Pelagibacter ubique

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Pelagibacter ubique
Pelagibacter.jpg
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

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]

Contents

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

The name of the genus (Pelagibacter) stems from the Latin neuter noun (but with masculine ending) 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]

See also

Related Research Articles

Riboswitch

In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules.

Planctomycetes Phylum of aquatic bacteria

Planctomycetes are a phylum of aquatic bacteria and are found in samples of brackish, and marine and fresh water. They reproduce by budding. In structure, the organisms of this group are ovoid and have a holdfast, at the tip of a thin cylindrical extension from the cell body called the stalk, at the nonreproductive end that helps them to attach to each other during budding.

Rickettsiales Order of bacteria

The Rickettsiales, informally called rickettsias, are an order of small Alphaproteobacteria. Some are notable pathogens, including Rickettsia, which causes a variety of diseases in humans, and Ehrlichia, which causes diseases in livestock. Another genus of well-known Rickettsiales is the Wolbachia, which infect about two-thirds of all arthropods and nearly all filarial nematodes. Genetic studies support the endosymbiotic theory according to which mitochondria and related organelles developed from members of this group.

Last universal common ancestor Last recent common ancestor of all current life

The last universal common ancestor or last universal cellular ancestor (LUCA), also called the last universal ancestor (LUA), is the most recent population of organisms from which all organisms now living on Earth have a common descent—the most recent common ancestor of all current life on Earth. A related concept is that of progenote. LUCA is not thought to be the first life on Earth, but rather the only type of organism of its time to still have living descendants.

Alphaproteobacteria Class of bacteria

Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria. Its members are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like all Proteobacteria, its members are gram-negative and some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.

Cobalamin riboswitch

Cobalamin riboswitch is a cis-regulatory element which is widely distributed in 5' untranslated regions of vitamin B12 (Cobalamin) related genes in bacteria. Riboswitches are metabolite binding domains within certain messenger RNAs (mRNAs) that serve as precision sensors for their corresponding targets. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results in modulation of gene expression or translation of mRNA to yield a protein. Cobalamin in the form of adenosylcobalamin (Ado-CBL) is known to repress expression of proteins for vitamin B12 biosynthesis via a post-transcriptional regulatory mechanism that involves direct binding of Ado-CBL to 5' UTRs in relevant genes, preventing ribosome binding and translation of those genes. Before proof of riboswitch function, a conserved sequence motif called the B12 box was identified that corresponds to a part of the cobalamin riboswitch, and a more complete conserved structure was identified. Variants of the riboswitch consensus have been identified.

SAM-II riboswitch

The SAM-II riboswitch is a RNA element found predominantly in alpha-proteobacteria that binds S-adenosyl methionine (SAM). Its structure and sequence appear to be unrelated to the SAM riboswitch found in Gram-positive bacteria. This SAM riboswitch is located upstream of the metA and metC genes in Agrobacterium tumefaciens, and other methionine and SAM biosynthesis genes in other alpha-proteobacteria. Like the other SAM riboswitch, it probably functions to turn off expression of these genes in response to elevated SAM levels. A significant variant of SAM-II riboswitches was found in Pelagibacter ubique and related marine bacteria and called SAM-V. Also, like many structured RNAs, SAM-II riboswitches can tolerate long loops between their stems.

Archaeal Richmond Mine acidophilic nanoorganisms

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Mycoplasma laboratorium or Synthia refers to a synthetic strain of bacterium. The project to build the new bacterium has evolved since its inception. Initially the goal was to identify a minimal set of genes that are required to sustain life from the genome of Mycoplasma genitalium, and rebuild these genes synthetically to create a "new" organism. Mycoplasma genitalium was originally chosen as the basis for this project because at the time it had the smallest number of genes of all organisms analyzed. Later, the focus switched to Mycoplasma mycoides and took a more trial-and-error approach.

Archaea Domain of single-celled organisms

Archaea constitute a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this classification is obsolete.

