Nanoarchaeota Explained

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.

Taxonomy

Members of the Nanoarchaeota are associated with different host organisms and environmental conditions.^[2] 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.^[3]

The phylogeny of the Nanoarchaeota is anchored by its only cultured representative, Nanoarchaeum equitans, which clusters in a separate evolutionary group than other archaea,^{[4] [5]} 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.^[6]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)^[7] and the National Center for Biotechnology Information (NCBI).^[8]

• Class "Nanoarchaeia" Vazquez-Campos et al. 2021 ["Nanoarchaea" <small>Huber et al. 2011</small>;<ref name="Wiley-2015">{{Cite book |url=https://onlinelibrary.wiley.com/doi/book/10.1002/9781118960608 |title=Bergey's Manual of Systematics of Archaea and Bacteria |date=2015-04-17 |publisher=Wiley |isbn=978-1-118-96060-8 |editor-last=Trujillo |editor-first=Martha E |edition=1 |language=en |doi=10.1002/9781118960608.obm00129 |editor-last2=Dedysh |editor-first2=Svetlana |editor-last3=DeVos |editor-first3=Paul |editor-last4=Hedlund |editor-first4=Brian |editor-last5=Kämpfer |editor-first5=Peter |editor-last6=Rainey |editor-first6=Fred A |editor-last7=Whitman |editor-first7=William B}}</ref> Nanobdellia <small>Kato et al. 2022</small><ref name="Kato-2022">{{Cite journal |last1=Kato |first1=Shingo |last2=Ogasawara |first2=Ayaka |last3=Itoh |first3=Takashi |last4=Sakai |first4=Hiroyuki D. |last5=Shimizu |first5=Michiru |last6=Yuki |first6=Masahiro |last7=Kaneko |first7=Masanori |last8=Takashina |first8=Tomonori |last9=Ohkuma |first9=MoriyaYR 2022 |title=Nanobdella aerobiophila gen. nov., sp. nov., a thermoacidophilic, obligate ectosymbiotic archaeon, and proposal of Nanobdellaceae fam. nov., Nanobdellales ord. nov. and Nanobdellia class. nov. |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005489 |journal=International Journal of Systematic and Evolutionary Microbiology |year=2022 |volume=72 |issue=8 |pages=005489 |doi=10.1099/ijsem.0.005489 |pmid=35993221 |s2cid=251720962 |issn=1466-5034}}</ref>]
  • Order "Jingweiarchaeales" Rao et al. 2023
    • Family "Haiyanarchaeaceae" Rao et al. 2023
      • Genus ?"Candidatus Haiyanarchaeum" Rao et al. 2023
        • "Ca. H. thermophilum" 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 "Nanoarchaeales" Huber et al. 2011 [Nanobdellales <small>Kato et al. 2022</small><ref name="Kato-2022"/>]
    • Family "Nanoarchaeaceae" Huber et al. 2011
      • Genus "Nanoarchaeum" Huber et al. 2002^[9]
        • "N. equitans" Huber et al. 2002^[9]
    • Family "Nanopusillaceae" Huber et al. 2011 [Nanobdellaceae <small>Kato et al. 2022</small><ref name="Kato-2022"/>]
      • Genus Nanobdella Kato et al. 2022
        • N. aerobiophila Kato et al. 2022
      • Genus "Candidatus Nanoclepta" St. John et al. 2019^[10]
        • "Ca. N. minuta" St. John et al. 2019^[10]
      • Genus "Candidatus Nanopusillus" Wurch et al. 2016^[11]
        • "Ca. N. acidilobi" Wurch et al. 2016^[11]
        • "Ca. N. stetteri" (Castelle et al. 2015) Rinke et al. 2020^[12]
  • Order "Tiddalikarchaeales" Vazquez-Campos et al. 2021^[13]
    • Family "Tiddalikarchaeaceae" Vazquez-Campos et al. 2021^[13]
      • Genus "Candidatus Tiddalikarchaeum" Vazquez-Campos et al. 2021^[13]
        • "Ca. T. anstoanum" Vazquez-Campos et al. 2021^[13]
  • Order "Parvarchaeales" Rinke et al. 2020^[12]
    • Family "Parvarchaeaceae" Rinke et al. 2020 ["Acidifodinimicrobiaceae" <small>Luo et al. 2020</small><ref name="Luo-2020">{{Cite journal |last1=Luo |first1=Zhen-Hao |last2=Li |first2=Qi |last3=Lai |first3=Yan |last4=Chen |first4=Hao |last5=Liao |first5=Bin |last6=Huang |first6=Li-nan |date=2020 |title=Diversity and Genomic Characterization of a Novel Parvarchaeota Family in Acid Mine Drainage Sediments |journal=Frontiers in Microbiology |volume=11 |page=612257 |doi=10.3389/fmicb.2020.612257 |issn=1664-302X |pmc=7779479 |pmid=33408709|doi-access=free }}</ref>]
      • Genus ?"Candidatus Rehaiarchaeum fermentans" Rao et al. 2023
        • "Ca. R. fermentans" Rao et al. 2023
      • Genus "Candidatus Acidifodinimicrobium" Luo et al. 2020
        • "Ca. A. mancum" Luo et al. 2020
      • Genus "Candidatus Parvarchaeum" Baker et al. 2010^[14]
        • ?"Ca. P. tengchongense" Rao et al. 2023
        • "Ca. P. acidiphilum" Baker et al. 2010
        • "Ca. P. paracidiphilum" corrig. Baker et al. 2010

