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The candidate phyla radiation (also referred to as CPR group) is a large
The Candidate phyla radiation was found to be the most basal-branching lineage in bacteria according to some early phylogenetic analyses of this group based on ribosomal proteins and protein family occurrence profiles. These studies found the following phylogeny between phyla and superphyla. The superphyla are shown in bold.
However, several recent studies have suggested that the CPR belongs to
Most of the Tree of Life is a Complete Mystery
We know certain branches exist, but we have never seen the organisms that perch there. by Ed Yong, April 12, 2016, atlantic.com.
Ultra-Small, Parasitic Bacteria Found in Groundwater, Dogs, Cats — And You
on: SciTechDaily; July 21, 2020; source: Forsyth Institute * * {{Taxonbar, from=Q27110262 Bacteriology Candidatus taxa Bacteria phyla
evolutionary radiation
An evolutionary radiation is an increase in taxonomic diversity that is caused by elevated rates of speciation, that may or may not be associated with an increase in morphological disparity. Radiations may affect one clade or many, and be rapid ...
of bacterial lineages whose members are mostly uncultivated and only known from metagenomics
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microb ...
and single cell sequencing
Single-cell sequencing examines the sequence information from individual cells with optimized next-generation sequencing technologies, providing a higher resolution of cellular differences and a better understanding of the function of an individual ...
. They have been described as nanobacteria (not to be confused with non-living nanoparticles of the same name) or ultra-small bacteria due to their reduced size (nanometric) compared to other bacteria.
Originally (circa 2016), it has been suggested that CPR represents over 15% of all bacterial diversity and may consist of more than 70 different phyla. However,
the Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to breaking up paraph ...
(2018) based on relative evolutionary divergence found that CPR represents a single phylum, with earlier figures inflated by the rapid evolution of ribosomal proteins. CPR lineages are generally characterized as having small genome
In the fields of molecular biology and genetics, 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 g ...
s and lacking several biosynthetic pathways and ribosomal
Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to for ...
proteins. This has led to the speculation that they are likely obligate symbiont
Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasit ...
s.
Earlier work proposed a superphylum called Patescibacteria which encompassed several phyla later attributed to the CPR group. Therefore, Patescibacteria and CPR are often used as synonyms. The former name is not necessarily obsolete: for example, the GTDB uses this name because they consider the CPR group a phylum.
Characteristics
Although there are a few exceptions, members of the candidate phyla radiation generally lack several biosynthetic pathways for several amino acids and nucleotides. To date, there has been no genomic evidence that indicates that they are capable of producing the lipids essential for cell envelope formation. Additionally, they tend to lack complete TCA cycles and electron transport chain complexes, including ATP synthase. This lack of several important pathways found in most free-living prokaryotes indicates that the candidate phyla radiation is composed of obligate fermentative symbionts. Furthermore, CPR members have unique ribosomal features. While the members of CPR are generally uncultivable, and therefore missed in culture-dependent methods, they are also often missed in culture-independent studies that rely on16S rRNA 16S rRNA may refer to:
* 16S ribosomal RNA
16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure.
The g ...
sequences. Their rRNA genes appear to encode proteins and have self-splicing intron
Group I introns are large self-splicing ribozymes. They Biocatalysis, catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of nine paired regions (P1-P9). These fold t ...
s, features that are rarely seen in bacteria, although they have previously been reported. Owing to these introns, members of CPR are not detected in 16S-dependent methods. Additionally, all CPR members are missing the L30 ribosomal protein, a trait that is often seen in symbionts.
Many of its characteristics are similar or analogous to those of ultra-small archaea (DPANN
DPANN is a superphylum of Archaea first proposed in 2013. Many members show novel signs of horizontal gene transfer from other domains of life. They are known as nanoarchaea or ultra-small archaea due to their smaller size (nanometric) compared t ...
).
Phylogeny
The Candidate phyla radiation was found to be the most basal-branching lineage in bacteria according to some early phylogenetic analyses of this group based on ribosomal proteins and protein family occurrence profiles. These studies found the following phylogeny between phyla and superphyla. The superphyla are shown in bold.
However, several recent studies have suggested that the CPR belongs to Terrabacteria
Terrabacteria is a taxon containing approximately two-thirds of prokaryote species, including those in the gram positive phyla (Actinomycetota and Bacillota) as well as the phyla "Cyanobacteria", Chloroflexota, and Deinococcota.
It derives its ...
and is more closely related to Chloroflexota
The Chloroflexota are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for phot ...
. The evolutionary relationships that are typically supported by these studies are as follows.
