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DPANN

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DPANN
Parvarchaeum acidiphilum
Scientific classification Edit this classification
Domain: Archaea
Superphylum: DPANN
Rinke et al. 2013[1]
Phyla[2]
Synonyms
  • Nanobdellati Rinke, Schwientek, Sczyrba, Ivanova, Anderson, Cheng, Darling, Malfatti, Swan, Gies, Dodsworth, Hedlund, Tsiamis, Sievert, Liu, Eisen, Hallam, Kyrpides, Stepanauskas, Rubin, Hugenholtz and Woyke 2024[3] – the only validly published name

DPANN is a superphylum of Archaea first proposed in 2013.[1] Many members show novel signs of horizontal gene transfer from other domains of life.[1] They are known as nanoarchaea or ultra-small archaea due 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, Nanoarchaeota and Nanohaloarchaeota. Later Woesearchaeota and Pacearchaeota were discovered and proposed within the DPANN superphylum.[4] In 2017, another phylum Altiarchaeota was placed into this superphylum.[5] The monophyly of DPANN is not yet considered established, due to the high mutation rate of the included phyla, which can lead to the artifact of the long branch attraction (LBA) where the lineages are grouped basally or artificially at the base of the phylogenetic tree without being related.[6][7] These analyzes instead suggest that DPANN belongs to Euryarchaeota or is polyphyletic occupying various positions within Euryarchaeota.[6][7][8]

The DPANN groups together different phyla with a variety of environmental distribution and metabolism, ranging from symbiotic and thermophilic forms such as Nanoarchaeota, acidophiles like Parvarchaeota and non-extremophiles like Aenigmarchaeota and Diapherotrites. 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.[9]

Since the recognition of the kingdom rank by the ICNP, the only validly published name for this group is kingdom Nanobdellati.[10]

Characteristics

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They are characterized by being small in size compared to other archaea (nanometric size) and in keeping with their small genome, they have limited but sufficient catabolic capacities to lead a free life, although many are thought to be episymbionts that depend on a symbiotic or parasitic association with other organisms. Many of their characteristics are similar or analogous to those of ultra-small bacteria (CPR group).[4]

Limited metabolic capacities are a product of the small genome and are reflected in the fact that many lack central biosynthetic pathways for nucleotides, aminoacids, and lipids; hence most DPANN archaea, such as ARMAN archaea, which rely on other microbes to meet their biological requirements. But those that have the potential to live freely are fermentative and aerobic heterotrophs.[4]

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 lake sediments. They are rarely found on the ground or in the open ocean.[4]

Classification

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Phylogeny

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Tom A. Williams et al. 2017,[21] Castelle et al. 2015[4] and Dombrowski et al. 2020.[22] Jordan et al. 2017[8] Cavalier-Smith2020[7] and Feng et al 2021.[23]

DPANN may be the first divergent clade of archaea according to some phylogenetic analyses. Recent phylogenetic analyses have found the following phylogeny between phyla.[4][21][22]

Bacteria

Archaea

Other phylogenetic analyzes have suggested that DPANN could belong to Euryarchaeota or that it may even be polyphyletic occupying different positions within Euryarchaeota. It is also debated whether the phylum Altiarchaeota should be classified in DPANN or Euryarchaeota.[22][6] An alternative location for DPANN in the phylogenetic tree is as follows.[8][7][23] The groups marked in quotes are lineages assigned to DPANN, but phylogenetically separated from the rest.

Bacteria

Archaea

Taxonomy

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The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[24] and National Center for Biotechnology Information (NCBI).[25]

GTDB phylogeny of "DPANN"[26][27][28]
"Undinarchaeota"
"Undinarchaeia"

"Undinarchaeales"

Nanobdellati

Superphylum "DPANN" Rinke et al. 2013 (kingdom Nanobdellati)

  • Phylum Microcaldota Sakai et al. 2023
    • Class Microcaldia Sakai et al. 2023
      • Order ?Microcaldales Sakai et al. 2023
  • 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"
      • Order ?"Nanohydrothermales" Xie et al. 2022
      • Order ?"Nucleotidisoterales" Xie et al. 2022
  • Phylum Altarchaeota Probst et al. 2018 (SM1)
    • Class "Altarchaeia" corrig. Probst et al. 2014
      • Order "Altarchaeales" corrig. Probst et al. 2014
  • Phylum "Iainarchaeota" corrig. Rinke et al. 2013 ["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 Nanobdellota Huber et al. 2023
  • Phylum ?"Mamarchaeota"
  • Order ?"Wiannamattarchaeales"

See also

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References

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  1. ^ a b c Rinke 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. PMID 23851394. S2CID 4394530.
  2. ^ 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. PMID 29522741.
  3. ^ 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. ISSN 1466-5026. PMID 38252124.
  4. ^ a b c d e f g Castelle 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. Bibcode:2015CBio...25..690C. doi:10.1016/j.cub.2015.01.014. PMID 25702576.
  5. ^ 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. PMID 28798101.
  6. ^ a b c Nina Dombrowski, Jun-Hoe Lee, Tom A Williams, Pierre Offre, Anja Spang (2019). Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. Nature.
  7. ^ a b c d Cavalier-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. PMC 7203096. PMID 31900730.
  8. ^ a b c Jordan T. Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar, Karen G. Lloyd (2017). Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales. Frontiers.
  9. ^ 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. Bibcode:2017PLoSO..1274930L. doi:10.1371/journal.pone.0174930. PMC 5383146. PMID 28384184.
  10. ^ 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. ISSN 1466-5026. PMID 38252124.
  11. ^ Genomes Online Database
  12. ^ 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. Bibcode:2009ISMEJ...3..159C. doi:10.1038/ismej.2008.99. PMID 18946497.
  13. ^ 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. Bibcode:2006Sci...314.1933B. doi:10.1126/science.1132690. PMID 17185602. S2CID 26033384.
  14. ^ 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. Bibcode:2012ApEnM..78.1015M. doi:10.1128/AEM.06811-11. PMC 3272989. PMID 22156430.
  15. ^ 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. Bibcode:2010PNAS..107.8806B. doi:10.1073/pnas.0914470107. PMC 2889320. PMID 20421484.
  16. ^ 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. Bibcode:2016EnvMR...8..210O. doi:10.1111/1758-2229.12370. PMID 26711582.
  17. ^ 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. Bibcode:2001ApEnM..67.5750T. doi:10.1128/AEM.67.21.5750-5760.2001. PMC 93369. PMID 11722932.
  18. ^ 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. Bibcode:2012ISMEJ...6...81N. doi:10.1038/ismej.2011.78. PMC 3246234. PMID 21716304.
  19. ^ 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 of Nanoarchaeum 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. Bibcode:2003PNAS..10012984W. doi:10.1073/pnas.1735403100. PMC 240731. PMID 14566062.
  20. ^ 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. PMC 3655853. PMID 23607440.
  21. ^ a b Williams 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. Bibcode:2017PNAS..114E4602W. doi:10.1073/pnas.1618463114. PMC 5468678. PMID 28533395.
  22. ^ a b c Dombrowski 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. Bibcode:2020NatCo..11.3939D. doi:10.1038/s41467-020-17408-w. PMC 7414124. PMID 32770105.
  23. ^ a b Yutian 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.
  24. ^ J.P. Euzéby. "Parvarchaeota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.
  25. ^ Sayers; et al. "Parvarchaeota". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  26. ^ "GTDB release 09-RS220". Genome Taxonomy Database. Retrieved 10 May 2024.
  27. ^ "ar53_r220.sp_label". Genome Taxonomy Database. Retrieved 10 May 2024.
  28. ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2024.
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