Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 74, Issue 7

gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage ‘Asgard’ archaea, and proposal of the new archaeal phylum phyl. nov. and kingdom regn. nov. Open Access

Abstract

An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1, was isolated as a pure co-culture with sp. strain MK-MG from deep-sea methane seep sediment. This organism is, to our knowledge, the first cultured representative of ‘Asgard’ archaea, an archaeal group closely related to eukaryotes. Here, we describe the detailed physiology and phylogeny of MK-D1 and propose gen. nov., sp. nov. to accommodate this strain. Cells were non-motile, small cocci, approximately 300–750 nm in diameter and produced membrane vesicles, chains of blebs and membrane-based protrusions. MK-D1 grew at 4–30 °C with optimum growth at 20 °C. The strain grew chemoorganotrophically with amino acids, peptides and yeast extract with obligate dependence on syntrophy with H-/formate-utilizing organisms. MK-D1 showed the fastest growth and highest maximum cell yield when grown with yeast extract as the substrate: approximately 3 months to full growth, reaching up to 6.7×10 16S rRNA gene copies ml. MK-D1 had a circular 4.32 Mb chromosome with a DNA G+C content of 31.1 mol%. The results of phylogenetic analyses of the 16S rRNA gene and conserved marker proteins indicated that the strain is affiliated with ‘Asgard’ archaea and more specifically DHVC1/DSAG/MBG-B and ‘Lokiarchaeota’/‘Lokiarchaeia’. On the basis of the results of 16S rRNA gene sequence analysis, the most closely related isolated relatives were 3507LT (76.09 %) and RMAS (77.45 %) and the closest relative in enrichment culture was ‘Lokiarchaeum ossiferum’ (95.39 %). The type strain of the type species is MK-D1 (JCM 39240 and JAMSTEC no. 115508). We propose the associated family, order, class, phylum, and kingdom as fam. nov., ord. nov., class. nov., phyl. nov., and regn. nov., respectively. These are in accordance with ICNP Rules 8 and 22 for nomenclature, Rule 30(3)(b) for validation and maintenance of the type strain, and Rule 31a for description as a member of an unambiguous syntrophic association.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): anaerobe , deep-sea sediment , Promethearchaeum , syntrophy and ‘Asgard’ archaea
Funding
This study was supported by the:
  • Core Research for Evolutional Science and Technology (Award JPMJCR19S5)
    • Principle Award Recipient: MakotoMiyata
  • Gordon and Betty Moore Foundation (Award GBMF9743)
    • Principle Award Recipient: MasaruK. Nobu
  • Japan Society for the Promotion of Science (Award JP19H05689)
    • Principle Award Recipient: MoriyaOhkuma
  • Japan Society for the Promotion of Science (Award JP22H04985)
    • Principle Award Recipient: HiroyukiImachi
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006435
2024-07-05
2025-01-14
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/74/7/ijsem006435.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006435&mimeType=html&fmt=ahah

