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.

  • Letter
  • Published:

Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments

Nature Microbiology volume 5, pages 248–255 (2020)Cite this article

Subjects

An Author Correction to this article was published on 29 April 2020

This article has been updated

Abstract

The genomes of the Asgard superphylum of Archaea hold clues pertaining to the nature of the host cell that acquired the mitochondrion at the origin of eukaryotes1,2,3,4. Representatives of the Asgard candidate phylum Candidatus Lokiarchaeota (Lokiarchaeon) have the capacity for acetogenesis and fermentation5,6,7, but how their metabolic activity responds to environmental conditions is poorly understood. Here, we show that in anoxic Namibian shelf sediments, Lokiarchaeon gene expression levels are higher than those of bacterial phyla and increase with depth below the seafloor. Lokiarchaeon gene expression was significantly different across a hypoxic–sulfidic redox gradient, whereby genes involved in growth, fermentation and H2-dependent carbon fixation had the highest expression under the most reducing (sulfidic) conditions. Quantitative stable isotope probing revealed that anaerobic utilization of CO2 and diatomaceous extracellular polymeric substances by Lokiarchaeon was higher than the bacterial average, consistent with higher expression of Lokiarchaeon genes, including those involved in transport and fermentation of sugars and amino acids. The quantitative stable isotope probing and gene expression data demonstrate homoacetogenic activity of Candidatus Lokiarchaeota, whereby fermentative H2 production from organic substrates is coupled with the Wood–Ljungdahl carbon fixation pathway8. The high energetic efficiency provided by homoacetogenesis8 helps to explain the elevated metabolic activity of Lokiarchaeon in this anoxic, energy-limited setting.

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

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

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

Fig. 1: Lokiarchaeon gene expression increases in anoxic, sulfidic sediments.
Fig. 2: Lokiarchaeon gene expression across a hypoxic–sulfidic redox gradient.
Fig. 3: Potential Lokiarchaeon physiology based on metagenomes and metatranscriptomes.
Fig. 4: qSIP confirms high activity and anaerobic mixotrophy by Asgard archaea.

Similar content being viewed by others

Data availability

All metagenome, metatranscriptome and 16S rRNA gene data are publicly accessible in NCBI through BioProject number PRJNA525353. The raw version of the phylogenetic tree and the multiple sequence alignment are available in Supplementary Data 1 and 2.

Change history

References

  1. Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017).

    CAS  PubMed  Google Scholar 

  2. Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).

    CAS  PubMed  Google Scholar 

  4. Martin, W. F., Tielens, A. G. M., Mentel, M., Garg, S. G. & Gould, S. V. The physiology of phagocytosis in the context of mitochondrial origin. Microbiol. Mol. Biol. Rev. 81, e00008–e00017 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Sousa, F. L., Neukirchen, S., Allen, J. F., Lane, N. & Martin, W. F. Lokiarchaeon is hydrogen dependent. Nat. Microbiol. 1, 16034 (2016).

    CAS  PubMed  Google Scholar 

  6. Spang, A. et al. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism. Nat. Microbiol. 4, 1138–1148 (2019).

  7. Imachi, H. et al. Isolation of an archaeon at the prokaryote-eukaryote interface. Preprint at https://doi.org/10.1101/726976 (2019).

  8. Schuchmann, K. & Müller, V. Energetics and application of heterotrophy in acetogenic bacteria. Appl. Environ. Microbiol. 82, 4056–4069 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Lavik, G. et al. Detoxification of sulphidic African shelf waters by blooming chemolithotrophs. Nature 457, 581–584 (2009).

    CAS  PubMed  Google Scholar 

  10. Lin, Y. S. et al. Towards constraining H2 concentrations in subseafloor sediment: a proposal for combined analysis by two distinct approaches. Geochim. Cosmochim. Acta 77, 186–201 (2012).

    CAS  Google Scholar 

  11. Orsi, W. D. et al. Climate oscillations reflected within the microbiome of Arabian Sea sediments. Sci. Rep. 7, 6040 (2017).

