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Nanoarchaeota

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Nanoarchaeota
Nanoarcheotum Nanopusillus acidilobi attached to Acidilobus.
Scientific classification Edit this classification
Domain: Archaea
Superphylum: DPANN
Phylum: Nanoarchaeota
Class: Nanobdellia
Kato et al. 2022
Order
  • JAPDLS01
  • "Jingweiarchaeales"
  • Nanobdellales
  • "Pacearchaeales"
  • "Parvarchaeales"
  • "Tiddalikarchaeales"
  • "Woesearchaeales"
Synonyms
  • Nanobdellota Huber et al. 2023
  • "Pacearchaeota" Castelle et al. 2015
  • "Parvarchaeota" Rinke et al. 2013
  • "Woesearchaeota" Castelle et al. 2015

Nanoarchaeota (Greek, "dwarf or tiny ancient one") is a proposed phylum (Candidatus Nanoarchaeota) in the domain Archaea[1] that currently has only one representative, Nanoarchaeum equitans, which was discovered in a submarine hydrothermal vent and first described in 2002.[2]

Taxonomy

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Members of the Nanoarchaeota are associated with different host organisms and environmental conditions.[3] Despite small size, a reduced genome and limited respiration, members of the Nanoarchaeota have unusual metabolic features. For example, N. equitans has a complex and highly developed intercellular communication system.[4]

The phylogeny of the Nanoarchaeota is anchored by its only cultured representative, Nanoarchaeum equitans, which clusters in a separate evolutionary group than other archaea,[5][6] which have recently been reclassified. Further analysis has shown that N. equitans diverged early on in the evolution of Archaea, as indicated by the 16S rRNA sequence. This suggests that they occupy a deeply branching position within this group.[7]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[8] and the National Center for Biotechnology Information (NCBI).[9]

Phylogeny of Nanobdellota[10][11][12]
"Tiddalikarchaeales"
"Tiddalikarchaeaceae"

"Ca. Tiddalikarchaeum anstoanum"

"Jingweiarchaeales"
"Jingweiarchaeaceae"

"Ca. Jingweiarchaeum tengchongense"

"JAPDLS01"
"Haiyanarchaeaceae"

"Ca. Haiyanarchaeum thermophilum"

"Parvarchaeales"
"Parvarchaeaceae"

"Ca. Rehaiarchaeum fermentans"

"Ca. Acidifodinimicrobium mancum"

"Ca. Parvarchaeum"

"Ca. P. paracidiphilum"

"Ca. P. paracidiphilum"

"Ca. P. tengchongense"

"Pacearchaeales"

"Woesearchaeales"

Nanobdellales
"Nanoarchaeaceae"

"Nanoarchaeum equitans"

Nanobdellaceae

"Ca. Nanoclepta minuta"

Nanobdella aerobiophila

"Ca. Nanopusillus"

"Ca. N. acidilobi"

"Ca. N. stetteri"

