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. 2018 Apr;12(4):1021-1031.
doi: 10.1038/s41396-018-0060-x. Epub 2018 Feb 14.

Comparative Genomic Inference Suggests Mixotrophic Lifestyle for Thorarchaeota

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Free PMC article

Comparative Genomic Inference Suggests Mixotrophic Lifestyle for Thorarchaeota

Yang Liu et al. ISME J. .
Free PMC article

Abstract

Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen fixation, nitrite reduction, and arsenic detoxification. Interestingly, these Thorarchaeotal genomes are inferred to contain the tetrahydromethanopterin and tetrahydrofolate Wood-Ljungdahl (WL) pathways for CO2 reduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisphosphate carboxylase-like proteins (normally without RuBisCO activity) and a near-complete Calvin-Benson-Bassham cycle. The existence of eukaryotic selenocysteine insertion sequences and many genes for proteins previously considered eukaryote-specific in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryotic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their roles in ecosystems.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Phylogenetic analyses of new Thorarchaeota lineages. a The concatenated 16S and 23S rRNA genes maximum-likelihood tree rooted with bacteria. b The concatenated 55 archaeo-eukaryotic ribosomal proteins from Archaea and Eukarya Maximum-Likelihood tree re-rooted with DPANN and Euryarchaeota. The bootstrap support values above 50, 70 and 85 are indicated with empty, gray and black filled circles, respectively. c The relative abundance of Thorarchaeota in the five samples in Mai Po. The numbers of mapped reads were normalized by total number of sequenced raw reads
Fig. 2
Fig. 2
Pan-genome analysis of protein clusters within all Thorarchaeota genomes. The inner tree was constructed from matrix of protein annotation by COG function categories and eggNOG Orthologous Groups (LUCA, archaea, bacteria, and eukarya)
Fig. 3
Fig. 3
Inferred physiological capabilities of Thorarchaeota phylum. Metabolic reconstruction of the Thorarchaeota genomic bin MP8T_1 based on the genes identified using the KEGG database, NCBI non-redundant protein database and eggNOG-mapper annotation. Dashed line indicates absence and solid line indicates presence in bin MP8T_1, and gray line indicates presence in other Thorarchaeota genomic bins. Details about the genes are provided in Supplementary Table 4

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