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.
Environ Microbiol. 2021 Jul;23(7):3695-3709. doi: 10.1111/1462-2920.15349. Epub 2020 Dec 15.
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 CO -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 H F 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.
热变形菌门是广分布且在古菌域中具有重要生态地位的一门。由于可培养的物种和基因组数量有限，未被研究的热变形菌门代谢途径仍然未知。在本研究中，我们从丝状黑色恶臭水生沉积物的片段中获得了四个中高质量的古菌宏基因组组装基因组（MAG）。基于 16S rRNA 基因和核糖体蛋白系统发育树，这四个 MAG 属于先前未命名的热变形菌门 UBA10834 分支。我们建议将该分支（来自基因组分类数据库（GTDB）的五个参考基因组和本研究中的四个 MAG）视为一个新目，即候选古菌 Gimiplasmatales。代谢途径重建表明，候选古菌 Gimiplasmatales MAG 可以从头合成异戊二烯和核苷酸。此外，一些分类群具有甲醛和乙酸同化以及 Wood-Ljungdahl CO 固定途径的基因，表明它们具有混合营养生活方式。预测到了硫还原、氢代谢和砷解毒途径，表明它们具有硫、氢和砷转化潜力。比较基因组学表明，候选古菌 Gimiplasmatales 和甲烷八叠球菌目（Methanomassiliicoccales）的 HF Wood-Ljungdahl 途径可能是通过古菌域和厚壁菌门之间的种间水平基因转移获得的。总之，本研究阐明了新目的候选古菌 Gimiplasmatales 的分类和潜在代谢多样性，以及该亚群及其姐妹谱系甲烷八叠球菌目的进化。