    PubMed  PubMed Central  Google Scholar 

  12. Jorgensen, S. L. et al. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc. Natl Acad. Sci. USA 109, E2846–E2855 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Buckel, W. & Thauer, R. K. Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation. Biochim. Biophys. Acta 1827, 94–113 (2013).

    CAS  PubMed  Google Scholar 

  14. Becker, A. et al. Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase. Nat. Struct. Biol. 6, 969–975 (1999).

    CAS  PubMed  Google Scholar 

  15. Siebers, B. et al. Archaeal fructose-1,6-bisphosphate aldolases constitute a new family of archaeal type class I aldolase. J. Biol. Chem. 276, 28710–28718 (2001).

    CAS  PubMed  Google Scholar 

  16. Hetzel, M. et al. Acryloyl-CoA reductase from Clostridium propionicum. An enzyme complex of propionyl-CoA dehydrogenase and electron-transferring flavoprotein. Eur. J. Biochem. 270, 902–910 (2003).

    CAS  PubMed  Google Scholar 

  17. Schweiger, G., Dutscho, R. & Buckel, W. Purification of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. An iron-sulfur protein. Eur. J. Biochem. 169, 441–448 (1987).

    CAS  PubMed  Google Scholar 

  18. Hwang, W. C. et al. LUD, a new protein domain associated with lactate utilization. BMC Bioinform. 14, 341 (2013).

    Google Scholar 

  19. Buckel, W. & Thauer, R. K. Flavin-based electron bifurcation, a new mechanism of biological energy coupling. Chem. Rev. 118, 3862–3886 (2018).

    CAS  PubMed  Google Scholar 

  20. Seyler, L. M., McGuinness, L. M. & Kerkhof, L. J. Crenarchaeal heterotrophy in salt marsh sediments. ISME J. 8, 1534–1543 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Yu, T. et al. Growth of sedimentary Bathyarchaeota on lignin as an energy source. Proc. Natl Acad. Sci. USA 115, 6022–6027 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Lazar, C. S. et al. Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Environ. Microbiol. 18, 1200–1211 (2016).

    CAS  PubMed  Google Scholar 

  23. Martin, W. F., Neukirchen, S., Zimorski, V., Gould, S. B. & Sousa, F. L. Energy for two: new archaeal lineages and the origin of mitochondria. BioEssays 38, 850–856 (2016).

    PubMed  Google Scholar 

  24. He, Y. et al. Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments. Nat. Microbiol. 1, 16035 (2016).

    CAS  PubMed  Google Scholar 

  25. Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. & Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–D495 (2014).

    CAS  PubMed  Google Scholar 

  26. Aslam, S. N., Strauss, J., Thomas, D. N., Mock, T. & Underwood, G. J. C. Identifying metabolic pathways for production of extracellular polymeric substances by the diatom Fragilariopsis cylindrus inhabiting sea ice. ISME J. 12, 1237–1251 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Lovley, D. R. & Phillips, E. J. P. Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments. Geochim. Cosmochim. Acta 52, 2993–3003 (1988).

    CAS  Google Scholar 

  28. Schulz, H. D. et al. Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284, 493–495 (1999).

    CAS  PubMed  Google Scholar 

  29. Schink, B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262–280 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Ferdelman, T. et al. Sulfate reduction and methanogenesis in a Thioploca-dominated sediment off the coast of Chile. Geochim. Cosmochim. Acta 61, 3065–3079 (1997).

    CAS  Google Scholar 

  31. Seitz, K. W., Lazar, C. S., Hinrichs, K. U., Teske, A. P. & Baker, B. J. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J. 10, 1696–1705 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Lever, M. A. Acetogenesis in the energy-starved deep biosphere – a paradox? Front. Microbiol. 2, 284 (2012).

    PubMed  PubMed Central  Google Scholar 

  33. Lever, M. A. et al. Acetogenesis in deep subseafloor sediments of the Juan de Fuca Ridge Flank: a synthesis of geochemical, thermodynamic, and gene-based evidence. Geomicrobiol. J. 27, 183–211 (2009).

