"''Candidatus'' Pelagibacter", with the single species "''Ca.'' P. communis", was isolated in 2002 and given a specific name, although it has not yet been described as required by the

bacteriological code The International Code of Nomenclature of Prokaryotes (ICNP) formerly the International Code of Nomenclature of Bacteria (ICNB) or Bacteriological Code (BC) governs the scientific names for Bacteria and Archaea.P. H. A. Sneath, 2003. A short histor ...

. It is an abundant member of the

SAR11 clade 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 q ...

in the phylum ''

Alphaproteobacteria Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (formerly Proteobacteria). The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria. The Alphaproteobacteria are highly diverse and p ...

''. SAR11 members are highly dominant organisms found in both salt and fresh water worldwide and were originally known only from their

rRNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosoma ...

genes, first identified in the

Sargasso Sea The Sargasso Sea () is a region of the Atlantic Ocean bounded by four currents forming an ocean gyre. Unlike all other regions called seas, it has no land boundaries. It is distinguished from other parts of the Atlantic Ocean by its charac ...

in 1990 by

Stephen Giovannoni Stephen Joseph Giovannoni is an American microbiologist whose research mainly focuses on marine microbes. He is a fellow of the American Academy of Microbiology and a founding co-editor of the ''Annual Review of Marine Science''. Early life and ...

's laboratory at

Oregon State University Oregon State University (OSU) is a public land-grant, research university in Corvallis, Oregon. OSU offers more than 200 undergraduate-degree programs along with a variety of graduate and doctoral degrees. It has the 10th largest engineering co ...

and later found in oceans worldwide. "''Ca.'' P. communis" and its relatives may be the most abundant organisms in the ocean, and quite possibly the most abundant

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

in the entire world. It can make up about 25% of all microbial

plankton Plankton are the diverse collection of organisms found in Hydrosphere, water (or atmosphere, air) that are unable to propel themselves against a Ocean current, current (or wind). The individual organisms constituting plankton are called plankt ...

cells, and in the summer they may account for approximately half the cells present in temperate ocean surface water. The total abundance of "''Ca.'' P. communis" and relatives is estimated to be about 2 × 10²⁸ microbes. 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 In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...

takes up about 30% of the cell's volume. It is

gram negative The gram (originally gramme; SI unit symbol g) is a unit of mass in the International System of Units (SI) equal to one one thousandth of a kilogram. Originally defined as of 1795 as "the absolute weight of a volume of pure water equal to th ...

., Gauthier, Nicholas; Zinman, Guy; D’Antonio, Matteo; Abraham, Michael. Comparative Microbial Genomics DTU course. 2005. It recycles

dissolved organic carbon Dissolved organic carbon (DOC) is the fraction of organic carbon operationally defined as that which can pass through a filter with a pore size typically between 0.22 and 0.7 micrometers. The fraction remaining on the filter is called particu ...

. 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 The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and Earth's atmosphere, atmosphere of the Earth. Carbon is the main component of biological compounds as well as ...

. Its discovery was the subject of "Oceans of Microbes", Episode 5 of "Intimate Strangers: Unseen Life on Earth" by

PBS The Public Broadcasting Service (PBS) is an American public broadcasting, public broadcaster and Non-commercial activity, non-commercial, Terrestrial television, free-to-air television network based in Arlington, Virginia. PBS is a publicly fu ...

Cultivation

Several strains of "''Candidatus'' Pelagibacter communis" have been cultured thanks to improved isolation techniques. The most studied strain is HTCC1062 (high-throughput cultivation collection). The factors that regulate SAR11 populations are still largely unknown. They have sensors for

nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...

phosphate In chemistry, a phosphate is an anion, salt, functional group or ester derived from a phosphoric acid. It most commonly means orthophosphate, a derivative of orthophosphoric acid . The phosphate or orthophosphate ion is derived from phospho ...

, and

iron Iron () is a chemical element with symbol Fe (from la, ferrum) and atomic number 26. It is a metal that belongs to the first transition series and group 8 of the periodic table. It is, by mass, the most common element on Earth, right in f ...

limitation, and a very unusual requirement for reduced

sulfur Sulfur (or sulphur in British English) is a chemical element with the symbol S and atomic number 16. It is abundant, multivalent and nonmetallic. Under normal conditions, sulfur atoms form cyclic octatomic molecules with a chemical formula ...

compounds. 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. A population of "''Ca.'' P. communis" cells can double every 29 hours, which is fairly slow, but they can replicate under low nutrient conditions. "''Ca.'' P. communis" can be grown on a defined, artificial medium with additions of reduced sulfur, glycine, pyruvate and vitamins.

