or lack of FAME analysis^[15][16] whereas "Cadidatus Pelagibacter ubique" is not in ATCC [1] and DSMZ [2], nor has analysis of lipids and quinones been conducted.

HTTC1062 is the type strain of the species Pelagibacter ubique, which in turn is the type species of the genus Pelagibacter,^[1], which in turn is the type genus of the SAR11 clade or family "Pelagibacteraceae".^[17]

References

1. ^ ^{a b c} Michael S. Rappé, Stephanie A. Connon, Kevin L. Vergin, Stephen J. Giovannoni (2002). "Cultivation of the ubiquitous SAR11 marine bacterioplankton clade". Nature 418 (6898): 630–633. doi:10.1038/nature00917. PMID 12167859. 
2. ^ List of Candidate species entry in LPSN [Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int J Syst Bacteriol 47 (2): 590-2. doi:10.1099/00207713-47-2-590. ISSN 0020-7713. PMID 9103655. http://ijs.sgmjournals.org/cgi/reprint/47/2/590. ]
3. ^ R. M. Morris et al. (2002). "SAR11 clade dominates ocean surface bacterioplankton communities". Nature 420 (6917): 806–810. doi:10.1038/nature01240. PMID 12490947. 
4. ^ view "Oceans of Microbes" http://www.podcastdirectory.com/podshows/4339749
5. ^ Stingl, U.; Tripp, H. J.; Giovannoni, S. J. (2007). "Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site". The ISME Journal 1 (4). doi:10.1038/ismej.2007.49.  edit
6. ^ Giovannoni Lab http://giovannonilab.science.oregonstate.edu/
7. ^ ^{a b} Stephen J. Giovannoni, H. James Tripp et al. (2005). "Genome Streamlining in a Cosmopolitan Oceanic Bacterium". Science 309 (5738): 1242–1245. doi:10.1126/science.1114057. PMID 16109880. 
8. ^ Meyer MM, Ames TD, Smith DP et al. (2009). "Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'". BMC Genomics 10: 268. doi:10.1186/1471-2164-10-268. PMC 2704228. PMID 19531245. http://www.biomedcentral.com/1471-2164/10/268. Retrieved 2010-09-13. 
9. ^ Poiata E, Meyer MM, Ames TD, Breaker RR (November 2009). "A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria". RNA 15 (11): 2046–56. doi:10.1261/rna.1824209. PMC 2764483. PMID 19776155. http://rnajournal.cshlp.org/cgi/pmidlookup?view=long&pmid=19776155. Retrieved 2010-09-13. 
10. ^ Gregory R. Crane. "pelagus entry in Perseus Digital Library". Tufts University. http://www.perseus.tufts.edu/hopper/morph?l=pelagus&la=la#lexicon. Retrieved 22 May 2011. 
11. ^ Lapage, S.; Sneath, P.; Lessel, E.; Skerman, V.; Seeliger, H.; Clark, W. (1992). PMID 21089234.  edit
12. ^ http://www.bacterio.cict.fr/minimalstandards.html
13. ^ MURRAY (R.G.E.) and SCHLEIFER (K.H.): Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int. J. Syst. Bacteriol., 1994, 44, 174-176.
14. ^ JUDICIAL COMMISSION OF THE INTERNATIONAL COMMITTEE ON SYSTEMATIC BACTERIOLOGY: Minutes of the meetings, 2 and 6 July 1994, Prague, Czech Republic. Int. J. Syst. Bacteriol., 1995, 45, 195-196.
15. ^ Euzéby J.P. (2010). "Introduction". List of Prokaryotic names with Standing in Nomenclature. http://www.bacterio.cict.fr/nonvalid.html. Retrieved 2010-12-16. 
16. ^ Sneath, P.H.A (1992). Lapage S.P.; Sneath, P.H.A.; Lessel, E.F.; Skerman, V.B.D.; Seeliger, H.P.R.; Clark, W.A.. ed. International Code of Nomenclature of Bacteria. Washington, D.C.: American Society for Microbiology. ISBN 1-55581-039-X. PMID 21089234. 
17. ^ Thrash, J. C.; Boyd, A.; Huggett, M. J.; Grote, J.; Carini, P.; Yoder, R. J.; Robbertse, B.; Spatafora, J. W. et al. (2011). "Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade". Scientific Reports 1. doi:10.1038/srep00013.  edit

External links

• MicrobeWiki entry
• BBC News: Ocean bug has 'smallest genome'