  • Class Nanobdellia Kato et al. 2022[13] ["Nanoarchaea" Huber et al. 2011;[14] "Nanoarchaeia" Vazquez-Campos et al. 2021[15]]
    • Order Nanobdellales Kato et al. 2022[13] [Nanoarchaeales Huber et al. 2011[14]]
      • Family "Nanoarchaeaceae" Huber et al. 2011[14]
      • Family Nanobdellaceae Kato et al. 2022[13] ["Nanopusillaceae" Huber et al. 2011[14]]
        • Genus Nanobdella Kato et al. 2022[13]
          • N. aerobiophila Kato et al. 2022[13]
        • Genus "Candidatus Nanoclepta" St. John et al. 2019[16]
          • "Ca. N. minuta" St. John et al. 2019[16]
        • Genus "Candidatus Nanopusillus" Wurch et al. 2016[17]
          • "Ca. N. acidilobi" Wurch et al. 2016[17]
          • ?"Ca. N. massiliensis" Hassani et al. 2022
          • ?"Ca. N. phoceensis" Hassani et al. 2024
          • "Ca. N. stetteri" (Castelle et al. 2015) Rinke et al. 2020[18]
    • Order "Tiddalikarchaeales" Vazquez-Campos et al. 2021[15]
      • Family "Tiddalikarchaeaceae" Vazquez-Campos et al. 2021[15]
        • Genus "Candidatus Tiddalikarchaeum" Vazquez-Campos et al. 2021[15]
          • "Ca. T. anstoanum" Vazquez-Campos et al. 2021[15]
    • Order "Jingweiarchaeales" Rao et al. 2023
      • Family "Jingweiarchaeaceae" Rao et al. 2023
        • Genus "Candidatus Jingweiarchaeum" Rao et al. 2023
          • "Ca. J. tengchongense" Rao et al. 2023
    • Order JAPDLS01
      • Family "Haiyanarchaeaceae" Rao et al. 2023
        • Genus "Candidatus Haiyanarchaeum" Rao et al. 2023
          • "Ca. H. thermophilum" Rao et al. 2023
    • Order "Parvarchaeales" Rinke et al. 2020[18]
      • Family "Parvarchaeaceae" Rinke et al. 2020[18] ["Acidifodinimicrobiaceae" Luo et al. 2020[19]]
        • Genus "Candidatus Rehaiarchaeum" Rao et al. 2023
          • "Ca. R. fermentans" Rao et al. 2023
        • Genus "Candidatus Acidifodinimicrobium" Luo et al. 2020[19]
          • "Ca. A. mancum" Luo et al. 2020[19]
        • Genus "Candidatus Parvarchaeum" Baker et al. 2010[20]
          • "Ca. P. acidiphilum" Baker et al. 2010 [20]
          • "Ca. P. paracidiphilum" corrig. Baker et al. 2010 [20]
          • "Ca. P. tengchongense" Rao et al. 2023
Nanoarchaeum equitans

Characteristics

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Cells of N. equitans are spherical with a diameter of approximately 400 nm,[2] and have a very short and compact DNA sequence with the entire genome containing only 490,885 base pairs.[6] While they have the genetic code to carry out processing and repair, they cannot carry out certain biosynthetic and metabolic processes such as lipid, amino-acid, cofactor, or nucleotide synthesis.[6] Due to its limited machinery, it is an obligate parasite, the only one known in the Archaea.[6] Because of their unusual ss rRNA sequences, they are difficult to detect using standard polymerase chain reaction methods.[21] Cells of N. equitans contain a normal S-layer with sixfold symmetry with a 15 nm lattice constant.[21]

Genome structure

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Small cells between 100 and 400 nm in diameter and highly streamlined genomes of 0.491-0.606 Mbp characterize nanoarchaeotes.[22] The genomes of described nanoarchaeotes demonstrate different degrees of reduction, which is compatible with a host dependent lifestyle.[23] Certain nanaoarchaeotes still have genes for the CRISPR-Cas systems, archaeal flagella, and the gluconeogenesis pathway.[24]

Habitat

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Nanoarchaeotes are obligate symbionts that grow attached to an archaeal host known as Ignicoccus.[25] Both terrestrial hot springs and underwater hydrothermal vents have yielded isolates in the genus Nanoarchaeum .[26] However, there is evidence that nanoarcheotes reside in a variety of habitats outside of marine thermal vents.[3]  Genetic evidence for members of the Nanoarchaeota has been discovered to be pervasive in terrestrial hot springs and mesophilic hypersaline habitats using primers created based on the sequence of the 16S rRNA gene of Nanoarchaeum equitans.[3] In addition, the discovery of ribosomal sequences in photic-zone water samples taken distant from hydrothermal vents raises the possibility that Nanoarchaeota are an ubiquitous and diversified group of Archaea that can live in habitats with a variety of temperatures and geochemical settings.[3]

Metabolism

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Although much of the metabolism of members of the Nanoarchaeota is unknown, its host is an autotroph that grows on elemental sulphur as an electron acceptor and H2 as an electron donor.[26] The majority of recognized metabolic processes, such as the creation of monomers like amino acids, nucleotides, and coenzymes, lack recognizable genes in this organism.[26]