Provisional taxonomy
Because many CPR members are uncultivable, they cannot be formally put into thebacterial taxonomy
Bacterial taxonomy is the taxonomy, i.e. the rank-based classification, of bacteria.
In the scientific classification established by Carl Linnaeus, each species has to be assigned to a genus ( binary nomenclature), which in turn is a lower lev ...
, but a number of provisional, or ''Candidatus
In prokaryote nomenclature, ''Candidatus'' (Latin for candidate of Roman office) is used to name prokaryotic phyla that are well characterized but yet-uncultured. Contemporary sequencing approaches, such as 16S sequencing or metagenomics, provide m ...
'', names have been generally agreed on. As of 2017, two superphyla are generally recognized under CPR, Parcubacteria and Microgenomates. The Phyla under CPR include:
* ?" Elulimicrobiota" Rodriguez-R et al. 2020
* Clade "Patescibacteria" Rinke et al. 2013
** "Wirthbacteria
''Candidatus'' Wirthbacteria is a proposed bacterial phylum containing only one known sample from the Crystal Geyser aquifer, ''Ca. Wirthibacter wanneri''. This bacterium stands out in a basal position in some trees of life as it is closely re ...
" Hug et al. 2016
** Microgenomates Cluster
*** " Dojkabacteria" Wrighton et al. 2016 (WS6)
*** "Katanobacteria
Katanobacteria is a bacterial phylum formerly known as WWE3. It has candidate status, meaning there are no cultured representatives, and is a member of the Candidate Phyla Radiation
The candidate phyla radiation (also referred to as CPR group) ...
" Hug et al. 2016b (WWE3)
*** Superphylum Microgenomates
The Microgenomates are a proposed supergroup of bacterial candidate phyla in the Candidate phyla radiation, Candidate Phyla Radiation.
Organisms from the Microgenomates group have never been cultured in a lab; rather they have only been detected ...
**** " Woykebacteria" Anantharaman et al. 2016 (RIF34)
**** " Curtissbacteria" Brown et al. 2015
**** " Daviesbacteria" Brown et al. 2015
**** " Roizmanbacteria" Brown et al. 2015
**** " Gottesmanbacteria" Brown et al. 2015
**** " Levybacteria" Brown et al. 2015
**** " Shapirobacteria" Brown et al. 2015
**** Clade GWA2-44-7
***** ?" Genascibacteria" He et al. 2021
***** " Amesbacteraceaeia" Brown et al. 2015
***** " Blackburnbacteria" Anantharaman et al. 2016 (RIF35)
***** " Woesebacteria" Brown et al. 2015 (DUSEL-2, DUSEL-4)
**** Clade UBA1400
***** " Beckwithbacteria" Brown et al. 2015
***** " Collierbacteria" Brown et al. 2015
***** " Chazhemtonibacteraceae" corrig. Kadnikov et al. 2020
***** " Chisholmbacteria" Anantharaman et al. 2016 (RIF36)
***** " Cerribacteria" Kroeger et al. 2018
***** " Pacebacteria" Brown et al. 2015
** Gracilibacteria Cluster
*** " Absconditabacteria" Hug et al. 2016b (SR1)
*** "''Ca.'' Altimarinus" Rinke et al. 2013 (GN02)
*** " Abawacabacteria" Anantharaman et al. 2016 (RIF46)
*** " Peregrinibacteria" Brown et al. 2015 (PER)
*** "Fertabacteria
Fertabacteria is a Candidatus, candidate Bacterial phyla, bacterial phylum of the Candidate phyla radiation, Candidate Phyla Radiation, first proposed in 2017 after analysis of a genome from the mouth of a bottlenose dolphin. Members of this phylum ...
" Dudek et al. 2017 (DOLZORAL124_38_8)
*** " Peribacteria" Anantharaman et al. 2016
** Saccharibacteria Cluster
*** "Berkelbacteria
Berkelbacteria (formerly ACD58) is a bacterial phylum with candidate status, meaning there are no cultured representatives for this group. It is part of the Candidate Phyla Radiation
The candidate phyla radiation (also referred to as CPR grou ...
" Wrighton et al. 2014 (ACD58)
*** " Kazanbacteria" Jaffe et al. 2020 (Kazan)
*** " Howlettbacteria" Probst et al. 2018 (CPR2)
*** "Saccharibacteria
Saccharibacteria, formerly known as ''TM7'',
is a major bacterial lineage. It was discovered through 16S rRNA sequencing .
TM7x from the human oral cavity was cultivated and revealed that TM7x is an extremely small coccus (200-300 nm) an ...
