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Pelagibacterales

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Pelagibacteraceae
Scientific classification
(Candidatus)
Domain:
Bacteria
Phylum:
Proteobacteria
Class:
Alphaproteobacteria
Order:
Rickettsiales

The SAR11 clade, or Pelagibacteraceae,[1] defines a lineage of bacteria that is extremely common in the ocean.[2] Bacteria in the SAR11 clade make up roughly one in three cells at the ocean's surface. Overall, SAR11 bacteria are estimated to make up between a quarter and a half of all prokaryotic cells in the ocean.

SAR11 bacteria are classified as alphaproteobacteria, and include the highly abundant marine species Pelagibacter ubique. Bacteria in this clade are unusually small.[3]

Pelagibacter ubique and related species are oligotrophs — scavengers — and feed on dissolved organic carbon and nitrogen.[2] They are unable to fix carbon or nitrogen, but can perform the TCA cycle with glyoxylate bypass and are able to synthesise all amino-acids, except glycine,[4] and some cofactors.[5] They also have an unusual and unexpected requirement for reduced sulfur.[6]

Pelagibacter ubique and members of the oceanic subgroup I possess gluconeogenesis but not a typical glycolysis pathway, whereas other subgroups are capable of typical glycolysis.[7]

Unlike Acaryochloris marina, it is non-photosynthetic, but possesses proteorhodopsin (incl. retinol biosynthesis) for ATP production.[8]

SAR11 bacteria are responsible for much of the dissolved methane in the ocean surface. They extract phosphate from methylphosphonic acid.[9]

"Pelagibacteraceae" appear to be basal to the other three families in the order Rickettsiales.[10] The family derives its name from the type species Pelagibacter ubique. However, this species has not yet been validly published and, therefore, neither the familiar or the species has official taxonomic standing. Rickettsiales are currently defined by at least one shared feature: multiplying only inside host cells.[11] If the position of "Pelagibacteraceae" is correct, it might be possible to derive unique insight into the evolution from free-living to parasitic and symbiotic.[citation needed]

Subgroups

Currently the (unofficial) family is divided into five subgroups:[12]

  • Subgroup Ia, open ocean, crown group — includes Pelagibacter ubique HTCC1062
  • Subgroup Ib, open ocean, sister clade to Ia
  • Subgroup II, coastal, basal to Ia + Ib
  • Subgroup III, brackish, basal to I + II along with its sister clade IV
  • Subgroup IV, also known as LD12 clade, freshwater[13]
  • Subgroup V, which includes alphaproteobacterium HIMB59, basal to the remainder

Phylogenetic placement and Endosymbiotic theory

A 2011 study by researchers of the University of Hawaiʻi at Mānoa and the Oregon State University, indicate that SAR11 could be the ancestor of mitochondria in most eukaryotic cells.[1] However, the result can be tree reconstruction artefacts due to compositional bias.[14]

Schematic ribosomal RNA phylogeny of Alphaproteobacteria
  Magnetococcidae  

  Magnetococcus marinus

The cladogram of Rickettsidae has been inferred by Ferla et al. [15] from the comparison of 16S + 23S ribosomal RNA sequences.

References

  1. ^ a b J. Cameron Thrash, Alex Boyd, Megan J. Huggett, Jana Grote, Paul Carini, Ryan J. Yoder, Barbara Robbertse, Joseph W. Spatafora, Michael S. Rappé, Stephen J. Giovannoni (June 2011). "Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade" (PDF). Scientific Reports. 1: 13. doi:10.1038/srep00013. PMID 22355532.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ a b Morris RM, Rappé MS, Connon SA; et al. (2002). "SAR11 clade dominates ocean surface bacterioplankton communities". Nature. 420 (6917): 806–10. doi:10.1038/nature01240. PMID 12490947. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
  3. ^ Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (August 2002). "Cultivation of the ubiquitous SAR11 marine bacterioplankton clade". Nature. 418 (6898): 630–3. doi:10.1038/nature00917. PMID 12167859.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ H. James Tripp, Michael S. Schwalbach, Michelle M. Meyer, Joshua B. Kitner, Ronald R. Breaker, and Stephen J. Giovannoni (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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1126/science.1114057, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1126/science.1114057 instead.
  6. ^ H. James Tripp, Joshua B. Kitner, Michael S. Schwalbach, John W. H. Dacey, Larry J. Wilhelm, and Stephen J. Giovannoni (April 2008). "SAR11 marine bacteria require exogenous reduced sulfur for growth". Nature. 452 (7188): 741–4. doi:10.1038/nature06776. PMID 18337719.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 19889000, please use {{cite journal}} with |pmid=19889000 instead.
  8. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1038/nature04032, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1038/nature04032 instead.
  9. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1038/ncomms5346, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1038/ncomms5346 instead.
  10. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1038/srep00013, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1038/srep00013 instead.
  11. ^ Don J. Brenner, Noel R. Krieg, James T. Staley (July 26, 2005) [1984(Williams & Wilkins)]. George M. Garrity (ed.). The Proteobacteria. Bergey's Manual of Systematic Bacteriology. Vol. 2C (2nd ed.). New York: Springer. p. 1388. ISBN 978-0-387-24145-6. British Library no. GBA561951.{{cite book}}: CS1 maint: multiple names: authors list (link)
  12. ^ Robert M. Morris, K.L.V., Jang-Cheon Cho, Michael S. Rappé, Craig A. Carlson, Stephen J. Giovannoni, Temporal and Spatial Response of Bacterioplankton Lineages to Annual Convective Overturn at the Bermuda Atlantic Time-Series Study Site" Limnology and Oceanography 50(5) p. 1687-1696.
  13. ^ Salcher, M.M., J. Pernthaler, and T. Posch, Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria 'that rule the waves' (LD12). ISME J, 2011.
  14. ^ Rodríguez-Ezpeleta N, Embley TM. (2012). "The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria". PLoS One. 7 (1): e30520. doi:10.1371/journal.pone.0030520. PMID 22291975.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  15. ^ Ferla MP, Thrash JC, Giovannoni SJ, Patrick WM (2013). "New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability". PLOS ONE. 8 (12): e83383. Bibcode:2013PLoSO...883383F. doi:10.1371/journal.pone.0083383. PMC 3859672. PMID 24349502.
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