Characteristics

Cells of N. equitans are spherical with a diameter of approximately 400 nm,^[9] and have a very short and compact DNA sequence with the entire genome containing only 490,885 base pairs. 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. Due to its limited machinery, it is an obligate parasite, the only one known in the Archaea. Because of their unusual ss rRNA sequences, they are difficult to detect using standard polymerase chain reaction methods.^[15] Cells of N. equitans contain a normal S-layer with sixfold symmetry with a 15 nm lattice constant.

Genome structure

Small cells between 100 and 400 nm in diameter and highly streamlined genomes of 0.491-0.606 Mbp characterize nanoarchaeotes.^[16] The genomes of described nanoarchaeotes demonstrate different degrees of reduction, which is compatible with a host dependent lifestyle.^[17] Certain nanaoarchaeotes still have genes for the CRISPR-Cas systems, archaeal flagella, and the gluconeogenesis pathway.^[18]

Habitat

Nanoarchaeotes are obligate symbionts that grow attached to an archaeal host known as Ignicoccus. Both terrestrial hot springs and underwater hydrothermal vents have yielded isolates in the genus Nanoarchaeum . However, there is evidence that nanoarcheotes reside in a variety of habitats outside of marine thermal vents.  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. 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.

Metabolism

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. The majority of recognized metabolic processes, such as the creation of monomers like amino acids, nucleotides, and coenzymes, lack recognizable genes in this organism.