References

  1. Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 2015; 521:173–179 [View Article] [PubMed]
     [Google Scholar]
  2. Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 2017; 541:353–358 [View Article] [PubMed]
     [Google Scholar]
  3. Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG. Archaea and the origin of eukaryotes. Nat Rev Microbiol 2017; 15:711–723 [View Article] [PubMed]
     [Google Scholar]
  4. Liu Y, Makarova KS, Huang W-C, Wolf YI, Nikolskaya AN et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 2021; 593:553–557 [View Article]
     [Google Scholar]
  5. Williams TA, Cox CJ, Foster PG, Szöllősi GJ, Embley TM. Phylogenomics provides robust support for a two-domains tree of life. Nat Ecol Evol 2020; 4:138–147 [View Article] [PubMed]
     [Google Scholar]
  6. Baker BJ, Appler KE, Gong X. New microbial biodiversity in marine sediments. Annu Rev Mar Sci 2021; 13:161–175 [View Article]
     [Google Scholar]
  7. Hoshino T, Doi H, Uramoto G-I, Wörmer L, Adhikari RR et al. Global diversity of microbial communities in marine sediment. Proc Natl Acad Sci U S A 2020; 117:27587–27597 [View Article] [PubMed]
     [Google Scholar]
  8. Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M et al. Isolation of an archaeon at the prokaryote–eukaryote interface. Nature 2020; 577:519–525 [View Article] [PubMed]
     [Google Scholar]
  9. Aoki M, Ehara M, Saito Y, Yoshioka H, Miyazaki M et al. A long-term cultivation of an anaerobic methane-oxidizing microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor. PLoS One 2014; 9:e105356 [View Article] [PubMed]
     [Google Scholar]
  10. Imachi H, Nobu MK, Miyazaki M, Tasumi E, Saito Y et al. Cultivation of previously uncultured microorganisms with a continuous-flow down-flow hanging sponge (DHS) bioreactor, using a syntrophic archaeon culture obtained from deep marine sediment as a case study. Nat Protoc 2022; 17:2784–2814 [View Article] [PubMed]
     [Google Scholar]
  11. Oren A. Emendation of principle 8, rules 5b, 8, 15, 33a, and appendix 7 of the International Code of Nomenclature of Prokaryotes to include the categories of kingdom and domain. Int J Syst Evol Microbiol 2023; 73:006123 [View Article]
     [Google Scholar]
  12. Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R et al. International Code of Nomenclature of Prokaryotes. Prokaryotic code (2022 revision). Int J Syst Evolut Microbiol 2023; 73:005585 [View Article]
     [Google Scholar]
  13. Göker M, Oren A. Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2023; 73:005650 [View Article]
     [Google Scholar]
  14. Göker M, Oren A. Valid publication of names of two domains and seven kingdoms of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006242 [View Article] [PubMed]
     [Google Scholar]
  15. Toki T, Higa R, Ijiri A, Tsunogai U, Ashi J. Origin and transport of pore fluids in the Nankai accretionary prism inferred from chemical and isotopic compositions of pore water at cold seep sites off Kumano. Earth Planets Space 2014; 66: [View Article]
     [Google Scholar]
  16. Nunoura T, Takaki Y, Kazama H, Hirai M, Ashi J et al. Microbial diversity in deep-sea methane seep sediments presented by SSU rRNA gene tag sequencing. Microbes Environ 2012; 27:382–390 [View Article] [PubMed]
     [Google Scholar]
  17. Tahara YO, Miyata M. Visualization of peptidoglycan structures of Escherichia coli by quick-freeze deep-etch electron microscopy. In Minamino T, Miyata M, Namba K. (editors) Bacterial and Archaeal Motility. Methods in Molecular Biology 2023; 2646299–307 [View Article]
     [Google Scholar]
  18. Nakahara N, Nobu MK, Takaki Y, Miyazaki M, Tasumi E et al. Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi. Int J Syst Evol Microbiol 2019; 69:1185–1194 [View Article] [PubMed]
     [Google Scholar]
  19. Yoshimura T, Takano Y, Naraoka H, Koga T, Araoka D et al. Chemical evolution of primordial salts and organic sulfur molecules in the asteroid 162173 Ryugu. Nat Commun 2023; 14:5284 [View Article] [PubMed]
     [Google Scholar]
  20. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  21. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article] [PubMed]
     [Google Scholar]
  22. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  23. Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E et al. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res 2018; 46:D335–D342 [View Article]
     [Google Scholar]
  24. Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016; 44:W54–W57 [View Article] [PubMed]
     [Google Scholar]
  25. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41:D590–6 [View Article] [PubMed]
     [Google Scholar]
  26. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012; 28:3150–3152 [View Article] [PubMed]
     [Google Scholar]
  27. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  28. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
     [Google Scholar]
  29. Lemoine F, Domelevo Entfellner J-B, Wilkinson E, Correia D, Dávila Felipe M et al. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data. Nature 2018; 556:452–456 [View Article] [PubMed]
     [Google Scholar]
  30. Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalizedand complete genome-based taxonomy. Nucleic Acids Res 2022; 50:D785–D794 [View Article] [PubMed]
     [Google Scholar]