    Google Scholar 

  34. Glasemacher, J., Bock, A. K., Schmid, R. & Schönheit, P. Purification and properties of acetyl-CoA synthetase (ADP-forming), an archaeal enzyme of acetate formation and ATP synthesis, from the hyperthermophile Pyrococcus furiosus. Eur. J. Biochem. 244, 561–567 (1997).

    CAS  PubMed  Google Scholar 

  35. Knoll, A. H. The early evolution of eukaryotes: a geological perspective. Science 256, 622–627 (1992).

    CAS  PubMed  Google Scholar 

  36. Lyons, T. W., Reinhard, C. T. & Planavsky, N. J. The rise of oxygen in Earth’s early ocean and atmosphere. Nature 506, 307–315 (2014).

    CAS  PubMed  Google Scholar 

  37. Martin, W. & Muller, M. The hydrogen hypothesis for the first eukaryote. Nature 392, 37–41 (1998).

    CAS  PubMed  Google Scholar 

  38. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–33 (2011).

    Google Scholar 

  39. Cline, J. D. Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol. Oceanogr. 14, 454–458 (1969).

    CAS  Google Scholar 

  40. Strickland, J. D. & Parsons, T. R. A Practical Handbook of Seawater Analysis (Fisheries Research Board of Canada, 1972).

  41. Ortega-Arbulu, A. S., Pichler, M., Vuillemin, A. & Orsi, W. D. Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon. Environ. Microbiol. 21, 374–388 (2019).

    CAS  PubMed  Google Scholar 

  42. Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).

    CAS  PubMed  Google Scholar 

  43. Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).

    CAS  PubMed  Google Scholar 

  44. Orsi, W. D., Richards, T. A. & Francis, W. R. Predicted microbial secretomes and their target substrates in marine sediment. Nat. Microbiol. 3, 32–37 (2018).

    CAS  PubMed  Google Scholar 

  45. Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).

    CAS  PubMed  Google Scholar 

  46. Seitz, K. W. et al. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat. Commun. 10, 1822 (2019).

    PubMed  PubMed Central  Google Scholar 

  47. Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018).

    PubMed  PubMed Central  Google Scholar 

  48. Keeling, P. J. et al. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 12, e1001889 (2014).

    PubMed  PubMed Central  Google Scholar 

  49. Spang, A., Caceres, E. F. & Ettema, T. J. G. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357, eaaf3883 (2017).

    PubMed  Google Scholar 

  50. Vuillemin, A. et al. Archaea dominate oxic subseafloor communities over multimillion-year time scales. Sci. Adv. 5, eaaw4108 (2019).

    PubMed  PubMed Central  Google Scholar 

  51. Guillard, R. R. L. & Hargraves, P. E. Stichochrysis immobilis is a diatom, not a chrysophyte. Phycologia 32, 234–236 (1993).

    Google Scholar 

  52. Inthorn, M., Wagner, T., Scheeder, G. & Zabel, M. Lateral transport controls distribution, quality and burial of organic matter along continental slopes in high-productivity areas. Geology 34, 205–208 (2006).

    CAS  Google Scholar 

  53. Compton, J. S. & Bergh, E. W. Phosphorite deposits on the Namibian shelf. Mar. Geol. 380, 290–314 (2016).

    CAS  Google Scholar 

  54. Coskun, O. K., Pichler, M., Vargas, S., Gilder, S. & Orsi, W. D. Linking uncultivated microbial populations with benthic carbon turnover using quantitative stable isotope probing. Appl. Environ. Microbiol. 84, e01083–18 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Dunford, E. A. & Neufeld, J. D. DNA stable-isotope probing (DNA-SIP). J. Vis. Exp. 42, 2027 (2010).

    Google Scholar 

  56. Youngblut, N. D., Barnett, S. E. & Buckley, D. H. HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments. PLoS ONE 13, e0189616 (2018).

