"Candidatus Pelagibacter ubique" Rappé et al. 2002
"Candidatus Pelagibacter", with the single species "Ca. P. communis", was isolated in 2002 and given a specific name,[2] although it has not yet been described as required by the
bacteriological code.[3] 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 and later found in oceans worldwide.[4] "Ca. P. communis" 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 "Ca. P. communis" and relatives is estimated to be about 2 × 1028 microbes.[5]
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 Pelagibactergenome takes up about 30% of the cell's volume.[6] It is
gram negative.[7] 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.[8]
Cultivation
Several strains of "Candidatus Pelagibacter communis" have been cultured thanks to improved isolation techniques.[9] The most studied strain is HTCC1062 (high-throughput cultivation collection).[2]
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.[10] 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.[11]
A population of "Ca. P. communis" cells can double every 29 hours, which is fairly slow, but they can replicate under low nutrient conditions.[12]
"Ca. P. communis" can be grown on a defined, artificial medium with additions of reduced sulfur, glycine, pyruvate and vitamins.[13]
Genome
The genome of "Ca. P. communis" strain HTCC1062 was completely sequenced in 2005 showing that "Ca. P. communis" has the smallest
genome (1,308,759 bp) of any free-living organism[6] encoding only 1,354 open reading frames (1,389 genes total).[14] The only species with smaller genomes are symbionts and parasites, such as Mycoplasma genitalium or Nanoarchaeum equitans[6] 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.[6] Its genome has been
streamlined. This streamlining concept is important because it reduces the amount of energy required for cell replication.[7] "Ca. P. communis" 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.[7]
Non-coding RNAs have been identified in "Ca. P. communis" 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.[15][16] 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.[17]
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.[18]
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[19]). 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.[20]
The term "Candidatus" is used for proposed species for which the lack of information[21] prevents it from being a validated species according to the bacteriological code,[22][23] such as deposition in two public cell repositories or lack of
FAME analysis,[24][25] whereas "Candidatus Pelagibacter communis" is not in
ATCC and
DSMZ, nor has analysis of
lipids 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",[2] which in turn is the type genus of the SAR11 clade or family "Pelagibacteraceae".[26]
Bacteriophage
It was reported in Nature in February 2013 that the
bacteriophageHTVC010P, which attacks "Ca. P. communis", has been discovered and "it probably really is the commonest organism on the planet".[27][28]
^Judicial Commission of the International Committee on Systematic Bacteriology: Minutes of the meetings, 2 and 6 July 1994, Prague, Czech Republic". International Journal of Systematic and Evolutionary Microbiology 1995; 45, 195–196.
^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.
^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.
ISBN978-1-55581-039-9.
PMID21089234.
^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.
PMID23407494.
S2CID4348619.