  31. Criscuolo A, Gribaldo S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 2010; 10:210 [View Article] [PubMed]
     [Google Scholar]
  32. Schrempf D, Lartillot N, Szöllősi G. Scalable empirical mixture models that account for across-site compositional heterogeneity. Mol Biol Evol 2020; 37:3616–3631 [View Article] [PubMed]
     [Google Scholar]
  33. Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet 2000; 16:276–277 [View Article] [PubMed]
     [Google Scholar]
  34. Sára M, Sleytr UB. S-Layer proteins. J Bacteriol 2000; 182:859–868 [View Article] [PubMed]
     [Google Scholar]
  35. Albers S-V, Meyer BH. The archaeal cell envelope. Nat Rev Microbiol 2011; 9:414–426 [View Article] [PubMed]
     [Google Scholar]
  36. BD Bionutrients™ Technical Manual Advanced Bioprocessing, 3rd edn New Jersey: BD Biosciences; 2006
     [Google Scholar]
  37. Yokooji Y, Tomita H, Atomi H, Imanaka T. Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea. J Biol Chem 2009; 284:28137–28145 [View Article] [PubMed]
     [Google Scholar]
  38. Sakai S, Imachi H, Sekiguchi Y, Tseng I-C, Ohashi A et al. Cultivation of methanogens under low-hydrogen conditions by using the coculture method. Appl Environ Microbiol 2009; 75:4892–4896 [View Article] [PubMed]
     [Google Scholar]
  39. Villanueva L, Damsté JSS, Schouten S. A re-evaluation of the archaeal membrane lipid biosynthetic pathway. Nat Rev Microbiol 2014; 12:438–448 [View Article] [PubMed]
     [Google Scholar]
  40. Nobu MK, Narihiro T, Mei R, Kamagata Y, Lee PKH et al. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome 2020; 8:111 [View Article] [PubMed]
     [Google Scholar]
  41. Takai K, Horikoshi K. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 1999; 152:1285–1297 [View Article] [PubMed]
     [Google Scholar]
  42. Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA, Reysenbach AL. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl Environ Microbiol 1999; 65:4375–4384 [View Article] [PubMed]
     [Google Scholar]
  43. Takai K, Komatsu T, Inagaki F, Horikoshi K. Distribution of archaea in a black smoker chimney structure. Appl Environ Microbiol 2001; 67:3618–3629 [View Article] [PubMed]
     [Google Scholar]
  44. Bulzu P-A, Andrei A-Ş, Salcher MM, Mehrshad M, Inoue K et al. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat Microbiol 2019; 4:1129–1137 [View Article] [PubMed]
     [Google Scholar]
  45. Rinke C, Chuvochina M, Mussig AJ, Chaumeil P-A, Davín AA et al. A standardized archaeal taxonomy for the genome taxonomy database. Nat Microbiol 2021; 6:946–959 [View Article] [PubMed]
     [Google Scholar]
  46. Eme L, Tamarit D, Caceres EF, Stairs CW, De Anda V et al. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 2023; 618:992–999 [View Article] [PubMed]
     [Google Scholar]
  47. Rodrigues-Oliveira T, Wollweber F, Ponce-Toledo RI, Xu J, Rittmann SK-MR et al. Actin cytoskeleton and complex cell architecture in an Asgard archaeon. Nature 2023; 613:332–339 [View Article] [PubMed]
     [Google Scholar]
  48. Birrien J-L, Zeng X, Jebbar M, Cambon-Bonavita M-A, Quérellou J et al. Pyrococcus yayanosii sp. nov., an obligate piezophilic hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2011; 61:2827–2881 [View Article] [PubMed]
     [Google Scholar]
  49. de Bok FAM, Harmsen HJM, Plugge CM, de Vries MC, Akkermans ADL et al. The first true obligately syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov., co-cultured with Methanospirillum hungatei, and emended description of the genus Pelotomaculum. Int J Syst Evol Microbiol 2005; 55:1697–1703 [View Article] [PubMed]
     [Google Scholar]
  50. Qiu Y-L, Sekiguchi Y, Hanada S, Imachi H, Tseng I-C et al. Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens. Arch Microbiol 2006; 185:172–182 [View Article] [PubMed]
     [Google Scholar]
  51. Imachi H, Sakai S, Ohashi A, Harada H, Hanada S et al. Pelotomaculum propionicicum sp. nov., an anaerobic, mesophilic, obligately syntrophic, propionate-oxidizing bacterium. Int J Syst Evol Microbiol 2007; 57:1487–1492 [View Article] [PubMed]
     [Google Scholar]
  52. Qiu Y-L, Hanada S, Ohashi A, Harada H, Kamagata Y et al. Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the first cultured anaerobe capable of degrading phenol to acetate in obligate syntrophic associations with a hydrogenotrophic methanogen. Appl Environ Microbiol 2008; 74:2051–2058 [View Article] [PubMed]
     [Google Scholar]
  53. Sakai HD, Nur N, Kato S, Yuki M, Shimizu M et al. Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses. Proc Natl Acad Sci U S A 2022; 119:e2115449119 [View Article] [PubMed]
     [Google Scholar]
  54. Kato S, Ogasawara A, Itoh T, Sakai HD, Shimizu M et al. Nanobdella aerobiophila gen. nov., sp. nov., a thermoacidophilic, obligate ectosymbiotic archaeon, and proposal of Nanobdellaceae fam. nov., Nanobdellales ord. nov. and Nanobdellia class. nov. Int J Syst Evol Microbiol 2022; 72:005489 [View Article]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006435
Loading
Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage ‘Asgard’ archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov.
Int J Syst Evol Microbiol 74, 006435 (2024); https://doi.org/10.1099/ijsem.0.006435
/content/journal/ijsem/10.1099/ijsem.0.006435
/content/journal/ijsem/10.1099/ijsem.0.006435
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error