Asgardarchaeota

    Disentangling taxonomic knots in the realm of Asgard

    The recent flood of novel Asgardarchaeota lineages has triggered this post in an attempt to identify and resolve overlapping taxonomic groups and to perform rank normalisation.

     

    Summary
    The discovery of Asgard archaea, proposed to comprise the closest living prokaryotic relatives to eukaryotes, is arguably one of the major milestones achieved by microbiology research over the last decade. The first Asgard lineage, Lokiarchaeota, was proposed in 2014 [1], and was soon followed by manuscripts introducing us to Thorarchaeota [2], Odin- and Heimdallarchaeota [3], Helarchaeota [4], and most recently a study proposing to split off a new lineage termed Gerdarchaeota from Heimdallarchaeota [5]. This equals about one new Asgard lineage per year. However, recently this pace has changed considerably, with seven (!) new Asgard lineages proposed over the last few months. Our paper describing two new Asgard lineages got caught up in the middle of this, therefore I wrote this blog post to detail our attempt to resolve this situation.

    Note
    While Asgard archaea were originally introduced as a superphylum, the subsequent classification in the Genome Taxonomy Database (GTDB), based on taxonomic rank normalisation using relative evolutionary divergence (RED), assigned this lineage to the rank of phylum [6]. Subsequently, the name Asgardarchaeota with the classes Lokiarchaeia, Thorarchaeia, and Heimdallarchaeia were proposed as Latin placeholder names [6]. Hence, I will be using the GTDB classifications in this blog post.

    The situation

    In a recent paper (https://www.nature.com/articles/s43705-021-00032-0) we conducted an in-depth analysis of two novel Asgardarchaeota lineages and focuses on the role and evolutionary history of stop codon recodings. While our paper was in review, seven new lineages were proposed, with the latest paper published this month. Therefore, we added a “note in proof” to our manuscript where we performed additional phylogenetic inferences. The goal of this exercise was to identify and resolve overlapping taxonomic groups and to perform rank normalisation.

     

    Our proposed solution

    In a nutshell, here is what we found.  

    Our results support the rank of class for four of the recently proposed lineages, the “Hermodarchaeota” [7, 8], “Sifarchaeota” [9], “Baldrarchaeota” and “Wukongarchaeota” [7], from now on referred to as Hermodarchaeia, Sifarchaeia, Baldrarchaeia, and Wukongarchaeia (Fig. 1).

    The remaining novel lineages “Kariarchaeota”, “Hodarchaeota”, and “Borrarchaeota” [7], were placed within these classes and represent the orders Kariarchaeales (LC-2) and Hodarchaeales (LC-3) in Heimdallarchaeia, and the family Borrarchaeaceae within Sifarchaeia, respectively.

    We found that one of the two classes proposed in our manuscript (indicated by green MAG names) is synonymous with the recently proposed lineage “Sifarchaeota” which is in turn synonymous with the even more recently proposed “Borrarchaeota”. Due to its publication priority, we have used the type material of “Sifarchaeota” as the base name for this lineage, noting that it represents a class (Sifarchaeia) according to rank normalisation. We have also proposed the intermediate ranks of family and order, and a corrected spelling of the genus Ca. Sifarchaeotum, i.e. Ca. Sifarchaeum, as well as the species Ca. Borrarchaeum weybense.

    We hope that this proposed solution disentangles the potentially chaotic situation in the Asgardarchaeota.


     Asgardarchaeota tree GTDB rank normalised RED

    Fig. 1 | Asgardarchaeota taxonomy including recently published lineages. Decorated, rank normalised IQTREE (C10, PMSF) from a concatenated protein sequence alignment of 53 archaeal markers.

     

    References

    1. Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 2015; 521: 173–179.
    2. Seitz KW, Lazar CS, Hinrichs K-U, Teske AP, Baker BJ. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J 2016; 10: 1696–1705.
    3. Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 2017; 541: 353–358.
    4. Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J, Sieber JR, et al. Asgard archaea capable of anaerobic hydrocarbon cycling. Nature Communications 2019; 10: 1822.
    5. Cai M, Liu Y, Yin X, Zhou Z, Friedrich MW, Richter-Heitmann T, et al. Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation. Sci China Life Sci 2020.
    6. Rinke C, Chuvochina M, Mussig AJ, Chaumeil P-A, Waite DW, Whitman WB, et al. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology 2021; 10.1038.
    7. Liu Y, Makarova KS, Huang W-C, Wolf YI, Nikolskaya AN, Zhang X, et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 2021; 1–5.
    8. Zhang J-W, Dong H-P, Hou L-J, Liu Y, Ou Y-F, Zheng Y-L, et al. Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. The ISME Journal 2021; 1–18.
    9. Farag IF, Zhao R, Biddle JF. “Sifarchaeota” a novel Asgard phylum from Costa Rica sediment capable of polysaccharide degradation and anaerobic methylotrophy. Appl Environ Microbiol 2021.

        Our paper: Sun, Jiarui, Paul N. Evans, Emma J. Gagen, Ben J. Woodcroft, Brian P. Hedlund, Tanja Woyke, Philip Hugenholtz, and Christian Rinke. 2021. “Recoding of Stop Codons Expands the Metabolic Potential of Two Novel Asgardarchaeota Lineages.” ISME Communications 1 (1): 1–14. https://doi.org/10.1038/s43705-021-00032-0.

     

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