A wide variety of non-coding RNAs have been identified in various species of organisms known to science. However, RNAs have also been identified in "metagenomics" sequences derived from samples of DNA or RNA extracted from the environment, which contain unknown species. Initial work in this area detected homologs of known bacterial RNAs in such metagenome samples. Many of these RNA sequences were distinct from sequences within cultivated bacteria, and provide the potential for additional information on the RNA classes to which they belong.

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

CrcB RNA motif

The crcB RNA motif is a conserved RNA structure identified by bioinformatics in a wide variety of bacteria and archaea. These RNAs were later shown to function as riboswitches that sense fluoride ions. These "fluoride riboswitches" increase expression of downstream genes when fluoride levels are elevated, and the genes are proposed to help mitigate the toxic effects of very high levels of fluoride.

GlnA RNA motif

The glutamine riboswitch is a conserved RNA structure that was predicted by bioinformatics. It is present in a variety of lineages of cyanobacteria, as well as some phages that infect cyanobacteria. It is also found in DNA extracted from uncultivated bacteria living in the ocean that are presumably species of cyanobacteria.

SAM-V riboswitch

SAM-V riboswitch is the fifth known riboswitch to bind S-adenosyl methionine (SAM). It was first discovered in the marine bacterium Candidatus Pelagibacter ubique and can also be found in marine metagenomes. SAM-V features a similar consensus sequence and secondary structure as the binding site of SAM-II riboswitch, but bioinformatics scans cluster the two aptamers independently. These similar binding pockets suggest that the two riboswitches have undergone convergent evolution.

Marine microorganisms Any life form too small for the naked human eye to see that lives in a marine environment

Marine microorganisms are defined by their habitat as microorganisms living in a marine environment, that is, in the saltwater of a sea or ocean or the brackish water of a coastal estuary. A microorganism is any microscopic living organism or virus, that is too small to see with the unaided human eye without magnification. Microorganisms are very diverse. They can be single-celled or multicellular and include bacteria, archaea, viruses and most protozoa, as well as some fungi, algae, and animals, such as rotifers and copepods. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists also classify biologically active entities such as viruses and viroids as microorganisms, but others consider these as non-living.

"Candidatus Scalindua" is a bacterial genus, and a proposed member of the order Planctomycetes. These bacteria lack peptidoglycan in their cell wall and have a compartmentalized cytoplasm. They are ammonium oxidizing bacteria found in marine environments.

HTVC010P is a virus which was discovered by Stephen Giovannoni and colleagues at Oregon State University. The Economist reports that a February 2013 paper in Nature says that "it probably really is the commonest organism on the planet". It is a bacteriophage that infects the extremely abundant bacteria Pelagibacter ubique in the Pelagibacterales order.

Genomic streamlining is a theory in evolutionary biology and microbial ecology that suggests that there is a reproductive benefit to prokaryotes having a smaller genome size with less non-coding DNA and fewer non-essential genes. There is a lot of variation in prokaryotic genome size, with the smallest free-living cell's genome being roughly ten times smaller than the largest prokaryote. Two of the bacterial taxa with the smallest genomes are Prochlorococcus and Pelagibacter ubique, both highly abundant marine bacteria commonly found in oligotrophic regions. Similar reduced genomes have been found in uncultured marine bacteria, suggesting that genomic streamlining is a common feature of bacterioplankton. This theory is typically used with reference to free-living organisms in oligotrophic environments.

Marine prokaryotes Marine bacteria and marine archaea

Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular life forms can be divided into prokaryotes and eukaryotes. Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, whereas prokaryotes are the organisms that do not have a nucleus enclosed within a membrane. The three-domain system of classifying life adds another division: the prokaryotes are divided into two domains of life, the microscopic bacteria and the microscopic archaea, while everything else, the eukaryotes, become the third domain.

References

  1. 1 2 3 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. S2CID   4352877.
  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. S2CID   4360530.
  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. 1 2 3 4 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. S2CID   16221415.
  6. 1 2 3 "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. S2CID   205212536.
  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. S2CID   4349881.
  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. S2CID   4348619.
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