    PubMed  PubMed Central  Google Scholar 

  57. Hungate, B. A. et al. Quantitative microbial ecology through stable isotope probing. Appl. Environ. Microbiol. 81, 7570–7581 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by the Deutsche Forschungsgemeinschaft through Project OR 417/4-1 (W.D.O.), and the F/S Meteor Expedition M148/2 ‘EreBUS’. We thank the captain and crew of the F/S Meteor for assistance during the oceanographic expedition, as well as S. Littmann, T. Wilkop, G. Klockgether and K. Imhoff who assisted in obtaining samples and providing chemical data. This work was performed in part through the Masters in Geobiology and Paleontology Program at LMU Munich. G.V.G.-S. was funded by the Deutsche Forschungsgemeinschaft project DI 842/6-1.

Author information

Authors and Affiliations

  1. Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany

    William D. Orsi, Aurèle Vuillemin, Paula Rodriguez & Ömer K. Coskun

  2. GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany

    William D. Orsi

  3. Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany

    Gonzalo V. Gomez-Saez

  4. Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany

    Gaute Lavik & Timothy G. Ferdelman

  5. Baltic Sea Research Institute, Warnemünde, Rostock, Germany

    Volker Mohrholz

Authors
  1. William D. Orsi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Aurèle Vuillemin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Paula Rodriguez
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ömer K. Coskun
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gonzalo V. Gomez-Saez
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Gaute Lavik
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Volker Mohrholz
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Timothy G. Ferdelman
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

W.D.O. conceived the idea for the study and wrote the paper. T.G.F. organized and led the expedition. A.V., P.R., O.K.C., G.V.G.-S., V.M. and T.G.F. produced data. W.D.O., A.V., P.R., G.L. and O.K.C. analysed data. T.G.F., G.V.G.-S. and W.D.O. acquired the samples. W.D.O. supervised the study.

Corresponding author

Correspondence to William D. Orsi.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Dissolved oxygen profile in the water column and the sampled core.

(Left) Dissolved oxygen profile in the water column above the sampled core. Blue color represents measurements made on the downcast, red color are measurements made on the upcast. (Right) Photograph of the 30 cm long sediment core taken from the bottom of the OMZ with the seawater/seafloor interface still intact.

Extended Data Fig. 2 Relative abundance Lokiarchaeon OTUs (Loki1 and Loki2) throughout the core.

The in situ relative abundance of 16S rRNA genes from the two Lokiarchaeon OTUs (Loki1 and Loki2) that were detected in the core. For the phylogenetic analysis see Fig. 4c.

Extended Data Fig. 3 qSIP results from 13C- labeled bicarbonate and 13C-dEPS after 10 day anoxic incubations.

Each point represents a separate OTU, the x axis represents percent of 13C-labeled carbon atoms in 16S rRNA genes per population. Error bars represent 90% confidence intervals across three biological replicates (0.25 indicates 25% of C atoms are 13C labeled), and the points are mean values across the three replicates. Positive atom fraction excess values with confidence intervals not overlapping zero are statistically significant. The EAF values for the OTUs are vertically arranged from top to bottom for each major group (the “y axis”) from the highest EAF value (most 13C enriched OTU) gradually decreasing to the OTU with the lowest EAF value.

Extended Data Fig. 4 Similarity of key ORFs to Lokiarchaeon genomes.

Each point represents a separate ORF detected in either the metagenomes (filled circles) or metatranscriptomes (white circles) that had a predicted protein in a Lokiarchaeon genome as its top hit in DIAMOND searches, which are displayed in the metabolic reconstruction in Fig. 3 in the main text. The abbreviations in Fig. 3 are shown at the top of the plot, the full names appear at the bottom of the plot.

Extended Data Fig. 5 Sequencing and assembly statistics for the metagenomes and metatranscriptomes.

Sequencing and assembly statistics for the metagenomes and metatranscriptomes.

Supplementary information

Reporting Summary

Supplementary Data 1

FASTA alignment file for the phylogenetic tree in Fig. 4c.

Supplementary Data 2

The tree file for the 16S rRNA gene phylogenetic analysis presented in Fig. 4c.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Orsi, W.D., Vuillemin, A., Rodriguez, P. et al. Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments. Nat Microbiol 5, 248–255 (2020). https://doi.org/10.1038/s41564-019-0630-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41564-019-0630-3

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