Jump to content

DPANN

From Wikipedia, the free encyclopedia
(Redirected fromMicrarchaeota)

DPANN
Parvarchaeum acidiphilum
Scientific classificationEdit this classification
Domain: Archaea
Superphylum: DPANN
Rinke et al. 2013
Phyla[1]

DPANNis a superphylumofArchaeafirst proposed in 2013.[2]Many members show novel signs ofhorizontal gene transferfrom other domains of life.[2]They are known asnanoarchaeaorultra-small archaeadue to their smaller size (nanometric) compared to other archaea.

DPANN is an acronym formed by the initials of the first five groups discovered,Diapherotrites,Parvarchaeota,Aenigmarchaeota,NanoarchaeotaandNanohaloarchaeota.LaterWoesearchaeotaandPacearchaeotawere discovered and proposed within the DPANN superphylum.[3]In 2017, another phylum Altiarchaeota was placed into this superphylum.[4]Themonophylyof DPANN is not yet considered established, due to the highmutationrate of the included phyla, which can lead to the artifact of thelong branch attraction(LBA) where the lineages are grouped basally or artificially at the base of thephylogenetic treewithout being related.[5][6]These analyzes instead suggest that DPANN belongs toEuryarchaeotaor ispolyphyleticoccupying various positions within Euryarchaeota.[5][6][7]

The DPANN groups together different phyla with a variety of environmental distribution and metabolism, ranging from symbiotic andthermophilicforms such asNanoarchaeota,acidophileslikeParvarchaeotaand non-extremophiles likeAenigmarchaeotaandDiapherotrites.DPANN was also detected in nitrate-rich groundwater, on the water surface but not below, indicating that these taxa are still quite difficult to locate.[8]

Since the recognition of the kingdom rank by theICNP,the proposed name for this group is kingdomNanobdellati.[9]

Characteristics

[edit]

They are characterized by being small in size compared to otherarchaea(nanometric size) and in keeping with their smallgenome,they have limited but sufficient catabolic capacities to lead a free life, although many are thought to beepisymbiontsthat depend on asymbioticor parasitic association with other organisms. Many of their characteristics are similar or analogous to those ofultra-small bacteria(CPR group).[3]

Limited metabolic capacities are a product of the small genome and are reflected in the fact that many lack centralbiosyntheticpathways fornucleotides,aminoacids,andlipids;hence most DPANN archaea, such asARMAN archaea,which rely on othermicrobesto meet their biological requirements. But those that have the potential to live freely arefermentativeandaerobicheterotrophs.[3]

They are mostly anaerobic and have not been cultivated. They live in extreme environments such as thermophilic, hyperacidophilic, hyperhalophilic or metal-resistant; or also in the temperate environment of marine and lakesediments.They are rarely found on the ground or in the open ocean.[3]

Classification

[edit]

Phylogeny

[edit]
Tom A. Williams et al. 2017,[20]Castelle et al. 2015[3]and Dombrowski et al. 2020.[21] Jordan et al. 2017[7]Cavalier-Smith2020[6]and Feng et al 2021.[22]

DPANN may be the first divergent clade of archaea according to some phylogenetic analyses. Recent phylogenetic analyses have found the following phylogeny between phyla.[3][20][21]

Bacteria

Archaea

Other phylogenetic analyzes have suggested that DPANN could belong toEuryarchaeotaor that it may even bepolyphyleticoccupying different positions within Euryarchaeota. It is also debated whether the phylum Altiarchaeota should be classified in DPANN or Euryarchaeota.[21][5]An alternative location for DPANN in the phylogenetic tree is as follows.[7][6][22]The groups marked in quotes are lineages assigned to DPANN, but phylogenetically separated from the rest.