Genome

The genome of "''Ca.'' P. communis" strain HTCC1062 was completely sequenced in 2005 showing that "''Ca.'' P. communis" has the smallest

(1,308,759 bp) of any free-living organism encoding only 1,354 open reading frames (1,389 genes total). The only species with smaller genomes are intracellular symbionts and parasites, such as ''

Mycoplasma genitalium ''Mycoplasma genitalium'' (''MG'', commonly known as Mgen) is a sexually transmitted, small and pathogenic bacterium that lives on the mucous epithelial cells of the urinary and genital tracts in humans. Medical reports published in 2007 and 201 ...

'' or ''

Nanoarchaeum equitans ''Nanoarchaeum equitans'' is a species of marine archaea that was discovered in 2002 in a hydrothermal vent off the coast of Iceland on the Kolbeinsey Ridge by Karl Stetter. It has been proposed as the first species in a new phylum. Strains of th ...

'' 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 In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reac ...

for all 20

amino acids Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...

and most co-factors. Its genome has been

streamlined Streamlines, streaklines and pathlines are field lines in a fluid flow. They differ only when the flow changes with time, that is, when the flow is not steady. Considering a velocity vector field in three-dimensional space in the framework of ...

. This streamlining concept is important because it reduces the amount of energy required for cell replication. "''Ca.'' P. communis" saves energy by using the

base pairs A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...

A and T (≈70.3% of all base pairs) because they contain less

, a resource that is hard for organisms to acquire.

Non-coding RNA A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-c ...

s have been identified in "''Ca.'' P. communis" through a

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

screen of the published genome and metagenomic data. Examples of ncRNA found in these organisms include the

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 consen ...

, and other cis-regulatory elements like the ''rpsB'' motif. Another example of an important ncRNA in "''Ca.'' P. communis" 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. It is found to have proteorhodopsin

genes In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

, which help power light-mediated

proton pumps A proton pump is an integral membrane protein pump that builds up a proton gradient across a biological membrane. Proton pumps catalyze the following reaction: : n one side of a biological membrane/sub> + energy n the other side of the membr ...

. Subtle differences arise in the expression of its

codon The genetic code is the set of rules used by living cells to translate information encoded within genetic material ( DNA or RNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links ...

sequences when it is subjected to either light or dark treatments. More genes for

oxidative phosphorylation Oxidative phosphorylation (UK , US ) or electron transport-linked phosphorylation or terminal oxidation is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine tri ...

are expressed when it is subjected to darkness.

Name

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

pelagus Pelagus is a state constituency in Sarawak, Malaysia, that has been represented in the Sarawak State Legislative Assembly The Sarawak State Legislative Assembly is the legislative chamber of the unicameral legislature of the Malaysian state o ...

'' ("sea") combined with the suffix

-bacter The suffix -bacter is in microbiology for many genera and is intended to mean "bacteria". Meaning Bacter is a new Latin (i.e. Modern Latin) term coined from bacterium, which in turn derives from the Greek βακτήριον, meaning small staff ( ...

(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 Greek may refer to: Greece Anything of, from, or related to Greece, a country in Southern Europe: *Greeks, an ethnic group. *Greek language, a branch of the Indo-European language family. **Proto-Greek language, the assumed last common ancestor ...

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'', the Greek word being a 3rd declension neuter in -ος (pl. -η) unrelated with 2nd declension latin words in ''-us''). 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 t
rule 12c
of the IBCN. The term "''

Candidatus In prokaryote nomenclature, ''Candidatus'' (Latin for candidate of Roman office) is used to name prokaryotic phyla that are well characterized but yet-uncultured. Contemporary sequencing approaches, such as 16S sequencing or metagenomics, provide m ...

''" is used for proposed species for which the lack of information (''cf''. ) prevents it from being a validated species according to the bacteriological code, such as deposition in two public cell repositories or lack of FAME analysis whereas "''Candidatus'' Pelagibacter communis" is not in ATC

and DSM

nor has analysis of

lipids Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include ...

and

quinones The quinones are a class of organic compounds that are formally "derived from aromatic compounds uch as benzene or naphthalene">benzene.html" ;"title="uch as benzene">uch as benzene or naphthalene] by conversion of an even number of –CH= group ...

been conducted. HTTC1062 is the type strain of the species "''Ca.'' P. communis", which in turn is the type species of the genus "''Candidatus'' Pelagibacter", which in turn is the type genus of the SAR11 clade or family "''Pelagibacteraceae''".

Bacteriophage

It was reported in '' Nature (journal), Nature'' in February 2013 that the

bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacteri ...

HTVC010P 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 (journal), Nature'' says that "it probably really is the commonest organism ...

, which attacks "''Ca.'' P. communis", has been discovered and "it probably really is the commonest organism on the planet".

References

External links