State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China.
ISME J. 2024 Jan 8;18(1). doi: 10.1093/ismejo/wrad033.
The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria-Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia, and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.
产甲烷菌的起源可以追溯到非 DPANN 古菌的共同祖先，而盐杆菌（或盐杆菌）被认为是通过多次进化事件从产甲烷菌祖先进化而来的。然而，由于适应高盐环境的蛋白质的快速进化和组成偏向，盐杆菌与产甲烷菌表现出很大的进化分歧，而与盐杆菌关系最密切的产甲烷菌（无论是 Methanonatronarchaeia 还是其他分类群）的鉴定仍然存在争议。在这里，我们从中国内蒙古鄂尔多斯高原的苏打盐湖中获得了五个具有高完整性的宏基因组组装基因组，并为这个新的类群提出了候选鄂尔多斯古菌的名称。系统发育分析表明，候选鄂尔多斯古菌位于 Methanonatronarchaeia 和盐杆菌-希拉古菌谱系之间的中值位置附近。功能预测支持候选鄂尔多斯古菌的过渡状态，具有非产甲烷和需氧化能异养代谢的潜力，这与甲基胺/二甲胺/三甲胺代谢和辅酶 M 生物合成的基因序列残留物一致。基于 Methanonatronarchaeia 中甲基辅酶 M 还原酶基因 mcrBGADC 与系统发育上较远的产甲烷菌的相似性，提出了一个替代的进化情景，即 Methanonatronarchaeia、候选鄂尔多斯古菌、候选希拉古菌和盐杆菌共享一个最初失去 mcr 基因的共同祖先。然而，某些 Methanonatronarchaeia 成员随后通过与远缘产甲烷菌的水平基因转移获得了 mcr 基因。这个假设得到了合并似然估计、系统发育分析和基因排列模式的支持。总之，候选鄂尔多斯古菌基因组阐明了 Methanonatronarchaeia 与盐杆菌的姐妹关系，并为从产甲烷菌到盐杆菌的进化提供了新的见解。
