Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

Reply to ‘Evolutionary placement of Methanonatronarchaeia’

Nature Microbiology volume 4, pages 560–561 (2019)Cite this article

Subjects

Sorokin, D. Y. et al. reply — Different phylogenetic methods applied to different gene sets yield alternative positions for the proposed archaeal class ‘Methanonatronarchaeia’ in the archaeal tree. A more representative sampling of archaeal genomes is essential to resolve this phylogenetic impasse.

We appreciate the interest of Aouad and colleagues1 in our work on the archaeal class Methanonatronarchaeia2,3 and their effort to clarify the phylogenetic position of this unique group of extremely halophilic, methyl-reducing methanogens. In our analysis, Methanonatronarchaeia formed a clade with the class Halobacteria — the non-methanogenic euryarchaeal extreme halophiles. Notably, this phylogenetic placement is 100% bootstrap-supported in maximum-likelihood (ML) phylogenetic trees for both 16S ribosomal (r)RNA and concatenated alignments of ribosomal proteins3. Given the congruence of the two trees, the strong support for the Methanonatronarchaeia–Halobacteria clade, the biological plausibility of this affinity and the fact that these trees conformed with the currently favoured solutions for difficult problems in archaeal phylogeny (such as the monophyly of the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota (DPANN) superphylum and the euryarchaeal assemblage including Class I methanogens and Thermococci), we did not perform a more thorough phylogenetic analysis. Such an in-depth analysis was undertaken by Aouad and colleagues1. Their results suggest a different position for Methanonatronarchaeia — much deeper in the archaeal tree, sitting outside the branch that consists of Methanomicrobia (formerly, Class II Methanogens), including Halobacteria (denoted ‘Stenosarchaea’ by Aouad et al.) and the class Archaeoglobi, and at the base of the group (which Aouad et al. denote the ‘superclass Methanotecta’)1. This difference between the results of the two phylogenetic analyses stems primarily from the increasingly stringent removal of fast-evolving sites from the alignment prior to the phylogenetic tree construction that was applied by Aouad and colleagues. After a certain fraction of the fastest sites was removed, the tree topology abruptly transitioned to the deep placement of Methanonatronarchaeia. This procedure is supposed to eliminate the false signal produced by sites with multiple substitutions, and therefore Aouad et al. conclude that the affinity of Methanonatronarchaeia with Halobacteria was an artefact caused by such sites. Aouad et al. also obtained the ‘deeper’ placement of Methanonatronarchaeia with extended sets of conserved protein families and expanded taxon sampling in these cases, even without removing the fast-evolving sites.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

References

  1. Aouad, M., Borrel, G., Brochier-Armanet, C. & Gribaldo, S. Nat. Microbiol. https://doi.org/10.1038/s41564-019-0359-z (2019).

    Article  PubMed  Google Scholar 

  2. Sorokin, D. Y. et al. Nat. Microbiol. 2, 17081 (2017).

    Article  CAS  Google Scholar 

  3. Sorokin, D. Y. et al. Int. J. Syst. Evol. Micr. 68, 2199–2208 (2018).

    Article  CAS  Google Scholar 

  4. Felsenstein, J. (Sinauer Associates, Inc., Sunderland, 2004).

  5. Wagele, J. W. & Rodding, F. Mol. Phylogenet. Evol. 9, 358–365 (1998).

    Article  CAS  Google Scholar 

  6. Vollmer, A. C. & Bark, S. J. Adv. Appl. Microbiol. 102, 1–36 (2018).

    Article  Google Scholar 

  7. Prangishvili, D. et al. Nat. Rev. Microbiol. 15, 724–739 (2017).

    Article  CAS  Google Scholar 

  8. Aouad, M. et al. Mol. Phylogenet. Evol. 127, 46–54 (2018).

    Article  CAS  Google Scholar 

  9. Williams, T. A. et al. Proc. Natl Acad. Sci. USA 114, E4602–E4611 (2017).

    Article  CAS  Google Scholar 

  10. Waters, E. et al. Proc. Natl Acad. Sci. USA 100, 12984–12988 (2003).

    Article  CAS  Google Scholar 

  11. Brochier, C., Gribaldo, S., Zivanovic, Y., Confalonieri, F. & Forterre, P. Genome Biol. 6, R42 (2005).

    Article  Google Scholar 

  12. Petitjean, C., Deschamps, P., Lopez-Garcia, P. & Moreira, D. Genome Biol. Evol. 7, 191–204 (2014).

    Article  Google Scholar 

  13. Parks, D. H. et al. Nat. Biotechnol. 36, 996–1004 (2018).

    Article  CAS  Google Scholar 

  14. Townsend, J. P. & Lopez-Giraldez, F. Syst. Biol. 59, 446–457 (2010).

    Article  CAS  Google Scholar 

  15. Pick, K. S. et al. Mol. Biol. Evol. 27, 1983–1987 (2010).

    Article  CAS  Google Scholar 

  16. Ngugi, D. K. & Stingl, U. Genome Announc. 6, e00383–18 (2018).

    PubMed  PubMed Central  Google Scholar 

  17. Price, M. N., Dehal, P. S. & Arkin, A. P. PLoS ONE 5, e9490 (2010).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Winogradsky Institute of Microbiology, Research Centre for Biotechnology, Russian Academy of Sciences, Moscow, Russia

    Dimitry Y. Sorokin & Alexander Y. Merkel

  2. Department of Biotechnology, Delft University of Technology, Delft, the Netherlands

    Dimitry Y. Sorokin, Ben Abbas & Mark C. M. van Loosdrecht

  3. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

    Kira S. Makarova, Yuri I. Wolf & Eugene V. Koonin

  4. Institute of Catalysis, CSIC, Madrid, Spain

    Manuel Ferrer

  5. School of Biological Sciences, Bangor University, Gwynedd, UK

    Peter N. Golyshin

  6. Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms University, Bonn, Germany

    Erwin A. Galinski

  7. Proteomics Facility, Centro Nacional de Biotecnología, CSIC, Madrid, Spain

    Sergio Ciorda & María Carmen Mena

Authors
  1. Dimitry Y. Sorokin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kira S. Makarova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ben Abbas
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Manuel Ferrer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Peter N. Golyshin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Erwin A. Galinski
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Sergio Ciorda
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. María Carmen Mena
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Alexander Y. Merkel
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yuri I. Wolf
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Mark C. M. van Loosdrecht
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Eugene V. Koonin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Dimitry Y. Sorokin or Eugene V. Koonin.

Ethics declarations

Competing interests

The authors declare no competing interests.

Supplementary Information

Supplementary File 1

Legend for txt file.

Supplementary Dataset 1

Phylogenetic tree of the UspA family.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sorokin, D.Y., Makarova, K.S., Abbas, B. et al. Reply to ‘Evolutionary placement of Methanonatronarchaeia’. Nat Microbiol 4, 560–561 (2019). https://doi.org/10.1038/s41564-019-0358-0

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41564-019-0358-0

This article is cited by

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology