Candidate phyla radiation (also referred to as CPR group) is a large evolutionary radiation of bacterial lineages whose members are mostly uncultivated and only known from metagenomics and single cell sequencing. They have been described as nanobacteria or ultra-small bacteria due to their reduced size (nanometric) compared to other bacteria. Originally, it has been suggested that CPR represents over 15% of all bacterial diversity and may consist of more than 70 different phyla.[1] However,
a recently proposed standardized bacterial taxonomy based on relative evolutionary divergence found that CPR represents a single phylum.[2] CPR lineages 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.[3][4]
Earlier work proposed a superphylum called Patescibacteria which encompassed several phyla later attributed to the CPR group.[5] Therefore, Patescibacteria and CPR are often used as synonyms.[6]
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.[4] 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.[7]
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.[8] 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.[7]
Many of its characteristics are similar or analogous to those of ultra-small archaea (DPANN).[4]
Phylogeny[]
A 2016 tree of life based on ribosomal proteins.[3]
Phylogeny of bacteria and archaea based on ribosomal proteins and RNA polymerase subunits [9]
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.[4][3]
However, several recent studies have suggested that the CPR belongs to Terrabacteria and is more closely related to Chloroflexi.[10][11][12] The evolutionary relationships that are typically supported by these studies are as follows.
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.[5][13][14] As of 2017, two superphyla are generally recognized under CPR, Parcubacteria and Microgenomates.[1] The Phyla under CPR include:
^Beam, Jacob P.; Becraft, Eric D.; Brown, Julia M.; Schulz, Frederik; Jarett, Jessica K.; Bezuidt, Oliver; Poulton, Nicole J.; Clark, Kayla; Dunfield, Peter F.; Ravin, Nikolai V.; Spear, John R.; Hedlund, Brian P.; Kormas, Konstantinos A.; Sievert, Stefan M.; Elshahed, Mostafa S.; Barton, Hazel A.; Stott, Matthew B.; Eisen, Jonathan A.; Moser, Duane P.; Onstott, Tullis C.; Woyke, Tanja; Stepanauskas, Ramunas (2020). "Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN". Frontiers in Microbiology. 11: 1848. doi:10.3389/fmicb.2020.01848. PMC7507113. PMID33013724.
^ abBrown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. (July 2015). "Unusual biology across a group comprising more than 15% of domain Bacteria". Nature. 523 (7559): 208–11. Bibcode:2015Natur.523..208B. doi:10.1038/nature14486. OSTI1512215. PMID26083755. S2CID4397558.
^Martinez-Gutierrez CA, Aylward FO. "Phylogenetic signal, congruence, and uncertainty across bacteria and archaea". Molecular Biology and Evolution. doi:10.1093/molbev/msab254. PMID34436605.
^Coleman GA, Davín AA, Mahendrarajah TA, Szánthó LL, Spang A, Hugenholtz P, Szöllősi GJ, Williams TA. "A rooted phylogeny resolves early bacterial evolution". Science. doi:10.1126/science.abe0511. PMID33958449.
^Martinez-Gutierrez CA, Aylward FO. "Phylogenetic signal, congruence, and uncertainty across bacteria and archaea". Molecular Biology and Evolution. doi:10.1093/molbev/msab254. PMID34436605.
^Taib N, Megrian D, Witwinowski J, Adam P, Poppleton D, Borrel G, Beloin C, Gribaldo S. "Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition". Nature Ecology and Evolution. doi:10.1038/s41559-020-01299-7. PMID33077930.
