Candidatus Pelagibacter ubique

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" Candidatus Pelagibacter ubique"
Systematics
Domain : Bacteria (bacteria)
Department : Proteobacteria
Class : Alphaproteobacteria
without rank: " Candidatus Pelagibacter"
without rank: " Candidatus Pelagibacter ubique"
Scientific name
" Candidatus Pelagibacter ubique"
Rappé et al. 2002

" Candidatus Pelagibacter ubique" is probably the most common type of bacteria . It was originally called SAR11 and was only known for its ribosomal RNA , which was first identified in 1990 samples from the Sargasso Sea . The bacteria responsible for this were isolated in 2002 and named Pelagibacter ubique . However, this did not take place according to the rules of the bacteriological code (ICBN), so that Pelagibacter ubique is not a valid published name and the bacterium is therefore known as " Candidatus Pelagibacter ubique" Rappé et al. 2002 is to be designated.

" Candidatus Pelagibacter ubique" occurs all over the world and lives as part of the plankton , ie freely swimming in the oceans. They are among the smallest cells capable of reproduction with a diameter of only 0.12 to 0.20 µm .

With only 1,354 genes , these bacteria have a relatively small genome . It contains fewer paralogues than any other free-living cell studied, no viral genes, and very little non-coding DNA . “ Candidatus Pelagibacter ubique” is therefore a very efficient form of life, which also confirms its massive occurrence.

General information about the bacteria

They are very small marine α – protebacteria, they are found in all oceans and make up about 25% of all cells there. It is the first cultivated member of the tiny α – protebacteria. It has the smallest genome of all known reproductive cells and has biosynthetic functions for all 20 amino acids . " Candidatus Pelagibacter ubique" grows through carbon compounds dissolved in the water and draws its energy from a light-controlled proteo rhodopsin pump and from cellular respiration. When examining the genome of " Candidatus Pelagibacter ubique" it was found that it contains genes that can accept DNA, and it is therefore assumed that the bacterium can take up foreign DNA . These studies also found that the proportion of guanine and cytosine in the genome is around 29.7%. Since most of the transporters in " Candidatus Pelagibacter ubique" have a very high substrate affinity, less energy is consumed in the form of ATP , which also explains the viability of large populations in nutrient-poor media.

Systematics

It is increasingly being questioned that " Candidatus Pelagibacter ubique" is actually a free living relative of the obligate parasitic rickettsiae . Rather, the degree of relationship statistically calculated according to the principle of maximum parsimony is likely to be based on an artifact called compositional bias . These results suggest an order Pelagibacterales as sister taxon to the Rickettsiales . Morris et al. (2005) and Gote et al. (2012) break them down into sub-groups as follows:

  • Subgroup Ia, open ocean, Crown Group ( English crown group ) - with " Candidatus Pelagibacter ubique" HTCC1062
  • Subgroup Ib, open ocean, sister class to Ia
  • Subgroup II, coast, basal to Ia + Ib
  • Subgroup III, brackish water, together with its sister class IV basal to I + II
  • Subgroup IV, also known as LD12 clade, fresh water
  • Subgroup V, with Alphaproteobacterium HIMB59, basal to the rest

Representation of these relationships in a cladogram of the Pelagibacterales:





Subgroup Ia (proposed as Pelagibacteraceae, with "Pelagibacter")


   

Subgroup Ib



   

Subgroup II



   


Subgroup IIIa


   

Subgroup IIIb



   

Subgroup IV (named Klade LD12, with SAR11 bacteria)




   

Subgroup V (with α-proteobacterium HIMB59)


cultivation

During the cultivation of " Candidatus Pelagibacter ubique", natural microbial communities were diluted and isolated in very low-dose nutrient media. The nutrient medium consisted of sterile coastal water from Oregon , which was supplemented with phosphate (KH 2 PO 4 ), ammonium (NH 4 Cl) and a mixture of defined carbon compounds. When isolating the cells, the fact that the substrate concentration in natural seawater is about a third of that in laboratory media was taken advantage of. After the isolation, the arrays of the “ Candidatus Pelagibacter ubique” cultures were marked using FISH (fluorescence in situ hybridization) in order to improve their visibility under the microscope .

After incubation at 15 ° C. for 23 days in the dark or in a 14 h / 10 h light-dark cycle, small volumes of the cultures were applied to a polycarbonate membrane. The intergenic nucleotide sequences of the isolated cultures were then examined and it was found that there are three genetically different groups, each of which only differs by a few nucleotides or by an insertion or deletion. Since in two of the three groups (the third contains only one culture) the incubation took place both in the light-dark cycle and only in the dark, it was possible to rule out any influence of light.

