Volume 23, Issue 7 p. 3695-3709
Special Issue Article

Metagenomic insights into the metabolism and evolution of a new Thermoplasmata order (Candidatus Gimiplasmatales)

Wenzhe Hu

Wenzhe Hu

School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China

Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China

These authors contributed equally to this study.Search for more papers by this author
Jie Pan

Jie Pan

Shenzhen key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China

These authors contributed equally to this study.Search for more papers by this author
Bin Wang

Bin Wang

Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China

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Jun Guo

Jun Guo

Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China

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Meng Li

Corresponding Author

Meng Li

Shenzhen key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China

For correspondence. E-mail [email protected] (M.L); Tel. +86-755-26979250; Fax +86-755-26001356; [email protected] (M. Xu); Tel. +86-20-87137655; Fax +86-20-87684587.

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Meiying Xu

Corresponding Author

Meiying Xu

Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China

For correspondence. E-mail [email protected] (M.L); Tel. +86-755-26979250; Fax +86-755-26001356; [email protected] (M. Xu); Tel. +86-20-87137655; Fax +86-20-87684587.

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First published: 09 December 2020
Citations: 20

Summary

Thermoplasmata is a widely distributed and ecologically important archaeal class in the phylum Euryarchaeota. Because few cultures and genomes are available, uncharacterized Thermoplasmata metabolisms remain unexplored. In this study, we obtained four medium- to high-quality archaeal metagenome-assembled genomes (MAGs) from the filamentous fragments of black-odorous aquatic sediments (Foshan, Guangdong, China). Based on their 16S rRNA gene and ribosomal protein phylogenies, the four MAGs belong to the previously unnamed Thermoplasmata UBA10834 clade. We propose that this clade (five reference genomes from the Genome Taxonomy Database (GTDB) and four MAGs from this study) be considered a new order, Candidatus Gimiplasmatales. Metabolic pathway reconstructions indicated that the Ca. Gimiplasmatales MAGs can biosynthesize isoprenoids and nucleotides de novo. Additionally, some taxa have genes for formaldehyde and acetate assimilation, and the Wood–Ljungdahl CO2-fixation pathway, indicating a mixotrophic lifestyle. Sulfur reduction, hydrogen metabolism, and arsenic detoxification pathways were predicted, indicating sulfur-, hydrogen-, and arsenic-transformation potentials. Comparative genomics indicated that the H4F Wood–Ljungdahl pathway of both Ca. Gimiplasmatales and Methanomassiliicoccales was likely obtained by the interdomain lateral gene transfer from the Firmicutes. Collectively, this study elucidates the taxonomic and potential metabolic diversity of the new order Ca. Gimiplasmatales and the evolution of this subgroup and its sister lineage Methanomassiliicoccales.

Data availability

The metagenome raw sequence data reported in this article have been deposited in the Genome Sequence Archive in National Genomics Data Center (NGDC, https://bigd.big.ac.cn/gsa/) under accession number CRA003538. The MAGs described in this study have been deposited at JGI IMG/MER (https://gold.jgi.doe.gov/) under the Study ID Gs0140400 (accessions number: Ga0373720, Ga0373721, Ga0373731 and Ga0373734) and also at the National Omics Data Encyclopedia (NODE, https://www.biosino.org/node) under the Project ID OEP001066 (accessions number: OEZ006378, OEZ006395, OEZ006364 and OEZ006391).