|Candidate phyla radiation|
|Representation of a bacterium of this phylum.|
|(unranked):||Bacteria candidate phyla|
|Infrakingdom:||Candidate phyla radiation|
Candidate phyla radiation (also referred to as CPR group) is a large evolutionary radiation of bacterial candidate phyla and superphyla, whose members are largely uncultivable and only known from metagenomics. They are known as nanobacteria or ultra-small bacteria due to their smaller size (nanometric) compared to other bacteria. It is suggested that it represents over 15% of all bacterial diversity and may consist of more than 70 different phyla. They are generally characterized as having small genomes and lacking several biosynthetic pathways and ribosomal proteins. This has led to the speculation that they are likely obligate symbionts. Member phyla form a huge CPR monophyletic clade, on a level around the infrakingdom.
Earlier work proposed that many phyla under the CPR group form a superphylum called Patescibacteria. However, since many of the "phyla" are now considered superphyla, the rank is no longer appropriate.
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 on 16S rRNA sequences. Their rRNA genes appear to encode proteins and have self-splicing introns, 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.
Candidate phyla radiation is the first clade to separate from bacteria according to phylogenetic analyzes. Some analyzes have even found that they can be paraphyletic. Recent phylogenetic analyzes have found the following phylogeny between phyla and superphyla. The superphyla are shown in bold.
Because many CPR members are uncultivable, they cannot be formally put into the bacterial taxonomy, but a number of provisional, or Candidatus, names have been generally agreed on. As of 2017, two superphyla are generally recognized under CPR, Parcubacteria and Microgenomates. The Phyla under CPR include:
- Parvkingdom? Parcubacteria Cluster
- Superphylum Parcubacteria
- Phylum Kerfeldbacteria
- Phylum Doudnabacteria – forms a monophyletic group with the paraphyletic Parcubacteria
- Phylum KAZAN
- Phylum CPR2
- Phylum Berkelbacteria (ACD58)
- Phylum Gracilibacteria
- Phylum Saccharibacteria (TM7) – one member, TM7x, cultivated
- Phylum Peregrinibacteria
- Phylum Peribacteria
- Superphylum Parcubacteria
- Parvkingdom? Microgenomates Cluster
The current phylogeny is based on ribosomal proteins (Hug et al., 2016). Other approaches, including protein family existence and 16S ribosomal RNA, produce similar results at lower resolutions.
- Bacterial phyla § Uncultivated phyla and metagenomics for some of the phyla in CPR.
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- Bokhari, RH; Amirjan, N; Jeong, H; Kim, KM; Caetano-Anollés, G; Nasir, A (1 March 2020). "Bacterial Origin and Reductive Evolution of the CPR Group". Genome Biology and Evolution. 12 (3): 103–121. doi:10.1093/gbe/evaa024. PMC 7093835. PMID 32031619.