Pelagibacterales

The Pelagibacterales are an order in the Alphaproteobacteria composed of free-living bacteria that make up roughly one in three cells at the ocean's surface.[1][2][3] Overall, members of the Pelagibacterales are estimated to make up between a quarter and a half of all prokaryotic cells in the ocean.

Pelagibacteraceles
Scientific classification
Domain:
Bacteria
Phylum:
Proteobacteria
Class:
Alphaproteobacteria
Subclass:
Rickettsidae
Order:
Pelagibacterales

Initially, this taxon was known solely by metagenomic data and was known as the SAR11 clade. It was first placed in the Rickettsiales, but was later raised to the rank of order, and then placed as sister order to the Rickettsiales in the subclass Rickettsidae.[3]

It includes the highly abundant marine species Pelagibacter ubique. Bacteria in this clade are unusually small.[4] Due to their small genome size and limited metabolic function, Pelagibacterales have become a model organism for 'streamlining theory'.[5]

P. 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,[6] and some cofactors.[7] They also have an unusual and unexpected requirement for reduced sulfur.[8]

P. ubique and members of the oceanic subgroup I possess gluconeogenesis, but not a typical glycolysis pathway, whereas other subgroups are capable of typical glycolysis.[9]

Unlike Acaryochloris marina, it is not photosynthetic – specifically, it does not use light to increase the bond energy of an electron pair, but it does possess proteorhodopsin (incl. retinol biosynthesis) for ATP production from light.[10]

SAR11 bacteria are responsible for much of the dissolved methane in the ocean surface. They extract phosphate from methylphosphonic acid.[11]

The taxon derives its name from the type species Pelagibacter ubique(status Candidatus species). However, this species has not yet been validly published, and therefore neither the order name nor the species name has official taxonomic standing.[12]

Subgroups

Currently, the (unofficial) order is divided into five subgroups:[13]

  • 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[14]
  • Subgroup V, which includes alphaproteobacterium HIMB59, basal to the remainder

The above results in a cladogram of the Pelagibacterales as follows:

 
 
 
 

Subgroup Ia (named Pelagibacteraceae, includes Pelagibacter)

 
 

Subgroup Ib

 
 
 

Subgroup II

 
 
 
 
 

Subgroup IIIa

 
 

Subgroup IIIb

 
 
 

Subgroup IV (named LD12 clade, includes SAR11 bacteria)

 
 
 
 

Subgroup V (includes α-proteobacterium HIMB59)

 

Phylogenetic placement and endosymbiotic theory

A 2011 study by researchers of the University of Hawaiʻi at Mānoa and Oregon State University, indicated that SAR11 could be the ancestor of mitochondria in most eukaryotic cells.[1] However, the result can be tree reconstruction artifacts due to compositional bias.[15]

Schematic ribosomal RNA phylogeny of Alphaproteobacteria
  Magnetococcidae  

  Magnetococcus marinus

 
 
  Caulobacteridae  
 

  Rhodospirillales, Sphingomonadales,
  Rhodobacteraceae, Rhizobiales, etc.

 
 

  Holosporales

 
 
  Rickettsidae  
  Pelagibacterales  
  Pelagibacteraceae  
 

  Pelagibacter

 
 
 

  Subgroups Ib, II, IIIa, IIIb, IV and V

 
 
 
 

  Proto-mitochondria

 
 
  Anaplasmataceae  
 
 
 

  Ehrlichia

 
 

  Anaplasma

 
 
 

  Wolbachia

 
 
 

  Neorickettsia

 
 
 
  Midichloriaceae  
 

  Midichloria

 
 
  Rickettsiaceae  
 

  Rickettsia

 
 

  Orientia

 
 
 
 
 
 
 
The cladogram of Rickettsidae has been inferred by Ferla et al. [3] from the comparison of 16S + 23S ribosomal RNA sequences.

References
  1. 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". Scientific Reports. 1: 13. Bibcode:2011NatSR...1E..13T. doi:10.1038/srep00013. PMC 3216501. PMID 22355532.
  2. Morris RM, Rappé MS, Connon SA, et al. (2002). "SAR11 clade dominates ocean surface bacterioplankton communities". Nature. 420 (6917): 806–10. Bibcode:2002Natur.420..806M. doi:10.1038/nature01240. PMID 12490947.
  3. 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. doi:10.1371/journal.pone.0083383. PMC 3859672. PMID 24349502.
  4. Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (August 2002). "Cultivation of the ubiquitous SAR11 marine bacterioplankton clade". Nature. 418 (6898): 630–3. Bibcode:2002Natur.418..630R. doi:10.1038/nature00917. PMID 12167859.
  5. Giovannoni, Stephen J. (2017-01-03). "SAR11 Bacteria: The Most Abundant Plankton in the Oceans". Annual Review of Marine Science. 9: 231–255. Bibcode:2017ARMS....9..231G. doi:10.1146/annurev-marine-010814-015934. ISSN 1941-0611. PMID 27687974.
  6. H. James Tripp; Michael S. Schwalbach; Michelle M. Meyer; Joshua B. Kitner; Ronald R. Breaker & 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.
  7. Giovannoni, S. J.; Tripp, H. J.; Givan, S.; Podar, M.; Vergin, K. L.; Baptista, D.; Bibbs, L.; Eads, J.; Richardson, T. H.; Noordewier, M.; Rappé, M. S.; Short, J. M.; Carrington, J. C.; Mathur, E. J. (2005). "Genome Streamlining in a Cosmopolitan Oceanic Bacterium". Science. 309 (5738): 1242–1245. Bibcode:2005Sci...309.1242G. doi:10.1126/science.1114057. PMID 16109880.
  8. H. James Tripp; Joshua B. Kitner; Michael S. Schwalbach; John W. H. Dacey; Larry J. Wilhelm & Stephen J. Giovannoni (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.
  9. Schwalbach, M. S.; Tripp, H. J.; Steindler, L.; Smith, D. P.; Giovannoni, S. J. (2010). "The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity". Environmental Microbiology. 12 (2): 490–500. doi:10.1111/j.1462-2920.2009.02092.x. PMID 19889000.
  10. Giovannoni, S. J.; Bibbs, L.; Cho, J. C.; Stapels, M. D.; Desiderio, R.; Vergin, K. L.; Rappé, M. S.; Laney, S.; Wilhelm, L. J.; Tripp, H. J.; Mathur, E. J.; Barofsky, D. F. (2005). "Proteorhodopsin in the ubiquitous marine bacterium SAR11". Nature. 438 (7064): 82–85. Bibcode:2005Natur.438...82G. doi:10.1038/nature04032. PMID 16267553.
  11. Carini, P.; White, A. E.; Campbell, E. O.; Giovannoni, S. J. (2014). "Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria". Nature Communications. 5: 4346. Bibcode:2014NatCo...5.4346C. doi:10.1038/ncomms5346. PMID 25000228.
  12. 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. 2C (2nd ed.). New York: Springer. pp. 1388. ISBN 978-0-387-24145-6. British Library no. GBA561951.
  13. 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.
  14. 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.
  15. 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. Bibcode:2012PLoSO...730520R. doi:10.1371/journal.pone.0030520. PMC 3264578. PMID 22291975.
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