Pelagibacter ubique
Encyclopedia
Pelagibacter, with the single species P. ubique, was isolated in 2002 and given a specific name, although it has not yet been validly published according to 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 — possibly the most numerous bacteria in the world (perhaps 1028 individual cells) 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.
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. It recycles dissolved organic carbon. It undergoes regular seasonal cycles in abundance - in summer reaching ~50% of the cells in the temperate ocean. 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
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. 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.
(1,308,759 bp) of any free living organism. The only species with smaller genomes are endocellular symbionts and parasites, such as Mycoplasma genitalium
or Nanoarchaeum equitans
Non-coding RNA
s have been identified in P. ubique through a bioinformatics
screen of the published genome and metagenomic data. Examples of ncRNA found in this organisms include the SAM-V riboswitch
, and other cis-regulatory elements like the rpsB motif.
(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 an Greek-like irregular nominative plural pelagē and not pelagi). The name of the specific epithet (ubique) is a Latin adverb meaning "everywhere"; it should be noted 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.
The term "Candidatus" 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 "Cadidatus Pelagibacter ubique" is not in ATCC http://www.atcc.org/ and DSMZ http://www.dsmz.de/, 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,, which in turn is the type genus of the SAR11 clade or family "Pelagibacteraceae".
International Code of Nomenclature of Bacteria
The International Code of Nomenclature of Bacteria or Bacteriological Code governs the scientific names for bacteria, including Archaea. It denotes the rules for naming taxa of bacteria, according to their relative rank...
. It is an abundant member of the SAR11 clade
SAR11 clade
The SAR11 clade, or Pelagibacteraceae, defines a lineage of bacteria that is extremely common in the ocean. Bacteria in the SAR11 clade make up roughly one in three cells at the ocean's surface...
in the phylum Alphaproteobacteria
Alphaproteobacteria
Alphaproteobacteria is a class of Proteobacteria. Like all Proteobacteria, they are Gram-negative.-Characteristics:The Alphaproteobacteria comprise most phototrophic genera, but also several genera metabolising C1-compounds , symbionts of plants and animals, and a group of pathogens, the...
. SAR11 members are highly dominant organisms found in both salt and fresh water worldwide — possibly the most numerous bacteria in the world (perhaps 1028 individual cells) and were originally known only from their rRNA genes, which were first identified in environmental samples from the Sargasso Sea
Sargasso Sea
The Sargasso Sea is a region in the middle of the North Atlantic Ocean, surrounded by ocean currents. It is bounded on the west by the Gulf Stream; on the north, by the North Atlantic Current; on the east, by the Canary Current; and on the south, by the North Atlantic Equatorial Current. This...
in 1990 by Stephen Giovannoni's laboratory in the Department of Microbiology at Oregon State University
Oregon State University
Oregon State University is a coeducational, public research university located in Corvallis, Oregon, United States. The university offers undergraduate, graduate and doctoral degrees and a multitude of research opportunities. There are more than 200 academic degree programs offered through the...
and later found in oceans worldwide.
It is rod or crescent shaped and one of the smallest self-replicating cells known, with a length of 0.37-0.89 µm
Micrometre
A micrometer , is by definition 1×10-6 of a meter .In plain English, it means one-millionth of a meter . Its unit symbol in the International System of Units is μm...
and a diameter of only 0.12-0.20 µm. It recycles dissolved organic carbon. It undergoes regular seasonal cycles in abundance - in summer reaching ~50% of the cells in the temperate ocean. Thus it plays a major role in the Earth's carbon cycle
Carbon cycle
The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth...
.
Its discovery was the subject of "Oceans of Microbes", Episode 5 of "Intimate Strangers: Unseen Life on Earth" by PBS
Cultivation
Several strains of Pelagibacter ubique 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
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
, phosphate
Phosphate
A phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
, and iron
Iron
Iron is a chemical element with the symbol Fe and atomic number 26. It is a metal in the first transition series. It is the most common element forming the planet Earth as a whole, forming much of Earth's outer and inner core. It is the fourth most common element in the Earth's crust...
limitation, and a very unusual requirement for reduced sulfur
Sulfur
Sulfur or sulphur is the chemical element with atomic number 16. In the periodic table it is represented by the symbol S. It is an abundant, multivalent non-metal. Under normal conditions, sulfur atoms form cyclic octatomic molecules with chemical formula S8. Elemental sulfur is a bright yellow...
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.
Genome
The genome of P. ubique strain HTCC1062 was completely sequenced in 2005 showing that P. ubique has the smallest genomeGenome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
(1,308,759 bp) of any free living organism. The only species with smaller genomes are endocellular symbionts and parasites, such as Mycoplasma genitalium
Mycoplasma genitalium
Mycoplasma genitalium is a small parasitic bacterium that lives on the ciliated epithelial cells of the primate genital and respiratory tracts. M. genitalium is the smallest known genome that can constitute a cell, and the second-smallest bacterium after the recently-discovered endosymbiont...
or Nanoarchaeum equitans
Non-coding RNA
Non-coding RNA
A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
s have been identified in P. ubique through a bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
screen of the published genome and metagenomic data. Examples of ncRNA found in this organisms include the SAM-V riboswitch
SAM-V riboswitch
SAM-V riboswitch is the fifth known riboswitch to bind S-adenosyl methionine . It was first discovered in the marine organism 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...
, and other cis-regulatory elements like the rpsB motif.
Name
The name of the genus (Pelagibacter) stems from the Latin masculin noun pelagus ("sea") combined with the suffix -bacter-bacter
-Meaning:Bacter is a Neolatin 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 original πέλαγος (pelagos) (the word pelagus is a Greek word used in Latin poetry, it is a 2nd declension noun with an Greek-like irregular nominative plural pelagē and not pelagi). The name of the specific epithet (ubique) is a Latin adverb meaning "everywhere"; it should be noted 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.
The term "Candidatus" 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
Fatty acid methyl ester
A fatty acid methyl ester can be created by an alkali catalyzed reaction between fats or fatty acids and methanol. The molecules in biodiesel are primarily FAMEs, usually obtained from vegetable oils by transesterification....
whereas "Cadidatus Pelagibacter ubique" is not in ATCC http://www.atcc.org/ and DSMZ http://www.dsmz.de/, 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,, which in turn is the type genus of the SAR11 clade or family "Pelagibacteraceae".