Candidatus Pelagibacter communis

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"Candidatus Pelagibacter communis"
Pelagibacter.jpg
Scientific classification
( Candidatus )
Domain:
Bacteria
Phylum:
Pseudomonadota
Class:
Alphaproteobacteria
Subclass:
Rickettsidae
Order:
Pelagibacterales
Family:
"Pelagibacteraceae"
Genus:
"Candidatus Pelagibacter"

Rappé et al. 2002
Species:
"Ca. P. communis"
Binomial name
"Candidatus Pelagibacter communis"
corrig. Rappé et al. 2002
Synonyms [1]
  • "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 Pelagibacter genome 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 intracellular 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]

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 [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 bacteriophage HTVC010P, which attacks "Ca. P. communis", has been discovered and "it probably really is the commonest organism on the planet". [27] [28]

See also

Related Research Articles

<span class="mw-page-title-main">Riboswitch</span>

In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules.

<span class="mw-page-title-main">Chlamydiota</span> Phylum of bacteria

The Chlamydiota are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. Historically it was believed that all Chlamydiota had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins.

<span class="mw-page-title-main">Rickettsiales</span> Order of bacteria

The Rickettsiales, informally called rickettsias, are an order of small Alphaproteobacteria. They are obligate intracellular parasites, and some are notable pathogens, including Rickettsia, which causes a variety of diseases in humans, and Ehrlichia, which causes diseases in livestock. Another genus of well-known Rickettsiales is the Wolbachia, which infect about two-thirds of all arthropods and nearly all filarial nematodes. Genetic studies support the endosymbiotic theory according to which mitochondria and related organelles developed from members of this group.

<span class="mw-page-title-main">Alphaproteobacteria</span> Class of bacteria

Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota. The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria. The Alphaproteobacteria are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like all Proteobacteria, its members are gram-negative, although some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.

"Candidatus Midichloria" is a candidatus genus of Gram-negative, non-endospore-forming bacteria, with a bacillus shape around 0.45 µm in diameter and 1.2 µm in length. First described in 2004 with the temporary name IricES1, "Candidatus Midichloria" species are symbionts of several species of hard ticks. They live in the cells of the ovary of the females of this tick species. These bacteria have been observed in the mitochondria of the host cells, a trait that has never been described in any other symbiont of animals.

<span class="mw-page-title-main">SAM-II riboswitch</span>

The SAM-II riboswitch is an RNA element found predominantly in Alphaproteobacteria that binds S-adenosyl methionine (SAM). Its structure and sequence appear to be unrelated to the SAM riboswitch found in Gram-positive bacteria. This SAM riboswitch is located upstream of the metA and metC genes in Agrobacterium tumefaciens, and other methionine and SAM biosynthesis genes in other alpha-proteobacteria. Like the other SAM riboswitch, it probably functions to turn off expression of these genes in response to elevated SAM levels. A significant variant of SAM-II riboswitches was found in Pelagibacter ubique and related marine bacteria and called SAM-V. Also, like many structured RNAs, SAM-II riboswitches can tolerate long loops between their stems.

Mycoplasma laboratorium or Synthia refers to a synthetic strain of bacterium. The project to build the new bacterium has evolved since its inception. Initially the goal was to identify a minimal set of genes that are required to sustain life from the genome of Mycoplasma genitalium, and rebuild these genes synthetically to create a "new" organism. Mycoplasma genitalium was originally chosen as the basis for this project because at the time it had the smallest number of genes of all organisms analyzed. Later, the focus switched to Mycoplasma mycoides and took a more trial-and-error approach.

<span class="mw-page-title-main">Archaea</span> Domain of single-celled organisms

Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotic. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

<span class="mw-page-title-main">Nitrososphaerota</span> Phylum of archaea

The Nitrososphaerota are a phylum of the Archaea proposed in 2008 after the genome of Cenarchaeum symbiosum was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Thermoproteota. Three described species in addition to C. symbiosum are Nitrosopumilus maritimus, Nitrososphaera viennensis, and Nitrososphaera gargensis. The phylum was proposed in 2008 based on phylogenetic data, such as the sequences of these organisms' ribosomal RNA genes, and the presence of a form of type I topoisomerase that was previously thought to be unique to the eukaryotes. This assignment was confirmed by further analysis published in 2010 that examined the genomes of the ammonia-oxidizing archaea Nitrosopumilus maritimus and Nitrososphaera gargensis, concluding that these species form a distinct lineage that includes Cenarchaeum symbiosum. The lipid crenarchaeol has been found only in Nitrososphaerota, making it a potential biomarker for the phylum. Most organisms of this lineage thus far identified are chemolithoautotrophic ammonia-oxidizers and may play important roles in biogeochemical cycles, such as the nitrogen cycle and the carbon cycle. Metagenomic sequencing indicates that they constitute ~1% of the sea surface metagenome across many sites.