See also

• List of Archaea genera

Further reading

• Clingenpeel. Scott. 4. Kan. Jinjun. Macur. Richard E.. Woyke. Tanja. Lovalo. Dave. Varley. John. Inskeep. William P.. Nealson. Kenneth. McDermott. Timothy R.. Yellowstone Lake Nanoarchaeota. Frontiers in Microbiology. 11 September 2013. 4. 274. 10.3389/fmicb.2013.00274. 24062731. 3769629. free.
• Hohn . MJ . Hedlund BP . Huber H . 2002 . Detection of 16S rDNA sequences representing the novel phylum 'Nanoarchaeota': indication for a wide distribution in high temperature biotopes . Syst. Appl. Microbiol. . 25 . 551–554 . 12583716 . 10.1078/07232020260517698 . 4.
• Huber . H . 4 . Hohn MJ . Rachel R . Fuchs T . Wimmer VC . Stetter KO . 2002 . A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont . Nature . 417 . 63–67 . 11986665 . 10.1038/417063a . 6884. 2002Natur.417...63H . 4395094 .
• Stackebrandt . E . 4 . Frederiksen W . Garrity GM . Grimont PA . Kampfer P . Maiden MC . Nesme X . Rossello-Mora R . Swings J . Truper HG . Vauterin L . Ward AC . Whitman WB . 2002 . Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology . Int. J. Syst. Evol. Microbiol. . 52 . 1043–1047 . 12054223 . 10.1099/ijs.0.02360-0 . Pt 3.
• Christensen . H . 4 . Bisgaard M . Frederiksen W . Mutters R . Kuhnert P . Olsen JE . 2001 . Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision) . Int. J. Syst. Evol. Microbiol. . 51 . 2221–5 . 11760965 . Pt 6 . 10.1099/00207713-51-6-2221. free .
• Gurtler . V . Mayall BC . 2001 . Genomic approaches to typing, taxonomy and evolution of bacterial isolates . Int. J. Syst. Evol. Microbiol. . 51 . 3–16 . 11211268 . Pt 1 . 10.1099/00207713-51-1-3.
• Dalevi . D . Hugenholtz P . Blackall LL . 2001 . A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data . Int. J. Syst. Evol. Microbiol. . 51 . 385–91 . 11321083 . Pt 2 . 10.1099/00207713-51-2-385. free .
• Keswani . J . Whitman WB . 2001 . Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes . Int. J. Syst. Evol. Microbiol. . 51 . 667–78 . 11321113 . Pt 2 . 10.1099/00207713-51-2-667. free .
• Young . JM . 2001 . Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy . Int. J. Syst. Evol. Microbiol. . 51 . 945–53 . 11411719 . Pt 3 . 10.1099/00207713-51-3-945.
• Christensen . H . 4 . Angen O . Mutters R . Olsen JE . Bisgaard M . 2000 . DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA . Int. J. Syst. Evol. Microbiol. . 50 . 1095–102 . 10843050 . 10.1099/00207713-50-3-1095 . 3. free .
• Xu . HX . 4 . Kawamura Y . Li N . Zhao L . Li TM . Li ZY . Shu S . Ezaki T . 2000 . A rapid method for determining the G+C content of bacterial chromosomes by monitoring fluorescence intensity during DNA denaturation in a capillary tube . Int. J. Syst. Evol. Microbiol. . 50 . 1463–9 . 10939651 . 10.1099/00207713-50-4-1463 . 4. free .
• Young . JM . 2000 . Suggestions for avoiding on-going confusion from the Bacteriological Code . Int. J. Syst. Evol. Microbiol. . 50 . 1687–9 . 10939677 . 10.1099/00207713-50-4-1687 . 4. free .
• Hansmann . S . Martin W . 2000 . Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis . Int. J. Syst. Evol. Microbiol. . 50 . 1655–63 . 10939673 . 10.1099/00207713-50-4-1655 . 4. free .
• Tindall . BJ . 1999 . Proposal to change the Rule governing the designation of type strains deposited under culture collection numbers allocated for patent purposes . Int. J. Syst. Bacteriol. . 49 . 1317–1319 . 10490293 . 10.1099/00207713-49-3-1317 . 3. free .
• Tindall . BJ . 1999 . Proposal to change Rule 18a, Rule 18f and Rule 30 to limit the retroactive consequences of changes accepted by the ICSB . Int. J. Syst. Bacteriol. . 49 . 1321–1322 . 10425797 . 10.1099/00207713-49-3-1321 . 3. free .
• Tindall . BJ . 1999 . Misunderstanding the Bacteriological Code . Int. J. Syst. Bacteriol. . 49 . 1313–1316 . 10425796 . 10.1099/00207713-49-3-1313 . 3. free .
• Tindall . BJ . 1999 . Proposals to update and make changes to the Bacteriological Code . Int. J. Syst. Bacteriol. . 49 . 1309–1312 . 10425795 . 10.1099/00207713-49-3-1309 . 3. free .
• Palys . T . Nakamura LK . Cohan FM . 1997 . Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data . Int. J. Syst. Bacteriol. . 47 . 1145–1156 . 9336922 . 10.1099/00207713-47-4-1145 . 4. free .
• Euzeby . JP . 1997 . List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet . Int. J. Syst. Bacteriol. . 47 . 590–592 . 9103655 . 10.1099/00207713-47-2-590 . 2. free .
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Notes and References