Bacteria

Archaea

Taxonomy

[edit]

The currently accepted taxonomy is based on theList of Prokaryotic names with Standing in Nomenclature(LPSN)[23]andNational Center for Biotechnology Information(NCBI).[24]

GTDBphylogeny of "DPANN"[25][26][27]


DPANN
"Undinarchaeota"
"Undinarchaeia"

"Undinarchaeales"

DPANN

Superphylum"DPANN"Rinke et al. 2013(= proposedkingdomNanobdellatiRinke, Schwientek, Sczyrba, Ivanova, Anderson, Cheng, Darling, Malfatti, Swan, Gies, Dodsworth, Hedlund, Tsiamis, Sievert, Liu, Eisen, Hallam, Kyrpides, Stepanauskas, Rubin, Hugenholtz and Woyke 2024[28])

  • Phylum "Undinarchaeota"Dombrowski et al. 2020
    • Class "Undinarchaeia"Dombrowski et al. 2020
      • Order "Undinarchaeales"Dombrowski et al. 2020
  • Phylum "Huberarchaeota"Probst et al. 2019
    • Class "Huberarchaeia"corrig. Probst et al. 2019
      • Order "Huberarchaeales"Rinke et al. 2020
  • Phylum "Aenigmatarchaeota"corrig. Rinke et al. 2013(DSEG, DUSEL2)
    • Class "Aenigmatarchaeia"corrig. Rinke et al. 2020
      • Order "Aenigmatarchaeales"corrig. Rinke et al. 2020
  • Phylum "Nanohalarchaeota"corrig. Rinke et al. 2013
    • Class "Nanohalobiia"corrig.La Cono et al. 2020
      • Order "Nanohalobiales"La Cono et al. 2020
    • Class? "Nanohalarchaeia"corrig. Narasingarao et al. 2012
      • Order "Nanohalarchaeales"
  • PhylumAltarchaeotaProbst et al. 2018(SM1)
    • Class "Altarchaeia"corrig. Probst et al. 2014
      • Order "Altarchaeales"corrig. Probst et al. 2014
  • Phylum "Iainarchaeota" [ "Diapherotrites"Rinke et al. 2013] (DUSEL-3)
    • Class "Iainarchaeia"Rinke et al. 2020
      • Order "Forterreales"Probst & Banfield 2017
      • Order "Iainarchaeales"Rinke et al. 2020
  • Phylum "Micrarchaeota"Baker & Dick 2013
    • Class "Micrarchaeia"Vazquez-Campos et al. 2021
      • Order "Anstonellales"Vazquez-Campos et al. 2021(LFWA-IIIc)
      • Order "Burarchaeales"Vazquez-Campos et al. 2021(LFWA-IIIb)
      • Order "Fermentimicrarchaeales"Kadnikov et al. 2020
      • Order "Gugararchaeales"Vazquez-Campos et al. 2021(LFWA-IIIa)
      • Order "Micrarchaeales"Vazquez-Campos et al. 2021
      • Order "Norongarragalinales"Vazquez-Campos et al. 2021(LFWA-II)
  • Phylum "Nanoarchaeota"Huber et al. 2002
  • Phylum? "Mamarchaeota"
  • Order? "Wiannamattarchaeales"

See also

[edit]