See also

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References

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  1. ^ See the NCBI webpage on Nanoarchaeota. Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. Retrieved 2007-03-19.
  2. ^ a b c d Huber, Harald; Hohn, Michael J.; Rachel, Reinhard; Fuchs, Tanja; Wimmer, Verena C.; Stetter, Karl O. (May 2002). "A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont". Nature. 417 (6884): 63–67. Bibcode:2002Natur.417...63H. doi:10.1038/417063a. ISSN 1476-4687. PMID 11986665. S2CID 4395094.
  3. ^ a b c d Munson-McGee, Jacob H.; Field, Erin K.; Bateson, Mary; Rooney, Colleen; Stepanauskas, Ramunas; Young, Mark J. (2015-11-15). Wommack, K. E. (ed.). "Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs". Applied and Environmental Microbiology. 81 (22): 7860–7868. Bibcode:2015ApEnM..81.7860M. doi:10.1128/AEM.01539-15. ISSN 0099-2240. PMC 4616950. PMID 26341207.
  4. ^ Jarett, Jessica K.; Nayfach, Stephen; Podar, Mircea; Inskeep, William; Ivanova, Natalia N.; Munson-McGee, Jacob; Schulz, Frederik; Young, Mark; Jay, Zackary J.; Beam, Jacob P.; Kyrpides, Nikos C.; Malmstrom, Rex R.; Stepanauskas, Ramunas; Woyke, Tanja (2018-09-17). "Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis". Microbiome. 6 (1): 161. doi:10.1186/s40168-018-0539-8. ISSN 2049-2618. PMC 6142677. PMID 30223889.
  5. ^ Castelle, Cindy J.; Banfield, Jillian F. (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. ISSN 0092-8674. PMID 29522741. S2CID 3801477.
  6. ^ a b c d Waters, Elizabeth; Hohn, Michael J.; Ahel, Ivan; Graham, David E.; Adams, Mark D.; Barnstead, Mary; Beeson, Karen Y.; Bibbs, Lisa; Bolanos, Randall; Keller, Martin; Kretz, Keith; Lin, Xiaoying; Mathur, Eric; Ni, Jingwei; Podar, Mircea (2003-10-28). "The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism". Proceedings of the National Academy of Sciences. 100 (22): 12984–12988. Bibcode:2003PNAS..10012984W. doi:10.1073/pnas.1735403100. ISSN 0027-8424. PMC 240731. PMID 14566062.
  7. ^ Garrett, Roger A.; Klenk, Hans-Peter, eds. (2006-12-08). "Archaea". Malden, MA, USA: Blackwell Publishing Ltd. doi:10.1002/9780470750865. ISBN 978-0-470-75086-5. {{cite book}}: Missing or empty |title= (help)
  8. ^ J.P. Euzéby. "Phylum "Candidatus Nanoarchaeota"". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-11-17.
  9. ^ Sayers; et al. "Nanoarchaeota". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-06-05.
  10. ^ "GTDB release 09-RS220". Genome Taxonomy Database. Retrieved 10 May 2024.
  11. ^ "ar53_r220.sp_label". Genome Taxonomy Database. Retrieved 10 May 2024.
  12. ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2024.
  13. ^ a b c d e Kato, Shingo; Ogasawara, Ayaka; Itoh, Takashi; Sakai, Hiroyuki D.; Shimizu, Michiru; Yuki, Masahiro; Kaneko, Masanori; Takashina, Tomonori; Ohkuma, MoriyaYR 2022 (2022). "Nanobdella aerobiophila gen. nov., sp. nov., a thermoacidophilic, obligate ectosymbiotic archaeon, and proposal of Nanobdellaceae fam. nov., Nanobdellales ord. nov. and Nanobdellia class. nov". International Journal of Systematic and Evolutionary Microbiology. 72 (8): 005489. doi:10.1099/ijsem.0.005489. ISSN 1466-5034. PMID 35993221. S2CID 251720962.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  14. ^ a b c d Trujillo, Martha E; Dedysh, Svetlana; DeVos, Paul; Hedlund, Brian; Kämpfer, Peter; Rainey, Fred A; Whitman, William B, eds. (2015-04-17). Bergey's Manual of Systematics of Archaea and Bacteria (1 ed.). Wiley. doi:10.1002/9781118960608.obm00129. ISBN 978-1-118-96060-8.