1. See the NCBI webpage on Nanoarchaeota. Data extracted from the Web site: NCBI taxonomy resources . . 2007-03-19.
2. Munson-McGee . Jacob H. . Field . Erin K. . Bateson . Mary . Rooney . Colleen . Stepanauskas . Ramunas . Young . Mark J. . 2015-11-15 . Wommack . K. E. . Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs . Applied and Environmental Microbiology . en . 81 . 22 . 7860–7868 . 2015ApEnM..81.7860M . 10.1128/AEM.01539-15 . 0099-2240 . 4616950 . 26341207.
3. 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 . 10.1186/s40168-018-0539-8 . 2049-2618 . 6142677 . 30223889 . free .
4. 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 . 10.1016/j.cell.2018.02.016 . 29522741 . 3801477 . 0092-8674. free .
5. 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 . en . 100 . 22 . 12984–12988 . 2003PNAS..10012984W . 10.1073/pnas.1735403100 . 0027-8424 . 240731 . 14566062 . free.
6. Book: http://doi.wiley.com/10.1002/9780470750865 . Archaea . 2006-12-08 . Blackwell Publishing Ltd . 978-0-470-75086-5 . Garrett . Roger A. . Malden, MA, USA . en . 10.1002/9780470750865 . Klenk . Hans-Peter .
7. Web site: J.P. Euzéby . Phylum "Candidatus Nanoarchaeota" . 2021-11-17 . List of Prokaryotic names with Standing in Nomenclature (LPSN) .
8. Web site: Sayers . etal. Nanoarchaeota . 2021-06-05 . National Center for Biotechnology Information (NCBI) taxonomy database.
9. 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 . en . 417 . 6884 . 63–67 . 10.1038/417063a . 11986665 . 2002Natur.417...63H . 4395094 . 1476-4687.
10. 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 . en . 42 . 1 . 94–106 . 10.1016/j.syapm.2018.08.005 . 30195930 . 1470848 . 52178746 . 0723-2020. free .
11. 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 . en . 7 . 1 . 12115 . 10.1038/ncomms12115 . 2041-1723 . 4935971 . 27378076. 2016NatCo...712115W .
12. 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 . en . 946–959 . 10.1038/s41564-021-00918-8. 10.1101/2020.03.01.972265 . Nature Microbiology. 6 . 7 . 34155373 . 231984712 .
13. 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 . 10.3389/fmicb.2021.732575 . 1664-302X . 8561730 . 34737728. free .
14. 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 . en . 107 . 19 . 8806–8811 . 10.1073/pnas.0914470107 . 0027-8424 . 2889320 . 20421484. 2010PNAS..107.8806B . free .
15. 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 . en . 417 . 6884 . 63–67 . 10.1038/417063a . 11986665 . 2002Natur.417...63H . 4395094 . 0028-0836.
16. Web site: Nanoarchaeota - an overview ScienceDirect Topics . 2023-04-08 . www.sciencedirect.com.
17. Web site: Nanoarchaeota - an overview ScienceDirect Topics . 2023-04-08 . www.sciencedirect.com.
18. Web site: Nanoarchaeota - an overview ScienceDirect Topics . 2023-04-08 . www.sciencedirect.com.