Candidate phyla radiation

Candidate phyla radiation
Representation of a bacterium of this phylum.
Scientific classification
Domain: Bacteria
(unranked): Bacteria candidate phyla
Infrakingdom: Candidate phyla radiation

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]

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.[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]

Bacteria
 

The other bacteria

 
CPR
 

 Wirthbacteria

 
 
 
 

 Dojkabacteria

 
 
 

 Katanobacteria

 
 

 Microgenomates

 
 
 
 
 
 

 Berkelbacteria

 
 

 Saccharibacteria

 
 
 
 
 

 Peregrinibacteria

 
 
 

 Absconditabacteria

 
 

 Gracilibacteria

 
 
 
 

 Parcubacteria

 
 
 
 
 
 

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.


Bacteria 
 

Gracilicutes

 
Terrabacteria
 

DST

 
 
 

Cyanobacteria/Melainabacteria

 
 
 
 

Firmicutes (includes Tenericutes)

 
 

Actinobacteria

 
 
 
 
 

Armatimonadetes

 
 

Eremiobacteraeota

 
 
 
 

CPR

 
 
 

Dormibacteraeota

 
 

Chloroflexi

 
 
 
 
 
 
 
 

Provisional taxonomy

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:

Phylogeny of Patescibacteria[15][13]
 
 

"Wirthbacteria"

 
 
"Microgenomates"
 

"Dojkabacteria"

 
 
 

"Katanobacteria"

 
 

"Microgenomatia"

 
 
cluster
 
"Gracilibacteria"

"Gracilibacteria"

cluster
 
"Saccharibacteria"
 

"Berkelbacteria" (UBA1384)

 
 
 

"Kazanbacteria" (Kazan)

 
 
 

"Howlettbacteria"

 
 

"Saccharimonadia"

 
 
 
cluster
"Parcubacteria"
 
 

"Andersenbacteria"

 
 

"Doudnabacteria"

 
 
 
 
 

"Torokbacteria" (GCA-2792135)

 
 

ABY1

 
 
 

"Paceibacteria"

 
 
cluster
 
 
 
 
Phylogeny of Microgenomatia[15][13]
 
 
 

"Woykebacterales" (CG2-30-54-11)

 
 
 

"Curtissbacterales"

 
 

"Daviesbacterales"

 
 
 
 
 
 

"Roizmanbacterales" (UBA1406)

 
 
 

"Gottesmanbacterales" (UBA10105)

 
 

"Levybacterales"

 
 
 
 
 
 

"Shapirobacterales" (UBA12405)

 
GWA2‑44‑7
 

"Amesbacteraceae"

 
 
 

"Blackburnbacteraceae" (UBA10165)

 
 

"Woesebacteraceae" (UBA8517)

 
 
 
 
UBA1400
 

"Beckwithbacteraceae" (CG1-02-47-37)

 
 
 

"Chisholmbacteraceae"

 
 
 
 

"Collierbacteraceae" (UBA12108)

 
 

"Chazhemtobacteraceae"

 
 
 
 

"Cerribacteraceae" (UBA12028)

 
 

"Pacebacteraceae" (PJMF01)

 
 
 
 
 
 
 
 
Phylogeny of Gracilibacteria[15][13]
 
 
 

"Absconditabacterales"

 
 

"Gracilibacterales" (BD1-5)

 
 
 
 

"Abawacabacteriales" (RBG-16-42-10)

 
 
 

"Peregrinibacterales" (UBA1369)

 
 
 

"Fertabacterales" (UBA4473)

 
 

"Peribacterales"

 
 
 
 
 
Phylogeny of ABY1[15][13]
 
 

"Kerfeldbacterales" (SBBC01)

 
 
 
 
 

"Jacksonbacterales" (UBA9629)

 
 

"Kuenenbacterales" (UBA2196)

 
 
 
 

"Veblenbacterales"

 
 

"Komeilibacterales" (UBA1558)

 
 
 
 
 
 

"Falkowbacterales" (BM507)

 
 

"Buchananbacterales"

 
 
 
 

"Uhrbacterales" (GWA2-46-9)

 
 

"Magasanikbacterales"

 
 
 
 
 
Phylogeny of Paceibacteria[15][13]
 
 

"Moranbacterales"

 
 
UBA9983_A
 
 

"Nomurabacteraceae" (UBA9973)

 
 
 

"Vogelbacteraceae" (XYD1-FULL-46-19)

 
 

"Yonathbacteraceae" (UBA1539)

 
 
 
 
 
 

"Taylorbacteraceae" (UBA11359_A)

 
 

"Zambryskibacteraceae"

 
 
 
 

"Kaiserbacteraceae" (UBA2163)

 
 

"Campbellbacteraceae" (CSBR16-193)