  15. ^ a b c d e Vázquez-Campos, Xabier; Kinsela, Andrew S.; Bligh, Mark W.; Payne, Timothy E.; Wilkins, Marc R.; Waite, T. David (2021). "Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site". Frontiers in Microbiology. 12: 732575. doi:10.3389/fmicb.2021.732575. ISSN 1664-302X. PMC 8561730. PMID 34737728.
  16. ^ a b St. John, Emily; Liu, Yitai; Podar, Mircea; Stott, Matthew B.; Meneghin, Jennifer; Chen, Zhiqiang; Lagutin, Kirill; Mitchell, Kevin; Reysenbach, Anna-Louise (2019-01-01). "A new symbiotic nanoarchaeote (Candidatus Nanoclepta minutus) and its host (Zestosphaera tikiterensis gen. nov., sp. nov.) from a New Zealand hot spring". Systematic and Applied Microbiology. Taxonomy of uncultivated Bacteria and Archaea. 42 (1): 94–106. doi:10.1016/j.syapm.2018.08.005. ISSN 0723-2020. OSTI 1470848. PMID 30195930. S2CID 52178746.
  17. ^ a b Wurch, Louie; Giannone, Richard J.; Belisle, Bernard S.; Swift, Carolyn; Utturkar, Sagar; Hettich, Robert L.; Reysenbach, Anna-Louise; Podar, Mircea (2016-07-05). "Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment". Nature Communications. 7 (1): 12115. Bibcode:2016NatCo...712115W. doi:10.1038/ncomms12115. ISSN 2041-1723. PMC 4935971. PMID 27378076.
  18. ^ a b c Rinke, Christian; Chuvochina, Maria; Mussig, Aaron J.; Chaumeil, Pierre-Alain; Davin, Adrian A.; Waite, David W.; Whitman, William B.; Parks, Donovan H.; Hugenholtz, Philip (2021-02-17). "Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy". Nature Microbiology. 6 (7): 946–959. bioRxiv 10.1101/2020.03.01.972265. doi:10.1038/s41564-021-00918-8. PMID 34155373. S2CID 231984712.
  19. ^ a b c Luo, Zhen-Hao; Li, Qi; Lai, Yan; Chen, Hao; Liao, Bin; Huang, Li-nan (2020). "Diversity and Genomic Characterization of a Novel Parvarchaeota Family in Acid Mine Drainage Sediments". Frontiers in Microbiology. 11: 612257. doi:10.3389/fmicb.2020.612257. ISSN 1664-302X. PMC 7779479. PMID 33408709.
  20. ^ a b c Baker, Brett J.; Comolli, Luis R.; Dick, Gregory J.; Hauser, Loren J.; Hyatt, Doug; Dill, Brian D.; Land, Miriam L.; VerBerkmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F. (2010-05-11). "Enigmatic, ultrasmall, uncultivated Archaea". Proceedings of the National Academy of Sciences. 107 (19): 8806–8811. Bibcode:2010PNAS..107.8806B. doi:10.1073/pnas.0914470107. ISSN 0027-8424. PMC 2889320. PMID 20421484.
  21. ^ a b Huber, Harald; Hohn, Michael J.; Rachel, Reinhard; Fuchs, Tanja; Wimmer, Verena C.; Stetter, Karl O. (2002-05-02). "A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont". Nature. 417 (6884): 63–67. Bibcode:2002Natur.417...63H. doi:10.1038/417063a. ISSN 0028-0836. PMID 11986665. S2CID 4395094.
  22. ^ "Nanoarchaeota - an overview | ScienceDirect Topics". www.sciencedirect.com. Retrieved 2023-04-08.
  23. ^ "Nanoarchaeota - an overview | ScienceDirect Topics". www.sciencedirect.com. Retrieved 2023-04-08.
  24. ^ "Nanoarchaeota - an overview | ScienceDirect Topics". www.sciencedirect.com. Retrieved 2023-04-08.
  25. ^ Huber, Harald; Hohn, Michael J.; Rachel, Reinhard; Stetter, Karl O. (2006), Dworkin, Martin; Falkow, Stanley; Rosenberg, Eugene; Schleifer, Karl-Heinz (eds.), "Nanoarchaeota", The Prokaryotes: Volume 3: Archaea. Bacteria: Firmicutes, Actinomycetes, New York, NY: Springer, pp. 274–280, doi:10.1007/0-387-30743-5_14, ISBN 978-0-387-30743-5, retrieved 2023-04-08
  26. ^ a b c Amils, Ricardo (2011), "Nanoarchaeota", in Gargaud, Muriel; Amils, Ricardo; Quintanilla, José Cernicharo; Cleaves, Henderson James (Jim) (eds.), Encyclopedia of Astrobiology, Berlin, Heidelberg: Springer, p. 1106, doi:10.1007/978-3-642-11274-4_1040, ISBN 978-3-642-11274-4, retrieved 2023-04-08

Further reading

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