"''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. 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 and were originally known only from their rRNA genes, first identified in the Sargasso Sea 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 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., Gauthier, Nicholas; Zinman, Guy; D'Antonio, Matteo; Abraham, Michael. Comparative Microbial Genomics DTU course. 2005. 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 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.

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'' or '' Nanoarchaeum equitans'' 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 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. 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 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 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 sequences when it is subjected to either light or dark treatments. More genes for oxidative phosphorylation 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 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''" 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, 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 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 Nature is an inherent character or constitution, particularly of the Ecosphere (planetary), ecosphere or the universe as a whole. In this general sense nature refers to the Scientific law, laws, elements and phenomenon, phenomena of the physic ...

'' 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