The maximum cell density varies between 2.5 * 10 5 cells per ml and 3.5 * 10 6 cells per ml, which depends on where and when the samples were taken, but is independent of the carbon composition. Based on these results, it is believed that natural factors control the population of Candidatus Pelagibacter ubique. This is of great importance for oceanographic research, because it allows the conclusion that one could identify chemical factors in the water by studying the growth of " Candidatus Pelagibacter ubique". A BLAST search for paralog gene families revealed that " Candidatus Pelagibacter ubique" must have arisen from a duplication event.

literature

  • NA Logan, HM Lappin-Scott, PCF Oyston (Eds.): Prokaryotic Diversity: Mechanisms and Significance . Cambridge University Press, Cambridge and New York 2006, ISBN 0-521-86935-8 .
  • Stephen J. Giovannoni et al. a .: "Genome Streamlining in a Cosmopolitan Oceanic Bacterium". In: Science , August 19, 2005, pp. 1242-1245.
  • Steven Ashley: "Lean Gene Machine". In: Scientific American , December 2005, pp. 26-28.
  • Michael S. Rappé et al. a. : "Cultivation of the ubiquitous SAR11 marine bacterioplancton clade", "Nature" edition August 2002, pp. 630-633.

Web links

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  1. ^ Jean Euzéby, Aidan C. Parte: Some names included in the Candidatus category (Taxonomic category not covered by the Rules of the Bacteriological Code). In: List of Prokaryotic names with Standing in Nomenclature, Systematics of Bacteria (LPSN) . Retrieved December 16, 2019 .
  2. ^ Taxonomy Browser Candidatus Pelagibacter. In: National Center for Biotechnology Information (NCBI) website . Retrieved December 16, 2019 .
  3. ↑ Naiara Rodríguez-Ezpeleta, T Martin Embley: The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria . In: PLoS One . 7, No. 1, 2012, p. 22291975. doi : 10.1128 / JB.00934-06 . PMC 3264578 (free full text). Abstract: Although free living, members of the successful SAR11 group of marine alpha-proteobacteria contain a very small and A + T rich genome, two features that are typical of mitochondria and related obligate intracellular parasites such as the Rickettsiales. Previous phylogenetic analyzes have suggested that Candidatus Pelagibacter ubique, the first cultured member of this group, is related to the Rickettsiales + mitochondria clade whereas others disagree with this conclusion. In order to determine the evolutionary position of the SAR11 group and its relationship to the origin of mitochondria, we have performed phylogenetic analyzes on the concatenation of 24 proteins from 5 mitochondria and 71 proteobacteria. Our results support that SAR11 group is not the sister group of the Rickettsiales + mitochondria clade and confirm that the position of this group in the alpha-proteobacterial tree is strongly affected by tree reconstruction artefacts due to compositional bias. As a consequence, genome reduction and bias toward a high A + T content may have evolved independently in the SAR11 species, which points to a different direction in the quest for the closest relatives to mitochondria and Rickettsiales. In addition, our analyzes raise doubts about the monophyly of the newly proposed Pelagibacteraceae family.
  4. Jump up ↑ Robert M. Morris, Kevin L. Vergin, 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 , in: ASLO Limnology and Oceanography 50 (5) of November 18, 2005, pp. 1687-1696, doi: 10.4319 / lo.2005.50.5.1687
  5. ↑ Grote J, Thrash JC, Huggett MJ, Landry ZC, Carini P, Giovannoni SJ, Rappé MS: Streamlining and core genome conservation among highly divergent members of the SAR11 clade. . In: mBio . 3, No. 5, 2012, p. E00252-12. doi : 10.1128 / mBio.00252-12 . PMID 22991429 . PMC 3448164 (free full text).
  6. ↑ MM Salcher, J. Pernthaler, T. Posch: Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria 'that rule the waves' (LD12) , in: ISME J, 2011, doi: 10.1038 / ismej.2011.8 . PMID 21412347 .
  7. ↑ Hyun-Myung Oh, Kae Kyoung Kwon, Ilnam Kang, Sung Gyun Kang, Jung-Hyun Lee, Sang-Jin Kim, Jang-Cheon Cho: Complete Genome Sequence of “ Candidatus Puniceispirillum marinum” IMCC1322, a Representative of the SAR116 clade in the Alphaproteobacteria , in: Journal of Bacteriology, May 26, 2010, doi: 10.1128 / JB.00347-10 , PMID 20382761
  8. ↑ Ilnam Kang, Hyun-Myung Oh, Dongmin Kang, Jang-Cheon Cho: Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans , in: PNAS 110 (30), July 23, 2013, p. 12343– 12348, doi: 10.1073 / pnas.1219930110