DPANN explained

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.[2] 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.[3] In 2017, another phylum Altiarchaeota was placed into this superphylum.[4] 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. These analyzes instead suggest that DPANN belongs to Euryarchaeota or is polyphyletic occupying various positions within Euryarchaeota.

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.[5]

Since the recognition of the kingdom rank by the ICNP, the proposed name for this group is kingdom Nanobdellati.[6]

Characteristics

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).[3]

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.[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 lake sediments. They are rarely found on the ground or in the open ocean.[3]

Classification

Taxonomy

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

Superphylum "DPANN" Rinke et al. 2013 (= proposed kingdom 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[25])

See also

Notes and References

  1. 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 . Insights into the phylogeny and coding potential of microbial dark matter . En . Nature . 499 . 7459 . 431–437 . July 2013 . 23851394 . 10.1038/nature12352 . 2013Natur.499..431R . 4394530 . free .
  2. 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 . Insights into the phylogeny and coding potential of microbial dark matter . En . Nature . 499 . 7459 . 431–437 . July 2013 . 23851394 . 10.1038/nature12352 . 2013Natur.499..431R . 4394530 . free .
  3. 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 . Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling . Current Biology . 25 . 6 . 690–701 . March 2015 . 25702576 . 10.1016/j.cub.2015.01.014 . free .
  4. Spang A, Caceres EF, Ettema TJ . Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life . Science . 357 . 6351 . eaaf3883 . August 2017 . 28798101 . 10.1126/science.aaf3883 . free .
  5. Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL . Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater . PLOS ONE . 12 . 4 . e0174930 . 2017-04-06 . 28384184 . 5383146 . 10.1371/journal.pone.0174930 . free .
  6. Göker . Markus . Oren . Aharon . Valid publication of names of two domains and seven kingdoms of prokaryotes . International Journal of Systematic and Evolutionary Microbiology . 22 January 2024 . 74 . 1 . 10.1099/ijsem.0.006242 . 38252124 . en . 1466-5026.
  7. http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gi15106 Genomes Online Database
  8. Comolli LR, Baker BJ, Downing KH, Siegerist CE, Banfield JF . Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon . The ISME Journal . 3 . 2 . 159–167 . February 2009 . 18946497 . 10.1038/ismej.2008.99 . free .
  9. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF . Lineages of acidophilic archaea revealed by community genomic analysis . Science . 314 . 5807 . 1933–1935 . December 2006 . 17185602 . 10.1126/science.1132690 . 26033384 .
  10. Murakami S, Fujishima K, Tomita M, Kanai A . 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 . February 2012 . 22156430 . 3272989 . 10.1128/AEM.06811-11 .
  11. Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF . Enigmatic, ultrasmall, uncultivated Archaea . Proceedings of the National Academy of Sciences of the United States of America . 107 . 19 . 8806–8811 . May 2010 . 20421484 . 2889320 . 10.1073/pnas.0914470107 . free .
  12. Ortiz-Alvarez R, Casamayor EO . 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 . April 2016 . 26711582 . 10.1111/1758-2229.12370 .
  13. Takai K, Moser DP, DeFlaun M, Onstott TC, Fredrickson JK . Archaeal diversity in waters from deep South African gold mines . Applied and Environmental Microbiology . 67 . 12 . 5750–5760 . December 2001 . 11722932 . 93369 . 10.1128/AEM.67.21.5750-5760.2001 .
  14. Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE . De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities . The ISME Journal . 6 . 1 . 81–93 . January 2012 . 21716304 . 3246234 . 10.1038/ismej.2011.78 .
  15. 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 . 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 . October 2003 . 14566062 . 240731 . 10.1073/pnas.1735403100 . free .
  16. Podar M, Makarova KS, Graham DE, Wolf YI, Koonin EV, Reysenbach AL . 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 . December 2013 . 8 . 1 . 9 . 10.1186/1745-6150-8-9 . 23607440 . 3655853 . free .
  17. 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.
  18. Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJ, Embley TM . 6 . 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 . June 2017 . 28533395 . 10.1073/pnas.1618463114 . 5468678 . free .
  19. Dombrowski N, Williams TA, Sun J, Woodcroft BJ, Lee JH, Minh BQ, Rinke C, Spang A . 6 . Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution . Nature Communications . 11 . 1 . 3939 . August 2020 . 32770105 . 7414124 . 10.1038/s41467-020-17408-w .
  20. Nina Dombrowski, Jun-Hoe Lee, Tom A Williams, Pierre Offre, Anja Spang (2019). Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. Nature.
  21. 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.
  22. 10.1007/s00709-019-01442-7 . Multidomain ribosomal protein trees and the planctobacterial origin of neomura (Eukaryotes, archaebacteria) . 2020 . Cavalier-Smith . Thomas . Chao . Ema E-Yung . Protoplasma . 257 . 3 . 621–753 . 31900730 . 7203096 .
  23. Web site: J.P. Euzéby . Parvarchaeota . List of Prokaryotic names with Standing in Nomenclature (LPSN). 2021-06-27 .
  24. Web site: Sayers. et al.. Parvarchaeota . 2021-03-20 . National Center for Biotechnology Information (NCBI) taxonomy database.
  25. Göker . Markus . Oren . Aharon . Valid publication of names of two domains and seven kingdoms of prokaryotes . International Journal of Systematic and Evolutionary Microbiology . 22 January 2024 . 74 . 1 . 10.1099/ijsem.0.006242 . 38252124 . en . 1466-5026.

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