 
 
 
 
 
UBA6257
 

"Brennerbacteraceae"

 
 
 

"Jorgensenbacteraceae" (GWB1-50-10)

 
 
 

"Liptonbacteraceae" (2-01-FULL-56-20)

 
 
 

"Wolfebacteraceae" (UBA9933)

 
 
 

"Colwellbacteraceae" (UBA9933)

 
 

"Harrisonbacteraceae" (WO2-44-18)

 
 
 
 
 
 
 
 
 
 

"Parcunitrobacterales"

 
 

"Portnoybacterales"

 
 
"Paceibacterales"
 

"Gribaldobacteraceae" (CG1-02-41-26)

 
 
 

"Nealsonbacteraceae" (PWPS01)

 
 
 

"Wildermuthbacteraceae" (UBA10102)

 
 
 

"Staskawiczbacteraceae"

 
 

"Paceibacteraceae" ("Parcubacteria")

 
 
 
 
 
 
 
 

"Azambacterales" (UBA10092)

 
 
 

"Terrybacterales"

 
 
 

"Yanofskybacterales" (2-02-FULL-40-12)

 
 
 

"Spechtbacterales"

 
 
 

"Sungbacterales"

 
 
 

"Ryanbacterales"

 
 
 

"Tagabacterales"

 
"WO2‑41‑13"
 

"Giovannonibacteraceae" (2-01-FULL-45-33)

 
 

"Niyogibacteraceae" (1-14-0-10-42-19)

 
 
 
 
 
 
 
 
 
 
 
 
 
  •  ?"Elulimicrobiota" Rodriguez-R et al. 2020
  • Clade "Patescibacteria" Rinke et al. 2013
    • "Wirthbacteria" Hug et al. 2016
    • Microgenomates Cluster
      • "Dojkabacteria" Wrighton et al. 2016 (WS6)
      • "Katanobacteria" Hug et al. 2016b (WWE3)
      • Superphylum Microgenomates
        • "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
          • "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
          • "Chisholmbacteria" Anantharaman et al. 2016 (RIF36)
          • "Collierbacteria" Brown et al. 2015
          • "Chazhemtobacteriaceae" Kadnikov et al. 2020
          • "Cerribacteria" Kroeger et al. 2018
          • "Pacebacteria" Brown et al. 2015
    • Gracilibacteria Cluster
      • "Gracilibacteria" Rinke et al. 2013 (GN02)
      • "Abawacabacteria" Anantharaman et al. 2016 (RIF46)
      • "Absconditabacteria" Hug et al. 2016b (SR1)
      • "Fertabacteria" Dudek et al. 2017 (DOLZORAL124_38_8)
      • "Peregrinibacteria" Brown et al. 2015 (PER)
      • "Peribacteria" Anantharaman et al. 2016
    • Saccharibacteria Cluster
      • "Berkelbacteria" Wrighton et al. 2014 (ACD58)
      • "Kazanbacteria" Jaffe et al. 2020 (Kazan)
      • "Howlettbacteria" Probst et al. 2018 (CPR2)
      • "Saccharibacteria" 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)
        • "Jacksonbacteria" Anantharaman et al. 2016 (RIF38)
        • "Kuenenbacteria" Brown et al. 2015
        • "Veblenbacteria" Anantharaman et al. 2016 (RIF39)
        • "Komeilibacteria" Anantharaman et al. 2016 (RIF6)
        • "Falkowbacteria" Brown et al. 2015
        • "Buchananbacteria" Anantharaman et al. 2016 (RIF37)
        •  ?"Brownbacteria" Danczak et al. 2017
        • "Uhrbacteria" Brown et al. 2015
        • "Magasanikbacteria" Brown et al. 2015
      • Superphylum Parcubacteria
        • "Moranbacteria" Brown et al. 2015 (OD1-i)
        • Clade UBA9983_A
          • "Nomurabacteria" Brown et al. 2015
          • "Vogelbacteria" Anantharaman et al. 2016 (RIF14)
          •  ?"Llyodbacteria" Anantharaman et al. 2016 (RIF45)
          • "Yonathbacteria" Anantharaman et al. 2016 (RIF44)
          • "Taylorbacteria" Anantharaman et al. 2016 (RIF16)
          • "Zambryskibacteria" Anantharaman et al. 2016 (RIF15)
          • "Kaiserbacteria" Brown et al. 2015 [incl. "Adlerbacteria"]
          •  ?"Hugbacteria" Danczak et al. 2017
          • "Campbellbacteria" Brown et al. 2015
        • Clade UBA6257
          • "Brennerbacteria" Anantharaman et al. 2016 (RIF18)
          • "Jorgensenbacteria" Brown et al. 2015
          • "Liptonbacteria" Anantharaman et al. 2016 (RIF42)
          • "Wolfebacteria" Brown et al. 2015
          • "Colwellbacteria" Anantharaman et al. 2016 (RIF41)
          • "Harrisonbacteria" Anantharaman et al. 2016 (RIF43)
        • "Parcunitrobacteria" Castelle et al. 2017 (GWA2-38-13b)
        • "Portnoybacteria" Anantharaman et al. 2016 (RIF22)
        • Clade
          • "Gribaldobacteria" Probst et al. 2018
          • "Nealsonbacteria" Anantharaman et al. 2016 (RIF40)
          • "Wildermuthbacteria" Anantharaman et al. 2016 (RIF21)
          • "Parcubacteria" Rinke et al. 2013 (Paceibacteraceae)
          • "Staskawiczbacteria" Anantharaman et al. 2016 (RIF20)
        • "Azambacteria" Brown et al. 2015
        • "Terrybacteria" Anantharaman et al. 2016 (RIF13)
        • "Yanofskybacteria" Brown et al. 2015
        • "Spechtbacteria" Anantharaman et al. 2016 (RIF19)
        • "Sungbacteria" Anantharaman et al. 2016 (RIF17)
        • "Ryanbacteria" Anantharaman et al. 2016 (RIF10)
        • "Tagabacteria" Anantharaman et al. 2016 (RIF12)
        • Clade WO2-41-13
          • "Giovannonibacteria" Brown et al. 2015
          • "Niyogibacteria" Anantharaman et al. 2016 (RIF11)