References

[edit]
  1. ^Castelle CJ, Banfield JF (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.PMID29522741.
  2. ^abRinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T (July 2013)."Insights into the phylogeny and coding potential of microbial dark matter"(PDF).Nature.499(7459): 431–437.Bibcode:2013Natur.499..431R.doi:10.1038/nature12352.PMID23851394.S2CID4394530.
  3. ^abcdefgCastelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, Taylor RC, Williams KH, Banfield JF (March 2015)."Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling".Current Biology.25(6): 690–701.doi:10.1016/j.cub.2015.01.014.PMID25702576.
  4. ^Spang A, Caceres EF, Ettema TJ (August 2017)."Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life".Science.357(6351): eaaf3883.doi:10.1126/science.aaf3883.PMID28798101.
  5. ^abcNina Dombrowski, Jun-Hoe Lee, Tom A Williams, Pierre Offre, Anja Spang (2019).Genomic diversity, lifestyles and evolutionary origins of DPANN archaea.Nature.
  6. ^abcdCavalier-Smith, Thomas; Chao, Ema E-Yung (2020)."Multidomain ribosomal protein trees and the planctobacterial origin of neomura (Eukaryotes, archaebacteria)".Protoplasma.257(3): 621–753.doi:10.1007/s00709-019-01442-7.PMC7203096.PMID31900730.
  7. ^abcJordan T. Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar, Karen G. Lloyd (2017).Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales.Frontiers.
  8. ^Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL (2017-04-06)."Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater".PLOS ONE.12(4): e0174930.doi:10.1371/journal.pone.0174930.PMC5383146.PMID28384184.
  9. ^Göker, Markus; Oren, Aharon (22 January 2024)."Valid publication of names of two domains and seven kingdoms of prokaryotes".International Journal of Systematic and Evolutionary Microbiology.74(1).doi:10.1099/ijsem.0.006242.ISSN1466-5026.PMID38252124.
  10. ^Genomes Online Database
  11. ^Comolli LR, Baker BJ, Downing KH, Siegerist CE, Banfield JF (February 2009)."Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon".The ISME Journal.3(2): 159–167.doi:10.1038/ismej.2008.99.PMID18946497.
  12. ^Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF (December 2006). "Lineages of acidophilic archaea revealed by community genomic analysis".Science.314(5807): 1933–1935.doi:10.1126/science.1132690.PMID17185602.S2CID26033384.
  13. ^Murakami S, Fujishima K, Tomita M, Kanai A (February 2012)."Metatranscriptomic analysis of microbes in an Oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation".Applied and Environmental Microbiology.78(4): 1015–1022.doi:10.1128/AEM.06811-11.PMC3272989.PMID22156430.
  14. ^Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF (May 2010)."Enigmatic, ultrasmall, uncultivated Archaea".Proceedings of the National Academy of Sciences of the United States of America.107(19): 8806–8811.doi:10.1073/pnas.0914470107.PMC2889320.PMID20421484.
  15. ^Ortiz-Alvarez R, Casamayor EO (April 2016). "High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes".Environmental Microbiology Reports.8(2): 210–217.doi:10.1111/1758-2229.12370.PMID26711582.
  16. ^Takai K, Moser DP, DeFlaun M, Onstott TC, Fredrickson JK (December 2001)."Archaeal diversity in waters from deep South African gold mines".Applied and Environmental Microbiology.67(12): 5750–5760.doi:10.1128/AEM.67.21.5750-5760.2001.PMC93369.PMID11722932.
  17. ^Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE (January 2012)."De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities".The ISME Journal.6(1): 81–93.doi:10.1038/ismej.2011.78.PMC3246234.PMID21716304.
  18. ^Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M (October 2003)."The genome ofNanoarchaeum equitans:insights into early archaeal evolution and derived parasitism ".Proceedings of the National Academy of Sciences of the United States of America.100(22): 12984–12988.doi:10.1073/pnas.1735403100.PMC240731.PMID14566062.
  19. ^Podar M, Makarova KS, Graham DE, Wolf YI, Koonin EV, Reysenbach AL (December 2013)."Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park".Biology Direct.8(1): 9.doi:10.1186/1745-6150-8-9.PMC3655853.PMID23607440.
  20. ^abWilliams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, et al. (June 2017)."Integrative modeling of gene and genome evolution roots the archaeal tree of life".Proceedings of the National Academy of Sciences of the United States of America.114(23): E4602–E4611.doi:10.1073/pnas.1618463114.PMC5468678.PMID28533395.
  21. ^abcDombrowski N, Williams TA, Sun J, Woodcroft BJ, Lee JH, Minh BQ, et al. (August 2020)."Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution".Nature Communications.11(1): 3939.doi:10.1038/s41467-020-17408-w.PMC7414124.PMID32770105.
  22. ^abYutian Feng, Uri Neri, Sean Gosselin, Artemis S Louyakis, R Thane Papke, Uri Gophna, Johann Peter Gogarten (2021).The Evolutionary Origins of Extreme Halophilic Archaeal Lineages.Oxford Academic.
  23. ^J.P. Euzéby."Parvarchaeota".List of Prokaryotic names with Standing in Nomenclature(LPSN).Retrieved2021-06-27.
  24. ^Sayers; et al."Parvarchaeota".National Center for Biotechnology Information(NCBI) taxonomy database.Retrieved2021-03-20.
  25. ^"GTDB release 08-RS214".Genome Taxonomy Database.Retrieved6 December2021.
  26. ^"ar53_r214.sp_label".Genome Taxonomy Database.Retrieved10 May2023.
  27. ^"Taxon History".Genome Taxonomy Database.Retrieved6 December2021.
  28. ^Göker, Markus; Oren, Aharon (22 January 2024)."Valid publication of names of two domains and seven kingdoms of prokaryotes".International Journal of Systematic and Evolutionary Microbiology.74(1).doi:10.1099/ijsem.0.006242.ISSN1466-5026.PMID38252124.
[edit]


Retrieved from "https://en.wikipedia.org/w/index.php?title=DPANN&oldid=1234402000"