" Albertsen et al. 2013 (TM7)
** Parcubacteria Cluster
*** " Andersenbacteria" Anantharaman et al. 2016 (RIF9)
*** " Doudnabacteria" Anantharaman et al. 2016 (SM2F11)
*** " Torokbacteria" Probst et al. 2018
*** Clade ABY1
**** " Kerfeldbacteria" Anantharaman et al. 2016 (RIF4)
**** " Veblenbacteria" Anantharaman et al. 2016 (RIF39)
**** ?" Brownbacteria" Danczak et al. 2017
**** " Uhrbacteria" Brown et al. 2015 (SG8-24)
**** " Magasanikbacteria" Brown et al. 2015
**** " Kuenenbacteria" Brown et al. 2015
**** " Jacksonbacteria" Anantharaman et al. 2016 (RIF38)
**** " Komeilibacteria" Anantharaman et al. 2016 (RIF6)
**** " Moisslbacteria" Probst et al. 2018
**** " Falkowbacteria" Brown et al. 2015
**** " Buchananbacteria" Anantharaman et al. 2016 (RIF37)
*** Superphylum Parcubacteria
**** ?" Montesolbacteria " He et al. 2021
**** " Moranbacteria" Brown et al. 2015 (OD1-i)
**** Clade UBA6257
***** " Brennerbacteria" Anantharaman et al. 2016 (RIF18)
***** " Wolfebacteria" Brown et al. 2015
***** " Jorgensenbacteria" Brown et al. 2015
***** " Liptonbacteria" Anantharaman et al. 2016 (RIF42)
***** " Colwellbacteria" Anantharaman et al. 2016 (RIF41)
***** " Harrisonbacteria" Anantharaman et al. 2016 (RIF43)
**** Clade UBA9983_A
***** ?" Hugbacteria" Danczak et al. 2017
***** ?" Llyodbacteria" Anantharaman et al. 2016 (RIF45)
***** " Vogelbacteria" Anantharaman et al. 2016 (RIF14)
***** " Yonathbacteria" Anantharaman et al. 2016 (RIF44)
***** " Nomurabacteria" Brown et al. 2015
***** " Kaiserbacteria" Brown et al. 2015
***** " Adlerbacteria" Brown et al. 2015
***** " Campbellbacteria" Brown et al. 2015
***** " Taylorbacteria" Anantharaman et al. 2016 (RIF16)
***** " Zambryskibacteria" Anantharaman et al. 2016 (RIF15)
**** " Yanofskybacteria" Brown et al. 2015
**** " Azambacteria" Brown et al. 2015
**** " Sungbacteria" Anantharaman et al. 2016 (RIF17)
**** " Ryanbacteria" Anantharaman et al. 2016 (RIF10)
**** Clade UBA9983
***** " Giovannonibacteria" Brown et al. 2015
***** " Niyogibacteria" Anantharaman et al. 2016 (RIF11)
***** " Tagabacteria" Anantharaman et al. 2016 (RIF12)
**** " Terrybacteria" Anantharaman et al. 2016 (RIF13)
**** " Spechtbacteria" Anantharaman et al. 2016 (RIF19)
**** " Parcunitrobacteria" Castelle et al. 2017 (GWA2-38-13b)
**** " Portnoybacteria" Anantharaman et al. 2016 (RIF22)
**** Clade "Paceibacteria"
***** " Wildermuthbacteria" Anantharaman et al. 2016 (RIF21)
***** " Paceibacteria"
***** " Nealsonbacteria" Anantharaman et al. 2016 (RIF40)
***** " Gribaldobacteria" Probst et al. 2018
***** " Staskawiczbacteria" Anantharaman et al. 2016 (RIF20)
The current phylogeny is based on ribosomal protein
A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. ''E. coli'', other bacteria and Archaea have a 30S small subunit an ...
s (Hug et al., 2016). Other approaches, including protein family existence and 16S ribosomal RNA
16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure.
The genes coding for it are referred to as 16S rR ...
, produce similar results at lower resolutions.
See also
* for some of the phyla in CPR.References
External links
Most of the Tree of Life is a Complete Mystery
We know certain branches exist, but we have never seen the organisms that perch there. by Ed Yong, April 12, 2016, atlantic.com.
Ultra-Small, Parasitic Bacteria Found in Groundwater, Dogs, Cats — And You
on: SciTechDaily; July 21, 2020; source: Forsyth Institute * * {{Taxonbar, from=Q27110262 Bacteriology Candidatus taxa Bacteria phyla