"''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) or Prokaryotic Code, 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 ...

. 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'' or ''α-proteobacteria'', also called ''α-Purple bacteria'' in earlier literature, is a class of bacteria in the phylum '' Pseudomonadota'' (formerly "Proteobacteria"). The '' Magnetococcales'' and '' Mariprofundales'' ar ...

''. 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 ribosomal ...

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 is the only one without land boundaries. It is distinguished from other parts of the Atlantic Oc ...

in 1990 by Stephen Giovannoni's laboratory at

Oregon State University Oregon State University (OSU) is a Public university, public Land-grant university, land-grant research university in Corvallis, Oregon, United States. OSU offers more than 200 undergraduate degree programs and a variety of graduate and doctor ...

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 (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

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

plankton Plankton are the diverse collection of organisms that drift in Hydrosphere, water (or atmosphere, air) but are unable to actively propel themselves against ocean current, currents (or wind). The individual organisms constituting plankton are ca ...

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 The micrometre (Commonwealth English as used by the International Bureau of Weights and Measures; SI symbol: μm) or micrometer (American English), also commonly known by the non-SI term micron, is a unit of length in the International System ...

and a diameter of only 0.12–0.20 μm. The ''Pelagibacter''

genome 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 genes, other functional regions of the genome such as ...

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

gram negative Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists of ...

., 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 Operational definition, operationally defined as that which can pass through a filter with a pore size typically between 0.22 and 0.7 micrometre, micrometers. The fraction remain ...

. 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 a part of the biogeochemical cycle where carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of Earth. Other major biogeochemical cycles include the nitrogen cycle and the water cycl ...

. 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 broadcaster and non-commercial, free-to-air television network based in Arlington, Virginia. PBS is a publicly funded nonprofit organization and the most prominent provider of educat ...

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 a chemical element; it has Symbol (chemistry), symbol N and atomic number 7. Nitrogen is a Nonmetal (chemistry), nonmetal and the lightest member of pnictogen, group 15 of the periodic table, often called the Pnictogen, pnictogens. ...

phosphate Phosphates are the naturally occurring form of the element phosphorus. 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 orthop ...

, and

iron Iron is a chemical element; it has symbol Fe () 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, forming much of Earth's o ...

limitation, and a very unusual requirement for reduced

sulfur Sulfur ( American spelling and the preferred IUPAC name) or sulphur ( Commonwealth spelling) is a chemical element; it has symbol S and atomic number 16. It is abundant, multivalent and nonmetallic. Under normal conditions, sulfur atoms ...

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 symbionts and parasites, such as ''

Mycoplasma genitalium ''Mycoplasma genitalium'' (also known as ''MG','' Mgen, or since 2018, ''Mycoplasmoides genitalium'') is a sexually transmitted, small and pathogenic bacterium that lives on the mucous epithelial cells of the urinary and genital tracts in ...

'' 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, and is 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 ...

for all 20

amino acids Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the Proteinogenic amino acid, 22 α-amino acids incorporated into p ...

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 flow, steady. Considering a velocity vector field in three-dimensional space in the f ...

. 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 Translation (genetics), 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 imp ...

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

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

screen of the published genome and metagenomic data. Examples of ncRNA found in these organisms include the SAM-V riboswitch, and other

cis-regulatory ''Cis''-regulatory elements (CREs) or ''cis''-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morphoge ...

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 has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

, which help power light-mediated proton pumps. Subtle differences arise in the expression of its

codon Genetic code is a 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 prote ...

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 Cell (biology), cells use enzymes to Redox, oxidize nutrients, thereby releasing chemical energy in order ...

are expressed when it is subjected to darkness.

Name

The name of the genus (''Pelagibacter'') stems from the Latin neuter noun '' 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 Greek may refer to: 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 of all kno ...

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'' (abbreviated ''Ca.''; Latin for "candidate of Roman office") is used to name prokaryotic taxa that are well characterized but yet- uncultured. Contemporary sequencing approaches, such as 16S ribosomal R ...

''" is used for proposed species for which the lack of information 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 ATCC and

DSMZ The Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH (German: ''Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH''), located in Braunschweig, is a research infrastructure in the ...

, nor has analysis of

lipids Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins Vitamin A, A, Vitamin D, D, Vitamin E, E and Vitamin K, K), monoglycerides, diglycerides, phospholipids, and others. The fu ...

and

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

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 virus that infects and replicates within bacteria. The term is derived . Bacteriophages are composed of proteins that Capsid, encapsulate a DNA or RNA genome, and may have structu ...

HTVC010P, which attacks "''Ca.'' P. communis", has been discovered and "it probably really is the commonest organism on the planet".

References

External links