The current phylogeny is based on ribosomal proteins (Hug et al., 2016).[3] Other approaches, including protein family existence and 16S ribosomal RNA, produce similar results at lower resolutions.[16][1]

See also

References

  1. 1 2 3 Danczak RE, Johnston MD, Kenah C, Slattery M, Wrighton KC, Wilkins MJ (September 2017). "Members of the candidate phyla radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities". Microbiome. 5 (1): 112. doi:10.1186/s40168-017-0331-1. PMC 5581439. PMID 28865481.
  2. ↑ Parks, Donovan; Chuvochina, Maria; Waite, David; Rinke, Christian; Skarshewski, Adam; Chaumeil, Pierre-Alain; Hugenholtz, Philip (27 August 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100. Retrieved 13 January 2021.
  3. 1 2 3 4 Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. (April 2016). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. PMID 27572647.
  4. 1 2 3 4 Castelle CJ, Banfield JF (March 2018). "Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life". Cell. 172 (6): 1181–1197. doi:10.1016/j.cell.2018.02.016. PMID 29522741.
  5. 1 2 Rinke C; et al. (2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499 (7459): 431–7. Bibcode:2013Natur.499..431R. doi:10.1038/nature12352. PMID 23851394.
  6. ↑ 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. PMC 7507113. PMID 33013724.
  7. 1 2 Brown 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. OSTI 1512215. PMID 26083755. S2CID 4397558.
  8. ↑ Belfort M, Reaban ME, Coetzee T, Dalgaard JZ (July 1995). "Prokaryotic introns and inteins: a panoply of form and function". Journal of Bacteriology. 177 (14): 3897–903. doi:10.1128/jb.177.14.3897-3903.1995. PMC 177115. PMID 7608058.
  9. ↑ Martinez-Gutierrez CA, Aylward FO. "Phylogenetic signal, congruence, and uncertainty across bacteria and archaea". Molecular Biology and Evolution. doi:10.1093/molbev/msab254. PMID 34436605.
  10. ↑ 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. PMID 33958449.
  11. ↑ Martinez-Gutierrez CA, Aylward FO. "Phylogenetic signal, congruence, and uncertainty across bacteria and archaea". Molecular Biology and Evolution. doi:10.1093/molbev/msab254. PMID 34436605.
  12. ↑ 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. PMID 33077930.
  13. 1 2 3 4 5 6 "GTDB release 06-RS202". Genome Taxonomy Database.
  14. ↑ Sayers. "Patescibacteria group". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  15. 1 2 3 4 5 Mendler, K; Chen, H; Parks, DH; Hug, LA; Doxey, AC (2019). "AnnoTree: visualization and exploration of a functionally annotated microbial tree of life". Nucleic Acids Research. 47 (9): 4442–4448. doi:10.1093/nar/gkz246. PMC 6511854. PMID 31081040.
  16. ↑ Méheust, Raphaël; Burstein, David; Castelle, Cindy J.; Banfield, Jillian F. (13 September 2019). "The distinction of CPR bacteria from other bacteria based on protein family content". Nature Communications. 10 (1): 4173. Bibcode:2019NatCo..10.4173M. doi:10.1038/s41467-019-12171-z. PMC 6744442. PMID 31519891.
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