Pelagibacter ubique

Pelagibacter, with the single species P. ubique, was isolated in 2002 and given a specific name,[1] although it has not yet been described as required by 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 bacterium in the world, 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] P. ubique and its relatives may be the most abundant organisms in the ocean, and quite possibly the most abundant bacteria in the entire world. It can make up about 25% of all microbial plankton cells, and in the summer they may account for approximately half the cells present in temperate ocean surface water. The total abundance of P. ubique and relatives is estimated to be about 2 × 1028 microbes.[4]

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

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. The Pelagibacter genome takes up about 30% of the cell's volume.[5] It is gram negative.[6] It recycles dissolved organic carbon. It undergoes regular seasonal cycles in abundance – in summer reaching ~50% of the cells in the temperate ocean surface waters. 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.[7]

Cultivation

Several strains of Pelagibacter ubique have been cultured thanks to improved isolation techniques.[8] 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.[9] 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.[10]

A population of P. ubique cells can double every 29 hours, which is fairly slow, but they can replicate under low nutrient conditions.[11]

P. ubique can be grown on a defined, artificial medium with additions of reduced sulfur, glycine, pyruvate and vitamins.[12]

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[5] encoding only 1,354 open reading frames (1,389 genes total).[13] The only species with smaller genomes are intracellular symbionts and parasites, such as Mycoplasma genitalium or Nanoarchaeum equitans[5] It has the smallest number of open reading frames of any free living organism, and the shortest intergenic spacers, but it still has metabolic pathways for all 20 amino acids and most co-factors.[5] Its genome has been streamlined. This streamlining concept is important because it reduces the amount of energy required for cell replication.[6] P. ubique saves energy by using the base pairs A and T (≈70.3% of all base pairs) because they contain less nitrogen, a resource that is hard for organisms to acquire.[6]

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 these organisms include the SAM-V riboswitch, and other cis-regulatory elements like the rpsB motif.[14][15] Another example of an important ncRNA in P. ubique and other SAR11 clade members is a conserved, glycine-activated riboswitch on malate synthase, putatively leading to "functional auxotrophy" for glycine or glycine precursors in order to achieve optimal growth.[16]

It is found to have proteorhodopsin genes, which help power light-mediated proton pumps. Subtle differences arise in the expression of its codon sequences when it is subjected to either light or dark treatments. More genes for oxidative phosphorylation are expressed when it is subjected to darkness.[17]

Name
See also: Bacterial taxonomy

The name of the genus (Pelagibacter) stems from the Latin masculine 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 a Greek-like irregular nominative plural pelagē and not pelagi[18]). The name of the specific epithet (ubique) is a Latin adverb meaning "everywhere"; 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.[19]

The term "Candidatus" is used for proposed species for which the lack of information (cf.[20]) prevents it from being a validated species according to the bacteriological code,[21][22] such as deposition in two public cell repositories or lack of FAME analysis[23][24] whereas "Cadidatus Pelagibacter ubique" is not in ATCC and DSMZ , 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".[25]

Bacteriophage

It was reported in Nature in February 2013 that the bacteriophage HTVC010P, which attacks P. ubique, has been discovered and "it probably really is the commonest organism on the planet".[26][27]

gollark: Ah.
gollark: ENCODE and DECODE of what format?!
gollark: LyricLy knows K?!?!?!
gollark: I have occasionally found the index and stuff helpful, but it would be bettererererererererererererer if it had `enumerate` or something like Rust.
gollark: 2030.

