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

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.

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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.

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

  • 29 April 2020

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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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.

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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.

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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.

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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

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