<span class="mw-page-title-main">RNAs present in environmental samples</span>

A wide variety of non-coding RNAs have been identified in various species of organisms known to science. However, RNAs have also been identified in "metagenomics" sequences derived from samples of DNA or RNA extracted from the environment, which contain unknown species. Initial work in this area detected homologs of known bacterial RNAs in such metagenome samples. Many of these RNA sequences were distinct from sequences within cultivated bacteria, and provide the potential for additional information on the RNA classes to which they belong.

<span class="mw-page-title-main">Pelagibacterales</span> Order of bacteria

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 quarter and a half of all prokaryotic cells in the ocean.

<span class="mw-page-title-main">Glutamine riboswitch</span> Glutamine-binding RNA structure

The glutamine riboswitch is a conserved RNA structure that was predicted by bioinformatics. It is present in a variety of lineages of cyanobacteria, as well as some phages that infect cyanobacteria. It is also found in DNA extracted from uncultivated bacteria living in the ocean that are presumably species of cyanobacteria.

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 consensus sequence and secondary structure as the binding site of SAM-II riboswitch, but bioinformatics scans cluster the two aptamers independently. These similar binding pockets suggest that the two riboswitches have undergone convergent evolution.

<span class="mw-page-title-main">Lists of organisms by population</span>

This is a collection of lists of organisms by their population. While most of the numbers are estimates, they have been made by the experts in their fields. Species population is a science falling under the purview of population ecology and biogeography. Individuals are counted by census, as carried out for the piping plover; using the transect method, as done for the mountain plover; and beginning in 2012 by satellite, with the emperor penguin being first subject counted in this manner.

"Candidatus Scalindua" is a bacterial genus, and a proposed member of the order Planctomycetales. These bacteria lack peptidoglycan in their cell wall and have a compartmentalized cytoplasm. They are ammonium oxidizing bacteria found in marine environments.

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 says that "it probably really is the commonest organism on the planet". It is a bacteriophage that infects the extremely abundant bacteria Pelagibacter ubique in the Pelagibacterales order.

Nitrososphaera is a mesophilic genus of ammonia-oxidizing Crenarchaeota. The first Nitrososphaera organism was discovered in garden soils at the University of Vienna leading to the categorization of a new genus, family, order and class of Archaea. This genus is contains three distinct species: N. viennensis, Ca. N. gargensis, and Ca N. evergladensis. Nitrososphaera are chemolithoautotrophs and have important biogeochemical roles as nitrifying organisms.

The Pelagibacteraceae are a family in the Alphaproteobacteria composed of free-living marine bacteria.

Genomic streamlining is a theory in evolutionary biology and microbial ecology that suggests that there is a reproductive benefit to prokaryotes having a smaller genome size with less non-coding DNA and fewer non-essential genes. There is a lot of variation in prokaryotic genome size, with the smallest free-living cell's genome being roughly ten times smaller than the largest prokaryote. Two of the bacterial taxa with the smallest genomes are Prochlorococcus and Pelagibacter ubique, both highly abundant marine bacteria commonly found in oligotrophic regions. Similar reduced genomes have been found in uncultured marine bacteria, suggesting that genomic streamlining is a common feature of bacterioplankton. This theory is typically used with reference to free-living organisms in oligotrophic environments.

<span class="mw-page-title-main">Marine prokaryotes</span> Marine bacteria and marine archaea

Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular life forms can be divided into prokaryotes and eukaryotes. Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, whereas prokaryotes are the organisms that do not have a nucleus enclosed within a membrane. The three-domain system of classifying life adds another division: the prokaryotes are divided into two domains of life, the microscopic bacteria and the microscopic archaea, while everything else, the eukaryotes, become the third domain.

References

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  27. ↑ "Flea market: A newly discovered virus may be the most abundant organism on the planet". The Economist . 16 February 2013. Retrieved 16 February 2013.
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