See also

References
  1. 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. Bibcode:2002Natur.418..630R. 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". International Journal of Systematic and Evolutionary Microbiology. 47 (2): 590–2. doi:10.1099/00207713-47-2-590. PMID 9103655.]
  3. R. M. Morris, et al. (2002). "SAR11 clade dominates ocean surface bacterioplankton communities". Nature. 420 (6917): 806–810. Bibcode:2002Natur.420..806M. doi:10.1038/nature01240. PMID 12490947.
  4. "Candidatus Pelagibacter Ubique." European Bioinformatics Institute. European Bioinformatics Institute, 2011. Web. 08 Jan. 2012. http://www.ebi.ac.uk/2can/genomes/bacteria/Candidatus_Pelagibacter_ubique.html Archived December 1, 2008, at the Wayback Machine
  5. Stephen J. Giovannoni, H. James Tripp, et al. (2005). "Genome Streamlining in a Cosmopolitan Oceanic Bacterium". Science. 309 (5738): 1242–1245. Bibcode:2005Sci...309.1242G. doi:10.1126/science.1114057. PMID 16109880.
  6. "Archived copy" (PDF). Archived from the original (PDF) on 2006-03-05. Retrieved 2012-02-02.CS1 maint: archived copy as title (link), Gauthier, Nicholas; Zinman, Guy; D’Antonio, Matteo; Abraham, Michael. Comparative Microbial Genomics DTU course. 2005.
  7. View "Oceans of Microbes" http://www.podcastdirectory.com/podshows/4339749 Archived 2012-02-17 at the Wayback Machine
  8. 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): 361–71. doi:10.1038/ismej.2007.49. PMID 18043647.
  9. H. James Tripp; Joshua B. Kitner; Michael S. Schwalbach; John W. H. Dacey; et al. (April 2008). "SAR11 marine bacteria require exogenous reduced sulfur for growth". Nature. 452 (7188): 741–4. Bibcode:2008Natur.452..741T. doi:10.1038/nature06776. PMID 18337719.
  10. Giovannoni Lab http://giovannonilab.science.oregonstate.edu/ Archived 2011-07-20 at the Wayback Machine
  11. Giovannoni Stephen J.; Stingl Ulrich (2005). "Molecular diversity and ecology of microbial plankton". Nature. 437 (7057): 343–348. Bibcode:2005Natur.437..343G. doi:10.1038/nature04158. PMID 16163344.
  12. Carini, Paul; et al. (2012). "Nutrient requirements for growth of the extreme oligotroph '"Candidatus" Pelagibacter ubique' HTCC1062 on a defined medium". The ISME Journal. 7 (3): 592–602. doi:10.1038/ismej.2012.122. PMC 3578571. PMID 23096402.
  13. "Pelagibacter ubique genome". NCBI. Retrieved 27 November 2012.
  14. 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.
  15. 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.
  16. H. James Tripp; Michael S. Schwalbach; Michelle M. Meyer; Joshua B. Kitner; et al. (January 2009). "Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11". Environmental Microbiology. 11 (1): 230–8. doi:10.1111/j.1462-2920.2008.01758.x. PMC 2621071. PMID 19125817.
  17. Steindler Laura; Schwalbach Michael S.; Smith Daniel P.; Chan Francis; et al. (2011). "Energy Starved Candidatus Pelagibacter Ubique Substitutes Light-Mediated ATP Production for Endogenous Carbon Respiration". PLOS ONE. 6 (5): 9999. Bibcode:2011PLoSO...619725S. doi:10.1371/journal.pone.0019725. PMC 3090418. PMID 21573025.
  18. Gregory R. Crane. "pelagus entry in Perseus Digital Library". Perseus Digital Library Project. Tufts University. Retrieved 22 May 2011.
  19. Lapage, S.; Sneath, P.; Lessel, E.; Skerman, V.; Seeliger, H.; Clark, W. (1992). International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision. Washington, D.C.: ASM Press. PMID 21089234.
  20. "Archived copy". Archived from the original on 2013-01-27. Retrieved 2010-12-15.CS1 maint: archived copy as title (link)
  21. Murray, R. G. E.; Schleifer, K. H. (1994). "Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes". Int. J. Syst. Bacteriol. 44 (1): 174–176. doi:10.1099/00207713-44-1-174. PMID 8123559.
  22. 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.
  23. Euzéby J.P. (2010). "Introduction". List of Prokaryotic names with Standing in Nomenclature. Archived from the original on 2011-03-06. Retrieved 2010-12-16.
  24. 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. (eds.). International Code of Nomenclature of Bacteria. Washington, D.C.: American Society for Microbiology. ISBN 978-1-55581-039-9. PMID 21089234.
  25. Thrash, J. C.; Boyd, A.; Huggett, M. J.; Grote, J.; Carini, P.; Yoder, R. J.; Robbertse, B.; Spatafora, J. W.; Rappé, M. S.; Giovannoni, S. J. (2011). "Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade". Scientific Reports. 1: 13. Bibcode:2011NatSR...1E..13T. doi:10.1038/srep00013. PMC 3216501. PMID 22355532.
  26. "Flea market: A newly discovered virus may be the most abundant organism on the planet". The Economist. 16 February 2013. Retrieved 16 February 2013.
  27. Zhao, Y.; Temperton, B.; Thrash, J. C.; Schwalbach, M. S.; Vergin, K. L.; Landry, Z. C.; Ellisman, M.; Deerinck, T.; Sullivan, M. B.; Giovannoni, S. J. (2013). "Abundant SAR11 viruses in the ocean". Nature. 494 (7437): 357–360. Bibcode:2013Natur.494..357Z. doi:10.1038/nature11921. PMID 23407494.
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