Acidophilic archaea of the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group from the uncultured candidate phylum “Candidatus Micrarchaeota” have small genomes and cell sizes and are known to be metabolically dependent and physically associated with their Thermoplasmatales hosts. However, phylogenetically diverse “Ca. Micrarchaeota” are widely distributed in various nonacidic environments, and it remains uncertain because of the lack of complete genomes whether they are also devoted to a partner-dependent lifestyle. Here, we obtained nine metagenome-assembled genomes of “Ca. Micrarchaeota” from the sediments of a meromictic freshwater lake, including a complete, closed 1.2 Mbp genome of “Ca. Micrarchaeota” Sv326, an archaeon phylogenetically distant from the ARMAN lineage. Genome analysis revealed that, contrary to ARMAN “Ca. Micrarchaeota,” the Sv326 archaeon has complete glycolytic pathways and ATP generation mechanisms in substrate phosphorylation reactions, the capacities to utilize some sugars and amino acids as substrates, and pathways for de novo nucleotide biosynthesis but lacked an aerobic respiratory chain. We suppose that Sv326 is a free-living scavenger rather than an obligate parasite/symbiont. Comparative analysis of “Ca. Micrarchaeota” genomes representing different order-level divisions indicated that evolution of the “Ca. Micrarchaeota” from a free-living “Candidatus Diapherotrites”-like ancestor involved losses of important metabolic pathways in different lineages and gains of specific functions in the course of adaptation to a partner-dependent lifestyle and specific environmental conditions. The ARMAN group represents the most pronounced case of genome reduction and gene loss, while the Sv326 lineage appeared to be rather close to the ancestral state of the “Ca. Micrarchaeota” in terms of metabolic potential.

中文翻译：

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从淡水湖的基因组中发现古细菌门“ Micrarchaeota”的代谢多样性和进化史。

古细菌里士满矿嗜酸nanoorganisms（阿尔曼）从所述未培养候选门“组的嗜酸古细菌暂定Micrarchaeota”具有小的基因组和细胞大小，并且已知是代谢相关的，并且在物理上与它们相关联的Thermoplasmatales主机。然而，系统发育上的多样性“ Ca”。微囊藻”广泛分布在各种非酸性环境中，由于缺乏完整的基因组，它们是否也致力于依赖伴侣的生活方式，仍然不确定。在这里，我们得到的“九宏基因组组装基因组钙。来自淡紫色湖泊的沉积物中的“ Micrarchaeota”，包括完整，封闭的1.2 Mbp Ca的基因组。Micrarchaeota” Sv326，与ARMAN世系系统距离较远的古细菌。基因组分析表明，与ARMAN“ Ca ”相反。“ Micrarchaeota”，Sv326古细菌在底物磷酸化反应中具有完整的糖酵解途径和ATP生成机制，具有利用某些糖和氨基酸作为底物的能力，以及从头进行核苷酸生物合成的途径，但缺少需氧呼吸链。我们假设Sv326是一种自由的清除剂，而不是专性的寄生虫/共生体。钙的比较分析。代表不同阶级划分的“ Micrarchaeota”基因组表明“ Ca ”的进化。Micrarchaeota”从自由生活“暂定类花生四烯的祖先在不同世系中丢失了重要的代谢途径，在适应依赖伴侣的生活方式和特定环境条件的过程中获得了特定功能。ARMAN组代表了最明显的基因组减少和基因丢失情况，而Sv326谱系似乎非常接近“ Ca ”的祖传状态。在代谢潜能方面。